MX2008008729A - Calpastatin markers for fertility and longevity - Google Patents

Abstract

Aspects of the present invention provide novel compositions and methods based on novel calpastatin (CAST) genetic markers. Particular aspects provide novel markers for improved fertility and longevity in, for example, dairy cattle.

Description

FIELD OF THE INVENTION The present invention relates to the identification of genetic markers (individual nucleotide polymorphisms (SNPs) and a short tandem repeat (STR)) within the bovine genes encoding calpastatin (FIG. "CAST") and its associations with economically relevant attributes in dairy production. The invention also relates to methods and systems, including network-based processes, for handling SNP / STR data and other data related to specific animals and herds of animals, veterinary care, diagnostic data and quality control and management of cattle that, based on the determination of the genotype, have predictable attributes of fertility and longevity, breeding conditions, animal welfare, food safety information, verification of existing processes and field location data. BACKGROUND OF THE INVENTION Reproductive decline has been a challenge facing the dairy industry worldwide for several decades and has typically been blamed on the selection for increased milk production [Sheldon IM, Dobson H. Reproductive challenges facing the cattle industry at the beginning of the 2nd century. Reprod Suppl. 2003; 61: 1-13]. In the United States alone, the first coverage or service for the speed of conception has declined from approximately 65% in 1951 to 40% in 1996 [Butler WR. Review: effect of protein nutrition on ovarian and uterine physiology in dairy cattle. J, Dairy Sci. 1998; 81: 2533-2539], while the number of coverings per conception has increased from approximately 1.8 in 1970 to approximately 3 in 2000 [Lucy MC. Reproductive loss in high-producing dairy cattle: where will it end? J Dairy Sci. 2001; 84: 1277-1293]. This was reported in [Silvia WJ, Brown CH, McDaniel BT, McAllister AJ. Trends in reproductive performance in Southeastern Holstein and Jersey DHI herds. J Dairy Sci. 2002; 85: 244-251]. However, the available days were increased to 152 days for Jerseys and 168 days for Holsteins for 1997 to 1999. In the United Kingdom, the design speed for the first covering of dairy cows has declined by 65.4% (1975-82) to 44.3% (1995-98) at a rate of approximately 1% per year [Royal MD, Dar ash AO, Flint AP, Webb R, Woolliams JA, Lamming E. Declining fertility in dairy cattle; changes in traditional and endocrine pararaeters of fertility. Anim Sci 2000; 70: 487-502]. Equivalent decreases in the rate of conception of the first cover have also been observed in dairy cattle in Ireland [Roche JF, Mackey D, Diskin MD. Reproductive management of postpartum cows. Anim Reprod Sci 2000; 61: 703-712] and Australia [Macmillan KL, Lean IJ, estwood CT. The effects of lactation on the fertility of dairy cows. Aust Vet J 1996; 73: 141-147]. Understanding the genetic causes of reduced fertility is essential to stop the fertility decline currently observed in lactating dairy cows. To address the difficulties of achieving the desired levels of reproductive performance in dairy herds today, a new attribute of fertility, the rate of pregnancy of daughters (DPR) was introduced as an indicator of the fertility of the father or stallion for the selection genetics [VanRaden P, Sanders AH, Tooker ME, Miller RH, Norman HD, Kuhn MT, iggans GR. Development of a national genetic evaluation for cow fertility. Dairy Sci 2004; 87: 2285-2292]. The pregnancy rate is defined as the percentage of non-pregnant cows that become pregnant during each 21-day period. In fact, the data to calculate DPR are taken from the available days reported, which are calculated as the pregnancy date minus the previous due date. The pregnancy date is determined from the last reported reproduction or the duration of the subsequent pregnancy minus the expected pregnancy. For the calculation of genetic evaluations, the available days are converted at the rate of pregnancy of daughters by the linear transformation of the pregnancy rate = 0.25 (233 - days available). Evaluations are expressed as predicted transmission ability (PTA) for DPR, and calculations are generated as a direct result of performance of the bull daughters [VanRaden PM, Sanders AH, Tooker ME, Miller RH, Norman HD, Kuhn MT, Wiggans GR. Development of a national genetic evaluation for cow fertility. Dairy Sci 2004; 87: 2285-2292], In addition, the fertility of the cow is a major component of productive life (PL) or longevity. The improvement of both DPR and PL will lead to increased productivity and utilization of the dairy industry. Calpastatin (CAST) is an endogenous protease inhibitor that specifically acts on two independent proteases of Ca2 +, μ-calpain and m-calpain by binding and forming an inactive complex. CAST is widely expressed in mammalian cells and tissues, including those related to reproduction. For example, the CAST gene is expressed in the human pituitary gland [Kitahara A, Takano E, Ontsuki H, Kirihata Y, Yamagata Y, Knaagi R, Murachi T. Reversed distribution of calpains and calpastatin in human pituitary gland and selective localization of calpastatin in adrenocorticotropin-producing cells as demonstrated by immunohistochemistry. J Clin Endocrinol Metab 1986; 63: 343-348], the placenta, 'human [Thompson VF, Saldana S, Cong J, i Luedke DM, Goll DE. The 'calpain system in human placenta. Life Sci 2002; 70: 2493-508], the human oocyte [Ben-Aharon I, Ben-Yosef D, Amit A, Shalgi R. Expression and immunolocalization of the calpain-calpastatin system in the human oocyte. Fertile Steril 2005; 83: 1807-1813], the corpus luteum of cattle [Orwig E, Bertrand JE, Ou BR, Forsberg NE, Stormshak F. Invol ement of protein kinase-C, calpains, and calpastatin in prostaglandin F2 alpha-induced oxytocin secretion from the bovine corpus luteum. Endocrinology 1994; 134: 78-83], as well as spermatogenesis in human testes [Liang ZG, O 'Hern ??, Yavetz B, Yavetz H, Goldberg E. Human testis cDNAs identified by sera from infertile patients: a molecular biological approach to immunocontraceptive development. Reprod Fertile Dev 1994; 6: 297-305; Li S, Liang ZG, Wang GY, Yavetz B, im ED, Goldberg E. Molecular cloning and characterization of functional domains of a human testis-specific isoform of calpastatin. Biol Reprod 2000; 63: 172-178 and Wei SG, Wang LF, Miao SY, Zong SD, Koide SS. Expression of the calpastatin gene segment during spermiogenesis in human testis: an in situ hybridization study. Arch Androl 1995; 34: 9-12], mice [Li S, Goldberg E. A novel N-terminal domain directs membrane localization of mouse testis-specific calpastatin. Biol Reprod 2000; 63: 1594-1600] and rabbits [Wang LF, Miao SY, Yan YC, Li YH, Zong C, Koide SS. Expression of a sperm protein gene during spermatogenesis in mammalian testis: an in situ hybridization study. Mol Reprod Dev 1990; 26: 1-5]. Interestingly, the CAST protein was identified as one of the target antigens for anti-sperm antibodies found in infertile women [Koide SS, Wang L, beloved M. Antisperm antibodies associated with infertility: properties and encoding genes of target antigens. Proc Soc Exp Biol Med 2000; 224: 123-132]. 'In vivo, CAST anti-BS-17 antibodies can block the fertilizing capacity of mouse sperm to fertilize eggs by significantly reducing the numbers of developing embryos [Koide SS, Wang L, Kamada M. Antisperm antibodies associated with infertility: properties and encoding genes of target antigens. Proc Soc Exp Biol Med 2000; 224: 123-132]. All these results indicate that the CAST gene plays an important role in reproductive biology. The primary structure of the amino acid sequence of calpastatin includes four internally repeating domains (Domains 1-4) and a non-homologous domain at the amino-terminal end (Domain L) [Murachi T. Calpain and calpastatin. Rinsho Byori 1990; 38: 337-346]. However, a new 'N-terminal peptide domain, named XL domain, was identified in cattle [Cong M5 Thompson VF, Goll DE, Antin PB. The bovine calpastatin gene promoter and a new N-terminal region of the protein are targets for cAMP-dependent protein kinase activity. J Biol Chem 1998; 273: 660-666]. This region "XL" contains sixty-eight amino acids, but does not share homology with other regions of calpastatin or any of the known proteins. In vivo experiments showed that the "XL" region is a substrate for phosphorylation by the protein kinase [Cong M, Thompson VF, Goll DE, Antin PB. The bovine calpastatin gene promoter and a new N-terminal region of the protein are targets for cA P-dependent protein kinase activity. J Biol Chem 1998; 273: 660-666]. It remains advantageous to also provide SNPs / STRs that can more accurately predict the phenotypes of fertility and longevity of an animal and also a business method that provides increased production efficiencies in livestock, 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 document is available as the prior art for the present invention. BRIEF DESCRIPTION OF THE INVENTION The present invention relates to the identification of genetic markers (individual nucleotide polymorphisms (SNPs) and a short tandem repetition (STR)) within the bovine genes encoding calpastatin ("CAST") and their associations with economically relevant attributes in dairy production. 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 CAST gene which may comprise determining the genotype of each animal to be sub-grouped when determining the presence of a SNP / STR in the CAST gene, and by segregating individual animals into subgroups where each animal in a subgroup has a similar polymorphism in the CAST gene. The invention also encompasses a method for sub-grouping animals according to the genotype wherein the animals of each sub-group have a similar genotype in the CAST gene which may comprise determining the genotype of each animal to be sub-grouped when determining the presence of an individual nucleotide polymorphism (s) of interest in the CAST gene and by segregating the individual animals into subgroups depending on whether the animals have, or do not have, the nucleotide polymorphism (s) individual interest in the CAST gene. The genetic polymorphism (s) of interest can be selected from the group consisting of missense mutations in the XL domain region, especially missense mutations in exon 3 which result in G48D substitutions. and P52L (NM_174003.2: c.272G> A and 2830T), a G / T substitution in intron 3 (AAFC02060381.1: g.2110OT) and a short tandem repeat of GAAA in intron 8 (AAFC02060381. 1: g.6700 [(GAAA) 4] + [(GAAA) 5] The invention further relates to a method for sub-grouping animals according to the genotype wherein the animals of each subgroup have a similar genotype. in the CAST gene which may comprise determining the genotype of each animal to be sub-grouped by determining the presence of any of the previous SNPs / STRs, and by segregating the individual animals into sub-groups depending on whether the animals have, or not have any of the previous SNPs / STRs in the CAST gene, the invention is also links to a method for identifying an animal having a desirable phenotype as compared to the general population of animals in that species, which may comprise determining the presence of an individual nucleotide polymorphism in the CAST gene of the animal, wherein the presence of the SNP / STR is indicative of a desirable phenotype. In an advantageous embodiment, the animal can be a bovine. In another advantageous embodiment, the CAST gene can be a bovine CAST gene. The invention also encompasses computer-assisted methods and systems for improving production efficiency for livestock that have fertility and longevity and in particular the genotype of animals as it relates to CAST SNPs / STRs. The methods of the invention encompass obtaining a genetic sample from each animal in a herd of animals, 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. (SNPs) / STRs, group animals with similar genotypes and optionally, also sub-group the animals based on similar phenotypes. The methods of the invention may also include obtaining and maintaining data related to animals or herds, their breeding conditions, health and care and veterinary condition, genetic history or ancestry, and providing this data to others through systems which are based on the network, contained in a database, or linked to the animal itself such as by means of 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 / STR within the CAST gene related to fertility and longevity attributes of animal reproduction and association of that data with other data about the animal or its livestock, and maintain that data in ways that are accessible. Another aspect of the invention encompasses a computer-assisted method for predicting that livestock animals have a biological difference in fertility and longevity, and that may include the steps of 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 into the programmed computer through the input device data that include a genotype of an animal as it relates to any of the SNPs / STRs of CAST described herein, (b) correlate the fertility and longevity predicted by the CAST genotype using the processor and the data storage system and (c) output the correlated fertility and longevity output device with the CAST genotype, in order to predict that livestock animals have a particular fertility and longevity. Yet another aspect of the invention relates to a method for doing business to manage livestock that 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 medium for managing 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 of merit of intake, growth or channel in beef cattle and genotype is a CAST genotype. It is noted that in this description and particularly in the claims and / or paragraphs, the terms such as "comprises", "understood", "comprising" and the like can have the meaning attributed to it in the patent law of the United States. United; for example, they can mean "includes", "included", "including", and the like; and that the terms such as "consisting essentially of" and "consists essentially of" have the meaning ascribed to them in the United States patent law, for example, they allow elements not explicitly mentioned, but 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, but 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 comparative annotation of both human and bovine CAST genes. The annotation recovered the XL domain in the human CAST protein, which shows the same gene structure found in the bovine CAST gene. The sizes of each exon (human / cattle) are as follows: exon 1, 30 / 3'0bp; exon 2, 63/63 bp exon 3, 72/72 bp; exon 4, 60/60 bp; exon 5, 66 bp; exon 6, 42/42 bp; exon 7, 57/57 bp; exon 8, 114/114 bp; exon 9, 81/87 bp; exon 10, 69/69 bp; exon 11, 99/99 bp; exon 12, 81/81 bp; exon 13, 39/39 bp; exon 14, 93/93 bp; exon 15, 87/90 bp; exon 16, 102/102 bp; exon 17, 84/84 bp; exon 18, 48/48 bp; exon 19, 96/96 bp; exon 20, 96/93 bp; exon 21, 102/102 bp; exon 22, 84/84 bp; exon 23, 51/51 bp; exon 24, 72/72 bp; exon 25, 99/99 bp; exon 26, 105/108 bp; exon 27, 93/93 bp; exon 28, 45/48 bp; exon 29, 93/93 bp; exon 30, 72/72 bp; exon 31, 59/66 bp (including the partial non-coding sequence) and exon 32, 198/2045 bp (3'UTR sequences in both species). The 5'UTR is 148 bp in human and 128 bp long in cattle. The distance of space between any of the two exons is not proportional to the size of the intron. FIGS. 2A-2E provides a nucleotide sequence (SEQ ID NO: 1) of the promoter, 5'UTR (En Bold), exon 1 (Italic and Underline) and the partial intron 1 sequence of the bovine CAST gene (AAFC02060382). Each exon-intron limit is Encuadradol FIGS. 3A-3D provides a nucleotide sequence (SEQ ID NO: 2) of partial intron 1, exon 2 (Italic and Underlined) and the partial intron 2 sequence of the bovine CAST gene (AAFC0216139) - Each exon-intron limit is framed FIGS. 4A-4C provide a nucleotide sequence (SEQ ID NO: 3) of partial intron 2, exon 3 (Italic and Underline) and the partial intron 3 sequence of the bovine CAST gene (AAFC02179490). Each exon-intron limit is [Framed |. Three mutations: G / A, C / T and T / G (were in Bold), which were associated with both fertility and longevity in dairy cattle. FIGS. 5A-5F provide a nucleotide sequence (SEQ ID NO: 4) of partial intron 3, exon 4 (Italic and Underlined) and the partial intron 4 sequence of the bovine CAST gene (AÁFC02060385). Each exon-intron limit is in Framed, FIG. 6A-6E provide a nucleotide sequence (SEQ ID NO: 5) of partial intron 5, exons 5 - 16 (Italic and Underlined), introns 5 - 15 and the partial intron 16 sequence of the bovine CAST gene (AAFC02060381). Each exon-intron limit is | framed |. A STR polymorphism (GAAA) was In Bold and associated with fertility and longevity in dairy cattle. FIG. 7 provides a nucleotide sequence (SEQ ID NO: 6) of partial intron 16, exon 17 (Italic and Underlined) and the sequence of partial intron 17 of the bovine CAST gene (AAFC02197217). Each exon-intron limit is Framed FIGS. 8A-8H provides a nucleotide sequence (SEQ ID NO: 7) of partial intron 17, exons 18-32. { Cursive and Underlined), introns 18 - 31 and the 3'UTR sequence of the bovine CAST gene (AAFC02067026). Each exon-intron limit is framed FIGS. 9A-9B provides a nucleotide sequence (SEQ ID NO: 7) and the amino acid sequence (SEQ ID NO: 8) of the coding sequence and the identification of cSNP in silica. The potential SNPs were Framed The FIGS. 10A-10C provide polymorphisms of a nucleotide sequence in the bovine CAST gene. A, two missense mutations A / G and C / T in exon 3 (SEQ ID NOS.10 and 11); B, a substitution of T / G in intron 3 (SEQ ID Nos. 12 and 13); and C, a GAAA repeat in intron 8 (SEQ ID NOS.14 and 15). Two haplotypes exist in the population: G-C-T-GAAAGAAAGAAAGAAA (SEQ ID NO: 16) (upper row) and A-T-G-GAAAGAAAGAAAGAAAGAAA (SEQ ID NO: 17) (bottom row).

FIG. 11 illustrates the genotyping by PCR-RFLP of a C / T substitution in exon 3 of the bovine CAST gene. TT = 308 bp, CT = 135 + 173 + 308 bp and CC = 135 + 173 bp, respectively. FIG. 12 illustrates a flowchart of data entry and output results of analysis and correlation of data pertaining to reproduction, veterinary histories and performance requirements of a group of animals such as a herd of cows and the flow Interactive data from the computer-aided device to a body of students learning the use of the method of the invention. FIG. 13 illustrates potential relationships between data elements' that are introduced into the system. Unidirectional arrows indicate, for example, that a stable is typically owned by only one farm, while a farm may own several stables. Similarly, a prescription may include veterinary products. FIG. 14A 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. I I FIG. 14B illustrates the flow of events through the sub-routines related to the input of data concerning the! farm management.

FIG. 14C illustrates the flow of events through the sub-routines related to the input of data concerning specific data for a company. FIG. 15 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 calpastatin gene (CñST) is widely expressed in tissues / reproductive organs. However, how this gene is related to fertility remains largely undetermined. In the present study, the inventors discovered previously unreported significant associations of the missense mutations in a recently identified XL domain of the bovine CAST gene with fertility (daughters pregnancy rate, DPR) and longevity (productive life, PL) in the dairy cattle using 652 parents or stallions derived from seven grandparents. Alignment of both the cDNA and the genomic DNA sequences revealed three provisional missense mutations, but two of these (G48D and P52L) in exon 3 (M_17 A 003.2: c .271G> and 2830T), which corresponds to the region of the XL domain, they were confirmed by sequencing analysis of two DNA accumulations and seven grandparents. These two confirmed missense mutations plus a mutation in intron 3 (AAFC02060381.1: g .2110OT) and a repeat GAAA in intron 8 (AAFC02060381.1: g.6700 [(GAAA) 4] + [(GAAA ) 5] formed only two haplotypes, a C / T transition was then genotyped with the restriction enzyme MspI and used for an initial association classification and a comprehensive analysis with final analysis through the family indicated that the individual genotype was a significant source of variation (P <; 0.0001) for DPR and PL, but not for milk attributes (P> 0.05). The heritabilities carried out were estimated to be 0.55 for DPR and 0.66 for PL, indicating that the bovine Calpastatin gene, when used in marker-assisted selection, should accelerate the improvement of fertility in dairy cattle. Particular aspects provide four novel polymorphisms that include two missense mutations that form two haplotypes in a new N-terminal domain of the bovine calpastatin gene that show significant associations with fertility and longevity in dairy cattle. In specific aspects, two mutations in the "XL" region of the bovine CAST gene were identified, which lead to amino acid changes (G48D and P52L) in both positions. The determination of the genotype of markers in 652 animals of families of seven parents revealed a source association with DPR and PL in dairy cattle. The present results indicate that different forms of the CAST gene could be involved in different routes of several cells / tissues by expressing a pleiotropic effect on different functions. Particular aspects provide novel markers for fertility (eg, daughters pregnancy speed, DPR) and longevity (eg, productive life, PL) in, for example, dairy cattle. Additional aspects provide novel methods comprising marker-assisted selection to improve fertility and / or longevity in dairy cattle. In particular embodiments, a combination of genetic selection based on one or more of the novel CAST markers, and high PTA potentials (predicted transmission ability) of milk production attributes, provides improved breeding attributes in association with attributes of high production of milk. continuous milk. Additional aspects disclose a previously unrecognized XL domain in the human CAST gene, and thus provide the use of mutants / variants of the human CAST XL domain as markers for fertility and human longevity. The practice of the present invention will employ, unless otherwise indicated, conventional techniques of molecular biology, microbiology, recombinant DNA technology and immunology, which are within the skill of the art. Such techniques fully explain 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 pres's, 1986); Perbal, B., A Practical Guide to Molecular Cloning (1984); the series, Methods In Enzymology (S. Colowick and N. aplan 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 DNA, polypeptide sequences, parameters of particular processes since such, of course, may vary. It is also to be understood that in the terminology used herein is for the purpose 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 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 can 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", "calf", "bull", "heifer" and the like. That also includes an individual animal at all stages of development, including embryonic and fetal stages. Animals as referred to herein may also include individuals or groups of individuals that are bred for different food production such as, but not limited to, transgenic animals for the production of biopharmaceuticals including antibodies and other proteins or 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 involved in hybridization, although it need not 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 equivalently to the disclosed oligonucleotides. A "complementary DNA" or "cDNA" gene includes recombinant genes synthesized by the 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 the purposes of the specification or claims, a label molecule (isotopic or non-isotopic) that is incorporated indirectly or directly into an oligonucleotide, wherein the label molecule facilitates detection of the oligonucleotide in which it is incorporated, for example when the oligonucleotide is hybridized to amplified gene polymorphic sequences. Thus, "detectable portion" is used synonymously with "brand molecule". Oligonucleotide synthesis can be performed 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 (PC) process of Mullis as described in US Pat. Nos. 4,683,195 and 4,683,202. Methods, devices and reagents as described in the patents North American Nos. 6, 951, 726; 6, 927, 024; 6, 924, 127; 6, 893, 863; 6, 887, 66; 6, 881, 559; 6, 855, 522; 6, 855, 521; 6, 849, 430; 6, 849, 404; 6, 846, 631; 6, 844, 158; 6, 84, 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, 487; 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, 475, 729; 6, 468, 743; 6, 465, 638; 6, 465, 637; 6, 465, 171; 6,448,014; 6, 32, 646; 6, 428, 987; 6,426, 215; 6, 423, 499; 6, 10, 223; 6, 403, 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, 3 > 84; 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, 143; D445, 907; 6.261, 31; 6.258, 570; 6, 258, 5; 67; 6, 258, 537; 6, 258, 529; 6, 251, 607; 6.248, 567; 6, 235, 4; 68; 6, 232, 079; 6, 225, 093; 6, 221, 595; D441, 091; 6, 218, 153; 6, 207, 25; 6, 183, 999; 6, 183, 963; 6, 180, 372; 6, 180, 349; 6, 17, 670; 6, 153, 12; . 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; , 976, 842; 5, 972, 602; 5, 968, 730; 5, 958, 686; 5, 955, 274; , 952, 200; 5, 936, 968; 5, 909, 468; 5, 905, 732; 5, 888, 740; , 883, 924; 5, 876, 978; 5, 876, 977; 5, 874, 221; 5, 869, 318; , 863, 772; 5, 863, 731; 5, 861, 251; 5, 861, 245; 5, 858, 725; , 858, 718; 5, 856, 086; 5, 853, 991; 5, 849, 497; 5, 837, 468; , 830, 663; 5, 827, 695; 5, 827, 661; 5, 827, 657; 5, 824, 516; , 824, 479; 5, 817, 797; 5, 814, 489; 5, 814, 53; 5, 811, 296; , 804, 383; 5, 800, 97; 5, 780, 271; 5, 780, 222; 5, 776, 686; , 774, 497; 5, 766, 889; 5, 759, 822; 5, 750, 347; 5, 747, 251; , 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; , 674, 717; 5, 665, 572; 5, 665, 539; 5, 656, 93; 5, 656, 461; , 654, 144; 5, 652, 102; 5, 650, 268; 5, 643, 765; 5, 639, 871; , 639, 611; 5, 639, 606; 5, 631, 128; 5, 629, 178; 5, 627, 054; , 618, 703; 5, 618, 7? 2; 5, 614, 388; 5, 610, 017; 5, 602, 756; , 599, 674; 5; 589, 333; 5, 585, 238; 5, 576, 197; 5, 565, 340; , 565, 339; 5, 556, 774; 5, 556, 773; 5, 538, 871; 5, 527, 898; , 527, 510; 5, 514, 568; 5, 512, 63; 5, 512, 62; 5, 501, 947; , 494, 795; 5, 491, 225; 5, 487, 993; 5, 487, 985; 5, 484, 699; ,476,774; 5,475,610; 5,447,839; 5,437,975; 5,436,144; 5,426,026; 5,420,009; 5,411,876; 5,393,657; 5,389,512; 5,364,790; 5,364,758; 5,340,728; 5,283,171; 5,279,952; 5,254,469; 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 DNA polymerase, sequences known as primers, and heating cycles, which separate the replicating deoxyribonucleic acid (DNA), the strands and exponentially amplify a gene of interest. Any type of PCR, such as quantitative PCR, RT-PCR, warm start PCR, LAPCR, multiple PCR, touch PCR, etc., can be used. Advantageously, real-time PCR is used. In general, the PCR amplification process involves a cyclic enzyme chain reaction to prepare exponential amounts of a specific nucleic acid sequence. This requires a small amount of a sequence to initiate the chain reaction and the oligonucleotide primers that will irritate the sequence. In the PCR, the primers are 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 recosido and extension results in the exponential accumulation of the specific sequence that is amplified. The extension product of the chain reaction will be a nucleic acid duplex described with a terminal, corresponding to the ends of the specific primers employed. By the terms "amplify enzymatically" or "amplify" it is proposed, for the purposes of the specification or claims, DNA amplification, ie 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 amplification methods include LCR (ligase chain reaction) using DNA ligase, and a probe consisting of two halves of a DNA segment that is complementary to the DNA sequence to be amplified, the QB replicase enzyme and a template of ribonucleic acid (RNA) sequence attached to a probe complementary to the copied DNA that is used to be a DNA template for the exponential production of complementary RNA; strand displacement amplification (S D), Qñ replicase amplification (QBRA); 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 to be 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 of the 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 a sequence. ordinate of nucleotides located in 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 "genotype" while the animal's physical attributes are described as its "phenotypes". By "heterozygous" or "heterozygous polymorphism" it is proposed that the two: alleles and a diploid cell or organism at a given site are different, that is, they have a different nucleotide exchanged for 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, that is, they have the same nucleotide exchange per nucleotide at the same place in their sequences. By "hybridization" or "hybrid" as used herein, is the formation of base pairs proposed? and C-G between the nucleotide sequence of a fragment of a segment of a polynucleotide and a nucleotide sequence complementary to an oligonucleotide. By complementary it is proposed that at the site of each A, C, G or T (or U in a ribonucleotide) in the fragment sequence, the sequenced oligonucleotide has a T, G, C or A, respectively. The hybridized fragment / oligonucleotide is called a "duplex". A "hybridization complex", such as in an intercalation assay, means a complex of nucleic acid molecules that includes at least the target nucleic acid and a sensing probe. That may ainclude a fixator probe. As used herein, the term "site" or "sites" refers to the site of a gene on a chromosome. Pairs of genes, known as "alleles" control the hereditary attribute produced by a gene site. Each particular combination of the allele animal is referred to as its "genotypes". 