Abstract:
The present invention provides for selection of livestock animals, including bovines, whose genotypes based in the STAT6 gene are correlated with phenotypes reflecting desirable carcass and feedlot traits. These phenotypes include back fat (BFAT), calculated yield grade (CALCYG), cutability (CUT), hot carcass weight (HCW), dry matter intake (DMI), days on feed (DOF), back fat rate (BFAT RATE) and average daily gain (ADG), based on the knowledge of the STAT6 genotypes. The predictive value is based in part on the discovery that certain single nucleotide polymorphisms (SNPs) within the STAT6 gene are linked to phenotypes of economically these important carcass and feedlot traits. Also provided are SNPs within the STAT6 gene useful in reliably distinguishing between a  Bos taurus  and a  Bos indicus  bovine. The invention provides methods and compositions for determining STAT6 genotypes and for screening livestock animals to predict which animals will have desirable carcass traits and feedlot traits, allowing producers to selectively breed and manage animals based on desired characteristics, thereby maximizing productivity and profitability in commercial meat production operations.

Description:
FIELD OF THE INVENTION 
       [0001]    The present application provides methods and compositions for using polymorphisms in the STAT6 gene that are associated with economically important feedlot and carcass traits in livestock animals. 
       BACKGROUND OF THE INVENTION 
       [0002]    The cost of feeding is the single largest variable cost in beef production systems, accounting for approximately 70% of the total production cost (Perry and Cecava, 1995,  Beef Cattle Feeding and Nutrition,  2nd Ed., Academic Press, San Diego, Calif.). Generally, about 70-75% of the total dietary energy consumed in a beef production system is used for maintenance (Ferrell and Jenkins 1984,  J. Anim. Sci.  58:234-243; NRC (National Research Council) 1996,  Nutrient Requirements of Beef Cattle,  Seventh Reviewed Edition, Washington, D.C.: National Academy Press). This means higher beef production costs, especially in large-sized breeding animals due to presumably higher maintenance energy needs, lower overall production system efficiency, and therefore lower profits. Indeed, compared to swine and poultry, which are able to convert about 14 and 22%, respectively, of the total energy intake into protein deposition, only 5% of the total energy intake in beef cattle is converted into deposited protein. Improvements in the efficiency of feed utilization by beef cattle would therefore lead to better economic returns from both beef cattle breeding operations and feedlots (Gibb and McAllister, 1999, “The impact of feed intake and feeding behaviour of cattle on feedlot and feedbunk management,” Pages 101-116. D. Korver and J. Morrison (ed). Proc. 20th Western Nutr. Conf. Canada; Liu et al., 2000,  Can. J. Anim. Sci.  80:435-441; Herd et al., 2003,  J. Anim. Sci.  81(E. Suppl. 1):E9-E17). According to Johnson et al. (2003)  J. Anim. Sci.  2003. 81:E27-E38, the reasons for the lack of change inbeefcattle energetic efficiency, despite several years of intensive production, include the lack of a consistent selection goal, loose and inconsistent definitions of efficiency, concentration on output traits, and emphasis on population similarities rather than individual variation. 
         [0003]    Efficient beef cattle production involves a complex summation of appropriate levels of available feed inputs and product outputs over a range of different production systems involving animals at different developmental stages. Thus, several indices have been proposed for determining the energetic efficiency of beef production, as comprehensively reviewed by Archer, et al. (1999)  Australian Journal ofAgricultural Research  50:147-161. These include feed conversion ratio (FCR), maintenance efficiency, partial efficiency of growth (PEG), cow-calf efficiency, and residual feed intake (RFI). Two other indices are relative growth rate (growth relative to instantaneous body size) and Kleiber ratio (weight gain per unit metabolic body size). 
         [0004]    Traditionally, feed efficiency has been expressed in terms of FCR, or its inverse (gross feed efficiency, GFE). This is usually measured as the ratio of feed consumed to gain in weight. It reflects the efficiency of use of the energy consumed for maintenance and growth and captures the relationship between input of feed and output of product (Herd et al., 2003, supra). Though FCR has been in existence for many years, it is difficult to improve through direct selection because it is difficult to measure on the individual and its genetic correlation with growth rate implies that selection for it can lead to an increase in body weight (BW) and feed intake, which is not always desirable (Gunsett, 1984,  J. Anim. Sci.  59: 1185-1193; Archer et al., 1999, supra; Crews, 2005,  Genet. Mol. Res.  4 (2): 152-165). On the other hand, several studies in different species have demonstrated considerable phenotypic and genetic variations among individual animals in feed intake above and below the predicted requirements for maintenance and growth (Foster et al., 1983,  Anim. Prod.  37:387-393; Luiting and Urff, 1991,  Poult. Sci.  70:1663-1672; Archer et al., 1998,  Anim. Sci.  67:171-182; Archer et al., 1999, supra). This variation in intake is usually measured as RFI, and was first proposed for use in cattle by Koch et al. (1963)  J. Anim. Sci.  22:486-494. 
         [0005]    Ultimately, the resulting phenotypic information collected using automated feed intake monitoring systems could be employed to dissect the molecular architecture of several economically relevant, but complex traits (ERT) in beef cattle. Molecular techniques can be employed to detect and map the chromosomal locations of genes contributing to variation in growth, feed intake, energetic efficiency, feeding behavior, and carcass merit. Several molecular tools and approaches, as well as statistical and computational techniques, are available that can be employed to quantify the number(s), location(s) and effect(s) of quantitative trait loci (QTL) through the use of genotypic information from genetic markers that are evenly spaced along chromosomes in the genome. A QTL is defined as the chromosomal location of individual or groups of genes, of unknown primary function, that show(s) significant association with a complex trait of interest (Lander and Kruglyuak, 1995,  Natural Genet  11: 241-247). In beef cattle, QTL have been detected for disease tolerance (Hanotte et al., 2003,  PNAS Agricultural Sciences  100:7443-7448), fertility and reproductive performance (Kirkpatrick et al., 2000,  Mammalian Genome  11:136-139), body conformation (Grobet et al., 1998,  Mammalian Genome  9: 210-213), birth weight and growth performance (Davis et al., 1998,  Proc.  6 th World Congr. Genet. Appl. Livest. Prod.  23: 441-444; Casas et al., 2003,  J. Anim. Sci.  81, 2976-83; Li et al., 2002,  J. Anim. Sci.  80:1187-1194; Kim et al., 2003,  J. Anim. Sci  81, 1933-42), and carcass and meat quality (Keele et al., 1999,  J. Anim. Sci  77, 1364-1371; Casas et al., 2000,  J. Anim. Sci.  78:560-569; MacNeil and Grosz, 2002,  J. Anim. Sci.  80:2316-2324; Casas et al., 2003, supra; Kim et al., 2003, supra; Moore et al., 2003,  J. Anim. Sci.  81:1919-1925; and Li et al., 2004,  J. Anim Sci.  2004 82: 967-972). 
         [0006]    It is possible to search for and identify associations between polymorphisms in specific candidate genes and measures of variation in feed intake, feed efficiency and feeding behavior. A candidate gene may be selected based on previously known biochemical or physiological information or may be chosen because it maps to or close to the location of a QTL (positional candidate gene). Of interest among these candidates are genes shown to affect feed intake, behavior, energy balance, and body composition, such as the appetite regulating gene leptin. Several polymorphisms in candidate genes have been shown to be associated with economically relevant traits in cattle (Chrenek et al., 1998,  Czech Journal of Animal Science  43, 541-544; Barendse et al., 2001, “The TG5 DNA marker test for marbling capacity in Australian feedlot cattle,” on the worldwide web at beef.crc.org.au/Publications/MarblingSymDay1/Tg5DNA;Ge et al., 2001,  J. Anim. Sci.  79:1757-1762; Grisart et al., 2002,  Genome Research  12:222-231; Buchanan et al., 2002;  Genet. Sel. Evol.  34:105-116; Moore et al., 2003,  J. Anim. Sci.  81:1919-1925; Li et al., 2004, supra; and Nkrumah et al., 2005,  J. Anim. Sci.  83:20-28). 
         [0007]    The bovine microsatellite ETH10, located on bovine chromosome 5, has recently been associated with marbling (deposition of intramuscular fat) in Asian breeds of cattle (Smith et al. 2001,  J. Animal Sci  79:3041-51; and U.S. Pat. No. 6,383,751 (“the &#39;751 patent”)). The &#39;751 patent suggests that differences in marbling score, between related cattle with different ETH10 genotypes, is likely due to a closely linked gene. The &#39;751 patent proposes that retinol dehydrogenase (11-cis and 9-cis) (RDH5), which maps 1.01 centi-rads (cR) from ETH10 on the bovine radiation hybrid map (Womack et al. 1997,  Mamm Genome  8:854-6), was the responsible gene. The association between ETH10 and marbling was highly significant with a P-value of &lt;0.00015. Even though strong linkage disequilibrium would exist in the population tested, a P-value of this magnitude suggests that the gene responsible might be more closely linked to ETH 10 than RDH5. 
         [0008]    Using a bioinformatics-based method to identify sequence homologies between bovine microsatellites and gene sequences from other species, it was demonstrated that ETH10 was putatively located within the 5′ UTR of the bovine STAT6 gene (Farber and Medrano, 2003,  Animal Genetics  34:11-18). To support the location of ETH10, a bovine sequence tagged site (STS) in the 3′ UTR of bovine STAT6 was designed from available EST sequences. 
         [0009]    STAT6 is the principal transcription factor involved in interlukin-4 (IL-4) and IL-13 signaling (Takeda et al. 1997,  J Mol Med  75:317-326). In this context, a polymorphic microsatellite (homologous to ETH10) in the first exon of human STAT6 has been associated with predisposition to allergic diseases, due to altered IL-4 and IL-13 signal transduction (Tamura etal. 2001,  Clinical and Experimental Allergy  31:1509-1514). More importantly, STAT6 has been shown to be activated by the full length form and not the truncated form of the leptin receptor in cell culture, implicating it as a potential mediator of the anti-obesity effects of leptin (Ghilardi et al. 1996,  Proc Natl Acad Sci USA  93:6231-6235). As a mediator of leptin signaling, different allelic forms of STAT6 could impact the level of circulating leptin, which would have a direct impact on the mass of adipocytes (Maffei et al. 1995,  Nature Med  1:1155-61). 
         [0010]    The present invention provides SNPs within the STAT6 gene that are correlated with economically important feedlot and carcass traits in livestock animals. 
       BRIEF SUMMARY OF THE INVENTION 
       [0011]    A variety of characteristics of livestock animals are considered important in determining the overall value of the finished product. Some factors are involved in the palatability of the meat produced, which is important to consumers, and which is reflected in the grading system used to classify meat. Still other factors affect the cost of producing an animal of given size and therefore affect the cost of meat that the consumer will ultimately pay, and which will result in improved profitability for producers of livestock as well as the operators of feedlots. As a result, methods of production that can improve the quality, or reduce the cost of production are desirable for all concerned in the production and consumption of meat from livestock. 
         [0012]    The present invention is based in part on the discovery of SNPs that are associated with a variety of parameters related to carcass and feedlot traits of livestock animals. Knowledge of the STAT6 genotype of livestock animals permits the development of genetic testing methods such that animals with the most desirable characteristics with regard to carcass weight and fat distribution, average daily weight gain and rib eye area can be identified and selected. This in turn leads to the development of methods of livestock management, wherein a higher degree of predictability about the eventual development of livestock animals becomes possible, once the genotype of animals with regard to the STAT6 gene is determined. 
         [0013]    Accordingly, the present inventions provides compositions and methods for using SNPs in the STAT6 gene to identify livestock animals (e.g.,  Bos,  bovines) with desirable feedlot and carcass traits. In one aspect, the invention provides methods of selecting individual livestock animals, e.g., bovines, with desirable traits based on the knowledge of the animal&#39;s STAT6 genotype. In some embodiments, the methods comprise the steps of: determining the STAT6 alleles of the animal, e.g., bovine, at one or more SNP IDs selected from the group consisting of 14636, 16084 and 19597 of a gene encoding STAT6; wherein the traits are selected from the group consisting of back fat, calculated yield grade, cutability, hot carcass weight, dry matter intake, days on feed, back fat rate and average daily gain, wherein: 
         [0014]    i) a “CC” genotype at SNP ID 16084 is indicative of decreased back fat, a lower calculated yield grade, and increased cutability in comparison to an “AC” or “AA” genotype; 
         [0015]    ii) an “AA” genotype at SNP ID 19597 is indicative of increased hot carcass weight, increased dry matter intake and fewer days on feed in comparison to a “AG” or “GG” genotype; 
         [0016]    iii) a “CC” genotype at SNP ID 14636 is indicative of increased back fat rate, fewer days on feed, and increased average daily gain in comparison to a “CG” or “GG” genotype. In some embodiments, the methods further comprise the step of selecting the livestock animal with the desirable trait based on the animal&#39;s STAT6 genotype. 
         [0017]    In another aspect, the invention provides methods for distinguishing bovines having one or more STAT6 gene polymorphisms. In some embodiments, the methods comprise
       a) amplifying one or more regions or alleles of the bovine STAT6 gene using an oligonucleotide pair to form nucleic acid amplification products comprising amplified STAT6 gene polymorphism sequences;   b) detecting one or more polymorphisms present in the bovine STAT6 gene at a SNP ID selected from the group consisting of 14636; 16084 and 19597; and   c) analyzing the one or more polymorphisms, wherein
           i) a “CC” genotype at SNP ID 16084 is indicative of decreased back fat, a lower calculated yield grade, and increased cutability in comparison to an “AC” or “AA” genotype;   ii) an “AA” genotype at SNP ID 19597 is indicative of increased hot carcass weight, increased dry matter intake and fewer days on feed in comparison to a “AG” or “GG” genotype; and   iii) a “CC” genotype at SNP ID 14636 is indicative of increased back fat rate, fewer days on feed, and increased average daily gain in comparison to a “CG” or “GG” genotype.   
               
