MX2008015001A - Polymorphisms in mitochondrial transcription factor a (tfam) gene and their associations with carcass traits. - Google Patents

Abstract

The physiological regulation of intake, growth and energy partitioning in animals is under the control of multiple genes, which may be important candidates for unraveling the genetic variation in economically relevant traits in beef production. The present invention relates to the identification of single nucleotide polymorphisms (SNPs) within the bovine gene encoding mitochondrial transcription factor A ("TFAM") and their associations with economically relevant traits in beef production. The invention further encompasses methods and systems, including network-based processes, to manage the SNP data and other data relating to specific animals and herds of animals, veterinarian care, diagnostic and quality control data and management of livestock which, based on genotyping, have predictable meat quality traits, husbandry conditions, animal welfare, food safety information, audit of existing processes and data from field locations.

Description

POLYMORPHISMS IN THE GENE OF THE MITOCONNIC TRANSCRIPTION FACTOR (FAM) AND ITS ASSOCIATIONS WITH CHANNEL ATTRIBUTES FIELD OF THE INVENTION The present invention relates to the identification of individual nucleotide polymorphisms (SNPs) within the bovine genes that encode mitochondrial transcription factor A ("TFAM") and their associations with economically relevant attributes in meat production. beef. The invention also relates to methods and systems, including network-based processes, for handling SNP data and other data related to specific animals and herds of animals, veterinary care, diagnostic and quality control data and livestock management. which, based on genotype determination, have predictable meat quality attributes, breeding conditions, animal welfare, feed safety information, verification of existing processes, and field location data. BACKGROUND OF THE INVENTION Significant improvements in animal performance, efficiency and carcass quality and meat have been made over the years through the application of standard animal breeding and selection techniques. However, such techniques of reproduction of classical animals they require several years of genetic evaluation of performance records on individual animals and their relatives and therefore are very expensive. Other efforts have been made to improve productivity and quality through the application of such management practices as the use of food additives, animal hormonal implants and chemotherapeutics. However, there is a significant political and regulatory resistance to the introduction and use of such methodologies. Such methodologies are also not inheritable and need to be applied differently in each production system. There is a need for methods that allow the relatively easy and more efficient selection and reproduction of farm animals with an advantage for a heritable attribute of circulating leptin levels, feed intake, growth rate, body weight, value of the carcass and composition of the channel. The economic significance of the use of genetic markers that are associated with specific economically important attributes (especially attributes with low heritability) in livestock through marker assisted selection can therefore not be overemphasized. Physiological regulation of the intake, growth and splitting of energy in animals is under the control of multiple genes, which may be candidates important to decipher the genetic variation in economically relevant attributes (ERT) in the production of beef. The polymorphisms in these candidate genes that show association with specific ERT are nucleotides of quantitative attributes useful for marker-assisted selection. The mitochondrial transcription factor A ("TFAM"), a member of a family of high mobility group proteins and the first identified mitochondrial transcription factor (Fisher and Clayton, Mol Cell Biol. 1988; 8: 3496-509), it is essential for the maintenance and biogenesis of mitochondrial DNA (mtDNA). First, TFAM performs a function similar to isone in the mitochondria, since it is closely associated with mtDNA as a major component of the nucleotide (Kanki et al., Mol Cell Biol. 2004; 24: 9823-34). Evidence has shown that an mtDNA molecule is packaged with -900 molecules of TFAM on average (Alam et al., Nucleic Acids Res. 2003; 31: 1640-5), which makes the mtDNA non-naked longer. Second, TFAM regulates the number of copies of mtDNA in mammals. Investigation using a combination of mice with overexpression of TFAM and inactivation of TFAM demonstrated that the copy number of mtDNA is directly proportional to the level of total TFAM protein in mouse embryos (Ekstrand et al., Hum Mol Genet., 2004; : 935-44). RNA interference from the expression of Endogenous TFAM in HeLa cells also indicated that the amount of mtDNA is correlated in parallel with the amount of TFAM (Kanki et al., Ann N and Acad Sci. 2004; 1011: 61-8). Third, TFAM stimulates the transcription of mtDNA. The TFAM protein possesses two domains of high mobility group in tandem, which makes the TFAM bind, unwind and fold the DNA without sequence specificity and thus facilitate the initiation of transcription of mtDNA (Gaspari et al., 2004; 1659: 148-52 ). Evidence has shown that the importation of wt-TFAM into liver mitochondria from hypothyroid rats increased RNA synthesis significantly up to 4 times (Garstka et al., Nucleic Acids Res. 2003; 31: 5039-47). It has been known for many years that adipose tissue plays a central role in the regulation and manipulation of energy metabolisms through the storage and productivity of triglycerides and through the secretion of factors that affect satiety and utilization of the supply. However, many key aspects of adipogenesis are accompanied by the stimulation of mitochondrial biogenesis (ilson-Fritch et al., Mol Cell Biol. 2003; 23: 1085-94). For example, the major ß-oxidation site of fatty acid occurs in the mitochondria (Reichert and Neupert, Trends Genet, 2004; 20: 555-62), which can provide key intermediaries for the synthesis of triglycerides via the action of pyruvate carboxylase (Owen et al., J Biol Chem. 2002; 277: 30409-12). In addition, a relatively large mitochondrial mass is necessary to generate acetyl-CoA for the activation of fatty acid before esterification into triglycerides. All these studies demonstrated the essential role and function of mitochondria in lipid metabolism. To further explore the mechanism of mitochondria involved in adipogenesis, Wilson-Fritch et al (Wilson-Fritch et al Mol Cell Biol. 2003; 23: 1085-94 and Wilson-Fritch et al., J Clin Invest. 2004; 114: 1281-9) studied the differentiation of the 3T3-L1 cell (representative of white adipocytes) by using both proteomic and genomic procedures. Proteomic analysis revealed a 20- to 30-fold increase in the concentration of numerous mitochondrial proteins, whereas genomic analysis with the profiling of gene expression using Affymetrix GeneChips detected a statistically significant increase in the expression of many mitochondrial genes encoded in the nucleus during adipogenesis. In particular, the authors found a profound decrease of approximately 50% in the levels of transcripts for nuclear encoded mitochondrial genes that accompany the onset of obesity (Wilson- Fritch et al., J Clin Invest. 2004; 114: 1281-9). It remains advantageous to provide additional SNPs that can more accurately predict the meat quality phenotype of an animal and also a business method that provides increased production efficiencies in cattle, as well as providing access to several animal records and allowing comparisons with expected or desired objectives with respect to the quality and quantity of animals produced. The citation or identification of any document in this application is not an admission that such a document is available as the prior art to the present invention. BRIEF DESCRIPTION OF THE INVENTION The present invention relates to the identification of individual nucleotide polymorphisms (SNPs) within the bovine genes that encode mitochondrial transcription factor A. { "TFAM") and its associations with economically relevant attributes in the production of beef. The invention encompasses a method for sub-grouping animals according to the genotype wherein the animals of each sub-group have a similar polymorphism in a TFAM gene which may comprise determining the genotype of each animal to be sub-grouped when determining the presence of an individual nucleotide polymorphism in the TFAM gene, and segregate individual animals into subgroups where each animal in a subgroup has a similar polymorphism in a TFAM gene. The invention also encompasses a method for sub-grouping animals according to the genotype wherein the animals of each subgroup have a similar genotype in the TFAM gene which may comprise determining the genotype of each animal to be subgrouped when determining the presence of an individual nucleotide polymorphism (s) of interest in the TFAM gene, and by segregating individual animals into subgroups depending on whether the animals have, or do not have, the individual nucleotide polymorphism (s) of interest in the TFAM gene. The individual nucleotide polymorphism (s) of interest can be selected from the group consisting of a substitution of A to C at the position of nucleotide -1220 in the promoter of the TFAM gene, a substitution of T to C at position -1212 in the promoter of the TFAM gene and a substitution of T a C at position -995 in the promoter of the TFAM gene. The invention furthermore relates to a method for sub-grouping animals according to the genotype wherein the animals of each subgroup have a similar genotype in the TFAM gene which may comprise of determining the genotype of each animal to be subgrouped when determining the presence of any of the previous SNPs, and by segregating the animals Individuals in sub-groups depending on whether the animals have, or do not have, any of the previous SNPs in the TFAM gene. The invention also relates to a method for identifying an animal having a desirable phenotype as compared to the general population of animals of that species, which may comprise determining the presence of an individual nucleotide polymorphism in the TFAM gene of the animal, in where the presence of the SNP is indicative of a desirable phenotype. In an advantageous embodiment, the animal can be a bovine. In another advantageous embodiment, the TFAM gene can be a bovine TFAM gene. The invention also encompasses computer-assisted methods and systems for improving production efficiency for cattle having softer meat marketable using multiple data, and in particular the genotype of animals as it relates to TFAM SNPs. The methods of the invention encompass obtaining a genetic sample from each animal in a herd of cattle, determining the genotype of each animal with respect to specific quality attributes as defined by a panel of at least two polynucleotides of individual polynucleotides. (SPNs), group the animals with similar genotypes, and optionally, also sublevel the animals based on similar phenotypes. The methods of the invention may also encompass obtaining and maintaining data related to animals or herds, their breeding conditions, health and care and veterinary condition, genetic history or kinship, and the provision of this data to others through systems that are network-based, contained in a database, or linked to the animal itself such as by an implanted microchip. An advantageous aspect of the present invention, therefore, is directed to a computer system and computer-assisted methods for tracking quality attributes for livestock that possess specific genetic predispositions. The present invention advantageously encompasses computer-assisted methods and systems for acquiring genetic data, particularly genetic data as defined by the absence or presence of a SNP within the TFAM gene related to quality attributes of the animal's reproduction meat and the association of that data with other data about the animal or herd, and the maintenance of that data in ways that are accessible. Another aspect of the invention encompasses a computer-assisted method for predicting which livestock animals have a biological difference in the quality of the meat, and which may include the steps of using a computer system, for example, a programmed computer comprising a computer. processor, a data storage system, an input device and an output device, the stages of: (a) entering into the programmed computer a. through the input device data that include a genotype of an animal as it relates to any of the TFAM SNPs described herein; (b) correlate the quality of the meat predicted by the TFAM genotype using the processor and the data storage system and (c) output the quality of the meat correlated with the TFAM genotype to the output device, in order to predict what livestock animals have a particular quality of meat. Yet another aspect of the invention relates to a method for doing business to manage livestock which comprises providing a user with the computer system for handling livestock comprising physical characteristics and genotypes corresponding to one or more animals or a computer readable means to handle livestock that comprises physical characteristics and genotypes corresponding to one or more animals or physical characteristics and genotypes corresponding to one or more animals, where a physical characteristic is the intake, growth or value of the channel in cattle for meat and the genotype is a TFAM genotype. It is noted that in this description and particularly in the claims and / or paragraphs, the I I terms such as "is understood", "understood", "comprising" and the like may have the meaning attrid to it in the United States patent law, for example, they may mean "included", "included" , "including" and the like; and that the terms such as "consisting essentially of" and "consisting essentially of" have the meaning ascribed to them in the United States patent law, for example, they allow elements not explicitly mentioned, exclude elements that are found in the prior art or that affect a basic or novel feature of the invention. These and other modalities are disclosed or are obvious from and encompassed by, the following Detailed Description. BRIEF DESCRIPTION OF THE DRAWINGS The following detailed description, given by way of example, not proposed to limit the invention only to the specific embodiments described, can be better understood in conjunction with the accompanying drawings, in which: FIG. 1 provides a schematic annotation of the cDNA and genomic DNA sequences of the bovine TFAM gene using a combination of the in silico procedure with amplification of the target PCR region.

FIG. 2 provides a nucleotide sequence of the region upstream of the bovine TFAM gene (SEQ ID NO: 1). This sequence corresponds to the 5 'flanking region and exon 1. The coding sequence is shaded. The putative transcription site was numbered as +1. Consensual sequences for SP1, NRF1 and the potential transcriptional repressor are shown by the arrows. Many potential mCpG sites are underlined. An extra AUG codon upstream of the normal translation site is in bold and marked. Both substitutions C / A and C / T are marked by arrows and numbers. FIG. 3 provides a demonstration of a C / A and C / T SNP in the region of the bovine TFAM promoter. Left: a homozygote with CC and CC; Right: a homozygote with AA and TT in two positions separated by 9 bp inclusive. FIG. 4 provides genotyping with PCR-RFLP of two SNPs in the bovine TFAM promoter. Strips 1 and 8: stairs of 100 bp. Strips 2-7: an 801 bp fragment was digested with the restriction enzyme Dpnll. Stripes 2 and 3, animals TT (55 + 68 + 135 + 241 + 302bp); strips 4 and 5, CT animals (55 + 68 + 135 + 241 + 302 + 543bp); and strips 6 and 7, CC animals (55 + 68 + 135 + 543bp). Strips 9-14: a fragment of 801 bp was digested with the restriction enzyme fíaelll. Strips 9 and 10, animals AA (152 + 187 + 462bp); strips 11 and 12, CA animals (83 + 104 + 152 + 187 + 462bp); and stripes 13 and 14, CC animals (83 + 104 + 152 + 462bp). FIG. 5 identifies genetic polymorphisms in bovine TFAM, TFB1M and TFB2M genes. A. A third substitution mutation C / T in the region of the TFAM promoter. B. Two mutations detected in the bovine TFB1M gene using accumulations of DNA. C. Five mutations developed in the bovine TFB2M gene using accumulations of DNA. FIG. 6A provides a cDNA sequence of TFAM of cattle cattle (2259bp) (SEQ ID N0: 2). FIG. 6B provides a genomic DNA sequence of TFAM from cattle (16666bp) (SEQ ID NO: 3).

The exons are shaded, as well as the mutation sites.