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 the heterozygote for the attribute. A "melting temperature" is proposed for the temperature at which the hybridized duplexes are dehybridized and returned to their single-stranded state. Likewise, hybridization will not occur in the first place between the two oligonucleotides, or, in the present, an oligonucleotide and a fragment, at temperatures above the melting temperature of the resulting duplex. It is currently advantageous that the difference in melting point temperatures of the oligonucleotide-fragment duplexes of this invention be 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), analogs of DNA or RNA generated using analogs of nucleotide, 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 the form of either single-stranded or double-stranded helix. This term refers only to the primary and secondary structure of the molecule, and is not limited to any of the particular tertiary forms. Thus, this term includes the double-stranded DNA found, inter alia, in linear DNA molecules (eg, 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 that is given only to the sequence in the 5 'to 3' direction throughout the non-transcribed strand of DNA (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) (or its 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 can be based on, or designed from, a genomic or cDNA sequence and is used to amplify, confirm or reveal the presence of an identical, similar or complementary DNA or RNA in a particular cell or tissue. The oligonucleotides can be chemically synthesized or can be used as primers or probes. Oligonucleotides is any nucleotide of more than 3 bases in length used to facilitate the detection or identification of a target nucleic acid, including probes and primers. A "polymerase" is an enzyme that catalyzes the sequential addition of monomer units to 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 which is complementary to a template molecule of a specific sequence. For example, DNA polymerases such as DNA pol 1 and Taq polymerase add deoxyribonucleotides to the 3 'end of a polynucleotide chain in a template-dependent manner, to thereby synthesize a nucleic acid that is complementary to the molecule. template. The polymerases can be used either to extend a primer once or repetitively or to amplify a polynucleotide by repetitively priming two complementary strands using two primers. A "thermostable polymerase" refers to a DNA or RNA polymerase enzyme that can withstand extremely high temperatures, such that approach 100 ° C. Frequently, thermostable polymerases are derived from organisms that live in extreme temperatures, such as Thermus aquaticus. Examples of thermostable polymerases include Taq, Tth, Pfu, Vent, deep vent, UlTma, and variations and derivatives thereof. A "polynucleotide" refers to a linear chain of nucleotides connected by a phosphodiester linkage between the 3'-hydroxyl group of a nucleoside and the 5'-hydroxyl group of a second nucleoside which in turn binds through its group 3 '-hydroxyl to the 5' -hydroxyl group of a third nucleoside and thus forms 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 "priming.r" is an oligonucleotide, the sequence of at least a portion of which is complementary to a segment of a DNA, of template that is going to be amplified or replicated. Typically the primers are used in performing the polymerase chain reaction (PCR). A hybrid primer with (or "recose" a) the template DNA and is used by the polymerase enzyme as the starting point for the replication / amplification process. The primers herein are selected to be "substantially" complementary to different strands of a particular target DNA sequence. This means that the primers must be sufficiently complementary to hybridize with their respective strands. Therefore, the sequence of the primer does not need to 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, non-complementary bases or longer sequences may be interdispersed 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 nucleic acid sequences of variable length oligonucleotides, used in the detection of identical, similar or complementary nucleic acid sequences by 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, plasmid vectors, DNA isolated from any sequence, RNA isolated from any sequence , probes and nucleic acid primers. A polynucleotide can comprise modified nucleotides, such as methylated nucleotides and nucleotide analogues, uracil, other sugars and linking groups such as fluororibose and thiolate, and nucleotide branching. The nucleotide sequence may also be modified after the polymerization, such as by conjugation, with a labeling component. Other types of modifications included in this definition are terminations, replacement of one or more of the >; nucleotides that occur naturally with an analog, and the introduction of means for joining the polynucleotide to proteins, metal ions, labeling components, other polynucleotides or solid support. 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 selling 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, in whole or in part, from sequences normally associated with it 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 not excluded, as it is understood in the art that thymidine (T) in a DNA sequence is considered equal to uracil (U) in an RNA sequence. Thus, the RNA sequences for the use of the invention, for example, for use in RNA vectors, can be derived from DNA sequences, by means of thymidine (T) in the DNA sequence that is considered equal to a uracil (U). ) in 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 translation detection codon 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 'to 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 regions, followed by digestion with single-stranded specific nucleases (s) and size determination of the digested fragments. DNA sequences that are substantially homologous can be identified in the Southern hybridization experiment under, for example, severe conditions, as defined for that 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; Nucleic 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 or 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 wash conditions of reduced severity that allow at most approximately 25-30% of base pair mismatches, for 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: 487-91). The term "capable of hybridizing under severe conditions" as used herein refers to the recoside of a first nucleic acid to a second nucleic acid under severe conditions as defined below. Severe hybridization conditions typically allow hybridization of nucleic acid molecules having at least 70% nucleic acid sequence identity to the nucleic acid molecule that is used as a probe in the hybridization reaction. For example, the first nucleic acid may be a test sample or probe, and the second nucleic acid may 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 high temperature and / or low salt content which tend to disfavor the hybridization of different nucleotide sequences. Alternatively, the hybridization of the first and second nucleic acids can be conducted under conditions of reduced safety, for example low temperature and / or high salt content which tend to favor hybridization of different nucleotide sequences. Hybridization conditions of low severity can be followed by conditions of high severity or intermediate medium severity conditions to increase the selectivity of the first and second nucleic acid linkages. Hybridization conditions may further include reagents such as, but not limited to, dimethyl sulfoxide (DMSO) or formamide to further disadvantage the hybridization of different nucleotide sequences. A suitable hybridization protocol may, for example, involve hybridization in 6 x SSC (where 1 x SSC comprises 0.015M sodium citrate and 0.15M 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 allow 30% less mismatch 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 a suitable hybridization protocol without undue experimentation. See, for example, Sambrook et al., (2001) Molecular Cloning: ? Laboratory Manual, 3rd ed .5 Cold Spring Harbor Press, the contents of which are hereby incorporated by reference in their entirety. Typically, severe conditions will be those in which the salt concentration is less than about 1.5M sodium ion, typically about 0.01 to 1.0M sodium ion concentration (or other salts) of about pH 7.0 at about pH 8.3 and the temperature is at least about 30 ° Celsius for short probes 1 (for example, 10 to 50 nucleotides) and at least about 60 ° C for long probes (for example, greater than 50 nucleotides). Severe conditions can also be achieved with the addition of destabilizing agents such as formamide. Exemplary low stringency conditions include hybridization with a buffer solution of 30 to 35% formamide, 1M NaCl, 1% SDS (sodium dodecyl sulfate) at 37 ° Celsius, and a wash in 1-2x SSC at 50 ° C. 55 ° Celsius. Exemplary moderate severity conditions include hybridization in 40% to 45% formamide, 1M NaCl, 1% SDS at 37 ° Celsius, and. a wash in 0.5-1 x SSC at 55 to 60 ° Celsius. Exemplary high stringency conditions include hybridization in 50% formamide, 1M NaCl, 1% SDS at 37 ° Celsius, and a wash in 0.1 x SSC 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 from an individual animal and detect genetic differences in the animals. In particular, a sample of genomic DNA from an animal can be evaluated by reference to one or more controls to determine whether a SNP, or a 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, amplimer sequencing, DNA sequencing, fluorescence spectroscopy, hybridization analysis based on fluorescence resonance energy transfer (or "FRET"), high throughput classification, mass spectroscopy, microsatellite analysis, nucleic acid hybridization, polymerase chain reaction (PCR), RFLP analysis and size chromatography (eg, capillary or gel chromatography), all of which are well known to one skilled in the art. In particular, methods for determining nucleotide polymorphisms, particularly individual nucleotide polymorphisms, are described in US Pat. 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 resisted by Chen and Sullivan, Pharmacogenomics J 2003; 3 (2): 7-96, the description of which are incorporated by reference and their totalities. The genotypic data useful in the methods of the invention and methods for the identification and selection of animal attributes are based on the presence of SNPs. A "restriction fragment" refers to a fragment of a polynucleotide generated by a restriction endonuclease (an enzyme that cleaves phosphodiester bonds within, of a polynucleotide chain) that cleaves DNA in response to a recognition site on the DNA. The recognition site (restriction site) consists of a specific sequence of nucleotides typically of 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 difference of only one nucleotide. For example, without limitation, the exchange of an A by a C, G or T in the complete sequence of the polynucleotide constitutes a SNP. It is possible to have more than one SNP in a particular polynucleotide. For example, in an Assignment 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 it refers to SNPs, the polynucleotide is more frequently DNA. As used herein, a "template" refers to an objective polynucleotide strand t, for example, without limitation a strand of DNA that occurs naturally unmodified, with a use of polymerase as a means to recognize which nucleotide should be then join in a growing strand to polymerize the complement of the strand that occurs naturally. Such a strand of DNA can be single-strand or can be part of a double-stranded DNA template. In applications of the present invention that require repeated cycles of polymerization, for example the polymerase chain reaction (PCR), the platelet 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 multi-step 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 the related polynucleotides. The difference can 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 nucleotide substitutions 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 "physical characteristics" or "phenotypes" refer to the advantageous properties of the animal 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, increase intramuscular fat. Physical characteristics include, but are not limited to, marbling, tender or lean meats. The terms can be used interchangeably. A "computer system" refers to the hardware means, software means and data storage medium used to compile the data of the present invention. The minimum hardware means of the computer-based systems of the invention may comprise a central processing unit (CPU), input means, output means and data storage means. Desirably, a monitor is provided to visualize the structure data. The data storage means may be RAM or other means for entering the computer readable medium of the invention. Examples of such systems are the microcomputer workstations available from Silicon Graphics Incorporated and Sun Microsystems running the operating systems based on Unix, Linux, Windows NT, XP or IBM OS / 2. "Computer readable medium" means any medium that can be read and entered directly by a computer, and includes, but is not limited to: magnetic storage media such as floppy disks, hard storage media and magnetic tape; optical storage medium such as optical discs or CD-ROM; means of electrical storage such as RAM and ROM; and hybrids of these categories, such as the magnetic / optical medium. By providing such a computer-readable medium, the data compiled on a particular animal can be routinely entered by a user, for example, a feedlot operator. The term "data analysis module" is defined herein to include any person 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, object or system that obtains a tissue sample