 
         [0024]    With respect to the methods for identifying animals with desirable feedlot or carcass traits based on their STAT6 genotype, in some embodiments, the step of determining or analyzing comprises determining the STAT6 allele of the animal at SNP ID 14636, wherein a “CC” genotype at SNP ID 14636 is indicative of increased back fat rate, fewer days on feed, and increased average daily gain in comparison to a “CG” or “GG” genotype. In some embodiments, the step of determining or analyzing comprises determining the STAT6 allele of the animal at SNP ID 16084, wherein a “CC” genotype at SNP ID 16084 is indicative of decreased back fat, a lower calculated yield grade, and increased cutability in comparison to an “AC” or “AA” genotype. In some embodiments, the step of determining or analyzing comprises determining the STAT6 allele of the animal at SNP ID 19597, wherein an “AA” genotype at SNP ID 19597 is indicative of increased hot carcass weight, increased dry matter intake and fewer days on feed in comparison to a “AG” or “GG” genotype. 
         [0025]    In some embodiments, the livestock animal is from the genus  Bos.  In some embodiments, the livestock animal is a bovine. In some embodiments, the livestock animal is a  Bos taurus.  In some embodiments, the livestock animal is a  Bos indicus.    
         [0026]    In some embodiments, two or more polymorphisms are determined, e.g., are amplified. In some embodiments, one, two or three polymorphisms are determined, e.g., are amplified. 
         [0027]    In some embodiments, the gene encoding bovine STAT6 shares at least 95% sequence identity to SEQ ID NO: 1 or the complement thereof. 
         [0028]    In some embodiments, the SNP ID 14636 of the gene encoding STAT6 is within a nucleic acid sequence having at least 95% sequence identity to a nucleic acid sequence of SEQ ID NO:2. In some embodiments, the SNP ID 16084 of the gene encoding STAT6 is within a nucleic acid sequence having at least 95% sequence identity to a nucleic acid sequence of SEQ ID NO:3. In some embodiments, the SNP ID 19597 of the gene encoding STAT6 is within a nucleic acid sequence having at least 95% sequence identity to a nucleic acid sequence of SEQ ID NO:4. 
         [0029]    In some embodiments, the STAT6 alleles are independently detected by an amplification reaction using polynucleotides that distinguish between alleles at SNP IDs 14636, 16084 or 19597. 
         [0030]    In some embodiments, the amplification reaction is selected from the group consisting of polymerase chain reaction (PCR), strand displacement amplification (SDA), nucleic acid sequence based amplification (NASBA), rolling circle amplification (RCA), T7 polymerase mediated amplification, T3 polymerase mediated amplification and SP6 polymerase mediated amplification. 
         [0031]    In some embodiments, the STAT6 alleles are independently detected by hybridization using polynucleotides that distinguish between alleles at SNP IDs 14636, 16084 or 19597. 
         [0032]    In some embodiments, the STAT6 alleles are independently detected by sequencing a subsequence of a gene encoding STAT6, the subsequence comprising SNP IDs 14636, 16084 or 19597. 
         [0033]    In some embodiments, the polymorphism or allele or position of the bovine STAT6 gene is at SNP ID 14636, and the oligonucleotide pair comprises a forward primer comprising a nucleic acid sequence selected from 5′-GCTGGTCACTCTTCCTAATC-3′ (SEQ ID NO: 11) and 5′-TCTGACTTAGGGATCACCTC-3′ (SEQ ID NO: 12); and a reverse primer comprising a nucleic acid sequence selected from 5′-GACCTCTATCTCTACCCTAC-3′ (SEQ ID NO:13); 5′-ACCTCTATCTCTACCCTACG-3′ (SEQ ID NO:14) and 5′-CTCTACCCTACGGGGAC-3′ (SEQ ID NO:15). 
         [0034]    In some embodiments, the polymorphism or allele or position of the bovine STAT6 gene is at SNP ID 16084, and the oligonucleotide pair comprises a forward primer comprising a nucleic acid sequence selected from 5′-TTTCCCTACTGCCCCATTGC-3′ (SEQ ID NO:16); 5′-TCAGAGAGCTTTCCCTACTG-3′ (SEQ ID NO:17); and 5′-CCTGTCTCTTACCCTCT-3′ (SEQ ID NO:18); and a reverse primer comprising the nucleic acid sequence 5′-TAATGGAGTGGGAAGAGCTG-3′ (SEQ ID NO: 19). 
         [0035]    In some embodiments, the polymorphism or allele or position of the bovine STAT6 gene is at SNP ID 19597, and the oligonucleotide pair comprises a forward primer comprising a nucleic acid sequence selected from 5′-CACACTCGTCACCAGGTATG-3′ (SEQ ID NO:20) and 5′-GAGCCCCCCTGCCTG-3′ (SEQ ID NO:21); and a reverse primer comprising a nucleic acid sequence selected from 5′-AACTCTGACCCTCCTGTTTC-3′ (SEQ ID NO:22) and 5′-GGGGTCTGCTCTCCA-3′ (SEQ ID NO:23). 
         [0036]    In a related aspect, the invention provides methods of distinguishing a  Bos taurus  from a  Bos indicus  based on one or more polymorphisms in a bovine STAT6 gene. In some embodiments, the methods comprise:
       determining one or more STAT6 alleles of a bovine at one or more SNP IDs selected from the group consisting of 10922, 14257, 24000 and 25999 of a bovine gene encoding STAT6, wherein:
           i) an “AA” genotype at SNP ID 10922 indicates that the bovine is a  Bos taurus,  and a “GG” genotype at SNP ID 10922 indicates that the bovine is a  Bos indicus;      ii) a “CC” genotype at SNP ID 14257 indicates that the bovine is a  Bos taurus , and a “AA” genotype at SNP ID 14257 indicates that the bovine is a  Bos indicus;      iii) a “TT” genotype at SNP ID 24000 indicates that the bovine is a  Bos taurus , and a “CC” genotype at SNP ID 24000 indicates that the bovine is a  Bos indicus;  and   iv) a “TT” genotype at SNP ID 25999 indicates that the bovine is a  Bos taurus , and an “CC” genotype at SNP ID 25999 indicates that the bovine is a  Bos indicus.      
               
 
         [0042]    In some embodiments, the methods of distinguishing a  Bos taurus  from a  Bos indicus  based on one or more polymorphisms in a bovine STAT6 gene comprise:
       a) amplifying one or more alleles of the bovine STAT6 gene using an oligonucleotide pair to form nucleic acid amplification products comprising amplified STAT6 gene polymorphism sequences;   b) detecting one or more polymorphisms present in the bovine STAT6 gene at a SNP ID selected from the group consisting of 10922, 14257, 24000 and 25999; and   c) analyzing the one or more polymorphisms, wherein
           i) an “AA” genotype at SNP ID 10922 indicates that the bovine is a  Bos taurus , and a “GG” genotype at SNP ID 10922 indicates that the bovine is a  Bos indicus;      ii) a “CC” genotype at SNP ID 14257 indicates that the bovine is a  Bos taurus , and a “AA” genotype at SNP ID 14257 indicates that the bovine is a  Bos indicus;      iii) a “TT” genotype at SNP ID 24000 indicates that the bovine is a  Bos taurus , and a “CC” genotype at SNP ID 24000 indicates that the bovine is a  Bos indicus ; and   iv) a “TT” genotype at SNP ID 25999 indicates that the bovine is a  Bos taurus , and an “CC” genotype at SNP ID 25999 indicates that the bovine is a  Bos indicus.      
               