See, for example, GenBank Accesses Nos. AAFC02110692 and AAFC0201944. FIG. 7 illustrates a flowchart of data entry and output of analysis results and the correlation of data pertaining to reproduction, veterinary histories and performance requirements of a group of animals such as a herd of cows and the Interactive flow of data from the computer-aided de to a body of students learning the use of the method of the invention. FIG. 8 illustrates the potential relationships between the data elements to be introduced into the system. Unidirectional arrows indicate, for example, that a stable it is typically owned by only one farm, while a farm can have several stables. Similarly, a prescription may include veterinary products. FIG 9A illustrates the flow of events in the use of the laptop-based system for the input of data on breeding and rearing a herd of cows. FIG. 9B illustrates the flow of events through the sub-routines related to the input of data concerning farm management. FIG. 9C illustrates the flow of events through subroutines related to the entry of data concerning company-specific data. FIG. 10 illustrates a flowchart of data entry and output of analysis results and correlation of data pertaining to reproduction, veterinary histories and performance requirements of a group of animals. DETAILED DESCRIPTION The practice of the present invention will employ, unless otherwise indicated, conventional techniques of molecular biology, microbiology, recombinant DNA technology, immunology, which are within the skill of the art. Such techniques are fully explained in the literature. See, for example, Sambrook et al. (2001) Molecular Cloning: A Laboratory Manual, 3rd ed., Cold Spring Harbor Press; DNA Cloning, Vols. I and II (D. N. Glover ed., 1985); Oligonucleotide Synthesis (M. J. Gait ed. 1984); Nucleic Acid Hybridization (B. D. Hames &S. J. Higgins eds, 1984); Animal Cell Culture. (R. K. Freshney ed. 1986); Immobilized Cells and Enzymes (IRL press, 1986); Perbal, B., A Practical Guide to Molecular Cloning (1984); the series, Methods In Enzymology (S. Colowick and N. Kaplan eds., Academic Press, Inc.); and Handbook of Experimental Immunology, Vols. I-IV (D. M. Weir and C. C. Blackwell eds., 1986, Blackwell Scientific Publications). Before describing the present invention in detail, it is to be understood that this invention is not limited to particular DNA, polypeptide sequences or process parameters since such, of course, may vary. It is also to be understood that the terminology used herein is for purposes of describing particular embodiments of the invention only, and is not intended to be limiting. Unless defined otherwise, all technical and scientific terms used herein have the same meaning as is commonly understood by one of ordinary skill in the art to which the invention pertains. Although a number of methods and materials similar or equivalent to those described herein may be used in the practice of the present invention, Preferred materials and methods are described herein. In the description of the present invention, the following terms will be employed and are proposed to be defined as indicated below. The term "cow" or "cattle" is generally used to refer to an animal of bovine origin of any age. Interchangeable terms include "bovine," "calf," "bull," "bull," "heifer," and the like. It also includes an individual animal at all stages of development, including the embryonic and fetal stages. The animals as referred to herein may also include individuals or groups of individuals that are created for different food production such as, but not limited to, transgenic animals for the production of biopharmaceuticals including antibodies and other proteins and protein products. For the term "complementarity" or "complementary" is proposed, for the purposes of the specification or claims, a sufficient number in the oligonucleotide of complementary base pairs in its sequence to specifically interact (hybridize) with a target nucleic acid sequence of the gene polymorphism to be amplified or detected. As is known to those skilled in the art, a very high degree of Complementarity is necessary for the specificity and sensitivity that hybridization involves, although it does not need to be 100%. Thus, for example, an oligonucleotide that is identical in nucleotide sequence to an oligonucleotide disclosed herein, except for a base change or substitution, may function in an equivalent manner to the disclosed oligonucleotides. A "complementary DNA" or "cDNA" gene includes recombinant genes synthesized by reverse transcription of messenger RNA ("mRNA"). A "cyclic polymerase mediated reaction" refers to a biochemical reaction in which a template molecule or a population of template molecules is periodically and repeatedly copied to create a complementary template molecule or complementary template molecules to thereby increase the number of Template molecules over time. By the term "detectable moiety" it is proposed, for purposes of the specification or claims, a brand molecule (isotopic and non-isotopic) that is incorporated directly or indirectly into an oligonucleotide, wherein the label molecule facilitates detection of the oligonucleotide in which is incorporated, for example, when the oligonucleotide is hybrid to amplified gene polymorphic sequences. Thus, "detectable portion" is used synonymously with "brand molecule". The synthesis of Oligonucleotide can be made by any of several methods known to those skilled in the art. Brand molecules, known to those skilled in the art as being useful for detection, include chemiluminescent, fluorescent or luminescent molecules. Several fluorescent molecules are known in the art that are suitable for use to label a nucleic acid for the method of the present invention. The protocol for such incorporation may vary depending on the fluorescent molecule used. Such protocols are known in the art for the respective fluorescent molecule. "DNA amplification" as used herein refers to any process that increases the number of copies of a specific DNA sequence by enzymatically amplifying the nucleic acid sequence. A variety of processes are known. One of the most commonly used is the polymerase chain reaction (PCR) process of Mullis as described in U.S. Patent Nos. 4,683,195 and 4,683,202. Methods, devices and reagents are described in U.S. Patent Nos. 6,951,726; 6,927,024; 6,924,127; 6,893,863; 6,887,664; 6,881,559; 6,855,522; 6,855,521; 6,849,430; 6,849,404; 6,846,631; 6,844,158; 6,844,155; 6, 818,437; 6,818,402; 6,794, 177; 6,794,133; 6,790,952; 6, 783, 940; 6, 773, 901; 6, 770,440; 6, 767, 724; 6, 750, 022; 6, 744,789; 6, 733, 999; 6, 733, 972; 6, 703, 236; 6, 699, 713; 6, 696, 277; 6, 664, 080; 6, 664, 064; 6, 664, 044; RE38, 352; 6, 650, 719; 6, 645, 758; 6, 645, 720; 6, 642, 000; 6, 638, 716; 6, 632, 653; 6, 617, 107; 6, 613, 560; 6, 610, 87; 6, 596, 492, 6, 586, 250; 6, 586, 233; 6, 569, 678; 6, 569, 627; 6, 566, 103, 6, 566, 067; 6, 566, 052; 6, 558, 929; 6, 558, 909; 6, 551, 783, 6, 544, 782; 6, 537, 752; 6, 524, 830; 6, 518, 020; 6, 514, 750, 6, 514, 706; 6, 503, 750; 6, 503,705; 6, 493, 640; 6, 92, 114, 6,485, 907; 6,485, 903; 6, 82, 588; 6, 75, 729; 6, 68, 743, 6, 465, 638; 6, 465, 637; 6, 465, 171; 6, 48, 014; 6, 432, 646 6, 428, 987; 6, 26, 215; 6, 423, 499; 6, 410, 223; 6, 03, 341 6, 399, 320; 6, 395, 518; 6, 391, 559; 6, 383, 755; 6, 379, 932 6, 372, 484; 6, 368, 834; 6, 365, 375; 6, 358, 680; 6, 355, 422 6, 348, 336; 6, 346, 384; 6, 319, 673; 6, 316, 195; 6, 316, 192 6, 312, 930; 6, 309, 840; 6, 309, 837; 6, 303, 343; 6, 300, 073 6, 300, 072; 6,287,781; 6, 284, 55; 6, 277, 605; 6, 270, 977 6, 270, 966; 6, 268, 153; 6, 268, 1 3; D445, 907; 6, 261, 431 6, 258, 570; 6, 258, 567; 6, 258, 537; 6, 258, 529; 6, 251, 607 6, 248, 567; 6, 235, 468; 6, 232, 079; 6, 225, 093; 6, 221, 595 D441, 091; 6.218, 153; 6, 207, 425; 6, 183,999; 6, 183, 963 6, 180, 372; 6, 180, 349; 6, 174, 670; 6, 153, 412; 6, 146, 834 6, 143, 496; 6, 140, 613; 6, 140, 110; 6, 103, 468; 6, 087, 097 6, 072, 369; 6, 068, 974; 6, 063, 563; 6, 048, 688; 6, 046, 039 6, 037, 129; 6, 033, 854; 6, 031, 960; 6, 017, 699; 6,015, 664 6, 015, 534; 6, 004, 747; 6, 001, 612; 6, 001, 572; 5, 985, 619, 5, 976, 842; 5, 972, 602; 5, 968, 730; 5, 958, 686; 5, 955, 274, 5, 952, 200; 5, 936, 968; 5, 909, 468; 5, 905, 732; 5, 888, 740 5, 883, 924; 5, 876, 978; 5, 876, 977; 5, 874, 221; 5, 869, 318 5, 863, 772; 5, 863, 731; 5, 861, 251; 5, 861, 245; 5, 858, 725 5, 858, 718; 5, 856, 086; 5, 853, 991; 5, 849, 497; 5, 837, 468 5, 830, 663; 5, 827, 695; 5, 827, 661; 5, 827, 657; 5, 824, 516 5, 824, 479; 5, 817, 797; ' 5, 814, 489; 5, 814, 453; 5, 811, 296 5, 804, 383; 5, 800, 997; 5, 780.271; 5, 780, 222; 5, 776, 686 5, 774, 497; 5, 766, 889; 5, 759, 822; 5, 750, 347; 5, 747, 251 5, 741, 656; 5, 716, 784; 5, 712, 125; 5, 712, 090; 5, 710, 381 5, 705, 627; 5,702, 884; 5, 693, 67; 5, 691, 146; 5, 681, 741 5, 674, 717; 5, 665, 572; 5, 665, 539; 5, 656, 93; 5, 656, 461 5, 654, 144; 5, 652, 102; 5, 650, 268; 5, 643, 765; 5, 639, 871 5, 639, 611; 5, 639, 606; 5, 631, 128; 5, 629, 178; 5, 627, 054 5, 618, 703; 5, 618, 702; 5, 614, 388; 5, 610, 017; 5, 602, 756 5, 599, 674; 5, 589, 333; 5, 585, 238; 5, 576, 197; 5, 565, 340 5, 565, 339; 5, 556, 77; 5, 556, 773; 5, 538, 871; 5, 527, 898 5, 527, 510; 5, 514, 568; 5, 512, 463; 5, 512, 462; 5, 501, 947 5, 494, 795; 5, 491, 225; 5, 487, 993; 5, 487, 985; 5, 484, 699 5, 476, 774; 5, 475, 610; 5, 447, 839; 5, 37, 975; 5, 436, 144 5, 426, 026; 5, 20, 009; 5, 411, 876; 5, 393, 657; 5, 389, 512 5, 364, 790; 5, 364, 758; 5, 340, 728; 5, 283, 171; 5,279, 952 5, 254, 69; 5, 241, 363; 5, 232, 829; 5, 231, 015; 5, 229, 297 5, 224, 778; 5, 219, 727; 5, 213, 961; 5, 198, 337; 5, 187, 060 5,142,033; 5,091,310; 5,082,780; 5,066,584; 5,023,171 and 5,008,182 may also be employed in the practice of the present invention. PCR involves the use of a thermostable polymerase DNA, sequences known as primers, and heating cycles, which separate the replicating deoxyribonucleic acid (DNA), strands and exponentially amplify a gene of interest. Any type of PCR, such as quantitative PCR, RT-PCR, warm start PCR, LAPCR, multiplex PCR, direct touch PCR, etc., can be used. Advantageously, real-time PCR is used. In general, the PCR amplification process involves a cyclic enzymatic chain reaction to prepare exponential amounts of the specific nucleic acid sequence. This requires a small amount of a sequence to initiate the chain reaction and the oligonucleotide primers that will hybridize to the sequence. In PCR the primers are recosening to denatured nucleic acid followed by extension with an induction agent (enzyme) and nucleotides. This results in newly synthesized extension products. Since these newly synthesized sequences become templates for the primers, repeated cycles of denaturation, primer annealing and extension results in the exponential accumulation of the specific sequence that is amplified. The extension product of the chain reaction will be a discrete nucleic acid duplex with terminals corresponding to the ends of the specific primers employed. By the terms "enzymatically amplified" or "amplified" it is proposed, for the purposes of the specification or claims, DNA amplification, that is, a process by which the nucleic acid sequences are amplified in number. There are several means for enzymatically amplifying nucleic acid sequences. Currently, the most commonly used method is the polymerase chain reaction (PCR). Other methods of amplification include LCR (ligase chain reaction) using ligated DNA, and a probe consisting of two halves of a DNA segment that is complementary to the DNA sequence to be amplified, QB replicase enzyme and a template of ribonucleic acid (RNA) sequence linked to a probe complementary to the DNA to be copied that is used to make a DNA template for the exponential production of complementary RNA; strand displacement amplification (SDA), amplification of 0_β replicase (Q RA); self-sustained replication (3SR) and NASBA (amplification based on nucleic acid sequence) that can be performed on RNA or DNA as the nucleic acid sequence is amplified. A "fragment" of a molecule such as a protein or nucleic acid is proposed to refer to any portion of the genetic sequence of amino acids or nucleotides. As used herein, the term "genome" refers to all genetic material in the chromosomes of a particular organism. Its size is usually given as its total number of base pairs. Within the genome, the term "gene" refers to an ordered sequence of nucleotides located at a particular position on a particular chromosome that encodes a specific functional product (e.g., a protein or RNA molecule). In general, the genetic characteristics of an animal, as defined by the nucleotide sequence of its genome, are known as its "genotypes", while the animal's physical attributes are described as its "phenotype". By "heterozygous" or "heterozygous polymorphism" it is proposed that the two alleles of a diploid cell or organism at a given site are different, ie they have a different nucleotide exchanged by the same nucleotide at the same place in their sequences. By "homozygous" or "homozygous polymorphism" it is proposed that the two alleles of a diploid cell or organism at a given site are identical, ie they have the same nucleotide exchange at the same place in their sequences.

By "hybridization" or "hybridizing" as used herein, the formation of base pairs A-T and C-G between the nucleotide sequences of a fragment of a segment of a polynucleotide and a nucleotide sequence complementary to an oligonucleotide is proposed. By complementary it is proposed that at the site of each A, C, G or T (or U in a ribonucleotide) in the sequence of the fragment, the sequenced oligonucleotide has a T, G, C or A, respectively. The hybridized fragment / oligonucleotide is called a "duplex". A "hybridization complex", such as an intercalation assay, means a complex of nucleic acid molecules that includes at least the target nucleic acid and a sensing probe. This can also include a fixed probe. As used herein, the term "site" or "sites" refers to the location of a gene on a chromosome. Pairs of genes, known as "alleles" control the hereditary attribute produced by a gene site. Each particular allele combination of the animal is referred to as its "genotype". Where both alleles are identical the individual is said to be homozygous for the attribute controlled by that pair of genes; where the alleles are different, the individual is said to be heterozygous for the attribute. A "melting temperature" is proposed in the temperature at which the hybridized duplexes are uninhibited and return to their state in a single strand. Likewise, hybridization will not occur in the first place between two oligonucleotides or, in the present, an oligonucleotide and a fragment, at temperatures above the melting temperature of the resulting duplex. It is presently advantageous that the difference in the melting point temperatures of oligonucleotide duplexes of a fragment of this invention is from about 1 ° C to about 10 ° C to be easily detectable. As used herein, the term "nucleic acid molecule" is intended to include DNA molecules (e.g., cDNA or genomic DNA), RNA molecules (e.g., mRNA), DNA or RNA analogs generated using analogs of nucleotides and derivatives, fragments and homologs thereof. The nucleic acid molecule can be single-stranded or double-stranded, but advantageously it is double-stranded DNA. "DNA" refers to the polymeric form of deoxyribonucleotides (adenine, guanine, thymine, or cytosine) in its either single-stranded or double-stranded helix form. This term refers only to the primary and secondary structure of the molecule, and does not limit it to any of the particular tertiary forms. Thus, this term includes double-stranded DNA found, inter alia, in linear DNA molecules (e.g. restriction fragments), viruses, plasmids and chromosomes. In the discussion of the structure of the particular double-stranded DNA molecules, the sequences can be described herein in accordance with the normal convention of given only the sequence in the 5 'to 3' direction along the strand not DNA transcript (ie, the strand that has a sequence homologous to mRNA). An "isolated" nucleic acid molecule is one that is separated from other nucleic acid molecules that are present in the natural source of the nucleic acid. A "nucleoside" refers to a base linked to a sugar. The base can be adenine (A), guanine (G) (or its substitute, inosine (I)), cytosine (C), or thymine (T) (osu substitute, uracil (U)). The sugar can be ribose (the sugar of a natural nucleotide in RNA) or 2-deoxyribose (the sugar of a natural nucleotide in DNA). A "nucleotide" refers to a nucleoside linked to a single phosphate group. As used herein, the term "oligonucleotide" refers to a series of linked nucleotide residues, the oligonucleotide having a sufficient number of nucleotide bases to be used in a PCR reaction. A short oligonucleotide sequence may be based on, or designed from, a genomic or cDNA sequence and used to amplify, confirm or reveal the presence of an identical DNA or RNA or similar complementary in a particular cell or tissue. The oligonucleotides can be chemically synthesized and can be used as probe primers. Oligonucleotide means any nucleotide of more than three bases in length used to facilitate the detection and identification of a target nucleic acid including probes and primers. A "polymerase" is an enzyme that catalyzes the sequential addition of monomer units or a polymer chain, or links two or more monomer units to start a polymer chain. The "polymerase" will work by adding monomeric units whose identity is determined by and that is complementary to a template molecule of a specific sequence. For example, DNA polymerases such as Taq polymerase pol 1 and deoxyribonucleotides added to 3 'end of a polynucleotide chain in a template-dependent manner, to thereby synthesize a nucleic acid which is complementary to the template molecule. The polymerases can be used either to extend a primer once or effectively or to amplify a polynucleotide by repetitively priming two strands supplemented using two primers. A "thermostable polymerase" refers to a DNA or RNA polymerase enzyme that can withstand extremely high temperatures such as those approaching 100 ° C. Frequently, polymerases Thermostats are derived from organisms that live in extreme temperatures, such as Thermus aquaticus. Examples of thermostable polymerases include Taq, Tth, Pfu, Vent, deep vent, UITma, and variations and derivatives thereof. A "polynucleotide" refers to a linear chain of nucleotides connected by a phosphodiester linkage between the 3'-hydroxyl group and the 5'-idroxyl group of a second nucleoside which in turn is linked through its 3'- group. hydroxyl to the 5'-hydroxyl group of a third nucleoside and so on to form a polymer comprised of nucleosides linked by a phosphodiester backbone. A "modified polynucleotide" refers to a polynucleotide in which one or more natural nucleotides have been partially, substantially or completely replaced with modified nucleotides. A "primer" is an oligonucleotide, the sequence of at least a portion of which is complementary to a segment of a template DNA that is to be amplified or replicated. Typical primers are used in the performance of the polymerase chain reaction (PCR). A hybrid primer with (or recose to "the DNA" template and is used by the polymerase enzyme that it uses as the starting point for the replication / amplification process.) The primers herein are selected to be "substantially" complementary. to different strands of a DNA sequence particular objective. This means that the primers must be sufficiently complementary to hybridize with their respective strands. Therefore, the sequence of primers need not reflect the exact sequence of the template. For example, a non-complementary nucleotide fragment can be attached to the 5 'end of the primer, with the remainder of the primer sequence being complementary to the strand. Alternatively, the non-complementary bases or their longer sequences can be interspersed in the primer, provided that the primer sequence has sufficient complementarity with the sequence of the strand to hybridize therewith and thus form the template for the synthesis of the extension product. "Probes" refers to oligonucleotides of variable length nucleic acid sequences, used in the detection of identical, similar or complementary nucleic acid sequences for hybridization. An oligonucleotide sequence used as a detection probe can be labeled with a detectable portion. The following are non-limiting examples of polynucleotides: a gene or gene fragment, exons, introns, mRNA, tRNA, rRNA, ribozymes, cDNA, recombinant polynucleotides, branched polynucleotides, plasmids, vectors, DNA isolated from any sequence, RNA isolated from any sequence, probes and nucleic acid primers. A The polynucleotide can comprise modified nucleotides, such as methylated nucleotides and nucleotide analogues, uracil, other sugars and linking groups such as fluororibose and thiolated, and nucleotide branches. The nucleotide sequence can be further modified after the polymerization, such as by conjugation, with a labeling component. Other types of modifications included in this definition are terminations, substitution of one or more of the naturally occurring nucleotides with an analog, and introduction of means for binding the polynucleotide to proteins, metal ions, labeling components, other polynucleotides or solid supports. An "isolated" polynucleotide or polypeptide is one that is substantially pure from the materials with which it is associated in its native environment. By substantially free, at least 50%, at least 55%, at least 60%, at least 65%, advantageously at least 70%, at least 75%, more advantageously at least 80%, is proposed , at least 85%, even more advantageously at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96 %, at least 97%, much more advantageously at least 98%, at least 99%, at least 99.5%, at least 99.9% free of these materials. An "isolated" nucleic acid molecule is a discrete and discrete nucleic acid molecule of the complete organism with which the molecule is found in nature; or a nucleic acid molecule free of, in whole or in part, sequences normally associated with this in nature; or a sequence, as it exists in nature, but which has heterologous sequences (as defined below) in association with it. The term "polynucleotide encoding a protein" as used herein refers to an isolated DNA fragment or DNA molecule that encodes a protein, or the strand complementary thereto; but, RNA is not excluded, since thermal is understood as thymidine (T) in a DNA sequence is considered equal to uracil (U) in an RNA sequence. Thus, the RNA sequences for use in the invention, for example, for use in RNA vectors, can be derived from DNA sequences, by thymidine (T) in the DNA sequence which is considered equal to uracil (U). ) in the RNA sequences. A "coding sequence" of DNA or a "nucleotide sequence encoding" a particular protein is a DNA sequence that is transcribed and translated into a polypeptide in vitro or in vivo when placed under the control of appropriate regulatory elements. The limits of the coding sequence are determined by a start codon at the 5 '(amino) terminal and a codon of translation stop at the 3 '(carboxy) terminal. A coding sequence can include, but is not limited to prokaryotic sequences, eukaryotic mRNA cDNA, genomic DNA sequences of eukaryotic (e.g., mammalian) DNA and even synthetic DNA sequences. A transcription termination sequence will usually be located 3 'for the coding sequence. "Homology" refers to the percent identity between two polynucleotides or two portions of polypeptide. Two DNA, or two polypeptide sequences are "substantially homologous" to each other when the sequences exhibit at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, preferably at least about 90%, 91%, 92%, 93%, 94% and much more preferably at least about 95%, 96%, 97%, 98%, 99%, 99.5%, 99.9% sequence identity over a defined length of the molecules. As used herein, "substantially homologous" also refers to sequences that exhibit complete identity (100% sequence identity) to the specified DNA or polypeptide sequence. Homology can be determined by hybridizing polynucleotides under conditions that form stable duplexes between homologous reactions, followed by digestion with single-stranded nuclease (s), and size determination of the digested fragments. The DNA sequences that are substantially homologous can be identified in low Southern hybridization experiments, for example, severe conditions, as defined for this particular system. The definition of appropriate hybridization conditions is within the skill of the technique. See, for example, Sambrook et al. Supra; DNA Cloning, supra; Nuclexc Acid Hybridization, supra. Two fragments of nucleic acid are considered to be "selectively hybridizable" to a polynucleotide if they are capable of specifically hybridizing to a nucleic acid a variant thereof or specifically priming a polymerase chain reaction: (i) under hybridization and washing conditions typical, as described, for example, in Sambrook et al., supra and Nucleic Acid Hybridization, supra, (ii) using reduced stringency wash conditions that allow at most approximately 25-30% of base pair pairings, by example: 2x SSC, 0.1% SDS, room temperature twice, 30 minutes each; then 2x SSC, 0.1% SDS, 37 ° C once, 30 minutes; then 2 x SSC room temperature twice, 10 minutes each, or (iii) select primers for use in typical polymerase chain reactions (PCR) under standard conditions (described for example in Saiki, et al., (1988) Science 239: 487-491). The term "able to hybridize under conditions "Severe" as used herein refers to the annealing of a first nucleic acid or a second nucleic acid under severe conditions as defined below The conditions of severe hybridization typically allow for the hybridization of nucleic acid molecules having at least 70 nucleic acids. % sequence identity of nucleic acid with the nucleic acid molecule that is used as a probe in the hybridization region For example, the first nucleic acid can be a test sample or probe, and the second nucleic acid can be the sense or antisense strand of a nucleic acid or a fragment thereof Hybridization of the first and second nucleic acids can be conducted under severe conditions, for example, at high temperature and / or low salt content which tends to disfavor hybridization of different nucleotide sequences.Alternatively, the hybridization of the first and the second nucleic acid can be conducted low with conditions of reduced severity, for example, low temperature and / or high salt content that tend to favor the hybridization of different nucleotide sequences. Hybridization conditions of low severity can be followed by conditions of high severity or intermediate severity conditions to increase the selectivity of the first and second nucleic acid linkage. Hybridization conditions may also include reagents such as, but not limited to, dimethyl sulfoxide (MDSO) or formamide to further disadvantage the hybridization of different nucleotide sequences. A suitable hybridization protocol can, for example, involve hybridization in 6 x SSC (wherein 1 x SSC comprises 0.015 M sodium citrate and 0.15 M sodium chloride), at 65 ° Celsius in an aqueous solution, followed by washing with 1 x SSC at 65 ° C. The formulas for calculating the appropriate hybridization and washing conditions to achieve hybridization that allows 30% or less mismatches between two nucleic acid molecules are disclosed, for example, in Meinkoth et al., (1984) Anal. Biochem. 138: 267-284; the content of which is incorporated herein by reference in its entirety. Protocols for hybridization techniques are well known to those of skill in the art and standard molecular biology manuals can be consulted to select an appropriate hybridization protocol without undue experimentation. See, for example, Sambrook et al., (2001) Molecular Cloning: A Laboratory Manual, 3rd ed. , Cold Spring Harbor Press, the contents of which are incorporated herein by reference in their entirety. ' Typically, severe conditions will be those in which the salt concentration is less than about 1.5 M sodium ion, typically about 0.01 to 1.0 M concentration of sodium ion (or other salts) from about pH 7.0 to about pH 8.3 and the temperature is at least about 30 ° Celsius for short probes (eg, 10 to 50 nucleotides) and so less about 60 ° C for long probes (for example, greater than 50 nucleotides). Severe conditions can also be achieved by the addition of destabilizing agents such as formamide. Exemplary low stringency conditions include hybridization with a formamide buffer solution at 30 to 35%, 1 M NaCl, 1% SDS (sodium dodecyl sulfate) at 37 ° Celsius, and a wash at 1-2 x SSC at 50 at 55 ° Celsius. Exemplary moderate severity conditions include hybridization in 40 to 45% formamide, 1 M NaCl, 1% SDS at 37 ° Celsius, and a 0.5-1 x SSC wash at 55 to 60 ° Celsius. Exemplary high stringency conditions include hybridization in 50% formamide, 1 M NaCl, 1% SDS at 37 ° Celsius, and a 0.1 x SSC wash at 60 to 65 ° Celsius. The methods and materials of the invention can be used more generally to evaluate a DNA sample from an animal, genetically the type of an individual animal and detect genetic differences in the animals. In particular, a genomic DNA sample from an animal can be evaluated by reference to one or more controls to determine whether a SNP, or group of SNPs, in a gene is present.