from an animal or embryo. For example and without limitation, the term may define, individually or collectively, 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, the 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, searching for 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 not limited to, the location, reproduction, period of accommodation, as well as the genetic history of the animals, including the ancestors and descendants thereof, genotype, phenotype, transgenic history if relevant and the like. The term "breeding conditions" as used herein refers to parameters related to the maintenance of the animals including, but not limited to, temperature of the shed or shelter, weekly mortality of a herd, water consumption, 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 groups of animals, including, but not limited to, type (s) of vaccine, serial number (s) of batch of vaccine, administered dose, target antigen, method of administering the vaccine to the animal (s) vaccinated numbers, age of the animals and the vaccinator. Data related to the serological or immunological response induced by the vaccine can also be included. "Veterinary history" as used herein is also proposed to include the medication histories of the target animal (s) (including, but not limited to, drugs and / or antibiotics administered to the animals including the type of medication administered. , quantity and dose proportions, by whom and when administered, by what route, for example oral, subcutaneously and the like, and the response to the medication including the desired and undesirable effects thereof The term "diagnostic data" as used herein refers to data related to the health of the animal (s) other than the data detailing the vaccination or medication history of the animal (s). The diagnosis can be a record of the infections experienced by the animal (s) and the response of the same to the medications provided to treat such medications. The composition of antibody or protein from serum or other biofluids can also be useful diagnostic data for introduction into the methods of the invention. Surgical data pertaining to the animal (s) may be included, such as the type of surgical manipulation, the effects of the surgery, and the complications arising from the surgical procedure. The "diagnostic data" may also include measurements of such parameters as weight, morbidity, and other characteristics noted 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 including, but not limited to, a history of reproduction, a veterinary history, a welfare profile , diagnostic data, quality control data or any combination thereof. The term "welfare profile" as used herein refers to parameters such as weight, meat density, levels of stacking in breeding or breeding enclosures, psychological behavior of the animal, proportion of growth and quality and Similar. The term "quality control" as used herein refers to the desired characteristics of the animal (s). For non-poultry animals 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, breeding ability and the like . The term "performance parameters" as used herein refers to such factors as meat yield, breeding performance, milk form, quality and yield of the meat, speed of pregnancy of daughters (ie fertility) productive life ( that is, longevity) and the similar ones that may be the desired objectives of the breeding and rearing 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, the time, place and manner of preparation, storage of the food product, route of transport, inspection records, texture, color, taste, smell, bacterial content, parasitic content and the like. It will be obvious to those skilled 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 therefore is not proposed to be limiting . 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 a modality wherein the gene of interest is bovine CAST, the bovine CAST nucleotide sequence can be selected from, but not limited to, the sequence corresponding to GenBank Access Nos. AAFC02060382 (SEQ ID NO: 1), AAFC02161394 (SEQ ID NO: 2), AAFC02179490 (SEQ ID NO: 3), AAFC02060385 (SEQ ID NO: 4), AAFC02060381 (SEQ ID NO: 5), AÁFC02197217 (SEQ ID NO: 6), AAFC02067026 (SEQ ID NO. : 7) 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 that can be selected from, but not limited to, the sequence corresponding to GenBank Access Nos. AAFC02060382 (SEQ ID NO: 1 ), AAFC02161394 (SEQ ID NO: 2), AAFC02179490 (SEQ ID NO: 3), AAFC02060385 (SEQ ID NO: 4), AAFC02060381 (SEQ ID NO: 5), AAFC02197217 (SEQ ID NO: 6), AAFC02067026 (SEQ ID NO: 7), or the complement thereof, or comprising the corresponding polymorphic site.

The individual nucleotide polymorphism (s) of interest may be selected from the group consisting of missense mutations in the XL domain region, especially missense mutations in exon 3 which result in the substitutions of G48D and P52L (NM_174003.2: c.271G >; A and 283CT), a substitution of G / T in intron 3 (AAFC02060381.1: g .21170G> 7) and a repeat of GAAA in intron 8 (AAFC02060381.1: g .6700 [(GAAA) 4 ] + [(GAAA) 5] The advantageous SNP / STR in the present invention is associated with certain economically valuable and heritable attributes related to fertility and longevity in bovines.Therefore, it is an objective of the present invention to determine the genotype of a given animal of interest defined by the CAST SNP / STR site in accordance with the present invention It is also contemplated that the genotype of the animal (s) may be defined by additional SNPs / STRs within the CAST gene or within other genes identified with desirable attributes or other characteristics, and in particular by a panel or panels of SNPs / STRs. There are many methods known in the art for determining the DNA sequence of a sample, and for identifying whether a given DNA sample contains a particular SNP / STR. 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 / STRs in their genomes and particularly with missense mutations in exon 3 of the CAST gene. The methods also allow, through the computer-assisted methods of the invention, to correlate the attributes associated with SNP / STR 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, that genomic DNA sample will be obtained from a tissue sample or cells taken from that animal. A sample of tissue or cells can be taken from an animal at any time the life course of an animal but before the identity of the channel is lost. The tissue sample may comprise hair, including roots, skin, bone, mouth rubs, blood, saliva, milk, semen, embryos, muscle or any of the internal organs. 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 critical to the present invention. For example, the body tissue may be selected from the group consisting of skin, endometrial, uterine and cervical tissue. Both normal and tumor tissues can be used. Typically, the tissue sample is marked with an identification number or other indication 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 clues can be changed in a regular manner that ensures that. the data, and any other associated data, can be related again to the animal from which the data were 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 moderate pressure in the area between the upper 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 labeled using a numbering system that carries a code corresponding to the animal, for example, to the ear tag of the animal. Therefore, the genotype of a particular animal easily traceable at all times. The sampling device and / or container can be supplied to the farmer as a trace or retailer. The sampling device advantageously takes a consistent and reproducible sample from individual animals while simultaneously avoiding any cross-contamination of tissue. Therefore, the size and volume of the sample tissues derived from individual animals would be consistent. The DNA can be isolated from the tissue / cells by techniques known to those skilled in the art (see, for example, US Pat. 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 which are incorporated by reference in their totalities). For example, high molecular weight DNA can be purified from cells or tissue 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 / STR of any of the genes of the present invention can be determined by sequencing the region of the genomic DNA sample encompassing 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, as described below, a DNA fragment encompassing the location of SNP / STR 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 automatic nucleic acid sequencer. The detection of a given SNP / STR 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 utilize oligonucleotides useful as primers to amplify the specific nucleic acid sequences of the CAST gene, advantageously from the region comprising a SNP / STR CAST. Such fragments must be of sufficient length to allow annealing or specific hybridization to the nucleic acid sample. The sequence will typically be from about 8 to about 44 nucleotides in length. Longer sequences, for example from about 14 to about 50, can be advantageous for certain modalities. The design of primers is well known to one of ordinary skill in the art. Inventive nucleic acid molecules include nucleic acid molecules that have at least 70% identity or homology or similarity to a CAST gene or probes or primers derived therefrom such as at least 75% identity or homology or similarity, preferences of at least 80% identity or homology or similarity, plus preferences of at least 85% identity or homology or similarity, such as at least 90% identity or homology or similarity, plus preferences of at least 95% of identity or homology or similarity, such as at least 97% identity or homology or similarity. The similarity or homology or nucleotide sequence identity 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 measurement of homology between two sequences. The sequence similarity percent 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 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 in accordance with the algorithm of ilbur 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 4, and computer-aided analysis and interpretation of data Sequences that include alignment can be conveniently performed using commercially available programs (eg Intelligenetics ™ Suite, Intelligenetics Inc. CA). When the RNA sequence is 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 may 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 a CAST gene that are unique to a 'CAST gene. As for PCR or hybridization of primers or 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 the: RNA sequence. 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, or a phage vector or the like. 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. Microbe!. 63: 1143-1147; Proudnikov & Mirzabekov (1996) Nucí. Acids Res. 24: 4532-4535). Alternatively, the oligonucleotide can be labeled with a radio label, for example, 3H, 125I, 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 the like is used to provide a nucleic acid probe for use in the present invention can purify the synthesized oligonucleotide labeled with a marker. An advantageous probe shape is one labeled with a fluorescent dye at the 3'- 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 ribose or 3'-end deoxyribose can be modified with a phosphate group or the similar 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 of severe affectation, to aid in hybridization. Detection by differential interruption is particularly advantageous for reducing or eliminating slipped hybridization between the probes and the target and for promoting 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 if a SNP is present in the target sequence. A method to determine the genotype at the site of the polymorphic gene involves obtaining a sample of nucleic acid, hybridizing the nucleic acid sample with a probe, and interrupting the hybridization to determine the required energy level of interruption where the probe has an energy of interruption different for- one allele as compared to another allele. In one example, there may be a lower interruption energy, for example melting temperature, for an allele that harbors a cytosine residue at a polymorphic site, and a higher required energy for an allele with a different residue that is needed or polymorphic. This can be achieved where the probe has 100% homology with one allele (a perfectly matched probe) but has a single unequal ion with an alternative allele. Since the perfectly matched probe is more tightly bound to the target DNA than the unequal probe, this 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 hybridizes regardless of which nucleotide is present in the polymorphic site. The fixator probe does not affect the interruption energy required to disassociate the hybridization complex if it does not, rather, contain 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 the control of electronic severity, either alone or in combination with the other factors listed. Through the use of stringency conditions in either or both of the target hybridization step or the censor 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. As an example, with the use of severity, the initial hybridization step may be completed in ten minutes or less, more advantageously five minutes in 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 hybridization complex market at the test sites. The detection site and the method may include, but are 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 labeled or unmarked probe linked to the target can be quantified. Such quantification may include statistical analysis. The labeled portion of the complex may be the target, the stabilizer, the probe or the hybridization complex in question. The labeling can be by fluorescent labeling selected from the group of, 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 labeling, bioluminescent labeling and / or chemiluminescent labeling can also perform the marking. Marking may also include energy transfer between molecules in the hybridization complex by analysis! of perturbation, rapid cooling, electron transport between donor and acceptor molecules, the latter of which can be facilitated by double-strand matching hybridization complexes. Optionally, if the hybridization complex is unlabelled, detection can be made 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 mass spectrometry, a fluorescent or other brand is not 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 spray ionization (ESI). Where mass spectrometry is contemplated, probes having 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.