 
         [0050]    With respect to the embodiments of the methods of distinguishing a  Bos taurus  from a  Bos indicus  based on polymorphisms in the STAT6 gene, in some embodiments two or more polymorphisms are determined, e.g., are amplified. In some embodiments, two, three, or four polymorphisms are determined, e.g., are amplified. 
         [0051]    In some embodiments, the polymorphism or allele or position of the bovine STAT6 gene is at SNP ID 10922, and the oligonucleotide pair comprises a forward primer comprising a nucleic acid sequence selected from 5′-TGTGATGGGTTGAACTCTGC-3′ (SEQ ID NO:24) and 5′-CTGCCTCTCAAAAATTTATATATTA-3′ (SEQ ID NO:25); and a reverse primer comprising a nucleic acid sequence selected from 5′-GGGTACCTCCTATGAATATG-3′ (SEQ ID NO:26) and 5′-GGGATATGTGATTTCAACATA-3′ (SEQ ID NO:27). 
         [0052]    In some embodiments, the polymorphism or allele or position of the bovine STAT6 gene is at SNP ID 14257, and the oligonucleotide pair comprises a forward primer comprising a nucleic acid sequence selected from 5′-GGGCCTCTGACTACCAATGT-3′ (SEQ ID NO:9); 5′-TTTTTCCACACACCCCATCC-3′ (SEQ ID NO:28); and 5′-GGGACGTGTTAAGGC-3′ (SEQ ID NO:29); and a reverse primer comprising a nucleic acid sequence selected from 5′-CCACACCCTTGAAGAGGAAC-3′ (SEQ ID NO:10); 5′-ACTTCCCCCCAACCCAGAG-3′ (SEQ ID NO:30) and 5′-TTGCCCTCCTTCCCC-3′ (SEQ ID NO:31). In some embodiments, the polymorphism or allele or position of the bovine STAT6 gene is at SNP ID 14257, and the oligonucleotide pair comprises forward primer 5′-GGGCCTCTGACTACCAATGT-3′ (SEQ ID NO:9) and reverse primer 5′-CCACACCCTTGAAGAGGAAC-3′ (SEQ ID NO:10). 
         [0053]    In some embodiments, the polymorphism or allele or position of the bovine STAT6 gene is at SNP ID 24000, and the oligonucleotide pair comprises a forward primer comprising a nucleic acid sequence selected from 5′-TCATTTCCCTGCTTCTGGAC-3′ (SEQ ID NO:32) and 5′-CCATCATCCATGCTCACCTTTTC-3′ (SEQ ID NO:33); and a reverse primer comprising a nucleic acid sequence selected from 5′-ATGGAATGCTTCCGGGTTAG-3′ (SEQ ID NO:34) and 5′-AGGGAGGAAGGGAGCT-3′ (SEQ ID NO:35). 
         [0054]    In some embodiments, the polymorphism or allele or position of the bovine STAT6 gene is at SNP ID 25999, and the oligonucleotide pair comprises a forward primer comprising a nucleic acid sequence selected from 5′-CCTCAGGATCATGCTGTGTC-3′ (SEQ ID NO:36) and 5′-CCCTTGCTCTGCTCAGA-3′ (SEQ ID NO:37); and a reverse primer comprising a nucleic acid sequence selected from 5′-TGGTTCAGGCAGCTGTCTTC-3′ (SEQ ID NO:38) and 5′-TTCTGCCATGGTCAC-3′ (SEQ ID NO:39). 
         [0055]    In some embodiments, the polymorphism detected is a restriction fragment length polymorphism. 
         [0056]    In some embodiments, the amplification reaction is selected from the group consisting of polymerase chain reaction (PCR), strand displacement amplification (SDA), nucleic acid sequence based amplification (NASBA), rolling circle amplification (RCA), T7 polymerase mediated amplification, T3 polymerase mediated amplification and SP6 polymerase mediated amplification. 
         [0057]    In some embodiments, the bovine STAT6 gene shares at least 95% sequence identity to SEQ ID NO: 1 or the complement thereof. 
         [0058]    In some embodiments, the SNP ID 10922 of the gene encoding STAT6 is within a nucleic acid sequence having at least 95% sequence identity to a nucleic acid sequence of SEQ ID NO:5. In some embodiments, the SNP ID 14257 of the gene encoding STAT6 is within a nucleic acid sequence having at least 95% sequence identity to a nucleic acid sequence of SEQ ID NO:6. In some embodiments, the SNP ID 24000 of the gene encoding STAT6 is within a nucleic acid sequence having at least 95% sequence identity to a nucleic acid sequence of SEQ ID NO:7. In some embodiments, SNP ID 25999 of the gene encoding STAT6 is within a nucleic acid sequence having at least 95% sequence identity to a nucleic acid sequence of SEQ ID NO:8. 
         [0059]    In a related aspect, the invention provides isolated polynucleotides for distinguishing the STAT6 SNP IDs 10922, 14257, 14636, 16084, 19597, 24000 and 25999. 
         [0060]    In some embodiments, the isolated polynucleotides distinguish STAT6 alleles at SNP ID 14257. In some embodiments, the isolated polynucleotide is SEQ ID NO:9. In some embodiments, the isolated polynucleotide is SEQ ID NO: 10. 
       DEFINITIONS 
       [0061]    Unless defined otherwise, all technical and scientific terms used herein generally have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Generally, the nomenclature used herein and the laboratory procedures in cell culture, molecular genetics, organic chemistry and nucleic acid chemistry and hybridization described below are those well known and commonly employed in the art. Standard techniques are used for nucleic acid and peptide synthesis. Generally, enzymatic reactions and purification steps are performed according to the manufacturer&#39;s specifications. The techniques and procedures are generally performed according to conventional methods in the art and various general references (see generally, Sambrook et al. MOLECULAR CLONING: A LABORATORY MANUAL, 3rd ed. (2001) Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. and Ausubel, ed., Current Protocols in Molecular Biology, 1990-2008, John Wiley Interscience), which are provided throughout this document. The nomenclature used herein and the laboratory procedures in analytical chemistry, and organic synthetic described below are those well known and commonly employed in the art. Standard techniques, or modifications thereof, are used for chemical syntheses and chemical analyses. 
         [0062]    STAT6 refers to nucleic acids and polypeptide polymorphic variants (including single nucleotide polymorphisms involving displacement, insertion, or deletion of a single nucleotide that may or may not lead to a change in an encoded polypeptide sequence), alleles, mutants, and interspecies homologs that: (1) have an amino acid sequence that has greater than about 90% amino acid sequence identity, for example, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% or greater amino acid sequence identity, preferably over a region of at least about 25, 50, 100, 200, 500, 1000, or more amino acids, or over the full-length, to an amino acid sequence encoded by a STAT6 nucleic acid (see, e.g., SEQ ID NO: 1 and GenBank Accession Nos. AB038383 ( Bos taurus ); NC_009149 ( Equus caballus ); BV726713 ( Sus scrofa ); EU439612.1 ( Canis lupus ); NM — 001012930 ( Gallus gallus )) or to an amino acid sequence of a STAT6 polypeptide (e.g., GenBank Accession Nos. BAA96475 ( Bos taurus ); ACA21821 (Canis lupus); and NP — 001012948 ( Gallus gallus ); (2) bind to antibodies, e.g., polyclonal antibodies, raised against an immunogen comprising an amino acid sequence of a STAT6 polypeptide (e.g., encoded by a nucleic acid sequence of SEQ ID NO: 1 or a nucleic acid of GenBank Accession Nos. AB038383; NC — 009149; BV726713; EU439612.1; and NM — 001012930; or an amino acid sequence of GenBank Accession Nos. BAA96475; ACA21821; and NP — 001012948), and conservatively modified variants thereof, (3) specifically hybridize under stringent hybridization conditions to an anti-sense strand corresponding to a nucleic acid sequence encoding a STAT6 protein, and conservatively modified variants thereof, (4) have a nucleic acid sequence that has greater than about 95%, preferably greater than about 96%, 97%, 98%, 99%, or higher nucleotide sequence identity, preferably over a region of at least about 25, 50, 100, 200, 500, 1000, or more nucleotides, or over the full-length, to a STAT6 nucleic acid. STAT6 nucleic acids include polynucleotides comprising the SNPs described herein. 
         [0063]    Positions within the STAT6 genomic nucleic acid sequence can be counted, for example, from nucleotide 1 of SEQ ID NO: 1, from position 10801 of the bovine STAT6 sequence in  FIG. 1 , in reference to the adenosine nucleotide of the ATG start codon, or alternatively, in reference to the intron or exon in which the SNP resides. A STAT6 polynucleotide or polypeptide sequence is typically from a domesticated livestock animal, for example, a bovine, ovine, equine, porcine or gallus. The nucleic acids and proteins of the invention include both naturally occurring or recombinant molecules. The STAT6 genomic nucleic acid sequence is provided as SEQ ID NO: 1, and also published as ENSEMBL accession number ENSBTAG00000006335 (which correlates to positions 17,194-26,693 of the STAT6 gene as defined in  FIG. 1 ). As used herein, a “STAT6 gene” will have a nucleic acid sequence that has greater than about 95%, preferably greater than about 96%, 97%, 98%, 99%, or higher nucleotide sequence identity, preferably over a region of at least about 500, 1000, 2000, 3000, 50000 or more nucleotides, or over the full-length, to a STAT6 genomic nucleic acid, for example, SEQ ID NO: 1 or ENSBTAG00000006335. 
         [0064]    The term “livestock animal” refers to any breed or population of animal kept by humans for a useful, commercial purpose. As used herein, a livestock animal can be mammal or avian. Generally, the livestock animal is an agricultural mammal, for example, bovine, equine, ovine, porcine. Livestock animals raised for the production of meat find use with the present invention, for example, beef cattle, pigs, goats, sheep, bison, chickens, turkeys, etc. The livestock animals can be in all stages of development, including embryonic, fetal, neonate, yearling, juvenile and adult stages. 
         [0065]    The term “bovine” refers to a domesticated (purebred or crossbreeds) or wild mammal that is a  Bovinae,  for example, of the genera  Bos  (e.g., cattle or oxen) or  Bison  (e.g., American buffalo). Exemplary mammals of the genus  Bos  include without limitation  Bos taurus, Bos bovis, Bos frontalis  (gayal),  Bos gaurus  (gaur),  Bos grunniens  (domestic yak),  Bos grunniens×Bos taurus  (dzo),  Bos indicus  (zebu cattle),  Bos indicus  gudali (Gudali zebu),  Bos indicus×Bos taurus  (hybrid cattle),  Bos javanicus  (banteng),  Bos primigenius  (aurochs), and  Bos sauveli  (kouprey).  Bos  species for the production of meat products, e.g., beef cattle are of use in the present invention. Exemplary breeds of  Bos  without limitation Black Angus, Red Angus, Horned Hereford, Polled Hereford, Charolais, Simmental, Limousine, Chianina, Brahman, Santa Gertrudis, and Wagyu. Other breeds of beef cattle of use are listed in Tables 1 and 2, infra. 
         [0066]    The term “carcass traits” refers to traits of an animal&#39;s carcass determined after the animal has been slaughtered. 
         [0067]    The term “feedlot traits” refers to traits of a live animal during the time period it is resident in a feedlot. 
         [0068]    The terms “nucleic acid” and “polynucleotide” are used interchangeably herein to refer to deoxyribonucleotides or ribonucleotides and polymers thereof in either single- or double-stranded form. The term encompasses nucleic acids containing known nucleotide analogs or modified backbone residues or linkages, which are synthetic, naturally occurring, and non-naturally occurring, which have similar binding properties as the reference nucleic acid, and which are metabolized in a manner similar to the reference nucleotides. Examples of such analogs include, without limitation, phosphorothioates, phosphoramidates, methyl phosphonates, chiral-methyl phosphonates, 2-O-methyl ribonucleotides, peptide-nucleic acids (PNAs). 
         [0069]    Unless otherwise indicated, a particular nucleic acid sequence also encompasses conservatively modified variants thereof (e.g., degenerate codon substitutions) and complementary sequences, as well as the sequence explicitly indicated. Specifically, degenerate codon substitutions may be achieved by generating sequences in which the third position of one or more selected (or all) codons is substituted with mixed-base and/or deoxyinosine residues (Batzer et al.,  Nucleic Acid Res.  19:5081 (1991); Ohtsuka et al.,  J. Biol. Chem.  260:2605-2608 (1985); Rossolini et al.,  Mol. Cell Probes  8:91-98 (1994)). The term nucleic acid is used interchangeably with gene, cDNA, mRNA, oligonucleotide, and polynucleotide. 
         [0070]    A “single nucleotide polymorphism” or “SNP” refers to polynucleotide that differs from another polynucleotide by a single nucleotide exchange. For example, without limitation, exchanging one A for one C, G or T in the entire sequence of polynucleotide constitutes a SNP. Of course, it is possible to have more than one SNP in a particular polynucleotide. For example, at one locus in a polynucleotide, a C may be exchanged for a T, at another locus a G may be exchanged for an A and so on. When referring to SNPs, the polynucleotide is most often DNA and the SNP is one that usually results in a change in the genotype that is associated with a corresponding change in phenotype of the organism in which the SNP occurs. 
         [0071]    A “variant” is a difference in the nucleotide sequence among related polynucleotides. The difference may be the deletion of one or more nucleotides from the sequence of one polynucleotide compared to the sequence of a related polynucleotide, the addition of one or more nucleotides or the substitution of one nucleotide for another. The terms “mutation,” “polymorphism” and “variant” are used interchangeably herein to describe such variants. As used herein, the term “variant” in the singular is to be construed to include multiple variances; i. e., two or more nucleotide additions, deletions and/or substitutions in the same polynucleotide. A “point mutation” refers to a single substitution of one nucleotide for another. 
         [0072]    A nucleic acid “that distinguishes” as used herein refers to a polynucleotide(s) that (1) specifically hybridizes under stringent hybridization conditions to an anti-sense strand corresponding to a nucleic acid sequence encoding a STAT6 protein, and conservatively modified variants thereof, or (2) has a nucleic acid sequence that has greater than about 80%, 85%, 90%, 95%, preferably greater than about 96%, 97%, 98%, 99%, or higher nucleotide sequence identity, preferably over a region of at least about 25, 50, 100, 200, 500, 1000, or more nucleotides, to a STAT6 nucleic acid (e.g., a sequence as set forth in SEQ ID NO: 1, or complements or a subsequences thereof. A nucleic acid that distinguishes a first STAT6 polymorphism from a second STAT6 polymorphism at the same position in the STAT6 sequence will allow for polynucleotide extension and amplification after annealing to a STAT6 polynucleotide comprising the first polymorphism, but will not allow for will not allow for polynucleotide extension or amplification after annealing to a STAT6 polynucleotide comprising the second polymorphism. In other embodiments, a nucleic acid that distinguishes a first STAT6 polymorphism from a second STAT6 polymorphism at the same position in the STAT6 sequence will hybridize to a STAT6 polynucleotide comprising the first polymorphism but will not hybridize to a STAT6 polynucleotide comprising the second polymorphism. 
         [0073]    The phrase “stringent hybridization conditions” refers to conditions under which a probe will hybridize to its target subsequence, typically in a complex mixture of nucleic acid, but to no other sequences. Stringent conditions are sequence-dependent and will be different in different circumstances. Longer sequences hybridize specifically at higher temperatures. An extensive guide to the hybridization of nucleic acids is found in Tijssen, Techniques in Biochemistry and Molecular Biology—Hybridization with Nucleic Probes, “Overview of principles of hybridization and the strategy of nucleic acid assays” (1993). Generally, stringent conditions are selected to be about 5-10° C. lower than the thermal melting point I for the specific sequence at a defined ionic strength pH. The Tm is the temperature (under defined ionic strength, pH, and nucleic concentration) at which 50% of the probes complementary to the target hybridize to the target sequence at equilibrium (as the target sequences are present in excess, at Tm, 50% of the probes are occupied at equilibrium). Stringent conditions will be those in which the salt concentration is less than about 1.0 M sodium ion, typically about 0.01 to 1.0 M sodium ion concentration (or other salts) at pH 7.0 to 8.3 and the temperature is at least about 30° C. for short probes (e.g., 10 to 50 nucleotides) and at least about 60° C. for long probes (e.g., greater than 50 nucleotides). Stringent conditions may also be achieved with the addition of destabilizing agents such as formamide. For selective or specific hybridization, a positive signal is at least two times background, optionally 10 times background hybridization. Exemplary stringent hybridization conditions can be as following: 50% formamide, 5×SSC, and 1% SDS, incubating at 42° C., or, 5×SSC, 1% SDS, incubating at 65° C., with wash in 0.2×SSC, and 0.1% SDS at 65° C. 
         [0074]    Nucleic acids that do not hybridize to each other under stringent conditions are still substantially identical if the polypeptides which they encode are substantially identical. This occurs, for example, when a copy of a nucleic acid is created using the maximum codon degeneracy permitted by the genetic code. In such cases, the nucleic acids typically hybridize under moderately stringent hybridization conditions. Exemplary “moderately stringent hybridization conditions” include a hybridization in a buffer of 40% formamide, 1 M NaCl, 1% SDS at 37° C., and a wash in 1×SSC at 45° C. A positive hybridization is at least twice background. Those of ordinary skill will readily recognize that alternative hybridization and wash conditions can be utilized to provide conditions of similar stringency. 
         [0075]    The phrase “selectively (or specifically) hybridizes to” refers to the binding, duplexing, or hybridizing of a molecule only to a particular nucleotide sequence under stringent hybridization conditions when that sequence is present in a complex mixture (e.g., total cellular or library DNA or RNA). 
         [0076]    The terms “isolated,” “purified,” or “biologically pure” refer to material that is substantially or essentially free from components that normally accompany it as found in its native state. Purity and homogeneity are typically determined using analytical chemistry techniques such as polyacrylamide gel electrophoresis or high performance liquid chromatography. A protein that is the predominant species present in a preparation is substantially purified. In particular, an isolated STAT6 nucleic acid is separated from open reading frames that flank the STAT6 gene and encode proteins other than STAT6. The term “purified” denotes that a nucleic acid or protein gives rise to essentially one band in an electrophoretic gel. Particularly, it means that the nucleic acid or protein is at least 85% pure, more preferably at least 95% pure, and most preferably at least 99% pure. 
         [0077]    The terms “polypeptide,” “peptide” and “protein” are used interchangeably herein to refer to a polymer of amino acid residues. The terms apply to amino acid polymers in which one or more amino acid residue is an artificial chemical mimetic of a corresponding naturally occurring amino acid, as well as to naturally occurring amino acid polymers and non-naturally occurring amino acid polymer. 
         [0078]    The term “amino acid” refers to naturally occurring and synthetic amino acids, as well as amino acid analogs and amino acid mimetics that function in a manner similar to the naturally occurring amino acids. Naturally occurring amino acids are those encoded by the genetic code, as well as those amino acids that are later modified, e.g., hydroxyproline, α-carboxyglutamate, and O-phosphoserine. Amino acid analogs refers to compounds that have the same basic chemical structure as a naturally occurring amino acid, i.e., an a carbon that is bound to a hydrogen, a carboxyl group, an amino group, and an R group, e.g., homoserine, norleucine, methionine sulfoxide, methionine methyl sulfonium. Such analogs have modified R groups (e.g., norleucine) or modified peptide backbones, but retain the same basic chemical structure as a naturally occurring amino acid. Amino acid mimetics refers to chemical compounds that have a structure that is different from the general chemical structure of an amino acid, but that functions in a manner similar to a naturally occurring amino acid. 
         [0079]    Amino acids may be referred to herein by either their commonly known three letter symbols or by the one-letter symbols recommended by the IUPAC-IUB Biochemical Nomenclature Commission. Nucleotides, likewise, may be referred to by their commonly accepted single-letter codes. 
         [0080]    “Conservatively modified variants” applies to both amino acid and nucleic acid sequences. With respect to particular nucleic acid sequences, conservatively modified variants refers to those nucleic acids which encode identical or essentially identical amino acid sequences, or where the nucleic acid does not encode an amino acid sequence, to essentially identical sequences. Because of the degeneracy of the genetic code, a large number of functionally identical nucleic acids encode any given protein. For instance, the codons GCA, GCC, GCG and GCU all encode the amino acid alanine. Thus, at every position where an alanine is specified by a codon, the codon can be altered to any of the corresponding codons described without altering the encoded polypeptide. Such nucleic acid variations are “silent variations,” which are one species of conservatively modified variations. Every nucleic acid sequence herein which encodes a polypeptide also describes every possible silent variation of the nucleic acid. One of skill will recognize that each codon in a nucleic acid (except AUG, which is ordinarily the only codon for methionine, and TGG, which is ordinarily the only codon for tryptophan) can be modified to yield a functionally identical molecule. Accordingly, each silent variation of a nucleic acid which encodes a polypeptide is implicit in each described sequence. 
         [0081]    As to amino acid sequences, one of skill will recognize that individual substitutions, deletions or additions to a nucleic acid, peptide, polypeptide, or protein sequence which alters, adds or deletes a single amino acid or a small percentage of amino acids in the encoded sequence is a “conservatively modified variant” where the alteration results in the substitution of an amino acid with a chemically similar amino acid. Conservative substitution tables providing functionally similar amino acids are well known in the art. Such conservatively modified variants are in addition to and do not exclude polymorphic variants, interspecies homologs, and alleles of the invention. 
         [0082]    The following eight groups each contain amino acids that are conservative substitutions for one another:
       1) Alanine (A), Glycine (G);   2) Aspartic acid (D), Glutamic acid (E);   3) Asparagine (N), Glutamine (Q);   4) Arginine I, Lysine (K);   5) Isoleucine (I), Leucine (L), Methionine (M), Valine (V);   6) Phenylalanine (F), Tyrosine (Y), Tryptophan (W);   7) Serine (S), Threonine (T); and   8) Cysteine (C), Methionine (M) (see, e.g., Creighton, Proteins (1984)).       
 