Any method for determining the genotype can be used to determine the genotype in the present invention. Such methods include, but are not limited to, amplification sequencing, DNA sequencing, fluorescence spectroscopy, hybridization analysis based on fluorescence resonance energy transfer (or "FRET") high performance classification, mass spectroscopy, microsatellite analysis, nucleic acid hybridization, polymerase chain reaction (PCR), R FL P analysis and size chromatography (for example, capillary or gel chromatography), all of which are well known for one of skill in technique. In particular, methods for determining nucleotide polymorphisms, particularly individual nucleotide polymorphisms, are described in U.S. Patent Nos. 6,514,700; 6,503,710; 6,468,742; 6,448,407; 6,410,231; 6,383,756; 6,358,679; 6,322,980; 6,316,230; and 6,287,766 and reviewed by Chen and Sullivan, Pharmacogenomics J 2003; 3 (2): 77 -96, the description of each of which are incorporated by reference in their totalities. The genotypic data useful in the methods of the invention and the methods for identifying animal attributes are based on the presence of SNPs. A "restriction fragment" refers to a fragment of a polynucleotide generated by an endonuclease of restriction (an enzyme that cleaves phosphodiester bonds within a polynucleotide chain) that cleaves DNA in response to a recognition site on DNA. The recognition site (restriction site) consists of a specific sequence of nucleotides typically about 4-8 nucleotides long. An "individual nucleotide polymorphism" or "SNP" refers to a variation in the nucleotide sequence of a polynucleotide that differs from another polynucleotide by a single nucleotide difference. For example, without limitation, the. exchange of an A by a C, G or T in the complete sequence of the polynucleotide constitutes SNP. It is possible to have more than one SNP in a particular polynucleotide. For example, in a position in a polynucleotide, a C can be exchanged for a T, in another position a G can be exchanged for an A and so on. When referring to SNPs, the polynucleotide is more frequently DNA. As used herein, a "template" refers to a strand of target polynucleotide, for example, without limitation, a strand of DNA that occurs naturally unmodified, a polymerase that is used as a means to recognize which nucleotide should be incorporated immediately. in a strand of growth to polymerize the complement of the strand that occurs naturally. Such a strand of DNA can be single-stranded or can be part of a DNA template of double strand In applications of the present invention that require repeated cycles of polymerization, for example the polymerase chain reaction (PCR) the template strand itself can be modified by the incorporation of modified nucleotides, but still serve as a template for a polymerase to synthesize additional polynucleotides. A "thermocyclic reaction" is a multistage reaction wherein at least two steps are carried out by changing the temperature of the reaction. A "variation" is a difference in the nucleotide sequence between related polynucleotides. The difference may be the deletion of one or more nucleotides from the sequence of a polynucleotide compared to the sequence of a related polynucleotide, the addition of one or more nucleotides or the replacement of one nucleotide by another. The terms "mutation", "polymorphism" and "variation" are used interchangeably in the present. As used herein, the term "variation" in the singular will be considered to include multiple variations; that is, two or more additions, deletions and / or substitutions of nucleotides in the same polynucleotide. A "point mutation" refers to a single substitution of one nucleotide for another. As used herein, the terms "attributes", "quality attributes" or "characteristics" "Physical" or "phenotypes" refer to advantageous animal properties that result from genetics.Quality attributes include, but are not limited to, the animal's genetic ability to efficiently metabolize energy, produce meat or milk, place fat Intramuscular Physical characteristics include, but are not limited to, marbled, soft or lean meats Terms can be used interchangeably A "computer system" refers to the hardware medium Software medium and data storage media used to compile the data of the present invention The minimum hardware means of computer-based systems of the invention may comprise a central processing unit (CPU), input means, output means and data storage means. a monitor is provided to visualize the structure data.The data storage medium can be RAM or other means to enter the computer readable medium of the invention. Examples of such systems are microcomputer workstations available from Silicon Graphics Incorporated and Sun Microsystems that operate based on Unix, Linux, Windows NT, XP or IBM OS / 2 operating systems. "Computer readable medium" means any media that can be read and entered directly by a computer, and includes, but is not limited to: magnetic storage such as soft disks, hard storage media and magnetic tape; optical storage medium such optical discs or CD-ROOM; electrical storage means such as RAM and ROM; and hybrids of those categories, such as magnetic / optical media. By providing such a computer-readable medium, the data compiled on a particular animal can be routinely entered by a user, for example, a feed batch operator. The term "data analysis module" is defined herein to include any individual or machine, individually or jointly, which analyzes the sample and determines the genetic information contained therein. The term may include a person or machine within a laboratory facility. As used herein, the term "data collection module" refers to any person or object or system that has a tissue sample from an animal or embryo. For example and without limitation, the term may individually or collectively define the person or machine in physical contact with the animal as the sample is taken, the containers containing the tissue samples, the packaging used to transport the samples and the like. Advantageously, the data collector is a person. More advantageously data collector is a cattle farmer, a breeder or a veterinarian. The term "network interface" is defined herein to include any person or computer system capable of entering data, depositing data, combining data, analyzing data, investigating data, transmitting data or storing data. The term is broadly defined to be a person who analyzes the data, the electronic hardware and software systems used in the analysis, the databases that store the data analysis and any storage medium capable of storing the data. Non-limiting examples of network interfaces include people, automated laboratory equipment, computers and computer networks, data storage devices such as, but not limited to, disks, hard drives or memory chips. The term "reproduction history" as used herein refers to a record of the life of an animal or group of animals that includes, but is not limited to, the location, reproduction, period of housing, as well as genetic history of the animals, including the kinship and descendants of the same, genotype, phenotype and transgenic history if relevant and similar. The term "breeding conditions" as used herein refers to parameters related to the maintenance of animals including, but not limited to, the temperature of the shed or lodging, weekly mortality of a herd, consumption of water, consumption of food, proportion and quality of ventilation, condition of the bait and the like. The term "veterinary history" as used herein refers to vaccination data of an animal or group of animals, including, but not limited to, type (s) of vaccine, serial number (s) of vaccine lot. , dose administered, target antigen, method of administering the vaccine to the recipient animal (s), number of vaccinated animals, age of the animals and the vaccinator. Data related to a serological or immunological response induced by the vaccine may also be included. "Veterinary history" as used herein is also proposed to include the medication history of the target animal (s), including but not limited to drug and / or antibiotics administered to the animals including the type of medication administered, amount and proportions of dosage, by whom and when they were administered, by what route, for example oral, subcutaneously and the like, and the response to the medication including the desired and undesirable effects of the same. The term "diagnostic data" as used herein refers to data related to the health of the animal (s) different from the data detailing the vaccination or medication history of the animal (s). For example, the diagnostic data may be a record of the infections experienced by the animal (s) and the response thereof to the medications provided to treat such medications. Serological data that include the composition of serum protein antibody or other biofluids may also be useful diagnostic data to be introduced into the methods of the invention. Surgical data pertaining to the animal (s) may be included, such as the type of surgical manipulation, effect of the surgery and complications arising from the surgical procedure. "Diagnostic data" may also include measurements of such parameters as weight, morbidity and other characteristics observed by a veterinary service such as the condition of the skin, the legs, etc. The term "welfare data" as used herein refers to the collective accumulation of data pertaining to an animal or group of animals that includes, but is not limited to, a history of reproduction, a veterinary history, a profile of welfare, diagnostic data, quality control data or any combination thereof. The term "welfare profile" as used herein refers to parameters such as weight, density of the meat, levels of stacking in breeding or breeding enclosures, psychological behavior of the animal, proportion of growth and quality of the similar. The term "quality control" as used herein refers to the desired characteristics of the animal (s). For animals other than poultry such as cattle and sheep, for example, such parameters include the amount and density of the muscle, fat content, meat softness, milk yield and quality, ability to reproduce the like . The term "performance parameters" as used herein refers to such factors as beef marbling, subcutaneous fat, meat yield, breeding performance, dairy form, meat yield quality, speed of pregnancy of daughters (ie, fertility), productive life (ie, longevity) and the like that may be the desired objectives of the reproduction and breeding of the animal (s). The performance parameters can be either generated from the animals themselves, or those parameters desired by a customer or the market. The term "nutritional data" as used herein refers to the composition, amount and frequency of food supply including water, provided to the animal (s).