In addition, if the purified target is amplified and the amplification is an exponential 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 winding circle or the transcriptional shift can also be used. Where it is desired to amplify a DNA fragment comprising a SNP / STR according to the present invention, the forward and rear 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 length up to including approximately 50 nucleotides in length. The sequences to which the forward and backward primers anneal are advantageously located on either side of the particular nucleotide position that is substituted in the SNP / STR to be amplified. A detected label can be incorporated into a nucleic acid during at least one cycle of an amplification reaction. Spectroscopic, photochemical, biochemical, immunochemical, electrical, optical or chemical media 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., 3H, 1251, 35S, 14C, 32P, etc.), enzymes ( for example, horseradish peroxidase, alkaline phosphatase, etc.) colorimetric labels such as colloidal gold or beads, colored glass or plastic (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 above, a wide variety of brands are used, with brand choice depending on the required sensitivity, ease of conjion with the compound, stability requirements, available instrumentation and waste supplies. Non-radioactive brands are frequently linked by indirect means. Polymerases can also incorporate fluorescent nucleotides during the synthesis of nucleic acids. 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. Commercial kits containing the 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 genomic DNA sequencing methods are known in the art, and any method of that kind 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 using any method known in the art. Advantageously, the nucleic acid sequencing is by automated methods (reviewed by Meldrum, (2000) Genome Res. 10: 1288-303, description of which is incorporated by reference in its entirety), for example using a Beckman Genetic Analysis System 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 specific SNP / STR probe can also be used in the detection of SNP / STR 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 / STR-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 probe1 of between 10 and 50 nucleotides in length allows the formation of a duplex molecule that is both stable and selective. Molecules having complementary sequence envelopes stretches greater than 12 bases in length are generally advantageous, in order to increase the stability and selectivity of the hybrid, and for this way improve the quality and the degree of particular hybrid molecules obtained. It is generally 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. Selling two or more different "allele-specific sodas" 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 intended to encompass at least nucleic acid sequences that are hybridizable to the nucleotide sequence disclosed herein, the complement or a fragment of the invention. same, or are functional sequence analogs of this sequence. It is also contemplated that a particular attribute of an animal can be determined by using a panel of SNPs / STRs associated with that attribute. Several economically relevant attributes can be characterized by the presence or absence of one or more SNPs / STRs and by a plurality of SNPs / STRs in different genes. One or more panels of SNPs / STRs 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 (e.g., paralogs) can be obtained under conditions of standard or stringent hybridization with all or a portion of the particular sequence as a probe using methods well known in the art for the hybridization and nucleic acid cloning. The genetic markers, probes thereof, methods and kits of the invention are also useful in a breeding program to select for breeding those animals having desirable phenotypes for various economically important attributes, such as fertility (speed Daughter Pregnancy ) and longevity (productive life). Continuous selection and breeding of animals, such as livestock, that are at least heterozygous and advantageously homozygous for desirable alleles of the polymorphic sites of the CAST gene associated with the economically relevant attributes growth, feed intake, efficiency and / or Valia of canal, and reproduction and longevity would lead to a reproduction, line or population that has high numbers of descendants with economically relevant attributes of growth, food intake, efficiency and value of the channel and reproduction and longevity. Thus, the CAST SNPs / STRs 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, additional channel value (additional channel value, $), average daily gain (ADG, lb / d), back fat thickness (BFAT, in), calculated live weight (Cale Lv t, Ib), calculated yield grade (cYG), days in food (DOF, d), percentage of fertilizer (DP,%), dry matter intake (DMI, Ib), intake of dry matter per day in the feed (DMI per DOF, lb / d), weight of the hot channel (HCW, Ib), weight value of the hot channel (HCW valued, $), 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 versus greater than or equal to the choice (QG, <Se vs.,> Ch), rib area (REA, in2), rib area weight percent HCW (REA / cwt HCW; in2 / 100 Ib), 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 livestock animals such as cattle vaccinated according to the genotype as defined by the SNPs / STRs panels, each panel comprising at least one SNP / STR, one or more of which are in the CñST gene of the present invention. Other SNPs that can be included in panels of SNPs include, but are not limited to, SNPs found in the GHR gene, FABP4 gene, ghrelin gene, leptin gene, NPY gene, ob gene, TFAM gene, CRM gene, UASMS1 gene, UASMS2 gene, UASMS3 gene and / or the UCP3 gene. The genetic selection and grouping methods of the present invention can be used in conjunction with other methods of conventional phenotypic clustering such as clustering of animals by visible features such as weight, size of structure, breeding attributes and the like. . The methods of the present invention provide the production of cattle having improved heritable attributes, and can be used to optimize the performance of herds of livestock in areas such as fertility, longevity, reproduction, food intake, carcass / 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 fertility and longevity. As described above, and in the Examples, there are several phenotypic attributes with which the SNPs / STRs 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 by using any of the suitable methods known in the art. Using the methods of the invention, a farmer, or feed batch operator, or the like, can group livestock according to each genetic protection, of the animal for a desired attribute such as growth rate, feed intake or behavior of feeding, as determined by the SNP / STR genotype. Cattle are tested to determine the homozygosity or heterozygosity with respect to the SNP / STR 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 food lots, and then sacrificed. Individual genotypic data derived from a panel or panels of SNPs / STRs for each animal or a herd of animals can be recorded and associated with various other animal data, for example, health information, ancestry, breeding conditions, vaccination history , record of the herd, safety data of subsequent food and the like. Such information may be provided to a government agency to provide traceability for an animal or meat product, or it may serve as the basis for reproduction information., food and marketing. 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 microchip 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. Other parameters include, but are not limited to, such as breeding objectives, dairy production management, vaccination levels of a herd. If the performance or properties of animals deviate from the desired objectives, computer-based methods can trigger an alert to allow the operator to adjust the dose of vaccination medications, feed etc., accordingly. The results of the analysis provide data that 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, or 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 ancestry, herd identification, health information including vaccinations, exposure to diseases, location of the food lot, diet and owner changes. Information such as dates and results of diagnostic or routine tests are easily stored and obtainable. Such information will be especially valuable for companies, particularly those who seek superior breeding lines. Each animal can be provided with a unique identifier. The animal can be tagged, as in traditional tracking programs or have implanted computer chips that provide stored and readable data or promoted with any other identification method that associates the animal with its unique identifier. The database that contains the SNP / STR-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, that can be useful in selecting attributes to group or sub-group an animal. For example, and not for limitation, the data pertaining to animals that have particular vaccination or medication 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 those attributes. The bases, data that can be usefully associated with the methods of the invention include, but are not limited to, specific or general scientific data. Specific data include, but are not limited to, breeding lines, stallions, mothers and the like, other animal genotypes, including whether or not other specific animals possess specific genes, including transgenic genetic elements, location of animals that share genetic characteristics similar or identical, and similar. General data includes, but is not limited to, scientific data such as genes that code for specific quality characteristics, reproduction association data, feed data, breeding trends, and the like. One method of the present invention includes 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. Advantageously, the packaging is encoded with a bar code label. The labels are coded with the same identifying indicia, 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 encoded with identification signs, advantageously with a barcode label. The method optionally includes a system in which a database account is established in the ordering of the equipment of the sampling equipment. The identifier of the database account corresponds to the identification signs of the labels and the packaging. In the shipment of the sampling equipment in compliance with the order, the identification signs are recorded in a database. Advantageously, the identifier is a bar code 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 registered in the database in the shipment of the bottle to the customer. Once the genotype determination 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 that contain information related to SNP-based DNA testing, vaccination, safe health pre-conditioning program, estrus and pregnancy outcomes, hormone levels, safety / food contamination, somatic cell counts, mastitis occurrence, diagnostic test results, milk protein levels, milk fat, vaccine status, health records, mineral levels, minor mineral levels, performance of the herd and the like.

The present invention thus encompasses computer-assisted methods for tracking breeding and veterinary histories of livestock animals comprising the use of a computer-based system comprising a programmed computer comprising a processor, a data storage system , an input device and an input device and an output device, and comprising the steps of generating a profile of the livestock animal by entering in the programmed computer through the input device the genotype data of the animal, where the animal can be defined by a panel of at least two individual nucleotide polymorphisms that produce at least one physical attribute of the animal, introducing in the programmed computer through the input device the welfare data of the animal, which correlates the data of well-being introduced with the phenotypic profile of the animal using the processor of the data storage system, and output a profile of the animal or group of animals to the output device. The data bases and the analysis thereof will be accessible to those to whom access has been provided. Access can be provided through rights to access, or by subscription to specific portions of the data. For example, the database can be entered by animal owners, the test site, the entity that provides the sample to the test site, the food lot personnel and the veterinarians. The data can be provided in any form such as when entering a network site, fax, email, sent correspondence, automated telephone or other methods for communication. This data can also be encoded on a portable storage device, such as a microchip, which can be implanted in the animal. Advantageously, the information can be read and new information added without removing the animal's microchip. The present invention comprises systems for performing the methods disclosed herein. Such systems comprise devices, such as computers, Internet connections, servers and storage devices for the data. The present invention also provides a method for transmitting data comprising the transmission of information from such methods discussed herein in the steps thereof, for example, by way of telecommunication, telephone, video conference, mass communication, by example, presentation such as a computer presentation (for example, POWERPOINT), internet, email, documentary communication such as computer programs (for example, WORD) and the like.

The systems of the present invention may comprise a data collection module, which includes a data collector for collecting data from an animal or embryo and transmitting the data to a data analysis module, a network interface for receiving data from the data analysis module, 1 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 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 another site 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 of an animal or embryo gene, and for example, such data is processed when the animal's feeding regime is planned. In a modality where the data is implanted in a microchip on a particular animal, the farmer can optimize the efficiency of managing the herd because the farmer is able to identify the genetic predispositions of an individual animal as well as the past, present and future treatments (for example, vaccinations and veterinary visits). The invention, therefore also provides input to other databases, for example, herd data related to genetic tests and data made by others, by data links to other sites. Therefore, data from other databases can be transmitted to the central database of the present invention via the network interface to receive data from the data analysis module of 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 input data on that animal, such as but not limited to, vaccinations and medication histories, DNA testing. , thyroglobulin test, leptin, MI (Meta morphix Inc.), diagnosis of spongiform encephalopathy coil (BSE), vaccination for brucellosis, vaccination for FMD (foot and mouth disease) vaccination for BVD (viral diarrhea coil), pre -Conditioning of Safe Health, results of estrus and pregnancy, tuberculosis, hormone levels, food safety / contamination, somatic cell counts, occurrences of mastitis, diagnostic test results, milk protein levels, milk fat , vaccine status, health records, mineral levels, levels. of minor minerals, 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 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 introducing into the computer programmed through the input device data comprising reproductive data, veterinary medication, diagnostic and the like of an animal, correlating a physical characteristic predicted by the genotype using the processor in the system of storage of data, output the physical characteristics correlated with the genotype, and feed the animal with a diet based on the physical characteristic, in order to improve livestock production. The invention further provides a computer-assisted method for optimizing the efficiency of livestock feed lots comprising using a computer system, for example, a programmed computer which comprises a processor, a data storage system, an input device and a computer. output device, and the steps of entering into the computer programmed through the input device data comprising reproduction, veterinary history of an animal, correlating reproduction, veterinary histories using the processor and data storage system, output to the output device the physical characteristics correlated with the genotype, and feed the animal with a diet based on the physical characteristic, in order to optimize the efficiency of the feed lots for the livestock. The invention further comprises methods for doing business to provide access to such readable means on computer and / or computer systems and / or data collected from animals to users, for example, the means and / or sequence data may be accessible to a user, for example on a subscription basis via the Internet or a global communication network / computer; or in 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 computer means for handling livestock comprising physical characteristics and veterinary histories corresponding to one or more animals. The invention further provides methods for doing business to manage livestock which comprises 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 comprises 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 further encompasses equipment useful for classifying nucleic acid isolated from one or more bovine individuals for the allelic variation of any of the mitochondrial transcription factor genes, and in particular for any of the SNPs described herein, wherein the equipment may comprising at least one oligonucleotide which selectively hybridizes to a nucleic acid comprising any of the one or more of which are CAST sequences described herein and instructions for using the oligonucleotide to detect variation in the nucleotide corresponding to the SNP of isolated nucleic acid .