         [0091]    The terms “identical” or percent “identity,” in the context of two or more nucleic acids or polypeptide sequences, refer to two or more sequences or subsequences that are the same or have a specified percentage of amino acid residues or nucleotides that are the same (i.e., share at least about 80% identity, for example, at least about 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% identity over a specified region to a reference sequence, e.g., SEQ ID NO: lor a polypeptide encoded by SEQ ID NO: 1), when compared and aligned for maximum correspondence over a comparison window, or designated region as measured using one of the following sequence comparison algorithms or by manual alignment and visual inspection. Such sequences are then said to be “substantially identical.” This definition also refers to the compliment of a test sequence. Preferably, the identity exists over a region that is at least about 25 amino acids or nucleotides in length, for example, over a region that is 50-100 amino acids or nucleotides in length, or over the full-length of a reference sequence. 
         [0092]    For sequence comparison, typically one sequence acts as a reference sequence, to which test sequences are compared. When using a sequence comparison algorithm, test and reference sequences are entered into a computer, subsequence coordinates are designated, if necessary, and sequence algorithm program parameters are designated. Default program parameters can be used, or alternative parameters can be designated. The sequence comparison algorithm then calculates the percent sequence identities for the test sequences relative to the reference sequence, based on the program parameters. For sequence comparison of nucleic acids and proteins to STAT6 nucleic acids and proteins, the BLAST and BLAST 2.0 algorithms and the default parameters discussed below are used. 
         [0093]    A “comparison window”, as used herein, includes reference to a segment of any one of the number of contiguous positions selected from the group consisting of from 20 to 600, usually about 50 to about 200, more usually about 100 to about 150 in which a sequence may be compared to a reference sequence of the same number of contiguous positions after the two sequences are optimally aligned. Methods of alignment of sequences for comparison are well-known in the art. Optimal alignment of sequences for comparison can be conducted, e.g., by the local homology algorithm of Smith &amp; Waterman, Adv. Appl. Math. 2:482 (1981), by the homology alignment algorithm of Needleman &amp; Wunsch, J. Mol. Biol. 48:443 (1970), by the search for similarity method of Pearson &amp; Lipman, Proc. Nat&#39;l. Acad. Sci. USA 85:2444 (1988), by computerized implementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group, 575 Science Dr., Madison, Wis.), or by manual alignment and visual inspection (see, e.g., Current Protocols in Molecular Biology (Ausubel et al., eds. 1995 supplement)). 
         [0094]    Examples of algorithms that are suitable for determining percent sequence identity and sequence similarity are the BLAST and BLAST 2.0 algorithms, which are described in Altschul et al. (1990) J. Mol. Biol. 215: 403-410 and Altschul et al. (1977) Nucleic Acids Res. 25: 3389-3402, respectively. Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information (on the worldwide web at ncbi.nlm.nih.gov/). The algorithm involves first identifying high scoring sequence pairs (HSPs) by identifying short words of length W in the query sequence, which either match or satisfy some positive-valued threshold score T when aligned with a word of the same length in a database sequence. T is referred to as the neighborhood word score threshold (Altschul et al, supra). These initial neighborhood word hits acts as seeds for initiating searches to find longer HSPs containing them. The word hits are then extended in both directions along each sequence for as far as the cumulative alignment score can be increased. Cumulative scores are calculated using, for nucleotide sequences, the parameters M (reward score for a pair of matching residues; always &gt;0) and N (penalty score for mismatching residues; always &lt;0). For amino acid sequences, a scoring matrix is used to calculate the cumulative score. Extension of the word hits in each direction are halted when: the cumulative alignment score falls off by the quantity X from its maximum achieved value; the cumulative score goes to zero or below, due to the accumulation of one or more negative-scoring residue alignments; or the end of either sequence is reached. The BLAST algorithm parameters W, T, and X determine the sensitivity and speed of the alignment. The BLASTN program (for nucleotide sequences) uses as defaults a word size (W) of 28, an expectation (E) of 10, M=1, N=−2, and a comparison of both strands. For amino acid sequences, the BLASTP program uses as defaults a word size (W) of 3, an expectation (E) of 10, and the BLOSUM62 scoring matrix (see Henikoff&amp; Henikoff, Proc. Natl. Acad. Sci. USA 89:10915 (1989)). 
         [0095]    The BLAST algorithm also performs a statistical analysis of the similarity between two sequences (see, e.g., Karlin &amp; Altschul, Proc. Nat&#39;l. Acad. Sci. USA 90:5873-5787 (1993)). One measure of similarity provided by the BLAST algorithm is the smallest sum probability (P(N)), which provides an indication of the probability by which a match between two nucleotide or amino acid sequences would occur by chance. For example, a nucleic acid is considered similar to a reference sequence if the smallest sum probability in a comparison of the test nucleic acid to the reference nucleic acid is less than about 0.2, more preferably less than about 0.01, and most preferably less than about 0.001. 
         [0096]    An indication that two nucleic acid sequences or polypeptides are substantially identical is that the polypeptide encoded by the first nucleic acid is immunologically cross reactive with the antibodies raised against the polypeptide encoded by the second nucleic acid, as described below. Thus, a polypeptide is typically substantially identical to a second polypeptide, for example, where the two peptides differ only by conservative substitutions. Another indication that two nucleic acid sequences are substantially identical is that the two molecules or their complements hybridize to each other under stringent conditions, as described below. Yet another indication that two nucleic acid sequences are substantially identical is that the same primers can be used to amplify the sequence. 
     