The term "food safety" as used herein refers to the quality of the meat of a livestock animal, including, but not limited to, time, place and manner of preparation, storage of the food product, transportation route. , inspection record, texture, color, taste, smell, bacterial content, parasitic content and the like. It will be apparent to those of skill in the art that data related to the health and maintenance of animals can be grouped variously depending on the source or intent of the data collector and any grouping in the present is therefore not proposed to be limitative. Unless otherwise defined, all technical and scientific terms used herein have the same meaning as is commonly understood by one of ordinary skill in the art of molecular biology. Although methods and materials similar or equivalent to those described herein may be used in the practice or testing of the present invention, suitable methods and materials are described herein. In one embodiment, wherein the gene of interest is bovine TFAM, the nucleotide sequence of bovine TFAM can be selected from, but not limited to, the sequence corresponding to GenBank Access Nos. AAFC0211069 or AAFC02019444 (SEQ ID NO: 3) or a fragment thereof or a region of the bovine genome comprising this sequence. The present invention, therefore, provides isolated nucleic acids that can hybridize specifically to the nucleotide sequence corresponding to GenBank Accession No. AAFC0211069 or AAFC02019444 (SEQ ID N0: 3), or the complement thereof, and which comprises the site polymorphic corresponding to nucleotide positions -1220, -1212 or -995. The individual nucleotide polymorphism (s) of interest can be selected from the group consisting of a substitution of A to C at the position of nucleotide -1220 in the promoter of the TFAM gene, a substitution of T to C at position -1212 in the promoter of the TFAM gene and a substitution of T a C at position -995 in the promoter of the TFAM gene. The advantageous SNP in the present invention is associated with certain economically valuable and heritable attributes related to the quality of beef in cattle. Therefore, it is an object of the present invention to determine the genotype of a given animal of interest as defined by the SNP of the TFAM site according to the present invention. It is also contemplated that the genotype of the animal (s) may be defined by additional SNPs within the TFAM gene or within other genes identified with desirable attributes or other characteristics, and in particular by a panel or panels of SNPs. There are many methods known in the art for determining the DNA sequence in a sample, and for identifying whether a given DNA sample contains a particular SNP. Any technique known in the art can be used in the performance of the methods of the present invention. The methods of the present invention allow animals with certain economically valuable heritable attributes to be identified based on the presence of SNPs in their genomes and particularly SNPs of the TFAM gene. The methods also allow, by means of computer-assisted methods of the invention, to correlate the attributes associated with SNP with other data pertinent to the welfare and productive capacity of the animals, or group of animals. To determine the genotype of a given animal according to the methods of the present invention, it is necessary to obtain a genomic DNA sample from that animal. Typically, the genomic DNA sample will be obtained from a tissue sample or cells taken from an animal. A tissue or cell sample can be taken from an animal at any time in the lifetime of an animal but before the identity of the channel is lost. The tissue sample may comprise hair, including roots, leather, bones, mouth rubs, blood, saliva, milk, semen, embryos, muscle or any of the internal organs. In the methods of the present invention, the source of the tissue sample, and thus also the source of the test nucleic acid sample, is not critical. For example, the test nucleic acid can be obtained from cells within a body fluid of the animal or from cells that constitute a body tissue of the animal. The particular body fluid from which the cells are obtained is also critical to the present invention. For example, the body fluid can be selected from the group consisting of blood, ascites, pleural fluid and spinal fluid. In addition, the particular body tissue from which the cells are obtained is also not critical to the present invention. For example, body tissue may be selected from the group consisting of skin, endometrium, uterine and cervical tissue. Both normal and tumor tissues can be used. Typically, the tissue sample is marked with an identification number or other legend that relates the sample to the individual animal from which the sample was taken. The identity of the sample advantageously remains constant by all the methods and systems of the invention in order to guarantee the integrity and continuity of the sample during the extraction and the analysis. Alternatively, the legends can be changed in a regular aspect that ensures that the data, and any other associated data, can be related again to the animal from which the data was obtained. The amount / size of sample required is known to those skilled in the art and for example, can be determined by the subsequent steps used in the method and system of the invention and the specific methods of analysis used. Ideally, the size / volume of the recovered tissue sample should be as consistent as possible within the type of sample and the animal species. For example, for cattle, non-limiting examples of sample sizes / methods include non-fat meat: 0.0002 gm-10.0 gm; skin: 0.0004 gm-10.0 gm; hair roots: at least one and advantageously greater than five; mouth rubs: 15 to 20 seconds of rubbing with light pressure in the area between the outer lip and the gum using, for example, a cytology brush; bone: 0.0002 gm-10.0 gm; blood: 30 μ? to 50 mi. Generally, the tissue sample is placed in a container that is marked using a numbering system that carries a code corresponding to the animal, for example, to the label of the animal's ear. Therefore, the genotype of a particular animal is easily traceable at all times. The sampling device and / or container can be supplied to the farmer, a trail or retailer. He Sampling device advantageously takes a consistent and reproducible sample from individual animals while simultaneously avoiding any cross-contamination of the tissue. Therefore, the size and volume of tissues from samples derived from individual animals would be consistent. DNA can be isolated from tissue / cells by techniques well known to those skilled in the art (see, for example, U.S. Patent Nos. 6,548,256 and 5,989,431; Hirota et al., (1989) Jinrui Idengaku Zasshi., 34: 217-23. and John et al., (1991) Nucleic Acids Res. 19: 408, the descriptions of each of which are incorporated by reference in their totalities). For example, high molecular weight DNA can be purified from cells or tissues using proteinase K extraction and ethanol precipitation. The DNA, however, can be extracted from an animal sample using any of other suitable methods known in the art. In one embodiment, the presence or absence of the SNP of any of the genes of the present invention can be determined by sequencing the region of the genomic DNA sample spanning the polymorphic site. Many methods for sequencing genomic DNA are known in the art, and any such method can be used, see for example, Sambrook et al., (2001) Molecular Cloning: A Laboratory Manual, 3rd ed., Cold Spring Harbor Press. For example, it is described below, a DNA fragment encompassing the location of the SNP of interest can be amplified using the polymerase chain reaction. The amplified region of the DNA form can then be sequenced using any method known in the art, for example, using an automated nucleic acid sequencer. The detection of a given SNP can then be performed using probe hybridization and / or using PCR-based amplification methods. Such methods are described in more detail below. The methods of the present invention can be oligonucleotides useful as primers for amplifying specific nucleic acid sequences of the TFAM gene, advantageously the region comprising a TFAM SNP. Such fragments must be of sufficient length to allow annealing or specific hybridization to the nucleic acid sample. The sequences will typically be from about 8 to about 44 nucleotides in length. Longer sequences, for example, from about 14 to about 50 may be advantageous for certain modalities. The design of primers is well known for one of ordinary skill in technique. Inventive nucleic acid molecules include nucleic acid molecules having at least 70% identity or homology or similarity to a TFAM gene or probes or primers derived therefrom such as at least 75% identity or homology or similarity, preferably at least 80% of identity or homology or similarity, more preferably at least 85% identity or homology or similarity such as at least 90% identity or homology or similarity, more preferably at least 95% identity or similar homology or similarity as at least 97% identity or homology or similarity. The similarity or identity homology of the nucleotide sequence can be determined using the "Align" program of Myers and Miller, ("Optimal Alignments in Linear Space", CABIOS 4, 11-17, 1988) and available from NCBI. Alternatively or additionally, the terms "similarity" or "identity" or "homology" for example, with respect to a nucleotide sequence, is proposed to indicate a quantitative measure of homology between two sequences. The percent sequence similarity can be calculated as (Nref-Ndif) * 100 / Nref, where Ndif is the total number of non-identical residues in the two sequences when they are aligned and where Nref is the number of residues in a of the sequences. Accordingly, the AGTCAGTC DNA sequence will have a sequence similarity of 75% with the sequence AATCAATC (Nref = 8; Ndif = 2). Alternatively or additionally, "similarity" with respect to sequences is refers to the number of positions with identical nucleotides divided by the number of nucleotides in the shorter of the two sequences where the alignment of the two sequences can be determined according to the algorithm of Wilbur and Lipman (Wilbur and Lipman, 1983 PNAS USA 80: 726), for example, using a window size of 20 nucleotides, a word length of 4 nucleotides, and a space sanction of, and computer-aided analysis and interpretation of sequence data including alignment it can be conveniently done using commercially available programs (for example, Intelligenetics ™ Suite, Intelligenetics Inc. CA). When the RNA sequences are said to be similar, or have a degree of sequence identity with the DNA sequence, thymidine (T) in the DNA sequence is considered equal to uracil (U) in the RNA sequence. A probe or primer can be any stretch of at least 8, preferably at least 10, more preferably at least 12, 13, 14 or 15, such as at least 20, for example, at least 23 or 25, for example at least 27 or 30 nucleotides in the TFñM gene that are unique to a TFñM gene. Regarding PCR or primers or hybridization probes and optimal lengths for them, reference is also made to Kajimura et al., GATA 7 (4): 71-79 (1990).

The RNA sequences within the scope of the invention are derived from the DNA sequences, by thymidine (T) in the DNA sequence which is considered equal to uracil (U) in RNA sequences. The oligonucleotides can be produced by a conventional production process for general oligonucleotides. They can be produced, for example, by a chemical synthesis process or by a microbial process that makes use of a plasmid vector, a phage vector or the . In addition, it is suitable for use as a nucleic acid synthesizer. To label an oligonucleotide with the fluorescent dye, one of the conventionally known labeling methods can be used (Tyagi &Kramer (1996) Nature Biotechnology 14: 303-308; Schofield et al., (1997) Appl. And Environ. Microbiol. 63: 1143-1147; Proudnikov &Mirzabekov (1996) Nucí Acids Res. 24: 4532-4535). Alternatively, the oligonucleotide can be labeled with a radiolabel, for example, 3H5 1251, 35S, 14C, 32P, etc. Well-known labeling methods are described, for example, in Sambrook et al., (2001) Molecular Cloning: A Laboratory Manual, 3rd ed. , Cold Spring Harbor Press. The tag is coupled directly or indirectly to a component of the oligonucleotide according to methods well known in the art. Reverse phase chromatography or similar ones used to provide a nucleic acid probe for use in the present invention can purify the synthesized oligonucleotide labeled with a marker. One advantageous probe shape is one labeled with a fluorescent dye at the 5'- or 5'- end and containing G or C as the base at the labeled end. If the 5'-end is labeled and the 3'-end is not labeled, the OH group on the C atom at the 3'-position of the 3'-end ribose - or deoxyribose can be modified with a phosphate group or the although no limitation is imposed in this respect. During the hybridization of the nucleic acid target with the probes, severe conditions can be used, advantageously together with other conditions that affect the severity, to aid in hybridization. Detection by differential interruption is particularly advantageous to reduce or eliminate slip hybridization between target probes, and to promote more effective hybridization. In still another aspect, severity conditions can be varied during the determination of stability of the hybridization complex to determine more precisely or rapidly whether a SNP is present in the target sequence. A method to determine the genotype at the polymorphic gene site involves obtaining a nucleic acid sample, hybridizing the nucleic acid sample or a probe, and interrupting the hybridization to determine the level of interruption energy required where the probe has a different interruption energy for one allele as compared to another allele. In one example, there may be a lower interruption energy, for example at melting temperature, for an allele that harbors a cytosine residue at a polymorphic site, and a higher required energy for an allele without a residue different from the polymorphic site. This can be achieved where the probe has 100% homology with one allele (a perfectly matched probe) but has a single mismatch with the alternative allele. Since the perfectly matched probe binds more tightly to the target DNA than the unequal probe, it requires more energy to cause the hybridized probe to dissociate. In a further step of the above method, a second probe ("fixator") can be used. Generally, the fixative probe is not specific to any allele, but hybridized regardless of which nucleotide is present at the polymorphic site. The fixator probe does not affect the interruption energy required to disassociate the hybridization complex but, instead, contains a complementary tag for use with the first probe ("sensor"). Hybridization stability can be influenced by numerous factors, including thermoregulation, chemical regulation, as well as electronic severity control, either alone or in combination with the other isolated factors. Through the use of severity conditions, in either or both of the target hybridization stage or the sensor oligonucleotide severity step, rapid completion of the process can be achieved. This is desirable to achieve appropriately indexed hybridization of the target DNA to achieve the maximum number of molecules at a test site with an accurate hybridization complex. By way of example, with the use of severity, the initial hybridization step can be completed in ten minutes or less. More advantageously five minutes or less, and much more advantageously two minutes or less. Globally, the analytical process can be completed in less than half an hour. In one mode, the hybridization complex is labeled and the step of determining the amount of hybridization includes detecting the amounts of the labeled hybridization complex at the test sites. The detection device and method may include, but is not limited to, optical image formation, electronic image formation, image formation with a CCD camera, integrated optical image formation, and mass spectrometry. In addition, the amount of the labeled and unmarked probe linked to the target can be quantified. Such quantification may include statistical analysis. The marked portion of the complex can be target, the stabilizer, the probe or the hybridization complex throughout. The labeling may be by fluorescent labeling selected from but not limited to, Cy3, Cy5, Bodipy Texas Red, Bodipy Far Red, Lucifer Yellow, Bodipy 630/650-X, Bodipy R6G-X and 5-CR 6G. Colorimetric marking, bioluminescent marking and / or chemiluminescent marking can also perform the marking. The labeling may also include the transfer of energy between molecules in the hybridization complex by perturbation analysis, rapid cooling, electronic transport between donor and acceptor molecules, the latter of which can be facilitated by double equalization hybridization complexes. strand. Optionally, if the hybridization complex is unlabelled, detection can be performed by measuring the conductance differential between double-stranded and non-double-stranded DNA. In addition, direct detection can be achieved by optical interferometry based on porous silicon or by mass spectrometry. When using non-fluorescent mass spectrometry or other brand is necessary. Rather, the detection is obtained by extremely high levels of mass resolution achieved by direct measurement, for example, by time of flight (TOF) or by electron dew ionization (ESI). Where mass spectrometry is contemplated, the probes that have a nucleic acid sequence of 50 bases or less are advantageous. The tag may be amplified, and may include, for example, branched or dendritic DNA. If the target DNA is purified, it can be unamplified or amplified. Furthermore, if the purified target is amplified and the amplification is a potential method, this may be, for example, DNA amplified by PCR or DNA amplified by strand displacement amplification (SDA). Linear methods of DNA amplification such as the rolling circle or tidal curve can also be used. Where it is desired to amplify a DNA fragment comprising a SNP according to the present invention, the forward and reverse primers may have contiguous stretches of about 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30 or any other length up to and including approximately 50 nucleotides in length. The sequences to which the reverse forward primers are reclined are advantageously located on either side of the particular nucleotide position that is substituted in the SNP to be amplified. A detectable label can be incorporated into a nucleic acid during at least one cycle of an amplification reaction. The spectroscopic, photochemical, biochemical, immunochemical, electrical, optical or chemical can detect such marks. Useful labels in the present invention include fluorescent dyes (e.g., fluorescein isothiocyanate, Texas red, rhodamine, and the like), radiolabels (e.g., 3 H, 125 I, 35 S, 14 C, 32 P, etc.), enzymes ( for example horseradish peroxidase, alkaline phosphatase, etc.), colorimetric labels such as colloidal gold or colored glass or plastic beads (for example - polystyrene, polypropylene, latex, etc.). The label is directly or indirectly coupled to a test component according to methods well known in the art. As indicated in the foregoing, a wide variety of brands are used, with the choice of brand that depends on the required sensitivity, ease of conjugation with the compound, stability requirement, available instrumentation and waste supplies. Non-radioactive brands are frequently linked by indirect means. Polymerases can also incorporate fluorescent nucleotides during nucleic acid synthesis. Reagents that allow sequencing of reaction products can be used herein. For example, chain termination nucleotides will often be incorporated into a reaction product during one or more cycles of a reaction. The teams commercially containing reagents most typically used for these DNA sequencing methods are available and widely used. PCR exonuclease digestion methods for DNA sequencing can also be used. Many methods of genomic DNA sequencing are known in the art, and any such method can be used see, for example Sambrook et al. (2001) Molecular Cloning: A Laboratory Manual, 3rd ed., Cold Spring Harbor Press. For example, as described below, a DNA fragment encompassing the location of the SNP of interest can be amplified using the polymerase chain reaction or some other cyclic polymerase-mediated amplification reaction. The amplified region of DNA can then be sequenced by subtilizing any method known in the art. Advantageously, nucleic acid sequencing is by automated methods (reviewed by Meldrum, (2000) Genome Res. 10: -1288-303, the description of which is incorporated by reference in its entirety), for example, using a System Genetic Analysis Beckman CEQ 8000 (Beckman Coulter Instruments, Inc.). Methods for sequencing nucleic acids include, but are not limited to, automated fluorescent DNA sequencing (see, for example, Watts &MacBeath, (2001) Methods Mol Biol. 167: 153-70 and MacBeath et al. (2001) Methods Mol. Biol. 167: 119-52), capillary electrophoresis (see, for example, Bosserhoff et al. (2000) Comb Chem High Throughput Screen 3: 455-66), DNA sequencing chips (see, for example, Jain, (2000) Pharmacogenomics 1: 289-307), mass spectrometry (see, for example, Yates, (2000) Trends Genet 16: 5-8), pyrosequencing (see, for example, Ronaghi, (2001) Genome Res. 11: 3-11), and ultra thin-layer gel electrophoresis (see, for example, Guttman &Ronai, (2000) Electrophoresis 21: 3952-64), the descriptions of which are incorporated in the present by reference in their totalities. . Sequencing can also be done by a commercial company. Examples of such companies include, but are not limited to, the University of Georgia Molecular Genetics Instrumentation Facility (Athens, Georgia) or Seq Wright DNA Technologies Services (Houston, Texas). A SNP-specific probe can also be used in the detection of the SNP in specific nucleic acid sequences amplified from the target gene, such as the amplified PCR products generated using the primers described above. In certain embodiments, these SNP-specific probes consist of oligonucleotide fragments. Advantageously, the fragments are of sufficient length to provide specific hybridization to the nucleic acid sample. The use of a hybridization probe between 10 and 50 nucleotides in length allows the formation of a duplex molecule that is both stable and selective. Molecules having complementary sequences on stretches greater than 12 bases in length are generally advantageous, in order to increase the stability and selectivity of the hybrid, and in this way improve the quality and the degree of particular hybrid molecules obtained. Generally, it will be preferred to design nucleic acid molecules having stretches of 16 to 24 nucleotides, or even longer where desired. A tag nucleotide region can be included, such as at the 5 'end of the primer that can provide a site to which an oligonucleotide sequencing primer can hybridize to facilitate sequencing of multiple PCR samples. The probe sequence must encompass the particular nucleotide position that can be substituted in the particular SNP to be detected. Advantageously, two or more different "allele-specific probes" can be used for the analysis of a SNP, a first allele-specific probe for the detection of one allele, and a second allele-specific probe for the detection of the alternative allele. It will be understood that this invention is not limited to the particular primers and probes disclosed herein and is proposed to encompass at least nucleic acid sequences that are hybridizable to the sequence of nucleotides disclosed herein, the complement or a fragment thereof, or are analogs of functional sequences of these sequences. It is also contemplated that a particular attribute of an animal can be determined by using a panel of SNPs associated with that attribute. Several economically relevant attributes can be characterized by the presence or absence of one or more SNPs and by a plurality of SNPs in different genes. One or more panels of SNPs can be used in the methods of the invention to define the phenotypic profile of the subject animal. Homologs (ie, nucleic acids derived from other species) or other related sequences (eg, paralogs) can be obtained under conditions of standard or severe hybridization conditions with a whole portion of the particular sequence as a probe using well-known methods in the technique for nucleic acid hybridization and cloning. The genetic markers, probes thereof, methods and equipment of the invention are also useful in a production schedule for selecting the reproduction of these animals that have desirable phenotypes for various economically important attributes, such as meat quality. The selection contains the reproduction of animals, such as cattle, which are at least heterozygous and advantageously desirable homozygous parallel from the sites polymorphic TFAM gene associated with economically relevant attributes of growth, food intake, efficiency and / or channel worth, and reproduction and longevity would lead to a reproduction, line or population that has higher numbers of descendants with economically relevant growth attributes , food intake, efficiency and value of the channel, and production and longevity. Thus, the TFAM SNPs of the present invention can be used as a selection tool. Desirable phenotypes include, but are not limited to, food intake, growth rate, body weight, value and composition of the carcass, and reproduction and longevity, and milk yield. Specific channel attributes with desirable phenotypes include, but are not limited to, the additional channel value (additional channel value, $), average daily gain (ADG, lb / d), posterior fat thickness (BFAT, in), weight calculated live (Cale Lv Wt, Ib), calculated yield grade (cYG), days in the food (DOF, d), percentage of fertilizer (DP,%), intake of matter (DMI, Ib), intake of dry matter per day on food (DMI per DOF, lb / d), weight of the hot channel (HCW, Ib), weight value of the hot channel (HCW valued, $), intramuscular fat content (IMF%,%), registration of marbling (MBS, 10 to 99), record of marbling divided between days on food (MBS / DOF), grade of quality, less than or equal to the selection versus greater than or equal to the choice (QG, <Se vs.,> Ch), ribeye area (REA, in2), ribeye area in weight percent HCW ( REA / cwt HCW, in2 / 100 lb of hot runner weight (HCW) and subcutaneous fat depth (SFD) One aspect of the present invention provides for the grouping of animals and methods for managing livestock production comprising grouping animals cattle such as cattle according to the genotype as defined with panels of SNPs, each panel comprising at least one SNP, one or more of which are in the TFAM gene of the present invention. being included in panels of SNPs include, but are not limited to, SNPs found in calpastatin, GHR gene, FABP4 gene, ghrelin gene, leptin gene, NPY gene, ob gene, UASMS1 gene, UASMS2 gene, UASMS3 gene and / or the UCP2 gene The genetic selection and the clustering method of the present invention It can be used in conjunction with other methods of conventional phenotypic groupings such as the grouping of animals by visible characteristics such as weight, body size, reproduction attributes and the like. The methods of the present invention provide the production of cattle that have improved heritable attributes, and can be used to optimize the performance of herds of cattle in areas such as breeding, food intake, canal / meat quality and milk production. The present invention provides methods for classifying cattle to determine those that most likely develop a desired body condition by identifying the presence or absence of one or more gene polymorphisms correlated with meat quality. As described in the above, and in the examples, there are several phenotypic attributes with which the SNPs of the present invention can be associated. Each of the phenotypic and genetic attributes can be tested using the methods described in the Examples, or using any of the suitable methods known in the art. Using the methods of the invention, a farmer, or food lot operator or the like, can group the livestock according to the genetic propensity of each animal for a desired attribute such as the growth rate, feed intake or behavior of the animal. feeding, as determined by the SNP genotype. Cattle are tested to determine the homozygosity or heterozygosity with respect to the SNP alleles of one or more genes so that they can be grouped such that each pen contains cattle with similar genotypes. Each animal pen then feeds and otherwise is maintained in a manner and for a time determined by the operator of the food lot and then sacrificed.