One embodiment of this aspect of the invention provides an oligonucleotide that specifically hybridizes to the nucleic acid molecule of this aspect of the invention, and wherein the oligonucleotide hybridizes a portion of the isolated nucleic acid molecule comprising any of the polymorphic sites in the CAST sequence 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 CAST 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 hybridizes specifically with. a polymorphic site of the CAST gene of the portion of the nucleic acid molecule. Another aspect of the invention in a method for identifying a CAST polymorphism in a nucleic acid sample comprising isolating a nucleic acid molecule encoding CAST 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 most likely to exhibit a biological difference in fertility and longevity comprising the steps of obtaining a sample of the genetic material of a bovine; and analyze the presence of genotype in cattle that is associated with fertility and longevity, the genotype characterized by a polymorphism in the bovine CAST gene. In other embodiments of this aspect of the invention, the analysis step is selected from the group consisting of: restriction fragment length polymorphism analysis (RFLP), minisequencing, MALD-TOF, heteroduplex analysis, conformational polymorphism 1 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 CAST gene to a portion thereof that contains the polymorphism. In other embodiments of the invention, the amplification may include the step of selecting a forward and rear sequence primer capable of amplifying a region of the CAST gene. Another aspect of the invention is a computer-assisted method for predicting that livestock animals have a biological difference in fertility and longevity which comprises: using a computer system, for example, a programmed computer comprising a processor, a computer system, storage of data, an input device and an output device, the steps of: (a) entering in the programmed computer through the input device data that. comprise a CAST genotype of an animal, (b) correlate the fertility and longevity predicted by the CAST genotype using the processor and the data storage system and (c) output the fertility and longevity correlated with the CAST genotype to the output device. , in order to predict that livestock animals have a particular fertility and longevity. Yet another aspect of the invention is a method for doing business to manage livestock that comprises providing a user with the computer system for managing livestock that comprises physical characteristics and genotypes corresponding to one or more animals or a computer readable medium for handling livestock. which 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 Animal Materials and Methods and DNA preparation. Semen samples from 652 stallions that have procreated several numbers of daughters plus seven grandparents were donated by the DNA depository of Dairy Bulls in Beltsville, Maryland for the analysis. Stallion PTAs for six attributes were obtained from the U.S. Department of Agriculture Animal Improvement Laboratory Programs for all Holstein sires (http: //aipl.arsusda.gob/). The attributes analyzed included the pregnancy rate of daughters (DPR), productive life (PL), protein yield (PY), milk yield (MY), fat yield (FY), somatic cell registration (SCS) and it was worth in dollars (NM). The average PTA, standard deviation and range of variation for each of these attributes in the sampled population of the inventors plus the global estimated heritability for each attribute is listed in Table 1. The sperm DNA was extracted using an extraction protocol and purification of phenol chloroform previously described [Ashwell MS, Heyen DW. Sonstegard TS, Van Tassell CP, Da Y, VanRaden PM, Ron M, Weller JI, Lewin HA. Detection of quantitative trait loci affecting milk production, health, and reproductive traits in Holstein cattle. J. Dairy Sci 2004; 87: 68-475]. Table 1. Phenotypic and genetic parameters of quantitative attributes in seven stallion families In silico mutation detection and primer design. A cDNA sequence of the bovine calpastatin gene (NM_174003) consisting of the new XL domain was used as a reference to search the genomic DNA sequences of the same gene against the bovine genome sequencing database (http: // www. hgsc.bcm.tmc.edu/projects/bovine/) A total of seven contiguous genomics (FIGS 1-8) were retrieved and alignment of both the cDNA and the genomic DNA sequences revealed 11 individual nucleotide polymorphisms (SNPs) potentials in the coding region (FIG 9). Among these, three provisional SNPs would result in amino acid changes in the protein sequence, including those located in putative exon 3 and one in putative exon 8 of the bovine gene. The new XL domain DNA sequence encompasses exons 1-3 and partial exon 4. Two pairs of primers were designed to cover both potential polymorphic exons based on the genomic DNA sequence. To ensure that each exon region was fully amplified and sequenced, at least 100 bp of flanking sequences were included in the products. The primer sequences to amplify the exon 3 product were: forward, 5'-AAA TTT GCG GTT GAC CAC ACT GTT A-3 (SEQ ID NO: 18) and rear, 5'-TGT TAT GCC TGT TGC TTT GTA CCT C-3 '(SEQ ID NO: 19) (access from GenBank number: AAFC02179 90): The primer sequences to amplify the full tentative exon 8 were: forward, 5'-GAT TCT TGC TGA ATT TGG AGG GAA G-3 '(SEQ ID NO: 20) and rear, 5' -GGG GTC TCA AAG AGT TGG ATA CGA T-3 '(SEQ ID NO: 21) (access from GenBank number: AAFC02060381). Mutation validation and detection by accumulated DNA sequencing. DNA from animals exhibiting extreme phenotypes accumulated to validate the putative mutations described above and to detect polymorphisms in both products that include exon 3 and exon 8 of the bovine CAST gene plus its flanking intron sequence. To address the phenotypes related to fertility, the animals were classified by PTA for DPR. Two samples of accumulated DNA were formed, using the upper 60 animals with the highest PTS 'for DPR and the 60 animals with the lowest PTS' for DPR. PCR reactions were performed using 25 ng of bovine genomic DNA as template in a final volume of 10 yL containing 12.5 ng of each primer, 200 μ of dNTPs, 1.5-3 mM MgCl2, 50 mM KCl, 20 mM Tris-HCl and 0.2u of Platinum Taq polymerase (Invitrogen, Carlsbad, CA). The contact PCR conditions were carried out as follows: 95 ° C for 10 min; 8 cycles of 94 ° C for 30 s, 71 ° C for 30 s and 72 ° C 30 s followed by 37 cycles of 94 ° C for 30 s, 63 ° C for 30 s and 72 ° C for 30 s plus 1 cycle to 72 ° C for 5 min and then an extended hold at 4 ° C until use. The PCR products were examined by electrophoresis through 1.5% agarose gel with IX TBE buffer in order to determine the quality and quantity for DNA sequencing. Sequencing was performed on an ABI 3730 sequencer at the Laboratory for Biotechnology and Bioanalysis (Washington State University) using a standard protocol. Nucleotide polymorphisms were identified by comparing sequence patterns between these DNA pools. Haplotype detection through the individual sequencing of the grandfather and the determination of the genotype of the marker. The accumulated DNA sequences of both products revealed genetic polymorphisms in the population of dairy stallions derived from seven grandparents. To determine the potential haplotypes among these mutations in the bovine CAST gene, the PCR products of the seven grandparents were amplified and subjected to sequencing individually. A total of four polymorphisms including three SNPs and one simple tandem repeat were observed, but they formed only two haplotypes among these seven grandparents. A substitution of C / T, therefore it was chosen to determine the genotype as it could be revealed using a PCR-RFLP (restriction fragment length polymorphism) procedure. The PCR amplicons containing the region of exon 3 and the flanking intron sequence were digested at 37 ° C for three hours with 2U of Mspl (New England Biolabs, Beverly, MA, USA). The visualization of the digestion of the enzyme and the registration of the genotype of the individuals was conducted by electrophoresis on a 2% agarose gel containing ethidium bromide. Association analysis of the CAST gene with fertility and longevity in dairy cattle. Three stages were used to investigate the association of the bovine Calpastatin gene with DPR and PL in the sampled population I of the inventors. The first step was to determine the genotype of the marker in 60 high DPR samples and 60 low DPR samples. Fisher's exact test was used to examine the 'differences in allele frequencies for the initial association classification between these two groups of animals. In the second stage, the same marker genotype was determined on the progeny of the stallion family with the highest PTA for DPR and the family of stallions with the lowest PTA for DPR. Fisher's exact test was used to examine the differences in allele frequencies to validate the initial associations identified in the first stage. The last stage was to comprehensively analyze the data of all individuals for the fertility attributes of DPR and PL, the attributes of milk yield, yield, protein, milk fat and total net merit value for all attributes combined. The association between the PTA's of the previously described attributes and the son's genotype, CC, CT and TT was examined, using! the mixed model function of SAS (Version 9.1 Carey C). The effect of the stallion family was also included in the model as a fixed effect and the genotype of the child as a random effect: yljk = μ + ¾ -i- g3 -i- eljk Where y ^ is the PTA of attributes examined; μ is the total average value of the attribute; If it is the effect of the stallion family (i = 1,2, ..., 7) and g \ is the genotypic effect of the son (j = CC, CT, TT). eijk is the residual effect corresponding to ¿jfc and it was assumed that it is normally distributed. The interaction effect between the stallion family and the son's genotype was also initially included in the model, but was excluded in the final model because it was not significant. The residual model was weighted by 1 / r in the analysis, where r is the reliability for PTA. The significance level of the model was adjusted to P < 0.05. After a significant F test, the individual means for the different genotypes were compared using the pre-planned pairwise comparisons using the pdiff function of SAS (Version 9.1, Carey NC). Comparative re-annotation of the human CAST gene. The current GenBank database revealed that the human CAST protein, even in its longest isoform only consisted of an N-terminal L domain and four repetitive calpain inhibition domains (domains 1-4), thus, lacking the XL domain which was detected in bovine CAST protein. To further validate that observation, the human CAST gene was re-annotated using a three-step process as follows: 1) BLAST searches against the "est_human" databases in GenBank using a full-length cDNA sequence of the bovine CAST gene as a reference for retrieving all human ESTs (expressed sequence tags) that are orthotologous to the specific sequence of the XL domain of the bovine gene; 2) assembly of freshly searched human ESTs with the current longer isoform of the cDNA sequence to form a full-length DNA sequence of the human gene and 3) newly annotated cDN7A sequence alignment and genomic DNA sequences to determine the organization complete genomics of the human CAST gene. Results Genomic organization and functional polymorphisms in the bovine CAST gene. A BLAST search using the cDNA sequence of the bovine CAST gene (NM_174003) retrieved seven contiguous genomes with a total sequence of 116, 129 bp from a 6X bovine genome sequence assembly (http: // www. Hgsc.cm.tmc. edu / proj ects / bovine /) (FIGS 2-9). The alignment of both the cDNA and the genomic DNA sequence indicated that the bovine CAST gene contained at least 32 exons and 31 introns (FIG 1). However, exons 1-31 are coding exons with coding sequence varying from 30 bp (exon 1) to 114 bp (exon 8) in length. Exon 31 also contained 12 bp of the 3 'untranslated sequence and exon 32 presented no coding sequence at all. Among the 31 introns, twenty-five had intron sequences, complete, intron 23 was the smallest intron with a sequence of 173 bp, while intron 4 could be the largest intron in the gene with more than 44 kb of sequence (FIG . 1). The XL domain of the protein encompassed exons 1-3 and part of exon 4; the L domain corresponds to part of exon 4, exons 5-9 and part of exon 10; domain 1 flanked part of exon 10 and exons 11-15; domain 2 was extended from exons 16-20 and part exon 21; domain 3 was encoded by exon 21, exons 22-25 and part of exon 26; and domain 4 included part of exon 26, exons 27-30 and part of exon 31, respectively (FIG 1). A cDNA search against the bovine genomic DNA database indicated that only one copy of the calpastatin gene existed in the bovine genome. The alignment of the cDNA sequence with the genomic DNA sequence of the bovine CAST gene also revealed 11 putative SNPs in the coding region; including four G / A transitions1, three C / T transitions, two T / A transversions, one G / T substitution, and one CA substitution (FIG.9). However, only three cSNPs were found that alter the amino acid sequence of bovine CAST protein: G48D, P52L and I128K. The remaining SNP 's were silent mutations. The substitutions of G48D and | P52L were located in exon 3, corresponding to the XL domain. I128L was located in exon 8 that codes for domain L. All three coding cSNPs of bad sense altered the second base in the codon, leading to amino acid changes. The accumulated high / low DNA sequences and seven individual grandparents confirmed the SNP 's of G48D and P52L in the XL domain (FIG 10A), but not the substitution of I128K in the L domain. As both PCR products contained intronic sequences partial, a G / T substitution was detected in intron 3 (FIG 10B) and a repeat of tetra ÷ -nucleotide GAAA in intron 8, close to the exon-intron junction region. The repetition of GAAA appeared in bi-allelic form: four repeats in one allele and five repetitions in another (FIG 10C). Among these four polymorphisms, only two haplotypes existed in the seven grandparents. Haplotype 1 was G-C- -G AAGAAAGAAAGAAA (SEQ ID NO: 16) and haplotype 2 was A-T-G-GAAAGAAAGAAAGAAAGAAA (SEQ ID NO: 17), respectively (FIG 10). Comparisons of high-low individual and family for the establishment of initial associations. As indicated in the above, only two haplotypes existed among the seven grandparents examined, so the determination of a genotype of one of the haplotypes was sufficient. Of the three SNPs identified in the products of exon 3, the C / T transition, which altered the amino acid at position 52 from a proline to leucine resulted in the gain / loss of a restriction enzyme cleavage site for Mspl. A fragment of 308 bp was amplified for the region, which contained only one cut-off site for the restriction enzyme. Therefore, digestion with Mspl produced three: bands of 135 bp, 173 bp and 308 bp, respectively (FIG 11). Animals homozygous for the C allele have an MspI site, and after complete digestion they exhibited two bands of 135 bp and 173 bp. Animals homozygous for the T allele lost their MspI site which resulted in a band of 308 bp after the digestion reaction. The heterozygous animals showed three bands after digestion of MspI (FIG 11). The C / T transition was then determined in genotype in the 60 upper and background individuals or the highest DPR values. Among the top 60 individuals, the number of genotypes T, CT and CC were 24 (40%), 22 (36.7%) and 14 (23.3%), respectively. However, of the 60 background individuals, TT genotypes accounted for 65% (39/60), while only three individuals (5%) showed CC genotype and 18 animals (30%) were heterozygous (Table 2). The chi-square analysis revealed an association between DPR and the genotype frequency between the upper and background groups (? 