    
     
       BRIEF DESCRIPTION OF THE DRAWINGS 
         [0097]      FIG. 1  illustrates the annotated sequence of the bovine STAT6 genomic sequence (SEQ ID NO:1). The positions of SNP IDs 10922, 14257, 14636, 16084, 19597, 24000 and 25999 and exons 1-21 are identified. Each exon is labeled with a letter “E” with the number of the exon, and is marked with a line above the corresponding sequence (“           ”). 
           [0098]      FIG. 2  illustrates a multiple sequence alignment of the STAT6 protein sequence, highlighting the high degree of conservation between bovine (SEQ ID NO:40), equine (SEQ ID NO:41), canine (SEQ ID NO:42), human (SEQ ID NO:43) and murine (SEQ ID NO:44) STAT6 amino acid sequences. 
       
    
    
     DETAILED DESCRIPTION 
     1. Introduction 
       [0099]    Single nucleotide polymorphisms (SNPs) can provide a useful way in which to distinguish different alleles of a gene. Furthermore, when the presence of a SNP can be associated with a specific phenotype, the SNP operates as a powerful marker and can be used to predict phenotypic outcomes based on an animal&#39;s genotypic makeup. The present invention relates to methods of managing livestock animals, for example, cattle, sheep, goats, horses and pigs, and taking advantage of genetic factors that affect an animal&#39;s fat distribution and disposition. By identifying animals with a particular genotype, with respect to herein described SNP alleles, it is possible to identify animals that will display phenotypes associated with carcass traits including back fat, carcass weight, and cutability; and feedlot traits including average daily gain, days on feed and dry matter intake, as compared to animals lacking the desired genotype. 
         [0100]    In particular, the present invention relates to methods for establishing the genetically determined predispositions of individual livestock animals, for example, cattle, sheep, goats, horses and pigs, within a group of such animals, to meet particular desired characteristics with respect to carcass and feedlot traits, based on the association of specific STAT6 alleles with statistically correlated carcass and feedlot phenotypes. 
         [0101]    The present invention provides methods for analyzing the genotype of animals with respect to the STAT6 gene, and using the genotype information to select animals with desired traits related to carcass and feedlot traits. Such knowledge further permits producers to charge a premium for the more desirable phenotype, and permits breeders to selectively breed animals for genotypes that will result in the most desirable phenotypes. 
         [0102]    The present invention is based in part on the unexpected discovery that the location of ETH10 is within the first exon of STAT6 (e.g., positions 13,805-13,844 of the bovine STAT6 genomic nucleic acid sequence in  FIG. 1 ). Using the bovine whole genome radiation hybrid panel, it was demonstrated that STAT6 mapped 0.3 cR from ETH10 with a LOD score of 20.4. Available EST sequences were assembled and part of the bovine STAT6 gene from cDNA was sequenced, confirming that the location of ETH 10 is indeed within the first exon of STAT6. The present invention provides a biological explanation for the association between the amount of marbling (the size and number of adipocytes within muscle tissue) and genotype at ETH10 and/or STAT6 alleles. 
         [0103]    In particular, three single nucleotide polymorphisms (SNPs) within the STAT6 gene, i.e., SNP ID 14636, SNP ID 16084 and SNP ID 19597, have been identified that are statistically correlated with economically important feedlot and carcass traits in livestock animals, for example, bovines, for example,  Bos taurus . In addition, four SNPS within the STAT6 gene, i.e., SNP ID 10922, SNP ID 14257, SNP ID 24000, and SNP ID 25999, have been identified that are fixed in  Bos taurus  and  Bos indicus , and are useful for genetically distinguishing these two  Bos  species that are oftentimes phenotypically indistinguishable. 
       2. Methods of Determining Desirable Traits in Livestock Animals by Determining SNPs in the STAT6 Gene 
       [0104]    a. Livestock Animals 
         [0105]    The present invention is useful for identifying desired phenotypes in a livestock animal based on its STAT6 genotype, particularly at SNP IDs 16084, 19597 and 14636. The livestock animal can be any animal that is raised commercially for meat production, for example, beef, pork, mutton, lamb or poultry. Oftentimes the livestock animal is a mammal. In some embodiments, the livestock animal is a bovine, ovine, equine, or porcine. In some embodiments, the livestock animal is a bovine, for example, of the genus  Bos , for example, beef cattle. 
         [0106]    The STAT6 genomic nucleic acid sequence, protein-encoding nucleic acid sequence (i.e., mRNA or cDNA), and amino acid sequence is conserved amongst mammalian species. The amino acid alignment in  FIG. 2  shows that the bovine STAT6 protein shares about 93% amino acid sequence identity with the STAT6 protein of horse and dog, and about 92% amino acid sequence identity with the murine STAT6 protein. The bovine STAT6-encoding nucleic acid sequence shares about 95% nucleic acid sequence identity with the STAT6-encoding nucleic acid sequence of horse and about 93% nucleic acid sequence identity with the STAT6-encoding nucleic acid sequence of dog. 
         [0107]    b. Biological Samples 
         [0108]    The methods of the present invention involve taking a biological sample comprising genomic DNA from the animal to be tested. The biological sample can be from solid tissue or a biological fluid that contains a nucleic acid comprising a single nucleotide polymorphism (SNP) described herein, e.g., a nucleic acid comprising a STAT6 gene. The biological sample can be tested by the methods described herein and include body fluids including whole blood, serum, plasma, cerebrospinal fluid, urine, lymph fluids, semen, and various external secretions of the respiratory, intestinal and genitourinary tracts, tears, saliva, milk, white blood cells, myelomas, and the like; and biological fluids such as cell extracts, cell culture supernatants; fixed tissue specimens; and fixed cell specimens. Biological samples can also be from solid tissue, including hair bulb, skin, biopsy or autopsy samples or frozen sections taken for histologic purposes. These samples are well known in the art. A biological sample is obtained from any livestock animal to be tested for STAT6 SNPs as described herein, including, e.g., a beef cow. A biological sample can be suspended or dissolved in liquid materials such as buffers, extractants, solvents and the like. 
         [0109]    c. SNPs in STAT6 Correlated with Desirable Traits 
         [0110]    Livestock mammals, including bovines, ovines, equines and porcines, are diploid organisms possessing pairs of homologous chromosomes. Thus, at a typical genetic locus, an animal has three possible genotypes that can result from the combining of two different alleles (e.g. A and B). The animal may be homozygous for one or another allele, or heterozygous, possessing one of each of the two possible alleles (e.g. AA, BB or AB). 
         [0111]    The STAT6 SNP IDs statistically correlated with desirable carcass and feedlot phenotypes include SNP ID 14636, SNP ID 16084 and SNP ID 19597. 
         [0112]    STAT6 SNP ID 14636 is identified in  FIG. 1 . As shown in  FIG. 1 , SNP ID 14636 is positioned at nucleotide 14989 of the sequence depicted in  FIG. 1 , or at position 4189 of SEQ ID NO:1. SNP ID 14636 is also positioned at nucleotide 656 of intron 1 of the STAT6 sequence depicted in  FIG. 1 . A homozygous “CC” genotype at STAT6 SNP ID 14636 is statistically correlated with the carcass and feedlot phenotypes of increased back fat rate, fewer days on feed, and increased average daily gain. A homozygous “GG” genotype at STAT6 SNP ID 14636 is statistically correlated with the carcass and feedlot phenotypes of decreased back fat rate, greater number of days on feed, and decreased average daily gain. See, Table 4. 
         [0113]    STAT6 SNP ID 16084 is identified in  FIG. 1 . As shown in  FIG. 1 , SNP ID 16084 is positioned at nucleotide 16437 of the sequence depicted in  FIG. 1 , or at position 5637 of SEQ ID NO: 1. SNP ID 16084 is also positioned at nucleotide 2104 of intron 1 of the STAT6 sequence depicted in  FIG. 1 . A homozygous “AA” genotype at STAT6 SNP ID 16084 is statistically correlated with the carcass phenotypes of increased back fat, increased calculated yield grade and decreased cutability. A homozygous “CC” genotype at STAT6 SNP ID 16084 is statistically correlated with the carcass phenotypes of decreased back fat, decreased calculated yield grade and increased cutability. See, Table 4. 
         [0114]    STAT6 SNP ID 19597 is identified in  FIG. 1 . As shown in  FIG. 1 , SNP ID 19597 is positioned at nucleotide 19950 of the sequence depicted in  FIG. 1 , or at position 9150 of SEQ ID NO: 1. SNP ID 19597 is also positioned at nucleotide 20 of intron 8 of the STAT6 sequence depicted in  FIG. 1 . A homozygous “AA” genotype at STAT6 SNP ID 19597 is statistically correlated with the carcass and feedlot phenotypes of increased hot carcass weight, increased dry matter intake and fewer days on feed. A homozygous “GG” genotype at STAT6 SNP ID 19597 is statistically correlated with the carcass and feedlot phenotypes of decreased hot carcass weight, decreased dry matter intake and greater number of days on feed. See, Table 4. 
         [0115]    d. Carcass Traits 
         [0116]    Carcass traits statistically correlated with the STAT6 SNPs identified in the present inventions include back fat thickness (BFAT), calculated yield grade (CALYG), cutability (CUT) and hot carcass weight (HCW). 
         [0117]    Back Fat Thickness (BFAT). Back fat thickness is expressed in tenths of an inch of the fat thickness at the 12th rib (as measured between the 12th and 13th ribs) of an animal&#39;s carcass. This is the amount of fat covering the ribeye. 
         [0118]    Hot Carcass Weight (HCW). Hot carcass weight is the weight expressed in pounds of an animal after slaughter. Hot carcass weight is obtained immediately after dressing (i. e., the viscera and hide are removed) and prior to carcass chilling. 
         [0119]    Calculated Yield Grade (CALYG) refers to a calculated value that includes back fat thickness (BFAT), ribeye area (REA), hot carcass weight (HCW), and kidney, pelvic, and heart fat percentage (KPH). This value is calculated using any of several known equations. Below are provided the calculated yield grade equations used by the USDA and by Iowa State University. 
         [0000]      Cal  YG= 2.46+2.49 ( B FAT )−0.13 ( REA )+0.0002 ( HCW )+0.115 ( KPH ) (Reference: 2000 Beef Research Report—Iowa State University—A. S. Leaflet R1730). 
         [0000]      Cal  YG= 2.5+2.5 ( B FAT)−0.32 ( REA )+0.0038 ( HCW )+0.2 ( KPH ) (USDA yield equation) 
         [0120]    Yield grades are used to identify carcasses that differ in yield of boneless, closely trimmed retail cuts from the round, loin, rib, and chuck. Yield grades range from 1 through 5. A yield grade 5 carcass would have the lowest cutability and would be characterized as light muscled and/or excessively fat. Accordingly, a lower calculated yield grade value is more desirable and a higher yield grade value is less desirable. 
         [0121]    Because current yield grades are too broad to clearly define value differences in retail yield, yield grades 2 and 3 have been divided into 2A and 2B and 3A and 3B respectively. Yield grades 2.0 to 2.5 are classified 2A and 2.5 to 3.0 are classified 2B. Similarly, yield grades 3.0 to 3.5 are classified 3A and 3.5 to 4.0 are classified 3B. Combining quality grade with yield grade more clearly defines carcass value than when quality grade alone is used. See, e.g., the worldwide web at caf.wvu.edu/˜forage/yieldgrd/yieldgrades.htm. 
         [0122]    Carcass traits considered in a calculated yield grade equation, are described, for example, on the worldwide web at ianrpubs.unl.edu/epublic/pages/publicationD.jsp?publicationId=19. 
         [0123]    As discussed above, external back fat thickness is measured in tenths of an inch and is the amount of fat covering the ribeye at the point of the 12th and 13th ribs. 
         [0124]    Hot carcass weight and REA work together as an indication of overall muscling of the animal. A heavy carcass is expected to have more total muscle than a lighter weight carcass. If a carcass does not have as much muscling as you would expect from an average carcass of that weight, it makes the yield grade less desirable. If a carcass has more muscling than average for that weight, it improves the yield grade. 
         [0125]    Percentage of KPH measures the amount of internal fat. All animals have some fat surrounding their internal organs such as the liver or heart. The less of this fat a carcass has, the better for the yield grade. The amount of KPH is expressed as a percentage of carcass weight. For example, an 800 pound carcass with 2.5% KPH has 20 pounds of internal fat.
       External adjusted fat thickness (more fat=less desirable yield grade)   Hot carcass weight (heavier weight=less desirable yield grade)   Percentage of kidney, pelvic and heart fat (more fat=less desirable yield grade)   Ribeye area (larger ribeye=more desirable yield grade)       
 