Individual genotypic data derived from a panel or panels of SNPs for each animal or a herd of animals can be recorded and associated with various other animal data, for example, health information, kinship, disease conditions, vaccination history, records of the herd, subsequent food safety data and the like. Such information may be directed to a government agency to provide traceability of an animal or meat product, or it may serve as the basis for reproduction, feeding and marketing information. Once the data has or has not been associated with other data, the data is stored in an accessible database, such as, but not limited to, a computer database or a micro chip implanted in the animal. The methods of the invention can provide an analysis of the input data that can be compared with parameters desired by the operator. These parameters include, but are not limited to, such as breeding objectives, egg-laying objectives, vaccination levels of a herd. If the performance of animal properties deviates from the desired objectives, computer-based methods can trigger an alert to allow the operator to adjust the doses of vaccination, medication, feed, etc. therefore. The results of the analysis provide data that they are associated with the individual animal or the herd, in whole or in part, from which the sample was taken. The data are then stored in an accessible database, and may or may not be associated with other data of that particular individual or other animals. The data obtained from individual animals can be stored in a database that can be integrated or associated with and / or cross matched with other databases. The database together with the associated data allows information about the individual animal that is known through each stage of the animal's life, that is, from conception to consumption of the animal product. Accumulated data and the combination of genetic data with other types of animal data provide access to information about kinship, herd identification, health information including vaccinations, disease exposure, location of diet feed lots and changes in owner. Information such as data and results of routine diagnostic tests are easily stored and are achievable. Such information would be especially valuable for companies, particularly those looking for superior breeding lines. Each animal can be provided with a unique identifier. The animal can be labeled, like traditional tracking programs or have chips implanted computers that provide stored and readable data or provided with any other identification method that associates the animal with its unique identifier. The database that contains the SNP-based genotype results for each animal or the data for each animal can be associated or linked to other databases that contain data, for example, which can be useful in selecting attributes for grouping or subbagging an animal. For example, and not for limitation, data pertaining to animals that have particular vaccination or meditation protocols, may optionally also be linked to data pertaining to animals that have food from certain food sources. The ability to refine a group of animals is limited only by the attributes sought and the databases that contain information related to these attributes. The databases that can be usefully associated with the methods of the invention include, but are not limited to, specific or general scientific data, the specific data include, but are not limited to, breeding lines, sires, mothers and the like. , other genotypes of animals, which include whether or not other specific animals possess specific genes, including transgenic genetic elements, location of animals who share similar or identical genetic characteristics, and the like. General data includes, but is not limited to, scientific data such as which genes code for specific quality characteristics, breeding association data, feed data, breeding trends and the like. One method of the present invention includes providing the animal owner or the customer with the sample collection equipment, such as swabs and tags useful for collecting samples from which genetic data can be obtained. Advantageously, the packaging is encoded with a bar code label. The labels are coded with the same identification legends, advantageously with an equalization bar code label. Optionally, the packaging contains means to send the labels to a laboratory for analysis. The optional packaging is also coded with identification legends, advantageously with a barcode label. The method optionally includes a system in which a database account establishes the ordering of the sampling equipment. The identifier of the database account corresponds to the legends of identification of labels and packaging. In the shipment of sampling equipment in compliance with order, the legends of identification only registered in a database. Advantageously, identifiers to a barcode label that is scanned when the labels are sent. When the labels are returned to the test facility, the identifier is again registered and matched with the information previously recorded in the database in the shipment of the vial to the customer. Once the genotype detection is complete, the information is recorded in the database and encoded with the unique identifier. The test results are also provided to the client or owner of the animal. The data stored in the genotype database can be integrated with or compared with other data or databases for the purpose of identifying animals based on genetic propensities. Other data or databases include, but are not limited to, those containing the SNP-based DNA test, vaccination, the safe pre-placement program for safe health, estrus and pregnancy outcomes, hormone levels, safety / contamination of the food, somatic cell count, occurrence of mastitis, diagnostic test result, milk protein levels, milk fat, vaccine status, health records, mineral levels, minor mineral levels, performance of the herd and the like.

The present invention, therefore, encompasses computer-assisted methods for tracking the breeding and veterinary histories of livestock animals comprising the use of a computer-based system comprising a programmed computer comprising a processor, a storage system, and a computer. data, an input device and an output device, and comprising the steps of generating an exploitation of the livestock animal by entering in the programmed computer through the input device genotype data of the animal, where the genotype can be defined For a panel of at least two individual nucleotide polymorphisms that predict at least one physical attribute of the animal, enter in the programmed computer through the input device the data must be of the animal, which correlates with the data of well-being introduced with the phenotypic profile of the animal using the processor and the to store data, and output a profile of the animal or group of animals to the output device. The databases and the analysis thereof will be accessible to those to whom access has been provided. Access can be provided through access rights or by subscription to specific portions of the data. For example, the database can be accessed by owners of the animal, the test site, identity that It provides the sample to the test site, the batch feeding staff and veterinarians. The data can be provided in any way by accessing a network site, fax, email, targeted mail, automated telephone or other methods for communication. This data can also be encoded to a portable storage device, such as micro chips, which can be implanted in the animal. Advantageously, the information can be read and new additional information without removing the animal's microchip. The present invention comprises systems for performing the methods disclosed herein. Such systems include devices such as computers, Internet connections, servers and storage devices for data. The present invention also provides a method for enabling data comprising the transmission of information of such methods discussed herein or steps thereof, for example, by way of telecommunication, telephone, video conference, mass communication, for example, the presentation such as a presentation on computers' (for example, POWERPOINT), Internet, email, documentary communication such as computer programs (for example, WORD) and the like. The systems of the present invention can comprise a data collection module, which includes a data collector to collect data from an animal or embryo and transmit the data to a data analysis module, a network interface to receive data from the data analysis module, and optionally further adapted to combine multiple data from one or more individual animals, and to transmit the data via a network to other sites, or to a storage device. More particularly, the systems of the present invention comprise a data collection module, a data analysis module, a network interface for receiving data from the data analysis module, and optionally further adapted to combine multiple data from one or more individual animals, and to transmit the data via a network to other sites and / or a storage device. For example, the data collected by the data collection module leads to a determination of the absence or presence of a SNP in the animal or embryo, and for example, such data is transmitted when the animal's feeding regime is planned. In a modality where the data are implanted in a microchip or a particular animal, the farmer can optimize the efficiency of the management of the herd because the farmer is able to identify the genetic predispositions of an individual animal as well as the treatments past, present and future (for example, vaccinations and veterinary visits). The invention therefore also provides input to other databases, for example, herd data related to genetic tests and related data by others, by linking data to other sites. Therefore, data from other databases can be transmitted to the central database of the present invention via a network interface to receive data from 1 data analysis module to the other databases. The invention relates to a computer system and a. computer readable medium for compiling data on an animal, the system that contains data entered on that animal, such as, but not limited to, vaccination and medication histories, DNA test, thyroglobulin test, leptin, MMI (Meta Morphix Inc. ), diagnosis of spongiform encephalopathy coil (BSE), brucellosis vaccination, FMD vaccination (paw and mouth disease), vaccination of BVD (bovine viral diarrhea), Safe Health preconditioning program, estrus and pregnancy results, tuberculosis, hormone levels, food safety / contamination, somatic cell count, mastitis occurrence, diagnostic test results, milk protein levels, milk fat, vaccine status, health records, mineral levels , lower mineral levels, performance of the herd and the like. Animal data may also include previous treatments as well as the suggested adjusted treatment depending on the genetic predisposition of that animal to a particular disease. The invention also provides a computer-assisted method for improving animal production comprising the use of a computer system, for example, a programmed computer comprising a processor, a data storage system, an input device and a device. of output, the steps of entering into the computer programmed through the input device data comprising reproductive, veterinary, medication and diagnostic data and the like of an animal, which correlates to a physical characteristic predicted by the genotype using the processor of the data storage system, output output device physical characteristics correlated with the genotype, and feed, the animal with a diet based on the physical characteristic for this way to improve livestock production. The invention further provides a computer-assisted method for optimizing the efficiency of livestock feed data comprising using a computer system, for example, a programmed computer comprising a processor, a storage system data, an input device and an output device, and the steps of entering into the computer programmed through the input device data comprising a reproduction, the veterinary history of an animal, correlated with the reproduction, veterinary histories using the processor and the data storage system, output output device to the physical characteristic correlated with the genotype and feed the animal with a diet based on the physical characteristic, in order to optimize the efficiency of feeding lots for livestock . The invention further comprises methods for doing business by providing access to such readable computer means and / or computer systems and / or data collected from animals to users; for example, the means and / or the sequence data may be accessible to a user, for example it is a subscription subscription base, via the Internet or a global communication / computer network; or, the computer system may be available to a user, on a subscription basis. In one embodiment, the invention provides a computer system for handling livestock comprising physical characteristics and databases corresponding to one or more animals. In another embodiment, the invention provides readable means in computers for handling livestock that comprises physical characteristics and specific histories corresponding to one or more animals. The invention further provides methods for doing business to manage livestock comprising providing a user with the computer system and means described in the foregoing or physical characteristics and veterinary histories corresponding to one or more animals. The invention further encompasses methods for transmitting information obtained in any method or stage thereof described herein or any information described herein, for example, by way of telecommunications, telephone, mass communications, mass media, presentations, Internet, mail electronic, etc. The invention also encompasses equipment useful for classifying nucleic acid isolated from one or more bovine individuals for allelic variation of any of the mitochondrial transcription factor genes, and in particular for any of the SNPs described herein, wherein the may comprise at least one oligonucleotide that selectively hybridizes a nucleic acid comprising any one or more of which are TFAM sequences described herein and instructions for using the oligonucleotide to detect variation in the oligonucleotide corresponding to the SNP of the acid nucleic isolated. One embodiment of this aspect of the invention provides an oligonucleotide that specifically hybridizes to the nucleic acid molecule isolated from that aspect of the invention, and wherein the oligonucleotide hybridizes to a portion of the isolated nucleic acid molecule comprising any of the sites polymorphic in the TFAM sequences described herein. Another embodiment of the invention is an oligonucleotide that specifically hybridizes under conditions of high stringency to any of the polymorphic sites of the TFAM gene, wherein the oligonucleotide is between about 18 nucleotides and about 50 nucleotides. In another embodiment of the invention, the oligonucleotide comprises a central nucleotide that specifically hybridizes with a polymorphic site of the TFAM gene of the portion of the nucleic acid molecule. Another aspect of the invention is a method for identifying a TFAM polymorphism in a nucleic acid sample comprising isolating a nucleic acid molecule encoding TFAM or a fragment thereof and determining the nucleotide at the polymorphic site. Another aspect of the invention is a method for classifying cattle to determine those cattle more likely to write a biological difference in the quality of meat that includes the steps of obtaining a sample of genetic materials from a bovine, and analyze for the presence of a genotype in cattle that is associated by the quality of meat, the genotype characterized by a polymorphism in any of the genes of the mitochondrial transcription factor. In other embodiments of this aspect of the invention, the step of analyzing is selected from the group consisting: restriction fragment length polymorphism analysis (RFLP), minisequencing, MALD-TOF, SINE, heteroduplex analysis, conformational polymorphism of a single strand (SSCP), denaturation gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE). In various embodiments of the invention, the method may further comprise the step of amplifying a region of the TFAM gene or a portion thereof that contains the polymorphism. In other embodiments of the invention, the amplification may include the step of selecting a forward and / or reverse sequence primer capable of amplifying a region of the TFAM gene. Another aspect of the invention is a computer-assisted method for predicting that livestock animals have a biological difference in the quality of meat that comprises: using a computer system, for example, a programmed computer comprising a processor, a data storage system, an input device and an output device, the steps of: (a) entering the programmed computer through of the input device data comprising a TFAM genotype of an animal, (b) correlating the growth, feed intake, efficiency or quality of the channel value predicted by the TFAM genotype using the processor and the data storage system and ( c) output the quality of meat correlated with the TFAM genotype to output device, in order to predict that livestock animals have a particular level of growth, food intake, efficiency or quality of the channel. Yet another aspect of the invention is a method for doing business to manage livestock which comprises providing a user with a computer system for handling livestock comprising physical characteristics and genotypes corresponding to one or more animals or a computer readable medium for handling livestock that it comprises physical characteristics and genotypes corresponding to one or more animals or physical characteristics and genotypes corresponding to one or more animals. The invention will now be described further by means of the following non-limiting examples.