2 = 11.10, P <; 0.01). This association between bovine CAST polymorphisms and DPR was also confirmed when determining the genotype of this marker on all the progeny of a family of high and low DPR stallions. This analysis supported the initial analysis and revealed a highly significant association between DPR and the genotype (? 2 = 92.91, P <0.0001, Table 2). Fisher's exact tests of differences in allele frequencies were also highly significant between the upper and background groups (p = 0.000146 Fisher) as well as between the high and low family progeny (p = 0.000000 Fisher) (Table 2 ). Table 2. Analysis of initial association of bovine CAST polymorphism with DPR in dairy cattle Group N e CT TT Signi fi ed c T Fisher p-value Level 60 14 22 24? 2 = íi.io 0. 42 0. 58 p = 0.000146 individual superior Fund 60 3 18 39 P < 0.01 0. .20 0. .80 Level of 60 27 42 0? 2 = 92.69 0. .70 0 .30 p = 0.000000 superior family Fund 60 0 17 42 P < 0.001 0 .13 0 .87 Significant associations of the CAST gene with fertility and longevity in dairy cattle. Initially, a total of 659 offspring from seven stallion families were genotyped for this C / T transition in the bovine CAST gene. After verification of the genotype based on pedigree analysis, seven animals were removed from the data set due to irregular genotypes. The remaining 652 animals included 62 homozygous CC animals, 378 homozygous TT animals and 212 heterozygous CT animals. The frequencies of C allele and T allele in the population were 0.26 and 0.74, respectively. Cross-family analysis for three genotypes of CC, CT and TT indicated that the individual genotype was a significant source of variation (P <0.0001) when examining DPR and PL, but it was not a significant source of variation when considering the milk production attributes (P> 0.05) (Table 3). In DPR values, the Cattle with the homozygous genotype. { CAST: c .283CC) had an additional 0.82 and 0.57 units of ??? (3.28 and 2.28 equivalent days available) compared to the homozygous CAST: c.283TT and the heterozygous animals CAST.C.283CT (P <0.05) (Table 1). The longevity ??? 1.22 units larger between CñST animals: c.283CC and TI and 0.89 different between animals CAST.C.283CC and CT (P <0.05). The improvement in both DPR and animal longevity CAST: c .283CC led to an increase in economic value of $ 67.86 and $ 51.14 per cow compared to homozygotes TT and heterozygous CT (P <0.05) (Table 3). The additive (a) and dominant (d) effects of the substitution C to T in their units in standard deviation (SD) are also listed in Table 3. Table 3. Associations of the bovine CAST gene (NM_174003.2: c.2830T) with reproductive and productive attributes in dairy cattle 1 The superscripts: different indicate a significant difference of P < .05 inside each row. 2 Additive effect. 3SD = Standard Deviation. ^ Dominant effect. The genotype determination of seven grandparents indicated that there was one CC stallion, two CT stallions and four T stallions. The grandfather's genotype was shown to be a significant source of variation for both DPR and PL (P <0.0001). When DPR is examined, the value ??? average for progeny of stallion CC was 1.50 (0.61 vs -0.89) and 0.94 units (0.60 vs -0.34) higher than that for the progeny of stallions TT and CT, respectively (P <0.05). The PL PTA values were 0.62, -0.51 and -1.24 in the progeny of the families of stallions CC, CT and TT, and were significantly different between any of two groups of stallion families (P <0.05). If the inventors consider the differences between the progeny of the CC and TT grandparents as selection differentials, and the differences between the CC and TT individuals of the crossed families as a selection response, the heritabilities carried out were estimated to be 0.55 (0.82 / 1.50 ) for DPR and 0.66 (1.22 / 1.86) for PL, respectively. Existence of the XL domain in the human CAST gene. The BLAST search against the "est_human" database in NCBI using the cDNA sequence of the bovine CAST gene (NM_174003) identified two human ESTs (BP2044772 and BU5644868) that showed high sequence similarity to the XL domain sequence of the bovine CAST gene. The assembly of these two EST sequences with the current longer form of the human CAST 'gene (NM_001750) generated a consensual sequence of 2,876 bp, including 151 bp 5'UTR, 2,331 bp of coding sequence and and 394 bp of 3' sequences UTR (FIG 1). Globally, the recently translated human CAST protein is 10 amino acids shorter than the bovine CAST protein sequence, but both have the same number of amino acids (68 amino acids) in the XL domain. The similarity of the XL domain between the human and bovine CAST gene was 85% in the nucleotide sequence and 77% in the amino acid sequence. Alignment of the freshly assembled human cDNA sequence with the genomic DNA sequence revealed that the longest human CAST gene contained 32 exons and 31 introns (FIG 1). Similar to bovine CAST gene, exons 1-31 are coding exons with coding sequence ranging from 30 bp (exon 1) to 114 bp (exon 8) in length. Exon 31 also contained 23 bp of 3 'untranslated sequence and exon 32 comprised the remaining 3'UTR sequence. Compared with the bovine CAST gene, the human gene had shorter coding sequences in exons 9, 15, 26, 28 and 31 by 6, 3, 3, 3 and 18 bp, respectively. However, exon 20 of the human CAST gene had a longer coding sequence of 3 bp than that observed in cattle. In the human CAST gene, intron 23 was also the smallest intron with a sequence of 89 bp, whereas intron 3 was the largest intron in the gene with approximately 27 kb of sequence (FIG 1). Discussion . It has been reported that the calpastatin gene is expressed in multiple reproductive tissues, including but not limited to the testes, ovary, uterus, pituitary, mammary gland, germ cells and the prostate gland [Kitahara A, Takano E, Ontsuki H, irihata Y, Yamagata Y, Knaagi 'R, Murachi T. Reversed distribution of calpains and calpastatin in human pituitary gland and selective localization of calpastatin in adrenocorticotropin-producing cells as demonstrated by immunohistochemistry. J Clin Endocrine! etab 1986; 63: 343-348; Thompson VF, Saldana S, Cong J, Luedke DM, Goll DE. The calpain system in human placenta. Life Sci 2002; 70: 2493-508; Ben-Aharon I, Ben-Yosef D, Amit A, Shalgi R. Expression and immunolocalization of the calpain-calpastatin system in the human oocyte. Fertile Steril 2005; 83: 1807-1813; Orwig KE, Bertrand JE, Ou BR, Forsberg NE, Stormshak F. Involvement of protein kinase-C, calpains, and calpastatin in prostaglandin F2 alpha-induced oxytocin secretion from the bovine corpus luteum. Endocrinology 1994; 134: 78-83; Liang ZG, O'Hern PA, Yavetz B, Yavetz H, Goldberg E. Human testis cDNAs identified by sera from infertile patients: a molecular biological approach to immunocontraceptive development. Reprod Fertile Dev 1994; 6: 297-305; Li S, Liang ZG, Wang GY, Yavetz B, Kim ED, Goldberg E. Molecular cloning and characterization of functional domains of a human testis-specific isoform of calpastatin. Biol Reprod 2000; 63: 172-178; Li S, Liang ZG, Wang GY, Yavetz B, Kim ED, Goldberg E. Molecular cloning and characterization of functional domains of a human testis-specific isoform of calpastatin. Biol Reprod 2000; 63: 172-178; Li S, Goldberg E. A novel N-terminal domains directs membrane localization of mouse testis-specific calpastatin. Biol Reprod 2000; 63: 1594-1600 and Wang LF, Miao SY, Yan YC, Li YH, Zong C, Koide SS. Expression of a sperm protein gene during spermatogenesis in mammalian testis: an in situ hybridization study. Mol Reprod Dev 1990; 26: 1-5]. A strong association was found between calpastatin and fertility in the present study. It was also observed that animals with the desirable genotype for fertility did not exhibit a decreased level of milk production: animals with higher PIA values for DPR exhibited similar milk production attributes as animals with less fertile genotypes (Table 3) . This is an optimal situation since it was initially thought that selection for fertility would result in a loss of milk production or vice versa. Therefore, the involvement of the calpastin gene in different physiological and / or biochemical pathways that led to several functions must be further evaluated. Pleothotropic effects of the CAST gene. As there is evidence that postmortem calpastatin activity is highly related to the softness of meat in different species [Koohmaraie M, Whipple G, Kxetchmar DH, Grouse J, Mersmann HJ. Postmortem proteolysis in longissimus muscle from beef, lamb, and pork carcasses. J Anim Sci 1991; 69: 617-624], several association studies have been conducted to look for genetic polymorphisms in calpastatin as a source of genetic markers that can influence the softness of the meat. For example, Schenkel and colleagues (unpublished data) identified a G / C substitution in intron 4 of the bovine CAST gene that was associated with shear force (P = 0.024) in cattle for beef. In pigs, Ciobanu and collaborators [Ciobanu DC, Bastiaansen JW, Lonergan SM, Thomsen H, Dekkers JC, Plastow GS, Rothschild MF. New alieles in calpastatin are associated with meat quality traits in pigs. J Anim Sci 2004; 82: 2829-2839] reported that a CAST haplotype was significantly associated with lower Warner-Bratzler shear strength, loss of cooking and higher juiciness. In the present study, the results clearly demonstrated that functional mutations in the CASI L bovine domain region were associated with fertility and longevity in Holstein dairy cattle. The haplotype G-C-T-GAAAGAAAGAAAGAAA (SEQ ID NO: 16) is more desirable than the haplotype A-T-G-GAAAGAAAGAAAGAAAGAAA (SEQ ID NO: 17) by increasing the values of ??? of 0.82 units in DPR and 1.22 units in PL (Table 3). These data indicate that the CAST gene plays a pleiotropic function in different physiological pathways and is involved in different functions. In addition, the present study reported two missense mutations in the bovine CAST gene, which are located in the region of the newly identified XL domain. The potential impact of this beneficial CAST haplotype for DPR and PL on meat quality warrants further investigation. Benefits of the CAST gene for marker-assisted selection. The reproductive decline in dairy cows has been largely blamed for intensive selection for milk attributes. For example, based on the linear regression of the reproduction values for the days available in the reproduction values by 3.7% FCM (milk corrected in fat), Abdallah and McDaniel [Abdallah JM, McDaniel BT. Genetic parameters and trends of milk, fat, days open, and body weight after calving in North Carolina experimental herds. J Dairy Sci 2000; 83: 1364-1370] estimated that for each 1000-kg increase in the reproduction values for 3.7% FCM, the reproduction values for the available days increased by 8 days. In Spain, milk yield per cow increased from 7800 kg in 1991 to 10,200 kg in 2000. However, each 1000 kg increase in average milk yield was accompanied by a decrease from 3.2% to 6% in the pregnancy rate, 4.4% to 7.6% in cyclicity, and an increase of 4.6% and 8% in the incidence of inactive ovaries [Lopez-Gatius F. Is fertility declining in dairy cattle? A retrospective study in northeastern Spain. The iogenology 2003; 60: 89-99]. Negative genetic correlations were also reported between milk yield and other reproductive attributes, such as range of breeding and first cover conception rates [Pryce JE, Veerkamp RF. The incorporation of fertility Indices in genetic improvement programs. In Fertility in the high producing dairy cows, British Society of Animal Science Occas 2003; 26: 237-249]. The results of the present study suggest that selection for the aelo / beneficial haplotype in the bovine CAST gene will not necessarily result in a decrease in milk production attributes in dairy cows. Therefore, the inventors anticipate that a combination of the genetic selection based on the CAST marker and high PTA potentials of the milk production attributes will improve the reproductive attributes while allowing the continuation of the high milk production attributes. In addition, if the CAST gene were to be applied in marker-assisted selection programs, the heritability of DPR could be markedly increased. Compared with the estimated heritability of 0.04 for DPR and 0.085 for 1? L (Table 1), the use of the calpastatin gene in marker-assisted selection in this way would accelerate the improvement of fertility in dairy cattle, which has declined by several decades The low frequency of the desirable allele / haplotype (0.26) in the current milk population studied was consistent with the low fertility exhibited in this population, indicating that marker-assisted selection is urgently needed. CAST gene and human infertility. Infertility is one of the most important social and economic health problems in humans. For example, although the population of the world has increased remarkably and is projected to I I I reach nine billion by 2050, it is estimated that 50-80 million couples in the world will remain without children due to infertility [Montoya JM, Bemal?, Borrero C. Diagnostics in assisted human reproduction Reprod Biomed Online 2002; 5: 198-210]. In the present study, the reanalysis of the human CAST gene revealed that the human gene also has the XL domain as the bovine gene. As the CAST protein was identified as one of the target antigens for antiesperm antibodies found in infertile women [Koide SS, Wang L, Kamada M. Antisperm antibodies associated with infertility: properties and encoding genes of target antigens. Proc Soc Exp Biol Med 2000; 224: 123-132], their involvement in human reproduction needs to be further explored. Example 2 FIG. 12 shows a flow diagram of the data entry and the output of the analysis and correlation of the data pertaining to the reproduction, veterinary histories and, performances of the performance of a group of animals such as bovines. The flow chart illustrated in FIG. 7 further indicates the interactive data flow of the computer-aided device to a group of students learning the use of the method of the invention and the correlation of such interactive data to present an output as a circular diagram indicating the progress of the class. The flow diagram 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. 