         [0130]    Cutability. The percent yield of the carcass is also called the cutability of the carcass. The cutability of the carcass is calculated from the following formula: 
         [0000]      % retail cuts=51.34−(5.78×Adj. Fat thickness)−(0.0088×hot carcass weight)−(0.462 ×KPH )+(0.740×ribeye area) 
         [0131]    Beef yield grades provide an estimate of how much lean, edible meat the carcass will produce. Yield grades are 1, 2, 3, 4 and 5, with 1 being a lean, heavy muscled carcass that will yield a high percentage of lean meat, and 5 being an overly fat, light muscled carcass. If all the bones and fat are removed from the major portions of the carcass (the rounds, loins, ribs and chucks), roughly 53-55% of a Yield Grade 1 carcass will become saleable, retail meat. From a Yield Grade 1, 800 pound carcass, you would expect approximately 430 lbs of meat. From an 800 pound, Yield Grade 5 carcass, you could expect a 43-45% yield, or about 350 lbs of meat. See, e.g., the worldwide web at ianrpubs.unl.edu/epublic/pages/publicationD.jsp?publicationId=19. 
         [0132]    e. Feedlot Traits 
         [0133]    Feedlot traits statistically correlated with the STAT6 SNPs identified in the present inventions include dry matter intake (DMI), days on feed (DOF), average daily gain, and back fat rate (BFAT RATE). These are arbitrary measurements from the time animals arrive in the feedlot until they are slaughtered. The measurements are used to recharge owners that subcontract feeding their animals in the feedlot, and or to calculate the economic efficiency of feeding different lots of animals. 
         [0134]    Days on feed (DOF) is measured in days fed in the feedlot from the time the animals enter the feedlot until they are slaughtered approximately when they have 0.4-0.5 in back fat or close to a Choice grade. 
         [0135]    Average daily gain (ADG) is the average daily weight gain of the animal in pounds in the feedlot measured from the time of arrival to the feedlot until the animal is slaughtered. 
         [0136]    Dry matter intake (DMI) is the amount of feed consumed in dry matter basis (pounds) by an animal in the feedlot measured from the time of arrival to the feedlot until the animal is slaughtered. 
         [0137]    Back Fat Rate (BFATRATE) is the rate of back fat accumulation on an animal measured on a daily basis. Back fat can be measured on the animal using any method known in the art, including for example, ultrasound techniques. 
         [0138]    f. Detection of SNPs 
         [0139]    The STAT6 SNPs can be detected using any methods known in art, including without limitation amplification, sequencing and hybridization techniques. Detection techniques for evaluating nucleic acids for the presence of a single base change involve procedures well known in the field of molecular genetics. Methods for amplifying nucleic acids find use in carrying out the present methods. Ample guidance for performing the methods is provided in the art. Exemplary references include manuals such as PCR Technology: PRINCIPLES AND APPLICATIONS FOR DNA AMPLIFICATION (ed. H. A. Erlich, Freeman Press, NY, N.Y., 1992); PCR PROTOCOLS: A GUIDE TO METHODS AND APPLICATIONS (eds. Innis, et al., Academic Press, San Diego, Calif., 1990); CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, Ausubel, 1990-2008, including supplemental updates; Sambrook &amp; Russell, Molecular Cloning, A Laboratory Manual (3rd Ed, 2001). 
         [0140]    According to one aspect of the present invention, there is provided a method for distinguishing livestock animals e.g., bovines having a STAT6 gene polymorphism. The method comprises the steps of first isolating a genomic DNA sample from a livestock animal, e.g., bovine, and then detecting, e.g., amplifying a region of the STAT6 gene using an oligonucleotide pair to form nucleic acid amplification products of STAT6 gene polymorphism sequences. Amplification can be by any of a number of methods known to those skilled in the art including PCR, and the invention is intended to encompass any suitable methods of DNA amplification. A number of DNA amplification techniques are suitable for use with the present invention. Conveniently such amplification techniques include methods such as polymerase chain reaction (PCR), strand displacement amplification (SDA), nucleic acid sequence based amplification (NASBA), rolling circle amplification, T7 polymerase mediated amplification, T3 polymerase mediated amplification and SP6 polymerase mediated amplification. The precise method of DNA amplification is not intended to be limiting, and other methods not listed here will be apparent to those skilled in the art and their use is within the scope of the invention. 
         [0141]    In some embodiments, the polymerase chain reaction (PCR) process is used (see, e.g., U.S. Pat. Nos. 4,683,195 and 4,683,202. PCR involves the use of a thermostable DNA polymerase, known sequences as primers, and heating cycles, which separate the replicating deoxyribonucleic acid (DNA), strands and exponentially amplify a gene of interest. Any type of PCR, including quantitative PCR, RT-PCR, hot start PCR, LA-PCR, multiplex PCR, touchdown PCR, finds use. In some embodiments, real-time PCR is used. 
         [0142]    The amplification products are then analyzed in order to detect the presence or absence of at least one polymorphism in the STAT6 gene that is associated with the desired phenotypes, as discussed herein. By practicing the methods of the present invention and analyzing the amplification products it is possible to determine the genotype of individual animals with respect to the polymorphism. 
         [0143]    In some embodiments, analysis may be made by restriction fragment length polymorphism (RFLP) analysis of a PCR amplicon produced by amplification of genomic DNA with the oligonucleotide pair. In order to simplify detection of the amplification products and the restriction fragments, those of skill will appreciate that the amplified DNA will further comprise labeled moieties to permit detection of relatively small amounts of product. A variety of moieties are well known to those skilled in the art and include such labeling tags as fluorescent, bioluminescent, chemiluminescent, and radioactive or colorigenic moieties. 
         [0144]    A variety of methods of detecting the presence and restriction digestion properties of STAT6 gene amplification products are also suitable for use with the present invention. These can include methods such as gel electrophoresis, mass spectroscopy or the like. The present invention is also adapted to the use of single stranded DNA detection techniques such as fluorescence resonance energy transfer (FRET). For FRET analysis, hybridization anchor and detection probes may be used to hybridize to the amplification products. The probes sequences are selected such that in the presence of the SNP, for example, the resulting hybridization complex is more stable than if there is a G or C residue at a particular nucleotide position. By adjusting the hybridization conditions, it is therefore possible to distinguish between animals with the SNP and those without. A variety of parameters well known to those skilled in the art can be used to affect the ability of a hybridization complex to form. These include changes in temperature, ionic concentration, or the inclusion of chemical constituents like formamide that decrease complex stability. It is further possible to distinguish animals heterozygous for the SNP versus those that are homozygous for the same. The method of FRET analysis is well known to the art, and the conditions under which the presence or absence of the SNP would be detected by FRET are readily determinable. 
         [0145]    Suitable sequence methods of detection also include e.g., dideoxy sequencing-based methods and Maxam and Gilbert sequence (see, e.g., Sambrook and Russell, supra). Suitable HPLC-based analyses include, e.g., denaturing HPLC (dHPLC) as described in e.g., Premstaller and Oefner, LC-GC Europe 1-9 (July 2002); Bennet et al., BMC Genetics 2:17 (2001); Schrimi et al., Biotechniques 28(4):740 (2000); and Nairz et al., PNAS USA 99(16):10575-10580 (2002); and ion-pair reversed phase HPLC-electrospray ionization mass spectrometry (ICEMS) as described in e.g., Oberacher et al.; Hum. Mutat. 21(1):86 (2003). Other methods for characterizing single base changes in STAT6 alleles include, e.g., single base extensions (see, e.g., Kobayashi et al, Mol. Cell. Probes, 9:175-182, 1995); single-strand conformation polymorphism analysis, as described, e.g, in Orita et al., Proc. Nat. Acad. Sci. 86, 2766-2770 (1989), allele specific oligonucleotide hybridization (ASO) (e.g., Stoneking et al., Am. J. Hum. Genet. 48:70-382, 1991; Saiki et al., Nature 324, 163-166, 1986; EP 235,726; and WO 89/11548); and sequence-specific amplification or primer extension methods as described in, for example, WO 93/22456; U.S. Pat. Nos. 5,137,806; 5,595,890; 5,639,611; and U.S. Pat. No. 4,851,331; 5′-nuclease assays, as described in U.S. Pat. Nos. 5,210,015; 5,487,972; and 5,804,375; and Holland et al., 1988, Proc. Natl. Acad. Sci. USA 88:7276-7280. 
         [0146]    Methods for detecting single base changes well known in the art often entail one of several general protocols: hybridization using sequence-specific oligonucleotides, primer extension, sequence-specific ligation, sequencing, or electrophoretic separation techniques, e.g., singled-stranded conformational polymorphism (SSCP) and heteroduplex analysis. Exemplary assays include 5′ nuclease assays, template-directed dye-terminator incorporation, molecular beacon allele-specific oligonucleotide assays, single-base extension assays, and SNP scoring by real-time pyrophosphate sequences. Analysis of amplified sequences can be performed using various technologies such as microchips, fluorescence polarization assays, and matrix-assisted laser desorption ionization (MALDI) mass spectrometry. In addition to these frequently used methodologies for analysis of nucleic acid samples to detect single base changes, any method known in the art can be used to detect the presence of the STAT6 SNPs described herein. 
         [0147]    For example FRET analysis can be used as a method of detection. Conveniently, hybridization probes comprising an anchor and detection probe, the design of which art is well known to those skilled in the art of FRET analysis, are labeled with a detectable moiety, and then under suitable conditions are hybridized a STAT6 amplification product containing the site of interest in order to form a hybridization complex. A variety of parameters well known to those skilled in the art can be used to affect the ability of a hybridization complex to form. These include changes in temperature, ionic concentration, or the inclusion of chemical constituents like formamide that decrease complex stability. The presence or absence of the STAT6 SNP is then determined by the stability of the hybridization complex. The parameters affecting hybridization and FRET analysis are well known to those skilled in the art. The amplification products and hybridization probes described herein are suitable for use with FRET analysis. 
         [0148]    In one embodiment, the detected polymorphism or allele or position of the bovine STAT6 gene is at SNP ID 14636, and the oligonucleotide pair comprises a forward primer comprising a nucleic acid sequence selected from 5′-GCTGGTCACTCTTCCTAATC-3′ (SEQ ID NO: 11) and 5′-TCTGACTTAGGGATCACCTC-3′ (SEQ ID NO: 12); and a reverse primer comprising a nucleic acid sequence selected from 5′-GACCTCTATCTCTACCCTAC-3′ (SEQ ID NO:13); 5′-ACCTCTATCTCTACCCTACG-3′ (SEQ ID NO:14) and 5′-CTCTACCCTACGGGGAC-3′ (SEQ ID NO:15). 
         [0149]    In one embodiment, the detected polymorphism or allele or position of the bovine STAT6 gene is at SNP ID 16084, and the oligonucleotide pair comprises a forward primer comprising a nucleic acid sequence selected from 5′-TTTCCCTACTGCCCCATTGC-3′ (SEQ ID NO: 16); 5′-TCAGAGAGCTTTCCCTACTG-3′ (SEQ ID NO: 17); and 5′-CCTGTCTCTTACCCTCT-3′ (SEQ ID NO:18); and a reverse primer comprising the nucleic acid sequence 5′-TAATGGAGTGGGAAGAGCTG-3′ (SEQ ID NO: 19). 