EXAMPLES Example 1 This example provides DNA sequences, genetic polymorphisms and significant associations with marbling and depth of subcutaneous fat in Wagyu x Limousin F2 crosses for the transgenic myocardial transcription factor A gene (TFAM). Factor A mitochondrial transcription (TFAM), a protein encoded in the nucleus, plays an important role in the initiation of transcription and mitochondrial DNA replication (mtDNA). Decreased expression in nuclear-encoded mitochondrial genes has been associated with the onset of obesity in mice. Therefore, it was hypothesized that genetic variants in the TFAM gene include in mitochondrial biogenesis consequently affecting the deposition of body fat and energy metabolism. In the present study, both cDNA sequences (2259 bp) and genomic DNA (16.666 bp) were generated for the bovine TFAM gene using a combination of in silico cloning with the PCR amplification of targeted region. The alignment of both cDNA and genomic sequences led to the determination of the genomic organization in the characterization of the promoter region of the bovine TFAM gene. Unfortunately, no polymorphisms were detected in the coding region, but two Single nucleotide polymorphisms (SNPs) of tightly linked A / C and C / T were found in the bovine TFAM promoter. Two of these SNPs were genotyped in 237 animals F2 Wagyu x Limousin with phenotypes registered for marbling and depth of subcutaneous fat (SFD). The statistical analysis showed that both SNPs were associated with marbling (P = 0.0153 for A / C and P = 0.0026 for C / T) and SFD (P = 0.0200 for A / C and P = 0.0039 for C / T), respectively . A search for transcriptional regulatory elements using Matlnspector indicated that both SNPs lead to a gain / loss of six putative link sites for genes relevant to fat deposition and energy metabolism. Compared with previous reports on the thyroglobulin, leptin and diacylglycerol 0-acyltranferase genes, the TFAM gene has the greatest effects on both marbling and SFD in this population, indicating its potential as a new target for marker-assisted selection in the industry of beef. The mitochondrial transcription factor A (TFAM), a member of a family of high mobility group proteins and the first identified mitochondrial transcription factor (Fisher and Clayton, 1988), is essential for the maintenance and biogenesis of mtDNA. First, TFAM plays a similar role to histone in the mitochondria, as it is closely associated with mtDNA as a principal component of the nucleotide (Kanki et al., 2004a). Evidence has shown that an mtDNA molecule is packaged with -900 molecules of TFAM on average (Alam et al., 2003), which makes the mtDNA non-naked longer. Second, T FAM regulates the number of mtDNA copies in mammals. Investigation using a combination of mice with T FAM overexpression and inactivation of T FAM demonstrated that the copy number of mtDNA is directly provided at the level of total T FAM protein in mouse embryos (Ekstrand et al., 2004). RNA interference from the expression of endogenous TFAM in HeLa cells also indicated that the amount of mtDNA is correlated in parallel with the amount of TFAM (Kanki et al., 2004b). Third, it stimulates the transcription of mtDNA. The TFAM protein possesses two domains of high mobility group in tandem, which makes the TFAM bind, unwind and fold the DNA without sequence specificity and thus facilitate the initiation of mtDNA transcription (Gaspari et al., 2004). The evidence has shown that the importation of wt-TFAM into mitochondria of the liver of hypothyroid rats increased the synthesis of RNA significantly up to 4 times (Garstka et al., 2003). It has been known for many years that adipose tissue plays a central role in the regulation and manipulation of energy metabolisms through the storage and productivity of triglycerides and through the secretion of factors that affect satiety and utilization of supply. However, many key aspects of adipogenesis are accompanied by the stimulation of mitochondrial biogenesis (Wilson-Fritch et al., 2003). For example, the major site of fatty acid ß-oxidation occurs in the mitochondria (Reichert and Neupert, 2004), which can provide key intermediates for the synthesis of triglycerides via the action of pyruvate carboxylase (Owen et al. 2002). Also, one. Relatively large mitochondrial mass is required to generate acetyl-CoA for the activation of fatty acid before esterification into triglycerides. All these studies demonstrated the essential role and function of mitochondria in lipid metabolism. To further explore the mechanism of the mitochondria involved in adipogenesis, Wilson-Fritch and colleagues (2003 and 2004) studied the differentiation of the 3T3-L1 cell (representative of white adipocytes) by using both proteomic and genomic procedures. Proteomic analysis revealed a 20 to 30-fold increase in the concentration of numerous mitochondrial proteins, while genomic analysis with profiling of gene expression using Affymetrix GeneChips detected a statistically significant increase in the expression of many mitochondrial genes encoded in the nucleus during adipogenesis. In particular, the authors found a profound decrease of approximately 50% in the levels of transcripts for the nuclear encoded mitochondrial genes that accompany the onset of obesity (Wilson-Fritch et al., 2004). As TFAM is one of the nuclear encoded mitochondrial genes, it was hypothesized that it plays an important role in adipogenesis or fat deposition via its function in mitochondrial biogenesis. Here, the evidence is presented to support the hypothesis by reporting significant associations of bovine TFAM promoter polymorphisms with marbling records and SFD measurements in Waygu x Limousin crosses. A Fi generation of an agyu x Limousin breed was developed at Washington State University and transferred to the Fort Eogh Livestock and Range Research Laboratory, ARS, USDA in the fall of 1998, including 6 Fi sires and 113 females. The intermingling of these animals Fi produced 71 F2 progenies in 2000, 90 in 2001 and 109 in 2003, respectively. Each calf was weighed within 24 h after birth and again at weaning when the calves averaged approximately 180 d of age. After weaning, the calves were returned to native range pastures and supplemented with 0. 7 kg per calf per day of both barley cakes and alfalfa pellets. In mid-January, the calves moved from the margin and were fed silage and chopped hay to achieve anticipated gains of 0.5 to 0.8 kg per day. They were then placed on a finishing diet for approximately 150 days followed by slaughter. Data on the growth rate and quality of the carcass and meat were collected in all F2 calves. Marbling records ranged from 4 = Light0 to 9.5 = Moderately Abundant50 (SD = 1.00) and SFD measurements ranged from 0.1 to 1.3 inches (SD = 0.18) in this population F2. Marbling was a subjective measure of the amount of intramuscular fat in the longissimus muscle based on USDA standards (http: // www. Ams. Usda. Gov /). SFD was measured at the interface of the 12-13th rib perpendicular to the outer surface at a three-quarter point the length of the longissimus muscle from its end of the spine bone. The DNA was extracted from blood samples. Based on the availability of both data and DNA samples, 246 observations were used in the current study. Unfortunately, both cDNA and genomic DNA sequences were not available for the bovine TFAM gene when the project was started. However, the bovine genome mapping project has advanced significantly in recent years. In particular, more than 500,000 bovine ESTs (sequence labels expressed) (http: / / www .ncbi.nlm.nih.gov /) and 3X bovine genome sequences (ht tp: //www.hgsc.bcrn.mc.edu/projcts/bovine/) have been released to the bases of public data. Therefore, a combination of an in silico comparative cloning with an objective PCR cloning procedure was developed and used to determine both of the cDNA and genomic DNA sequences of the bovine gene (FIG 1). The procedure included three steps: 1), BLAST searches against the public databases using a full-length cDNA sequence of the human TFAM gene as a reference to recover all bovine sequences that are orthologenic to the human gene; 2) annotation of both sequences of ESTs and genomic DNA in order to design primers for the amplification of the target region to close spaces if there are some; 3) alignment of the cDNA sequences and genomic DNA sequences to determine the full-length cDNA sequence and the genomic organization of the bovine TFAM gene. Two pairs of primers were designed to close two spaces for the genomic DNA sequence of the bovine TFAM gene (Table 1). PCR reactions were performed using 25 ng of bovine genomic DNA as a template in a final volume of 10 uL containing 12.5 ng of each primer, 200 μ? of dNTPs, 1.5 - 3 mM MgCl2, 50 mM C1, 20 mM Tris-HCl and 0.2U of Platinum Taq polymerase (Invitrogen, Carlsbad, CA). The PCR conditions were carried out as follows: 94 ° C for 2 min, 32 cycles of 94 ° C for 30 sec, 63 ° C for 30 sec and 72 ° C for 30 sec, followed by an extension of 5 min additional at 72 ° C. The PCR products were then examined by electrophoresis through a 1.5% agarose gel with IX TBE buffer to determine the quality and quantity for DNA sequencing. Sequencing was performed on the ABI 3730 sequencer at the Laboratory for Biotechnology and Bioanalysis (Washington State Uhiversity). The sequences of these two PCR amplified products spanning the space regions and three contiguous genome sequences derived from the draft Cattle genome sequence, were then assembled to form a complete genomic DNA sequence for the bovine TFAM gene. Table 1. Primers designed for closing the genomic space and mutation detection of the bovine TFAM gene. Region Primer sequences Annealed Size SEQ ID Objective (5 '-3') in bp Tm NO: Front Promoter: 801 61 ° C GTTGTTGCAGAAATCAGCTAAAATG 4 Rear: CATCCACTGAGACTATCGCTGACCT 5: 405 61 ° C CGCCTCCTAGCTAATCGGAAGTTAG_6_Rear: GTCGGAATCACAGGGCTAAGTCAGT 7 ???? 2 Front: 421 61 ° C TTCCCCTGGATAGGACAGGATTTTA 8 Rear: TACAGGCCATCACACAGAATGGTTA 9 ???? 3 Front: 407 57 ° C GAGCTAATGGATTATTCTTTCCTGA 10 Rear: ATGTGTTATCCAAGGTGAAGGTCTA 11 ???? 4 Front: 459 57 ° C TTATAAGTGGGATTTCAGAGTGCAT 12 Rear: AACTGAAGTCATTCTCTACCACGTC 13 ???? 5 Front: 392 57 ° C AACAATCGCATACTCATAATGTTCA 14 Rear: TGGTAAGAAAAAGGATTTTTAGGTC 15 Front Space: 222 57 ° C of GCACAAACAAAGGAACCATCAA 16 Intron 5 Rear: TTCCCTGACAATGATGTTGAGC 17 ???? 6 Forward: 408 57 ° C TACAGCTCAGAGTTTTGAGGAGTCT 18 Rear: CACTAAGTTACGAGGGACACTGTTT 19 Front Space: 736 57 ° C for TGAAAACTGGAAAAATCTCTCTA 20 Intron 6 Rear: & Exon 7 AACAGCTTCCGGTATTGAGACCT 21 The primers were designed to target the promoter region and all coding regions in order to classify genetic polymorphisms in the bovine TFAM gene (Table 1). Four accumulations of DNA were formed, one of all six Fi sires, one of 30 randomly selected Fi females, one of 30 high-marbling F2 progenies and one of 30 low-marbling F2 progenies. The PCR products for each pair of primers were amplified on these four DNA pools and directly sequenced on the ABI 3730 sequencer as described above. Nucleotide polymorphisms were identified by comparing sequence patterns between these four DNA pools. Unfortunately, no polymorphisms were detected in the coding sequence, but two SNPs, ie, C / A substitutions and C / T substitutions were found in the bovine TFAM promoter region. These two SNPs in the bovine promoter region were then determined in genotype in the F2 animals of Wagyu X Limousin that have both DNA samples and performance data for the marbling record and SFD measurements. Using the PCR-RFLP (restriction fragment length polymorphism) procedure, these two mutations were revealed by digestion at 37 ° C for three hours of 2U HaelII PCR amplicons for C / A substitution and 2U of Dpnl for the C / T substitution, followed by analysis in 4% agarose gels. The phenotypic data for the marbling records and the SFD measurements were adjusted for the effects of year, gender and age in collection (linear) before estimating the effects of the genotypes using the GLM procedure (general linear model) of SAS v9 .1 (SAS institute Inc., Gary, NC) to estimate the effects of the contemporary group and the genotype on the TFAM gene site. BLAST searches using the human TFAM cDNA (NM_003201) as a reference retrieved eight bovine orthologous EST sequences from the database of other ESTs at the National Center for Biotechnology Informatics (NCBI) and three contiguous genomes from the 3X genome assembly of cattle cow at Baylor College Medicine. Three ESTs (DN286575, DN285251 and CN793484) were selected to form a consensus cDNA sequence! of the bovine TFAM gene, but they left a space in the 3 'UTR (untranslated region) (FIG 1). However, the initial alignment of this EST sequence with the genomic DNA sequence revealed that the space of the cDNA sequence could be easily closed using the genomic DNA sequence corresponding to the 3'UTR region. The total length of the assembled mRNA sequence is 2,259 bp for the bovine TFAM gene. Three contiguous genomic DNAs (contiguous 45319, contiguous 729099 and contiguous 138856) have apparently not overlapped. The orientation of these three contiguous genomes to a 5'-3 'direction corresponding to the mRNA sequence made it possible to design primers for closures two spaces between them (FIG 1). Two PCR products of 222 bp and 736 bp (Table 1) were amplified and sequenced. The assembly of three contiguous genomic and these two PCR products made it possible to form a genomic DNA sequence of 16, 666 bp for the bovine TFAM gene (FIG 1). All eight bovine ESTs that are orthologous to the human TFAM gene are 99-100% identical to the assembled consensual mRNA sequence. The putative complete coding sequence of the bovine TFAM gene is 741 bp in length, which is identical to that in human (NM_003201, D'Errico et al., Gene 362, 125-132 (2005)), but 6 bp and 9 bp longer than that in the rat (NM_031326, Piantadosi and Suliman, J. Biol. Chem. 281 (1), 324-333 (2006)) and mouse (NM_009360, Noack et al., Biochim. Biophys. Acta 1760 (2) , 141-150 (2006)) and 48 bp shorter than that in chicken (NM_204100, Caldwell et al., Genome Biol. 6 (1), R5 (2005)), respectively. The translated amino acid sequence encoded by the bovine TFAM gene showed 91% identity with pig (AY923074), 71% with human (NM_003201), 65% with rat (NM_031326), 63% with mouse (NM_009360) and 43% with chicken (NM_204100), respectively. The total structure of the bovine TFAM gene was determined by comparing the genomic DNA sequence with the complete cDNA sequence determined in the study (FIG 1). Similar to that in human, mouse, rat and chicken, the genomic organization of the bovine TFAM gene consists of seven exons and six introns (FIG 1). It is estimated that the bovine genome is similar in size to the genomes of human and other mammals, which contain approximately 3 billion base pairs of DNA. The sequencing of the bovine genome began in December 2003 and the initial assembly based on the 3.3-fold coverage of the bovine genome was released on October 6, 2004, which can now be accessed through GenBank (www. Ncbi | nih. gov / Genbank) at NCBI. In addition, more than 500,000 bovine ESTs have also been released to the public and can be accessed through GenBank at NCBI. Both bovine ESTs and genome sequences provide valuable resources to revolutionize genome research in cattle. In the current study, a tool that combines an in silico comparative cloning with an objective PCR cloning procedure was developed and used to clone both of the cNA and genomic DNA sequences of the bovine TFAM gene. This procedure is very direct, simple, fast and inexpensive. Therefore, this procedure can serve as one of the model tools in identifying, mapping and understanding the function of genes in cattle, which will further advance the investigation of basic biology. FIG. 2 shows the nucleotide sequences for the 5 'upstream region and the complete exon 1 of the bovine TGAM gene. Analysis using the Mat Inspector program (Quandt et al., 1995) revealed a potential nuclear respiratory factor-1 (NRF1) and a stimulatory protein-1 binding site (SP1) in the bovine TFAM promoter region (FIG 2). However, the bovine TFAM promoter lacks the putative binding sites for nuclear respiratory factor 2 (NRF2). In the region of the human TFAM promoter, both binding sites NRF1 and NRF2 were found, whereas only the NRF2 binding sites existed in the rat and mouse TFAM promoters (Scarpulla, 2002). All TFAM promoters in the human, rat and mouse sites have the SPl binding. NRFl, NRF2 and SPl are the most prevalent factors associated with respiratory genes (Scarpulla, 2002). In addition to the NRF1 and SP1 binding sites, the bovine TFAM promoter contains a provisional transcriptional repressor binding site, which binds elements found predominantly in genes that participate in lipid metabolism (FIG 2). Although it is not clear whether the CpG islands are methylated in vivo, many potential methylated CpG sites are present in the bovine TFAM promoter (FIG 2). Interestingly, the bovine TFAM promoter may be one of the few promoters that contain the AUG codon that occurs naturally upstream of the normal translational start site (FIG 2). This AUG codon was also confirmed by sequencing with primers spanning the partial promoter, full exon 1 and partial intron 1 (see description below) in the study. The general rule of Kozak is that in most cases the AUG codon closest to the 5 'end is the unique site of translation initiation, because this "position effect" is observed in cases where a mutation creates a codon AUG upstream of the normal start site and translation shifts to the upstream site (Kozak, 2002). However, the first rule can be postulated when the next AUG triplet 5 'is followed shortly by a terminator codon, which makes the reinitiation in a possible downstream AUG codon (Kozak, 1995). It is observed that this extra AUG codon in the bovine TFAM promoter is not in the structure (FIG 2). If translated, it would generate precisely a peptide of 12 amino acids like MQWRFSGAYGAC (SEQ ID NO: 22). If and how this triplet next AUG 5 'interferes with the normal translation remains unknown. Therefore, the bovine TFAM gene could be a natural model gene for the investigation of mechanisms involved in the initiation of translation of mammalian genes. A total of eight pairs of primers were designed and used to classify genetic polymorphisms in the bovine TFAM gene. A pair of primers is directed to the promoter region, and the remaining primers amplify seven exons with one pair of primers per exon. However, the last pair of primers was used for both the enclosure of the space and the amplification of exon 7 (Table 1). In order to achieve the fully amplified and sequenced exon region, at least 100 bp of sequences from each flanking side were included in the products. No polymorphisms were found in all the coding sequences of the bovine TFAM gene, although the reference population includes two breeding races diverging from cattle: a Wagyu of Asian origin and a Limousin of European origin, which have characteristics that are very different between yes. However, two SNPs were detected in the promoter region (FIG 2 and FIG 3). These two SNPs are located just 9 bp apart, one substitution C / A and another substitution C / T. Both SNPs were revealed by digestion with HaelII and DpnII, respectively in an 801 bp fragment (FIG 4).

Since the fragment has three restriction sites, the digestion produces two invariant bands of 152 bp and 462 bp, and a band of 187 bp. That can be, depending on the nucleotide at position-1220 (FIG 2), also segmented into two bands of 83 bp and 104 bp (FIG 4). Therefore, animals homozygous with allele A have two HaelII sites, and reveal after complete digestion three bands: 152 bp, 187 bp and 462 bp, homozygous animals with the C allele have gained an additional tfaelll site in this position and result in four bands (83 bp, 104 bp, 152 bp and 462 bp) after complete digestion. However, heterozygous animals showed five bands after digestion of HaelII (FIG 4). These two common tfaelll sites were considered as internal controls of enzymatic digestion. In comparison, the fragments contain four Dpnll restriction sites including a polymorphic site. Therefore, digestion with DpnII produces three invariant bands of 55 bp, 68 bp and 135 bp, and three polymorphic bands of 241 bp, 302 bp and 543 bp, respectively (FIG 4). The homozygous animals with T allele have all four Dpnll sites, and reveal after the complete digestion five bands: 55 bp, 68bp, 135 bp, 241 bp and 302 bp, while animals homozygous with the C allele have lost a Dpnll site in position -1212 (FIG.2) and give by result four bands (55 bp, 68 bp, 135 bp and 543 bp) after complete digestion. However, the heterozygous animals showed six bands after digestion of DpnII (FIG 4). These three common Dpnll sites also served as internal controls for enzymatic digestion. The genotype determination of 237 F2 animals for both C / A and C / T SNPs revealed 75 homozygous CC animals, 45 homozygous AA animals and 117 CA heterozygous animals for the first SNP and 84 homozygous CC animals, 33 homozygous TT animals and 120 animals. CT heterozygous for the last SNP (Table 2). For the C / A substitution, the frequencies of the C allele and the A allele in the population were 0.56 and 0.44, respectively. The frequency of the C allele was slightly increased to 0.61 for the C / T substitution. However, both genotype distributions were in the Hardy-Weinberg equilibrium. The analysis of the general linear model clearly indicated that the effect of the genotype of any SNP reached statistical significance (for the substitution C / A, P = 0.0019 for the marbling record and P = 0.0200 for the measurement of SFD, and for substitution C / TP = 0.0011 for the marbling record and P = 0.0039 for the measurement of SFD) (Table 2). For C / A substitution, cattle with the homozygous (CC) genotype had an additional 0.047 inches of subcutaneous fat and 0.482 inches of marbling record compared to homozygous AA (P <0.05). However, the differences between two CC and TT homozygotes were also enlarged for the C / T substitution. The thickness of subcutaneous fat was 0.073 inches thicker and the marbling record was 0.634 higher in cattle with the homozygous genotype (CC) than homozygous TT (P <0.05) (Table 2). Only five haplotypes between these two promoter polymorphisms were observed in 237 Wagyu x Limousin F2 animals, including 75 CCCC, 108 CACT, 33 AATT, 12 AACT and 9 CACC, respectively. Due to relatively few samples, both haplotypes AACT and CACC were excluded in the additional statistical analysis. As indicated in Table 2, the haplotype had significant effects on both marbling and SFD in the reference population (P = 0.0004 for marbling and P = 0.0029 for SFD). The marbling record was 0.655 different between the CCCC and AATT animals and 0.518 different between the CCCC and CACT animals (P <0.05). For SFD measurements, cattle with the CCCC haplotype had 0.079 and 0.073 additional inches of subcutaneous fat compared to the CACT and AATT animals (P <0.05), respectively. The CCCC haplotype is observed to be associated with an increase in total body fat deposition in cattle. Table 2. Associations of the bovine TFAM promoter SNPs with marbling and SFD in crosses * F2 of Waygu x Limousin.