13 illustrates potential relationships between the data elements that are introduced into the system. The unidirectional arrows indicate, for example, that a stable is typically owned by only one farm, while a farm can have several stables. Similarly, a prescription may include veterinary products. FIG. 14A 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. 14B illustrates the flow of events through the sub-routines related to the input of data concerning the management of the farm. FIG. 14C illustrates the flow of events through the sub-routines related to the entry of data concerning specific data to a company. FIG. 15 illustrates a flow chart of a 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. The invention is further described by the following numbered paragraphs: 1. A method for sub-grouping animals according to the genotype wherein the animals of each sub-group have a similar polymorphism in a calpastatin ("CAST") gene comprising: (a) determine the genotype of each animal to be sub-grouped by determining the presence of SNPs / STRs in the CAST gene, and (b) segregating individual animals into sub-groups where each animal in a subgroup has a polymorphism similar in the CAST gene. 2. A method for sub-grouping animals according to the genotype where the animals of each subgroup have a similar genotype in the CAST gene comprising: (a) determining the genotype of each animal to be sub-grouped by determining the presence of SNPs / STRs of interest in the CAST gene, (b) segregating individual animals into sub-groups depending on whether the animals have, or do not have, the individual nucleotide polymorphism (s) / short tandem repeats of interest in the CAST gene. 3. The method of paragraphs 1 or 2, where the SNPs / STRs of interest are selected from the group consisting of I M missense mutations in exon 3 that result in substitutions of G48D or P52L (NM_174003.2: c.211G> A and 2830G), a substitution of G / T in intron 3 (AAFC02060381.1: g.21 1 0O T) and a repetition of GAAA in 'intron 8 (AAFC02060381.1: g.6700 [(GAAA) 4] + [(GAAA) 5] 4. A method for sub- group animals according to the genotype where the animals of each subgroup have a similar genotype in the CAS T gene comprising: (a) determining the genotype of each animal to be sub-grouped by determining the presence of mutations of poorly felt in exon 3 resulting in substitutions of G48D or P52L (NM_174003.2: c.211 G> A and 2830 T), a substitution of G / T in intron 3 (AAFC02060381.1: g.21 1 0O T) and a repeat of GAAA in intron 8 (AAFC02060381.1: g.6700 [(GAAA) 4] -l- [(GAAA) 5] and (b) segregate individual animals into subgroups depending on whether the animals have, or do not have, missense mutations in exon 3 that result in • substitutions of G48D or P52L (NM_174003.2: c.2 71 G> A and 283C> T), a substitution of G / T in intron 3 (AAFC02060381.1: g.2 71 0G> T) and a repeat of GAAA in intron 8 (AAFC02060381.1: g.600 [(GAAA) 4] + [(GAAA) 5] in the CAST gene. 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 a SNP / STR in the CAST gene of the animal, wherein the polymorphism is selected from the group consisting of missense mutations in exon 3 that result in substitutions of G48D or P52L (NM_174003.2: c.271G> A and 2830T), a substitution of G / in intron 3 (AAFC02060381.1: g.21.10G> T) and a repeat of GAAA in intron 8 (AAFC02060381.1: g.6700 [(GAAA) 4] -i- [(GAAA) 5] in the nucleotide polymorphism individual / short tandem repetition of the CAST gene is indicative of a desirable phenotype 6. The method of paragraph 5, where the desirable phenotype is the pregnancy pregnancy rate (DPR), productive life (PL), protein yield ( PY), milk yield (MY), fat yield (FY), somatic cell registration (SCS) and net worth in dollars (NM) or any combination thereof 7. The method of paragraph 5 or 6, in where the desirable phenotype is fertility, longevity and the additional economic net worth or any combination thereof 8. The method of any of paragraphs 1 to 7, wherein the animal is a bovine. paragraphs 1 to 8, where the CAST gene is a bovine CAST gene 10. An interactive computer-assisted method to track the 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 into the computer programmed through the input device data comprising a history of reproduction of a bovine or herd of cattle, (b) entering data programmed into the computer through the input device comprising a veterinary history of a bovine or herd of cattle, (c) correlating the veterinary data with the reproduction history of the bovine or herd of cattle using the processor and the data storage system and (d) outputting the reproduction history and the veterinary history of the bovine or herd of bovines. 11. The method according to paragraph 10, wherein the computer system is an interactive system by which modifications to the output of the computer-aided method can be correlated according to the input of the in-vivo device. 12. The method according to paragraph 10 or 11, which also includes the steps of entering diagnostic data related to the health of the cow or herd of cows into the programmed computer; and correlate the diagnostic data with the reproduction and veterinary history 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 paragraphs 10 to 13, wherein 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 histories of the reproduction and veterinary of the cow or herd of cows, to introduce in the programmed computer the parameters of performance 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 with the performance parameters of the bovine or herd of cattle, correlating the herd with the performance parameters of the cattle or herd of cattle, correlate the food safety data with the parameters of the performance of the cattle or herd of cattle, correlate the data of the breeding condition with the performance parameters of the cattle or herd of cattle, enter data into the programmed computer related to the national data of the bovine or herd of cattle; 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. 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 the 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 batches of feed for livestock comprising removing the output and veterinary history of the bovine or herd of cattle from the output device and feeding the animal. (the) animal (s) with a diet based on their breeding and veterinary history, in order to optimize the efficiency of the feed 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 consisting of telecommunication, telephone, video conference, 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 breeding and welfare histories of cows comprising reproduction 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. 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 breeding 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 for doing business to track breeding 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 20. 23. The method of making business in accordance with paragraph 21, which further comprises providing the animal owner or customer with sample collection equipment, such as swabs or tags useful for collecting samples from which genetic data can be obtained, and where the tags are optionally packed in a container that is coded with identification signs. 24. The method of 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, outputting 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 modifying 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 single nucleotide / STR polymorphism (s) of interest in the CAST gene. 26. The method of paragraph 25 wherein the single nucleotide polymorphism (s) / short tandem repeats of interest is selected from the group consisting of missense mutations in exon 3 which result in substitutions of G48D or P52L (NM_174003 - 2: c.271G >; A and 2830T), a substitution of G / T in intron 3 (AAFC02060381.1: g.2110G> T) and a repeat of GAAA in intron 8 (AAFC02060381 - 1: g.6700 [(GAAA) 4 ] + [(GAAA) 5.}. Of the CAST gene 27. A method for the diagnosis or monitoring of fertility and / or longevity in a subject, comprising: obtaining a biological sample from a subject, and determining, using a test adequate, presence or absence in the sample of one or more CAST markers of domain XL, as described in the present 28. The method of paragraph 27, where the subject is bovine 29. A method for marker-assisted selection to improve fertility and / or longevity, which comprises classifying, as part of a selection scheme, based on one or more XL domain CñST markers, as described herein, to increase the selection for fertility and / or 1ongevity 30. The method of paragraph 29, where the selection is to increase bovine fertility and / or longevity 31. The method of paragraph 29, which further comprises the genetic selection based on high PTA potential of one or more attributes of milk production, to provide improved fertility and / or longevity, in association with high milk production. 32. The method of paragraph 31, where the selection is to increase the fertility and / or longevity of cattle, in association with high milk production. * * * Having described in this manner in detail preferred embodiments of the present invention, it is to be understood that the invention defined by the preceding paragraphs will not be limited by the particular details set forth in the foregoing description, since many obvious variations thereof are possible without departing from the spirit or scope of the present invention.

Claims (19)

1. CLAIMS 1. A method for identifying an animal that has desirable fertility, longevity, milk production, or a combination thereof, as compared to the general population of animals of that species, characterized in that it comprises determining the presence of nucleotide polymorphisms individual / short tandem repeats in a calpastatin gene ("CAST"), the presence of a single nucleotide polymorphism / short tandem repeat in the CAST gene of the animal, where the single nucleotide polymorphism / short tandem repeat is indicative of fertility, longevity, desirable milk production, or a combination thereof. The method according to claim 1, further comprising sub-grouping animals according to the genotype, wherein the animals of each sub-group have a similar short tandem polymorphism / repeat in the CAST gene, the method characterized because it comprises: (a) determining the genotype of each animal to be sub-grouped by determining the presence of a single tandem repeat / short nucleotide polymorphism in the CAST gene, and (b) segregating individual animals into sub-groups depending on if the animals have, or do not have, the individual nucleotide polymorphisms / short tandem repeats of interest in the CAST gene. The method according to claim 1, characterized in that the single nucleotide polymorphism (s) / short tandem repeats of interest is selected from the group consisting of missense mutations in exon 3 which result in substitutions of G48D or P52L (NM_174003.2: c.211G> A and 2830T), a substitution of G / T in intron 3 (AAFC02060381.1: g.2110OT) and a repeat of GAAA in intron 8 (AAFC02060381.1: g.6700 [(GAAA) 4] + [(GAAA) 5] in the CAST gene 4. The method according to claim 1, characterized in that the animal is a bovine 5. The method according to the rei indication 1, characterized by the CAST gene is a bovine CAST 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 device, an input device, an output device, and an interactive device, the steps of: (a) entering into 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 into the computer programmed through the input device data 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 reproductive history, the veterinary history of the bovine or herd of cattle and the output device. the physical characteristic correlated with the genotype for a bovine or population of cattle, where the physical characteristic is the speed of pregnancy of daughters (DPR), productive life (PL), yield of protein (PY), yield of milk (Y) , fat yield (FY), somatic cell registration (SCS) and net worth in dollars (NM) desirable, or a combination thereof, as is compar with the general population of cattle, and the genotype is a single-nucleotide polymorphism / short tandem repeat in a CAST gene. 7. The method of compliance with the claim 6, characterized in that 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. 8. The method according to claim 6, characterized in that it 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. 9. 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 breeding condition data, herd history and food safety data. 11. The method according to claim 6, characterized in that it also comprises at least one additional step selected from the group consisting of entering in the programmed computer data related to the quality control of the bovine or herd of cattle and correlating the data of quality control with the histories of the reproduction and veterinary of the cow or herd of cows, introduce in the programmed computer the performance parameters of the cow or herd of cows; and correlate the required performance parameters of the bovine or herd of cattle 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 related data with the nutritional data of the bovine or herd of cattle; 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 single nucleotide polymorphism (s) / short tandem repeats of interest is selected from the group consisting of missense mutations in exon 3 which result in substitutions of G48D or P52L (NM_174003.2: c.2.110A and 2830T), a substitution of G / T in intron 3 (AAFC02060381.1: g.2110OT) and a repeat of GAAA in intron 8 (AAFC02060381.1: g .6700 [(GAAA) 4] + [(GAññ) 5] in the CAST gene 13. A method for transmitting data, characterized in that it comprises the transmission of information of such methods according to claim 6, selected from the group consisting of telecommunication, telephone, video conference, mass communication, a presentation, a computer presentation, a presentation on POWERPOINT ™, internet, email and documentary communication 14. An interactive computer system in accordance with the claim 6, characterized in that it is for tracking the reproduction and welfare histories of cows comprising reproduction and veterinary data corresponding to a bovine or herd of cattle, and wherein the computer system is configured to allow the operator thereof 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, characterized in that it comprises reproduction and veterinary data corresponding to one or more livestock animals comprising providing a user with the computer system of claim 14. 17. A method to do business to track breeding histories and * cattle welfare, characterized in that it comprises reproduction and veterinary data corresponding to one or more livestock animals comprising providing a user with the computer system of claim 1-3. 18. The method for doing business according to claim 16, characterized in that it further comprises providing the owner of the animal or client with sample collection equipment, such as swabs and tags useful for collecting samples from which genetic data can be obtained, and wherein the labels are optionally packaged in a container that is encoded with identification signs. 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 step 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.