         [0150]    In one embodiment, the detected polymorphism or allele or position of the bovine STAT6 gene is at SNP ID 19597, and the oligonucleotide pair comprises a forward primer comprising a nucleic acid sequence selected from 5′-CACACTCGTCACCAGGTATG-3′ (SEQ ID NO:20) and 5′-GAGCCCCCCTGCCTG-3′ (SEQ ID NO:21); and a reverse primer comprising a nucleic acid sequence selected from 5′-AACTCTGACCCTCCTGTTTC-3′ (SEQ ID NO:22) and 5′-GGGGTCTGCTCTCCA-3′ (SEQ ID NO:23). 
         [0151]    g. Selecting Livestock Animals with Desirable Traits 
         [0152]    The present invention provides a method of selecting individual livestock animals based on the knowledge of an animal&#39;s STAT6 genotype. With respect to the SNPs described in the present invention, livestock animals with alleles at SNP IDs 14636, 16084, 19597 correlated with desirable carcass and feedlot traits can be selected. 
         [0153]    For example, a “CC” homozygous genotype at SNP ID 16084 is correlated with the carcass phenotypes of decreased back fat, increased cutability and decreased calculated yield grade. An “AA” homozygous genotype at SNP ID 16084 is correlated with the carcass phenotypes of increased back fat, decreased cutability and increased calculated yield grade. 
         [0154]    Similarly, an “AA” homozygous genotype at SNP ID 19597 is correlated with the carcass and feedlot phenotypes of an increased hot carcass weight, increased dry matter intake and fewer days on feed. A “GG” homozygous genotype at SNP ID 19597 is correlated with the carcass and feedlot phenotypes of a decreased hot carcass weight, decreased dry matter intake and greater number of days on feed. 
         [0155]    A “CC” homozygous genotype at SNP ID 14636 is correlated with the carcass and feedlot phenotypes of an increased back fat rate, increased average daily gain and fewer days on feed. A “GG” homozygous genotype at SNP ID 14636 is correlated with the carcass and feedlot phenotypes of a decreased back fat rate, decreased average daily gain and greater number of days on feed. See, Table 4. 
         [0156]    According to the methods of the present invention, a livestock animal can be selected based on its STAT6 genotype at SNP IDs 16084, 19597 and 14636. With the knowledge of the animal&#39;s STAT6 genotype one can then identify and sort animals into groups of like phenotype(s), or otherwise use the knowledge of the genotype in order to predict which animals will have the desired phenotypes, for example, decreased back fat, increased cutability, decreased calculated yield grade, increased hot carcass weight, increased dry matter intake, fewer days on feed, increased or decreased back fat rate, and increased average daily gain. Knowledge of the animal&#39;s STAT6 genotype allows a breeder to encourage breeding between animals with a desired STAT6 genotype, and to discourage breeding between animals with an undesirable STAT6 genotype. 
         [0157]    Selecting or sorting can be taken to mean placing animals in physical groupings such as pens, so that animals of like genotype are kept separate from animals of a different genotype. This would be a useful practice in the case of breeding programs where it would be desirable to produce animals of particular genotypes. For example, it may be desirable to establish herds that are homozygous “CC” at SNP ID 16084, homozygous “AA” at SNP ID 19597 and homozygous “CC” at SNP ID 14636 within the STAT6 gene, such that breeding among these animals would only produce animals with a desired STAT6 genotype. On the other hand, it may also be desirable to decrease production of animals with an undesired STAT6 genotype. Separating out animals with the desired STAT6 genotype(s) would prevent animals with an undesired STAT6 genotype from breeding with animals possessing a desired STAT6 genotype, facilitating the reproduction of animals with an increased tendency to display the desired phenotypes associated with the STAT6 alleles. Furthermore, ensuring that at least one animal in a breeding pair possesses desired STAT6 alleles allows for the frequency of the desired STAT6 alleles to be increased in the next, and subsequent generations. For example, a favorable breed of  Bos  may not have a desired STAT6 genotype, but the desired STAT6 genotype could be bred into the genepool of the favorable breed of  Bos.    
         [0158]    Sorting may also be of a “virtual” nature, such that an animal&#39;s genotype is recorded either in a notebook or computer database. In this case, animals could then be selected based on their known genotype without the need for physical separation. This would allow one to select for animals of desired phenotype where physical separation is not required. 
         [0000]    3. Distinguishing  Bos taurus  from  Bos indicus  by Determining STAT6 SNPs 
         [0159]    In a related aspect, the invention provides a method for distinguishing bovines, in particular  Bos taurus  from  Bos indicus , based on STAT6 gene polymorphisms that are fixed in each species. The method comprises the steps of first isolating a genomic DNA sample from the bovine, and then detecting, e.g., amplifying a region of the STAT6 gene using an oligonucleotide pair to form nucleic acid amplification products of STAT6 gene polymorphism sequences. A biological sample comprising genomic DNA is taken from the bovine to be tested, as described above. The methods used to detect the STAT6 polymorphism can be any means of SNP detection known in the art, as discussed above, including without limitation, amplification, sequencing and hybridization techniques. Amplification can be by any of a number of methods known to those skilled in the art, as discussed above. Upon determining the species of the bovine based on genotypic analysis, the bovine is selected or rejected, either physically or virtually, as described above. 
         [0160]    a. STAT6 SNPs Useful to Distinguish  Bos taurus  from  Bos indicus    
         [0161]    STAT6 SNP ID 10922 is identified in  FIG. 1 . As shown in  FIG. 1 , SNP ID 10922 is positioned at nucleotide 10922 of the sequence depicted in  FIG. 1 , or at position 122 of SEQ ID NO: 1. SNP ID 10922 is also positioned at nucleotide 122 within the 5′-UTR of the STAT6 sequence depicted in  FIG. 1 . A homozygous “AA” genotype at STAT6 SNP ID 10922 indicates that the bovine is  Bos taurus . A homozygous “GG” genotype at STAT6 SNP ID 10922 indicates that the bovine is  Bos indicus . See, Table 3. 
         [0162]    STAT6 SNP ID 14257 is identified in  FIG. 1 . As shown in  FIG. 1 , SNP ID 14257 is positioned at nucleotide 14257 of the sequence depicted in  FIG. 1 , or at position 3457of SEQ ID NO: 1. SNP ID 14257 is also positioned at nucleotide 24 of intron 1 of the STAT6 sequence depicted in  FIG. 1 . A homozygous “CC” genotype at STAT6 SNP ID 14257 indicates that the bovine is  Bos taurus . A homozygous “AA” genotype at STAT6 SNP ID 14257 indicates that the bovine is  Bos indicus . See, Table 3. 
         [0163]    STAT6 SNP ID 24000 is identified in  FIG. 1 . As shown in  FIG. 1 , SNP ID 24000 is positioned at nucleotide 24353 of the sequence depicted in  FIG. 1 , or at position 13553 of SEQ ID NO: 1. SNP ID 24000 is also positioned at nucleotide 164 of intron 16 of the STAT6 sequence depicted in  FIG. 1 . A homozygous “TT” genotype at STAT6 SNP ID 24000 indicates that the bovine is  Bos taurus . A homozygous “CC” genotype at STAT6 SNP ID 24000 indicates that the bovine is  Bos indicus . See, Table 3. 
         [0164]    STAT6 SNP ID 25999 is identified in  FIG. 1 . As shown in  FIG. 1 , SNP ID 25999 is positioned at nucleotide 26352 of the sequence depicted in  FIG. 1 , or at position 15552 of SEQ ID NO: 1. SNP ID 25999 is also positioned at nucleotide 176 of intron 20 of the STAT6 sequence depicted in  FIG. 1 . A homozygous “TT” genotype at STAT6 SNP ID 25999 indicates that the bovine is  Bos taurus . A homozygous “CC” genotype at STAT6 SNP ID 25999 indicates that the bovine is  Bos indicus . See, Table 3. 
         [0165]    In one embodiment, the detected polymorphism or allele or position of the bovine STAT6 gene is at SNP ID 10922, and the oligonucleotide pair comprises a forward primer comprising a nucleic acid sequence selected from 5′-TGTGATGGGTTGAACTCTGC-3′ (SEQ ID NO:24) and 5′-CTGCCTCTCAAAAATTTATATATTA-3′ (SEQ ID NO:25); and a reverse primer comprising a nucleic acid sequence selected from 5′-GGGTACCTCCTATGAATATG-3′ (SEQ ID NO:26) and 5′-GGGATATGTGATTTCAACATA-3′ (SEQ ID NO:27). 
         [0166]    In one embodiment, the detected polymorphism or allele or position of the bovine STAT6 gene is at SNP ID 14257, and the oligonucleotide pair comprises a forward primer comprising a nucleic acid sequence selected from 5′-GGGCCTCTGACTACCAATGT-3′ (SEQ ID NO:9); 5′-TTTTTCCACACACCCCATCC-3′ (SEQ ID NO:28); and 5′-GGGACGTGTTAAGGC-3′ (SEQ ID NO:29); and a reverse primer comprising a nucleic acid sequence selected from 5′-CCACACCCTTGAAGAGGAAC-3′ (SEQ ID NO:10); 5′-ACTTCCCCCCAACCCAGAG-3′ (SEQ ID NO:30) and 5′-TTGCCCTCCTTCCCC-3′ (SEQ ID NO:3 1). In some embodiments, the polymorphism or allele or position of the bovine STAT6 gene is at SNP ID 14257, and the oligonucleotide pair comprises forward primer 5′-GGGCCTCTGACTACCAATGT-3′ (SEQ ID NO:9) and reverse primer 5′-CCACACCCTTGAAGAGGAAC-3′ (SEQ ID NO:10). 
         [0167]    In one embodiment, the detected polymorphism or allele or position of the bovine STAT6 gene is at SNP ID 24000, and the oligonucleotide pair comprises a forward primer comprising a nucleic acid sequence selected from 5′-TCATTTCCCTGCTTCTGGAC-3′ (SEQ ID NO:32) and 5′-CCATCATCCATGCTCACCTTTTC-3′ (SEQ ID NO:33); and a reverse primer comprising a nucleic acid sequence selected from 5′-ATGGAATGCTTCCGGGTTAG-3′ (SEQ ID NO:34) and 5′-AGGGAGGAAGGGAGCT-3′ (SEQ ID NO:35). 
         [0168]    In one embodiment, the detected polymorphism or allele or position of the bovine STAT6 gene is at SNP ID 25999, and the oligonucleotide pair comprises a forward primer comprising a nucleic acid sequence selected from 5′-CCTCAGGATCATGCTGTGTC-3′ (SEQ ID NO:36) and 5′-CCCTTGCTCTGCTCAGA-3′ (SEQ ID NO:37); and a reverse primer comprising a nucleic acid sequence selected from 5′-TGGTTCAGGCAGCTGTCTTC-3′ (SEQ ID NO:38) and 5′-TTCTGCCATGGTCAC-3′ (SEQ ID NO:39). 
         [0169]    In some embodiments, the amplicon produced can be further subjected to restriction endonuclease digestion. 
       4. Kits for Genotypic Analysis of STAT6 Polymorphisms 
       [0170]    The invention further provides diagnostic kits useful for determining the STAT6 genotypes of livestock animals, e.g., bovines. In general, each of the kits comprises one or more oligonucleotide primer pairs as described herein suitable to amplify the portions of the gene comprising the SNPs of the present invention, i.e., SNP IDs 10922, 14257, 14636, 16084, 19597, 24000 and 25999. The kits comprise forward and reverse primers suitable for amplification of a genomic DNA sample taken from an animal. As described above, the biological sample can be from any tissue or fluid in which genomic DNA is present. Conveniently, the sample may be taken from blood, skin or a hair bulb. 
       EXAMPLES 
       [0171]    The following examples are offered to illustrate, but not to limit the claimed invention. 
       Example 1  
     Cattle Breed DNA Resource for SNP Discovery 
       [0172]    The cattle breed DNA resource consists of approximately 6 animals of each of 12 cattle breeds (5 Black Angus, 6 Red Angus, 3 Horned Hereford, 3 Polled Hereford, 4 Charolais, 5 Simmental, 4 Limousine, Chianina, 6 Brahman, Santa Gertrudis, 3 Wagyu). The animals of each breed were selected to be unrelated at least 3 generations back. An effort was made to have the presence of diverse lines or types within each breed. At least 5 straws of semen were obtained from each animal. The semen came from 3 sources: purchased by Merial from semen Al companies, from Charles Farber (University of California at Davis) and from Milton Thomas (New Mexico State). Tables 1 and 2 show the details of the individual samples, source and number of semen straws. High quality DNA was extracted from one semen straw from each animal and four straws kept frozen for future use. DNA was extracted using PureGene DNA extraction kit, quantified on a UV spectrophotometer and tested for integrity on an agarose gel. The DNA panel was used as a SNP discovery resource by resequencing of the STAT6 gene as described below. 
         [0000]    
       