* Means within a column with different superindices that are significantly different (P <0.05). Previous efforts have identified candidate genes responsible for marbling and / or SFD in beef. Barendse et al. (1997) identified a TG5 polymorphism that occurs in the 5 'promoter region of the thyroglobulin (TG) gene. This marker had a genotype association with the marbling record in long-term cattle. Leptin is a 16-kilodalton protein produced by the obesity gene (ob). Mutations in the leptin gene. { LEP) cause the cattle to meat reach the weight for the fastest sacrifice and develop more marbling in the channel (Buchanan et al., 2002). A non-conservative K232A substitution in the gene DGAT1 (diacylglycerol O-acyltransferase) has been shown to affect the deposition of intramuscular fat (marbling) in beef (Thaller et al., 2003). The determination of the genotype of a C / T SNP in the TG gene, a C / T mutation in the LEP gene and an A / C polymorphism in the DGAT1 gene was also performed in this Waygu x Limousin crossover population (De et al. , 2004 and Wu et al., 2005, in press). The analysis of variation using a generalized linear model did not show some | significant differences between the genotypes in the LEP gene. However, the DGAT1 gene had a significant additive effect on SFD (P = 0.036), while the TG gene showed a dominant effect on marbling than the approximate meaning (P = 0.061). De and colleagues (2004) observed that in the TG gene, the genotype differences between CC and TT homozygotes were -0.074 ± 0.093 for marbling and -0.002 ± 0.015 inches for SFD (P> 0.05 for both attributes), while in the DGAT1 gene, AA homozygous animals were superior to CC homozygous animals for 0.092 ± 0.095 marbling record (P> 0.05) and 0.03210.015 inches for SFD (P <0.05), respectively. In the LEP gene, the same FIGs for genotype differences between CC and TT animals were 0.075 ± 0.116 for marbling and 0.019 ± 0.018 for SFD (P> 0.05 for both attributes) respectively. Obviously, the current study on the bovine TFAM gene indicated that the genotype differences between two homozygotes at any position exceeded any of the differences observed in the TG gene, DGAT1 and bovine LEP, respectively. In particular, the genotype differences between the CC and TT homozygotes in the bovine TFAM gene took into account 0.634 standard deviation in marbling and 0.402 standard deviation in SFD in these animals F2 of Wagyu X Limousin had a standard deviation of 1 marbling record and a standard deviation of 0.18 inches for SFD. Thus, among these four candidate genes studied so far in the reference population, the results showed that the TFAM gene had the greatest effects on both marbling and SFD, indicating a larger gene for both attributes. A search for transcriptional regulatory elements using Matlnspector (http: // www. gsf. de /) indicated that both SNPs in the bovine TFAM promoter unitarily or separately lead to a gain / loss of six putative binding sites for 1) heterodimer tal-lalfa / E47; 2), link protein 1 of the responsive element of cAMP; 3), heterodimers of the transcription factors of bHLH HAND2 (Thing2) and E12; 4), nuclear factor 1; 5), orphan alpha 1 receptor related to RAR and 6), zinc finger protein RP58 (ZNF238), which is preferentially associated with heterochromat ina. Reusch and Klemm (2002) reported that the binding protein of the cA P response element of the transcription factor (CREB) participates in adipogenesis, with. constitutively active forms of CREB that induce adipocyte differentiation and dominant negative forms of CREB that block this process. Evidence has shown that nuclear factor 1 is essential for the expression of the stearoyl-CoA desaturase gene during preadipocyte differentiation (Singh and Ntambi, 1998). The alfalpha receptor RAR-related orphan alphanumeric receptor related to RAR, or RORal forms a part of the multifactorial regulatory mechanisms that control the expression of the PPARgamma gene, which has been studied extensively for the past decade mainly due to its central function in promoting and maintain the adipocyte phenotype (Sundvold and Lien, 2001). However, as these two SNPs in the bovine TFAM promoter affect the binding efficiency for these genes, how these linkage alterations regulate the subsequent TFAM gene expression patterns and how these expression patterns stimulate mitochondrial biogenesis differently and thus lead to the differences in fat deposition and Energy metabolisms, need to be explored further. References: Alam et al., Nucleic Acids Res. 2003; 31: 1640-5. Barendse, 1997. Patent Application W09923248 PCT / AU98 / 00882. Buchanan et al., Genet Sel Evol. 2002; 34: 105-16. De and contributors, Proceedings, Western Section, American Society of Animal Science. 2004; 55: 95-98. Ekstrand and collaborators, Hum Mol Genet. 2004; 13: 935-44. Fisher and Clayton, Mol Cell Biol. 1988; 8: 3496-509. Garstka et al., Nucleic Acids Res. 2003; 31: 5039-47. Gaspari et al., 2004; 1659: 148-52. Kanki et al., Mol Cell Biol. 2004; 24: 9823-34. Kanki et al., Ann N and Acad Sci. 2004; 1011: 61-8. Kozak, Proc Nati Acad Sci U S A. 1995; 92: 2662-6. Kozak, Gene. 2002; 299: 1-34. Owen et al., J Biol Chem. 2002; 277: 30409- 12. Quandt et al., Nucleic Acids Res. 1995; 23: 4878-84. Reichert and Neupert, Trends Genet. 2004; 20: 555-62. Reusch and Klemm, 2002, J Biol Chem. 277, 1426-1432. Savell et al., (1986) Journal of Food Science 51, 838. Scarpulla, 2002. Biochim. Biophys. Acta. 1576: 1-14. Singh and Ntambi, 1998. Biochim Biophys Acta 1398, 148-156. Sundvold and Lien, 2001. Biochem Biophys Res Commun. 287, 383-390. Thaller and collaborators, Anini Genet. 2003 Oct; 34 (5): 354-7 ilson-Fritch et al., Mol Cell Biol. 2003; 23: 1085-9. Wilson-Fritch et al., J Clin Invest. 2004; 11: 1281-9. Wu and collaborators, Genetics. 2005 Sep; 125 (1): 103-13. Example 2 This example describes mitochondrial transcription genes encoded in the basal nucleus and meat quality in beef cattle. Evidence has shown that the machinery of Basal mitochondrial transcription directs mitochondrial biogenesis and gene expression, and thus can play an important role in the deposition of body fat and energy metabolism. Here the inventors report the sequence compilation, the development of the genetic marker and the association analysis of the TFAM, TFB1M and TFB2M genes with marbling and subcutaneous fat depth (SFD) in cattle using a reference population of F2 crossings. Wagyu x Limousin. Statistical analysis revealed that the bovine TFAM gene was significantly associated with marbling (F = 3.84, P = 0.0229) and SFD (F = 3.56, P = 0.0301). The genetic markers developed in the study can be used to determine how this mitochondrial complex is important for improving the quality of meat in the beef industry. Due to its limited protein coding capacity, the initiation and regulation of gene expression in mitochondrial DNA (mtDNA) is excessively dependent on a relatively small set of nuclear encoded mitochondrial regulatory proteins (Gleyzer et al., 2005). The basic mitochondrial transcription machinery consists of mitochondrial RNA polymerase. { POLRMT) and mitochondrial transcription factor A. { TFAM), Bl (TFB1M) and B2. { TFB2M). TFAM, a member of a high mobility protein family group and the first transcription factor identified mitochondrial, is essential for the maintenance and biogenesis of mtDNA (Fisher and Clayton, 1988). Both TFB1M and TFB2M are recently identified mitochondrial transcription factors and interact directly with POLRMT to form a heterodimer (Falkenberg et al., 2002). On the other hand, mitochondria carry out a large number of reactions in eukaryotic cells, including ß-oxidation of fatty acids, which provides key intermediates for the synthesis of triglycerides via the action of pyruvate carboxylase (Owen et al., 2002 ). As the basic mitochondrial transcription machinery directs mitochondrial biogenesis and gene expression, it has been contemplated that machinery can play an important role in the deposition of body fat and energy metabolism. Here the sequence compilation, the development of the genetic marker and the association analysis of the TFAM, TFB1M and TFB2M genes with the marbling and depth of subcutaneous fat (SFD) using a reference population of F2 crossing of Wagyu x Limousin are reported . The bioinformatics procedures used to recover both of the cDNA and genomic DNA sequences of those three bovine genes employed a three-step procedure. First, the cDNA sequences of the human orthologs were used as references to recover the ESTs orthologs against the 'GenBank data base' est_others "with a limited species option to Bos taurus. Second, several ESTs were selected and assembled to form a primary cDNA sequence for each cattle gene, which was then used to perform a species-specific EST search against the same database in order to expand the primary sequence to a full-length cDNA sequence. Finally, the full-length cDNA sequence was used to search the genomic DNA sequences of the same gene against the database of the 6X bovine genome sequence and thus determine its genomic organization. Primers were designed to direct the promoter regions and all the coding exons for all three bovine genes based on the genomic DNA sequences. To ensure that each exon region was fully amplified and sequenced, at least 100 bp of flanking sequences were included in the products. To facilitate the discovery of genetic polymorphisms in these genes, two accumulations of DNA were formed: one of 6 stallions Fi of agyu x Limousin and one of 113 Fi females of Wagyu x Limousin. PCR reactions were performed on these two DNA pools and sequenced on an ABI 3730 sequencer at the Laboratory for Biotechnology and Bioanalysis (Washington State University) using a standard protocol. Nucleotide polymorphisms were identified by comparison of sequence patterns between these DNA pools. A total of ten individual nucleotide polymorphisms (SNPs) were detected, including 3 in TFAM, 2 in TFB1M and 5 in TFB2M. Only one SNP in TFAM, two SNPs in TFB1M and one SNP in the bovine TFB2M gene were selected for genotyping using the PCR-RFLP and Bi-PASA techniques. The animals used in the study were the F2 progeny of the inter mating of 6 Fi Wagyu x Limousin sires and 113 females of Wagyu x Limousin as described above. Marbling records varied from 4 = Light0 to 9.5 = Moderately Abundant50 (SD = 1.00). SFD was measured at the interface of the 12-13th rib perpendicular to the outer surface at a point three-fourths of the length of the longissimus muscle from its end of the spinal bone, which varied from 0.1 to 1.3 inches (SD = 0.18) in this F2 population. The phenotypic data for the marbling and SFD records were analyzed with a mixed linear model using the PROC MIXED module in SAS v9.1. The source of variation included the year of birth, gender, age at collection and the genotype of each transfer marker as the fixed effects and a random effect to take into account the background of polygen. The covariance structure of the polygenic effect was defined by the calculated numerical ratio of the pedigree using SAS macro LORG. The residual effect was assumed to have identical independent distribution with unknown variation. The additive genetic variation and the components of residual variation were estimated using the Newton-Raphson algorithm stabilized at the edge for the maximum restricted probability estimation (REML). Marking effects tests were performed using the Kenward-Roger method to calculate word degrees of freedom. This method uses an adjusted covariance matrix estimator to reduce the deviation of the small sample. Comparisons similar to least squares mean pairs were performed using Fisher's less significant Protected Difference T (LSD) test procedure. The BLAST search based on human orthologous retrieved more than 20 ESTs for each of the TFAM, TFB1M and bovine TFB2M from the "est_others" database of GenBank. Several overlapping ESTs were selected and assembled to form the primary cDNA sequences for these genes. The primary cDNA sequence was then used as a reference for the search of ESTs of the same gene, in particular for their expansion of 5 'and 3' flanking sequence, which were omitted by the search of human orthologs due to the low sequence similarity in these regions. He final assembly produced a full-length cDNA sequence of 2,259 bp for the bovine TFAM gene, 2,617 bp for the bovine TFB1M gene and 1,991 bp for the bovine TFB2M gene, respectively. Using these full-length cDNA sequences as references, BLAST searches against the 6X cattle genome sequence databases retrieved three contiguous genomes of 16.666 bp for TFAM, four contiguous genomic ones of 108.966 bp for TFB1M and one contiguous genomic activity of 53, 542 bp for TFB2M, respectively. Similar in human, dog, mouse and rat, both bovine TFAM and TFB1M genes consist of seven exons, while the bovine TFB2M contains eight exons. In addition to two closely linked A / C and C / T SNPs described in Example 1, a third mutation with a C / T transition was also detected in the bovine TFAM promoter region (FIG 5A). A Bi-PASA assay was developed to determine the genotype of this marker on individuals. Direct sequencing of the PCR products on two DNA pools revealed two mutations in the TFB1M gene (FIG.5B) and five mutations in the TFB2M gene (FIG.5C), respectively. The PCR amplicons were digested with 2U of MspI and BanI to determine the genotype of T / G and GIC SNPs in the bovine TFB1M gene. The determination of the initial genotype of 48 samples using three of the five polymorphisms in the bovine TFB2M gene revealed that they are fixed in two haplotypes. Therefore, only one SNP was selected for the determination of the genotype by digestion with the restriction enzyme Acyl. The statistical analysis revealed that the bovine TFAM gene was significantly associated with marbling (F = 3.84, P = 0.0229) and SFD (F = 3.56, P = 0.0301). However, none of the markers in either TFB1M and TFB2M affected the significantly measured attributes (F < 1.70, P > 0.1842). The additive and dominance effects of each marker were estimated and listed in Table 3. Only the additive effect of the bovine TFAM gene on marbling reached a significant level (P = 0.0059) and the additive effects of TFAM and TFB2M on SFD were approximated the meaning (P = 0.0651 for TFAM and P = 0.1118 for TFB2M) (Table 3). The results indicate that the involvement of these three genes in promoting the initiation of mitochondrial genome transcription may be specific to the relevant tissue. That is, TFAM contributed significantly to both marbling and SFD, whereas TFB1M had no effect on any attribute. However, TFB2M contributed more to SFD, but almost nothing to marbling. Table 3. Additive and dominative effects of bovine TFAM, TFB1M and TFB2M markers on marbling and SFD. Marble Effect SFD (in inches) genetic Dear + S. E. t Pr > t Dear ± S.E. t Pr > t C / T in the bovine TFAM gene Aditivo -0.384 ± 0.138 -2.78 0.0059 -0.036 ± 0.019 -1.85 0.0651 Dominator 0.117 ± 0.088 0.17 0.2066 -0.007 ± 0.013 -0.56 0.5780 G / T in the bovine TFB1M gene Additive -0.206 ± 0.160 -1.28 0.2003 -0.007 ± 0.022 -0.33 0.7451 Dominative -0.017 ± 0.100 0.17 0.8646 -0.003 ± 0.014 -0.23 0.8209 C / G in the bovine TFB1M Additive 0.017 ± 0.186 0.09 0.9273 -0.005 ± 0.026 -0.19 0.8528 Dominative 0.074 ± 0.118 0.63 0.5288 -0.023 ± 0.017 1.41 0.1612 C / T in the bovine TFB2M gene Additive 0.121 ± 0.120 1.00 0.3188 -0.028 ± 0.018 1.60 0.1118 Dominative -0.112 ± 0.079 -1.41 0.1588 -0.000 ± 0.011 -0.03 0.9798 Both marbling and SFD have attracted a lot of publicity and interest for many years, since they are two of the greatest quantitative attributes that affect the quality of the channel and the production efficiency in beef cattle. The genetic markers developed in the study can be used to further determine how this mitochondrial complex is important to improve the quality of meat in the beef industry. References: Falkenberg et al., (2002) Nat Genet. 31: 289-94.

Fisher and Clayton (1988) Mol Cell Biol. 8-3496-3509. Gleyzer et al., (2005) Biochem Biophys Res Commun. 334: 516-23. Owen et al., J Biol Chem. 2002 Aug 23; 277 (34): 30409-12. Example 3 This example provides associations in the TFAM-I, TFA -2 and FABP4 markers and the channel attributes in steers and heifers of commercial feed lots. The following markers were evaluated: (1) a C to A substitution at the position of nucleotide 1220 in the promoter of the mitochondrial transcription factor A gene (TFAM-1), (2) a C to T substitution at the nucleotide position 1212 in the TFAM-2 promoter and (3) a G to C substitution at the position of nucleotide 7516 of the gene for protein 4 binding fatty acid (FABP4). Previous results indicate that they affect markers that affect marbling and subsequent fat. Initially, there were 1,589 records initially of steers and heifers. The target end point was 12.2 mm of posterior fat. The date of collection was predicted from the optimal economic end point for the animal. Contemporary groups included the source and sex. It was assumed that the type of reproduction was confused with the source. The final data set included the registration number based in the phenotypes and genotypes available for each attribute. The tested attributes are: weight of the hot channel (HCW, Ib), area of ribeye (REA, pg2), area of ribeye percent in weight HCW (REA / cwt HCW, pg2 / 100 Ib of weight of the hot channel (HCW) , weight value of the hot channel (HCW value, $), calculated live weight (Cale Lv Wt, Ib), dry matter intake (DMI, Ib), days in the food (DOF, d), intake of dry matter by day in feed (DMI per DOF, lb / d), average daily gain (ADG, lb / d), percentage of fertilizer (DP,%), posterior fat thickness (BFAT, pg), calculated yield grade (cYG) ), grade of quality, less than or equal to the selection versus greater than or equal to the choice (QG, <Se vs,> Ch), intramuscular fat content (IMF%,%), marbling record (MBS) , 10 to 99), marbling record divided by days in the feed (MBS / DOF), value of the additional channel (value of the additional channel,, $), adjusted net return - all costs removed (net return ajust. - all costs removed, $) and adjusted net return - value of the initial animal not removed (net return ajust. - value of initial animal not removed, $). The analysis models were the genotype, where the genotypes were adjusted as fixed effects and additive or allele substitution, which showed the regression in the number of alleles (0, 1, 2). Both models conform with the combinations of 2 markers. Another model of analysis is the haplotype, which shows the regression on the haplotype (expected) when adjusting multiple TFAM markers. Associations of significant individual markers are presented in Table 4 and combinations of 2 significant markers are presented in Table 5. t O Table 4: Analysis of a single marker for TFAM-1, TFAM-2 and FABP4 Adjustment of markers for substitution of allele: A for TFAM1; C for TFAM2 and FABP4 Marbling records vary from 10 to 99; 10 = PDO = Std, 99 = A90 = Prime QG Ch (1, 2, 5, 9, 20) implies Ch or better - includes Prime, Ch, CAB, Sterling Silver and Angus Pride; Alternate included Se, No Roll, Dark cutter and Hard bone Table 5: Analysis of two Markers for TFAM-1, TFAM-2 and FABP4 Marker adjustment for allele substitution: A for TFAM1; C for TFAM2 and FABP4 Marbling records vary from 10 to 99; 10 = PDO = Std, 99 = A90 = Prime QG Ch (1, 2, 5, 9, 20) implies Ch or better - includes Prime, Ch, CAB, Sterling and Angus Pride; Alternate included Se, No Roll, Dark cutter and Hard bone Example 4 FIG. 7 shows a flow chart of the data entry and the output of the analysis results and the correlation of the data pertaining to reproduction, veterinary histories and performance requirements of a group of animals such as bovines. The flow chart illustrated in FIG. 7 further indicates the interactive flow of data from the computer-aided device to a group of students who learn the use of the method of the invention and the correlation of such interactive data for. Present an output as a circular diagram that indicates the progress of the class. The flow chart further indicates modifications of the method of the invention in accordance with the information received from the students to advance the teaching process or optimize the method to meet the needs of the students. FIG. 8 illustrates potential relationships between the data elements that are introduced into the system. Unidirectional arrows indicate, for example, that a barn is typically owned by only one farm, while a barn can have several stables. Similarly, a pre-registration can include veterinary products. FIG. 9A illustrates the flow of events in the use of the laptop-based system for the entry of data on the reproduction and breeding of a herd of cows. FIG. 9B illustrates the flow of events through the subroutines related to the input of data concerning the management of the farm. FIG. 9C illustrates the flow of events through the subroutine related to the entry of data concerning specific data to a company. FIG. 10 illustrates a flowchart of data entry and output of analysis results and correlation of data pertaining to reproduction, veterinary histories and performance requirements of a group of animals. The invention is further described by the following numbered paragraphs: 1. A method for subgrouping animals according to the genotype wherein the animals of each subgroup have a similar polymorphism in a factor gene? of mitochondrial transcription ("TFAM") comprising: (a) determining the genotype of each animal that is subgrouped by determining the presence of an individual nucleotide polymorphism in the TFAM gene, and (b) segregating individual animals into subgroups where each animal in a subgroup has a similar polymorphism in the TFAM gene. 2. A method for sub-grouping animals according to the genotype where the animals of each subgroup have a similar genotype in the TFAM gene comprising: (a) determining the genotype of each animal that is subgrouped by determining the presence of an individual nucleotide polymorphism (s) of interest in the TFAM gene, (b) segregating individual animals into subgroups depending on whether the animals have, or do not have, the individual nucleotide polymorphism (s) of interest in the TFAM gene. 3. The method of paragraphs 1 or 2, wherein the individual nucleotide polymorphism (s) of interest is selected from the group consisting of a substitution of A to C at the nucleotide -1220 position in the TFAM gene promoter, a substitution of T a C in position -1212 in the promoter of the TFAM gene and a substitution of T a C in position -995 in the promoter of the TFAM gene. 4. A method for subgrouping animals according to the genotype wherein the animals of each subgroup have a similar genotype in the TFAM gene comprising: (a) determining the genotype of each animal that is subgrouped when determining the presence of a substitution of A to C at the position of nucleotide -1220 in the promoter of the TFAM gene, a substitution of T to C at position -1212 in the promoter of the TFAM gene and a. substitution of T to C at position -995 in the TFAM gene promoter, and (b) segregating individual animals into subgroups depending on whether the animals have, or do not have, a substitution of A to C at the position of nucleotide -1220 in the promoter of the TFAM gene, a substitution of T to C at position -1212 in the promoter of the TFAM gene and a substitution of T to C at position -995 in the TFAM gene promoter. 5. A method for identifying an animal having a desirable phenotype as compared to the general population of animals of that species, comprising determining the presence of an individual nucleotide polymorphism in the animal's TFAM gene, wherein the polymorphism is selected of the group consisting of a substitution of A to C at the position of nucleotide -1220 in the promoter of the TFAM gene, a substitution of T to C at position -1212 in the promoter of the TFAM gene and a substitution of T to C in the -995 position in the TFAM gene promoter where the individual nucleotide polymorphism is indicative of a desirable phenotype. 6. The method of paragraph 5, wherein the desirable phenotype is food intake, growth rate, body weight, carcass size and composition, milk yield or any combination thereof. 7. The method of paragraph 5 or 6, where the desirable phenotype is the value of the additional channel (value of the additional channel, $), average daily gain (ADG, lb / d), posterior fat thickness (BFAT, pg) , calculated live weight (Cale Lv Wt, Ib), degree of calculated yield (cYG), days in the food (DOF, d), percentage of fertilizer (DP,%), intake of dry matter (DMI, Ib), intake of dry matter by day in the feed (DMI per DOF, lb / d), weight of the hot channel (HCW, Ib), weight value of the hot channel (HCW value, $), intramuscular fat content (IMF%,%), record of marbling (MBS, 10 to 99), marbling record divided by days in the feed (MBS / DOF), grade of quality, less than or equal to the selection against greater than or equal to the choice (QG, < ,> Ch), ribeye area (REA, pg2), ribeye area by weight percent HCW (REA / cwt HCW, pg2 / 100 lb hot channel weight (HCW), subcutaneous fat depth (SFD) or any combination thereof 8. The method of any of paragraphs 1 to 7 wherein the animal is a bovine 9. The method of any of paragraphs 1 to 8 wherein the TFAM gene is a bovine TFAM gene. A method assisted by Interactive computer for tracking livestock cattle breeding comprising, using a computer system comprising a programmed computer comprising a processor, a data storage system, an input device, an output device and an interactive device, the steps of: (a) entering in the programmed computer through the input device data comprising a history of reproduction of a bovine or herd of cattle, (b) introducing into the computer programmed through the input device data comprising a veterinary history of a bovine or herd of cattle, (c) correlating veterinary data with the history of reproduction of the cattle or herds of cattle using the processor and the data storage system; and (d) outputting the output device to the veterinary history reproduction history of the bovine or herd of cattle. 11. The method according to paragraph 10, wherein the computer system is an interactive system whereby modifications to the output of the computer-assisted method can be correlated according to the input of the interactive device. 12. The method according to paragraph 10 or 11, further comprising the steps of entering diagnostic data related to the health of the cow or herds of cows into the programmed computer; and correlate the diagnostic data with the reproduction and veterinary histories of the cow or herd of cows. 13. The method according to any of paragraphs 10 to 12, wherein the veterinary data comprises a vaccination record for a cow or herd of cows. 14. The method according to any of the paragraphs 10 to 13, where the health data are selected from the group consisting of breeding condition data, herd history and food safety data. 15. The method according to any of paragraphs 10 to 14, further comprising at least one additional step selected from the group consisting of entering data related to the quality control of the bovine or herd of cattle and correlating to the programmed computer. the data of quality control with the reproduction and the veterinary histories of the cow or herd of cows, to introduce in the programmed computer the performance parameters of the cow or herd of cows; and correlating the required performance parameters of the bovine or herd of cattle to a specific performance requirement of a client, correlating the vaccine data to the performance parameters of the bovine or herd of cattle, correlating the herd with the performance parameters of the bovine or herd of cattle, correlate the safety data of the feed with the performance parameters of the cattle or herd of cattle, correlate the data of the breeding condition with the performance parameters of the bovine or herd of cattle, enter in the programmed computer related data with the nutritional data of the bovine or herd of cattle; and correlate the nutritional data with the performance parameters of the cattle or herd of cattle, and alert to undesirable changes in the parameters of performance in the bovine or herd of cattle. 16. The method according to any of paragraphs 10 to 15, further comprising the steps of entering into the programmed computer through the input device data comprising a genotype of a bovine; correlate a physical characteristic predicted by the genotype using the processor and the data storage system; and output output physical characteristic correlated with the genotype for a bovine or population of cattle and feed the animal (s) with a diet based on the physical characteristic, in order to improve the production of cattle. 17. The computer-assisted method according to any of paragraphs 10 to 16 to optimize the efficiency of the lots of feed for the livestock that comprises to make exit of the exit device the reproduction and veterinary history of the bovine or herd of cattle and to feed the animal (s) with a diet based on their reproduction and veterinary histories, in order to optimize the efficiency of the feeding lots for the cattle or herd of cattle. 18. A method for transmitting data comprising the transmission of information of such methods according to any of paragraphs 10 to 16, selected from the group which consists of telecommunication telephone, videoconference, mass communication, a presentation, a computer presentation, a presentation of POWERPOINT ™, Internet, email and documentary communication. 19. An interactive computer system according to any of paragraphs 10 to 16 to track reproduction and welfare histories of cows comprising reproduction and veterinary data corresponding to a bovine or herd of cattle and where the computer system it is configured to allow the operator of the same to exchange data with the device or with a remote database. 20. The interactive computer system according to paragraph 19, wherein the input and output devices are a personal digital assistant or a pocket computer. 21. A method for doing business to track reproduction and welfare stories of livestock comprising reproduction and veterinary data corresponding to one or more livestock animals comprising providing a user with the computer system of paragraph 19. 22. A method to do business to track reproduction and welfare stories of livestock that includes breeding and veterinary data corresponding to one or more livestock animals comprising providing a user with the computer system of paragraph 20. 23. The method of doing business in accordance with paragraph 21, which further comprises providing the owner of the animal or customer with collection equipment of samples, such as swabs and labels useful for collecting samples from which genetic data can be obtained, and where labels are optionally packaged in a container that is encoded with identification legends. 24. The method for doing business according to any of paragraphs 10 to 16, wherein the computer system further comprises a plurality of interactive devices and wherein the method further comprises the steps of receiving data from the interactive devices, compiling the data, output the data to indicate the response of a student or class of students to a question related to the operation of the computer-assisted method, and optionally modify the operation of the computer-assisted method according to the indication of the response. 25. The method of any of paragraphs 8 to 24, wherein the data comprises the presence or absence of one or more of an individual nucleotide polymorphism (s) of interest in the TFAM gene. 26. The method of paragraph 25, wherein the individual nucleotide polymorphism (s) is selected from the group consisting of a substitution of A to C at the position of nucleotide -1220 in the promoter of the TFAM gene, a substitution of T to C in the position -1212 in the promoter of the TFAM gene and a substitution of T to C in the position -995 in the promoter of the TFAM gene. * * * Having described in this manner in detail the preferred embodiments of the present invention, it is to be understood that the invention defined by the preceding paragraphs will not be limited to the particular details set forth in the foregoing description since many obvious variations. they are possible without departing from the spirit or scope of the present invention.

Claims (1)

1. CLAIMS 1. A method to identify an animal that has calculated live weight (Cale Lv Wt, Ib) desirable, calculated yield grade (cYG), days in the feed (DOF, d), dry matter intake (DMI, Ib) , intake of dry matter per day in the food (DMI per DOF, Ib / d), weight of the hot channel (HCW, Ib), weight value of the hot channel (HCW value, $), intramuscular fat content (IMF% ,%), marbling record (MBS, 10 to 99), marbling record divided by days in the food (MBS / DOF), grade of quality, less than or equal to the selection against greater than or equal to the choice ( QG, <Se vs,> Ch), ribeye area (REA, pg2), ribeye area by weight percent HCW (REA / cwt HCW, pg2 / 100 lb of hot channel weight (HCW), or a combination thereof, as compared to the general population of animals of that species, characterized in that it comprises determining the presence of a single nucleotide polymorphism in a gene of factor A d e mitochondrial transcription ("TFAM") of the animal, the presence of an individual nucleotide polymorphism in the TFAM gene of the animal, wherein the individual nucleotide polymorphism is indicative of calculated live weight (Cale Lv Wt, Ib) desirable, degree of calculated yield (cYG), days in the food (DOF, d), dry matter intake (DMI, Ib), dry matter intake per day in the food (DMI per DOF, lb / d), weight of the hot channel (HCW, Ib), weight value of the hot channel (HCW value, $), intramuscular fat content (IMF%,%), marbling record (MBS, 10 to 99), marbling record divided by days in the food (MBS / DOF), grade of quality, less than or equal to the selection against greater than or equal to the choice (QG, <Se vs.,> Ch), ribeye area (REA, pg2), area of ribeye percent by weight HCW (REA / cwt HCW, pg2 / 100 lb of hot runner weight (HCW), or a combination thereof 2. The method according to claim 1, which further comprises sub-packing animals according to the genotype, in which the animals of each subgroup have a similar polymorphism in the TFAM gene, the method characterized because it comprises: (a) determining the genotype of each animal that is subgrouped when determining the presence of an individual nucleotide polymorphism in the TFAM gene, and (b) segregating individual animals into subgroups depending on whether they animate them they have, or do not have, the individual nucleotide polymorphism of interest in the TFAM gene. 3. The method according to claim 1, characterized in that the individual nucleotide polymorphism (s) of interest is selected from the group consisting of a substitution from A to C at the nucleotide -1220 position. in the promoter of the TFAM gene, a substitution of T to C at position -1212 in the promoter of the TFAM gene and a substitution of T to C in position -995 in the promoter of the TFAM gene. 4. The method according to claim 1, characterized in that the animal is a bovine. 5. The method according to claim 1, characterized in that the TFAM gene is a bovine TFAM gene. 6. An interactive computer-assisted method for tracking the rearing of cattle, characterized in that it comprises, using a computer system comprising a programmed computer comprising a processor, a data storage system, an input device, a device of output and an interactive device, the steps of: (a) entering in the programmed computer through the input device data comprising a reproduction history of a bovine or herd of cattle and a genotype of a bovine; correlating a physical characteristic predicted by the genotype using the processor and the data storage system; (b) entering data into the computer programmed through the input device comprising a veterinary history of a bovine or herd of cattle, (c) correlate the veterinary data with the reproduction history of the bovine or herd of cattle using the processor and the data storage system, and (d) output the history of reproduction, the veterinary history of the bovine or herd of cattle and the physical characteristic correlated with the genotype for a bovine or population of cattle, where the physical characteristic is the calculated live weight (Cale Lv Wt) , Ib) desirable, calculated yield grade (cYG), days in the food (DOF, d), dry matter intake (DMI, Ib), dry matter intake per day in the food (DMI per DOF, lb / d ), weight of the hot channel (HCW, Ib), weight value of the hot channel (HCW value, $), intramuscular fat content (IMF%,%), marbling record (MBS, 10 to 99), marbling record divided between days in food (MBS / DOF), grade of quality, less than or equal to the selection versus greater than or equal to the choice (QG, <Se vs.,> Ch), ribeye area (REA, pg2), area of ribeye percent by weight HCW (REA / cwt HCW, pg2 / 100 lb of hot channel weight (HCW), or a combination of themselves, as compared to the general population of cattle, and the genotype is an individual nucleotide polymorphism in a TFAM gene. The method according to claim 6, characterized in that the computer system is an interactive system whereby the modifications to the output of the computer-assisted method can be correlated according to the input of the device Interactive 8. The method according to claim 6, characterized in that the method further comprises the steps of entering in the programmed computer diagnostic data related to the health of the cow or herd of cows; and correlating the diagnostic data with the breeding and veterinary histories of the cow or herd of cows. The method according to claim 6, characterized in that the veterinary data comprises a vaccination record for a cow or herd of cows. The method according to claim 6, characterized in that the health data are selected from the group consisting of the breeding condition data, herd history and food safety data. 11. The method according to claim 6, characterized in that the method further comprises at least one additional step selected from the group consisting of entering data related to the quality control of the bovine or herd of cattle in the programmed computer and correlating the quality control data with the reproduction and veterinary histories of the cow or herds of cows, introducing performance parameters of the cow or herd of cows into the programmed computer; and correlate the required performance parameters of the bovine or herd of bovine with a specific performance requirement of a client, correlate the vaccine data with the performance parameters of the bovine or herd of cattle, correlate the herd with the performance parameters of the bovine or herd of cattle, correlate the food safety data with the performance parameters of the bovine or herd of cattle, correlate the data of the breeding condition with the performance parameters of the bovine or herd of cattle, enter in the programmed computer data related to the nutritional data of the bovine or herd of bovines; and to correlate the nutritional data with the performance parameters of the bovine or herd of cattle, and to alert to the undesirable changes in the performance parameters of the bovine or herd of cattle. The method according to claim 6, characterized in that the individual nucleotide polymorphism (s) of interest is selected from the group consisting of a substitution of A to C at the nucleotide -1220 position in the TFAM gene promoter, a substitution of T to C at position -1212 in the promoter of the TFAM gene and a substitution of T to C at position -995 in the promoter of the TFAM gene. 13. A method for transmitting data, characterized in that it comprises the transmission of information according to claim 6, selected from the group consisting of telecommunication, telephone, video conference, Mass communication, a presentation, a computer presentation, a presentation of POWERPOINT ™, internet, email and documentary communication. 14. An interactive computer system according to claim 6, characterized in that it is for tracking the reproduction and welfare histories of cows comprising breeding and veterinary data corresponding to a bovine or herd of cattle, and wherein the The computer is configured to allow the operator to exchange data with the device or a remote database. 15. The interactive computer system according to claim 14, characterized in that the input and output devices are a personal digital assistant or a pocket computer. 16. A method for doing business to track breeding and welfare stories of livestock comprising reproduction and veterinary data corresponding to one or more livestock animals, characterized in that it comprises providing a user with the computer system of claim 1. 17. A method for doing business to track the breeding and welfare histories of livestock comprising reproduction and veterinary data corresponding to one or more livestock animals, characterized in that it comprises providing a user with the computer system of claim 14. 18. The method for doing business according to claim 16, characterized in that it further comprises providing the owner of the animal or customer with sample collection equipment, such as swabs and labels useful for collecting samples from which genetic data can be obtained, and where labels are optionally packaged in a container that is encoded with identification legends. The method for doing business according to claim 16, characterized in that the computer system further comprises a plurality of interactive devices and wherein the method further comprises the steps of receiving data from the interactive devices, compiling the data, outputting data to indicate the response of a student or class of students to a question related to the operation of the computer-assisted method, and optionally modify the operation of the computer-assisted method according to the indication of the response.