         
               
             
               
               
               
               
               
             
               
               
               
               
               
             
           
               
                 TABLE 1 
               
             
             
               
                   
               
               
                 DNA resource samples 
               
             
          
           
               
                 No. 
                 Source 
                 Breed 
                 Short Name 
                 Straws 
               
               
                   
               
             
          
           
               
                 1 
                 Select Sires 
                 Black Angus 
                 Predestined 
                 2 
               
               
                 2 
                 ABS Global 
                 Black Angus 
                 TRIPLE THREAT 
                 4 
               
               
                 3 
                 ABS Global 
                 Black Angus 
                 EASY FORTUNE 
                 3 
               
               
                 4 
                 ABS Global 
                 Black Angus 
                 CENTER CUT 
                 4 
               
               
                 5 
                 Charles Farber 
                 Black Angus 
                 P S Franco 064 157 
                 1 
               
               
                 6 
                 Milton Thomas 
                 Black Angus 
                 NMSU 302 
                 DNA 
               
               
                 7 
                 Select Sires 
                 Red Angus 
                 Field Day 
                 2 
               
               
                 8 
                 Select Sires 
                 Red Angus 
                 Vigor 
                 2 
               
               
                 9 
                 Select Sires 
                 Red Angus 
                 Ho Ho 
                 2 
               
               
                 10 
                 Select Sires 
                 Red Angus 
                 Heavenly 
                 2 
               
               
                 11 
                 Select Sires 
                 Red Angus 
                 Duke 
                 2 
               
               
                 12 
                 Select Sires 
                 Red Angus 
                 Rambler 
                 2 
               
               
                 13 
                 Select Sires 
                 Hereford Polled 
                 Formula 
                 2 
               
               
                 14 
                 ABS Global 
                 Hereford Polled 
                 JEDI 
                 4 
               
               
                 15 
                 ABS Global 
                 Hereford Polled 
                 MASTER DUTY 
                 4 
               
               
                 16 
                 ABS Global 
                 Horned 
                 HR ROBIN HOOD 
                 4 
               
               
                   
                   
                 Hereford 
               
               
                 17 
                 ABS Global 
                 Horned 
                 Star Donald 
                 4 
               
               
                   
                   
                 Hereford 
               
               
                 18 
                 Charles Farber 
                 Horned 
                 CL 1 Domino 0144K 
                 1 
               
               
                   
                   
                 Hereford 
                 1ET 
               
               
                 19 
                 Charles Farber 
                 Horned 
                 HH Advance 249B 
                 2 
               
               
                   
                   
                 Hereford 
               
               
                 20 
                 Select Sires 
                 Charolais 
                 Choice Plus 
                 2 
               
               
                   
                   
                 Creme 
               
               
                 21 
                 Select Sires 
                 Charolais 
                 Sir Prime Time 
                 2 
               
               
                   
                   
                 Creme 
               
               
                 22 
                 ABS Global 
                 Charolais 
                 SILVER EDGE 
                 4 
               
               
                   
                   
                 Polled 
               
               
                 23 
                 ABS Global 
                 Charolais 
                 SENTINAL RULER 
                 4 
               
               
                   
                   
                 scurred 
               
               
                 24 
                 Select Sires 
                 Simmental Red 
                 Autobahn 
                 2 
               
               
                 25 
                 Bovine Elite 
                 Simmental Red 
                 ER Americana 537B 
                 4 
               
               
                 26 
                 Bovine Elite 
                 Simmental Red 
                 NLC Good A Nuff 33G 
                 4 
               
               
                 27 
                 ABS Global 
                 Simmental 
                 FUTURE 
                 4 
               
               
                   
                   
                 Traditional 
                 MODERATOR 
               
               
                 28 
                 Universalsemensales 
                 Simmental 
                 BEL DUTCH 89X 
                 4 
               
               
                   
                   
                 Traditional 
               
               
                 29 
                 Bovine Elite 
                 Simmental 
                 Bar 5 Bernheim 405H 
                 4 
               
               
                   
                   
                 Traditional 
               
               
                 30 
                 ABS Global 
                 Gelbvieh Red 
                 TOP BRASS 
                 4 
               
               
                 31 
                 ABS Global 
                 Gelbvieh Red 
                 TABASCO 
                 4 
               
               
                 32 
                 ABS Global 
                 Gelbvieh Red 
                 SIR ARNOLD 
                 4 
               
               
                 33 
                 ABS Global 
                 Gelbvieh Red 
                 MODERATOR 
                 4 
               
               
                 34 
                 Select Sires 
                 Limousin Black 
                 Equity 
                 2 
               
               
                 35 
                 ABS Global 
                 Limousin Red 
                 POLLED 
                 4 
               
               
                   
                   
                   
                 MANHATTAN 
               
               
                 36 
                 ABS Global 
                 Limousin Red 
                 JUSTICE 
                 4 
               
               
                 37 
                 Bovine Elite 
                 Limousin Red 
                 EXLR Latigo 029M 
                 4 
               
               
                 38 
                 Universalsemensales 
                 Wagyu “A” 
                 BR Fukutsuru 0620 
                 4 
               
               
                 39 
                 Universalsemensales 
                 Wagyu “B” 
                 BR Takazakura 0604 
                 4 
               
               
                 40 
                 Universalsemensales 
                 Wagyu “C” 
                 BR Hirashigotayasu 
                 4 
               
               
                   
                   
                   
                 9645 
               
               
                 41 
                 Select Sires 
                 Brangus 
                 Carrarra 
                 2 
               
               
                 42 
                 Milton Thomas 
                 Brangus 
                 NMSU 830 
                 DNA 
               
               
                 43 
                 Milton Thomas 
                 Brangus 
                 NMSU 628 
                 DNA 
               
               
                 44 
                 Milton Thomas 
                 Brangus 
                 CCR INTEGRITY 
                 DNA 
               
               
                   
                   
                   
                 F386F2 
               
               
                 45 
                 Milton Thomas 
                 Brangus 
                 John Wayne 44L 
                 DNA 
               
               
                 46 
                 Milton Thomas 
                 Brangus 
                 NIMITZ OF BRINKS 
                 DNA 
               
               
                   
                   
                   
                 75L12 
               
               
                 47 
                 Milton Thomas 
                 Brangus 
                 Mr 304 (Lucky) 118 
                 DNA 
               
               
                 48 
                 Milton Thomas 
                 Brahman 
                 6X Sunland 874 
                 DNA 
               
               
                 49 
                 Milton Thomas 
                 Brahman 
                 SRW MR. FLYING W 
                 DNA 
               
               
                   
                   
                   
                 831 
               
               
                 50 
                 Milton Thomas 
                 Brahman 
                 JDH MR. SALLUTO 
                 DNA 
               
               
                   
                   
                   
                 MANSO 300/2 
               
               
                 51 
                 Select Sires 
                 Brahman 
                 852/5 
                 2 
               
               
                 52 
                 Select Sires 
                 Brahman 
                 Rojo Bueno 
                 2 
               
               
                 53 
                 Bovine Elite 
                 Brahman 
                 BB Mr Sting-Ray 10/0 
                 4 
               
               
                 54 
                 Bovine Elite 
                 Shorthorn 
                 ALM Tequila 
                 2 
               
               
                 55 
                 Bovine Elite 
                 Shorthorn 
                 SBR Storm Chaser 
                 4 
               
               
                 56 
                 Bovine Elite 
                 Shorthorn 
                 BG Spanky TPII 
                 4 
               
               
                 57 
                 Bovine Elite 
                 Romagnola 
                 Danure Hublo 
                 3 
               
               
                 58 
                 Universalsemensales 
                 Salers 
                 TV Big Red 
                 4 
               
               
                 59 
                 Bovine Elite 
                 Santa Gertrudis 
                 Gambler II 817 
                 4 
               
               
                 60 
                 Bovine Elite 
                 Senepol 
                 HBC 7115 48K 
                 4 
               
               
                 61 
                 Select Sires 
                 Beefmaster 
                 P.D.Q. 
                 2 
               
               
                   
               
             
          
         
       
     
         [0000]    
       
         
               
             
               
               
               
               
             
           
               
                 TABLE 2 
               
             
             
               
                   
               
               
                 DNA Repository (Samples Sequenced for STAT6) 
               
             
          
           
               
                 ID 
                 Source 
                 Breed 
                 Short Name 
               
               
                   
               
               
                 BA1 
                 Select Sires 
                 Black Angus 
                 Predestined 
               
               
                 BA2 
                 ABS Global 
                 Black Angus 
                 TRIPLE THREAT 
               
               
                 BA3 
                 ABS Global 
                 Black Angus 
                 EASY FORTUNE 
               
               
                 BA4 
                 ABS Global 
                 Black Angus 
                 CENTER CUT 
               
               
                 BA5 
                 Charles Farber 
                 Black Angus 
                 P S Franco 064 157 
               
               
                 RA1 
                 Select Sires 
                 Red Angus 
                 Field Day 
               
               
                 RA2 
                 Select Sires 
                 Red Angus 
                 Vigor 
               
               
                 RA3 
                 Select Sires 
                 Red Angus 
                 Ho Ho 
               
               
                 RA4 
                 Select Sires 
                 Red Angus 
                 Heavenly 
               
               
                 RA5 
                 Select Sires 
                 Red Angus 
                 Duke 
               
               
                 RA6 
                 Select Sires 
                 Red Angus 
                 Rambler 
               
               
                 HP1 
                 Select Sires 
                 Hereford Polled 
                 Formula 
               
               
                 HP2 
                 ABS Global 
                 Hereford Polled 
                 JEDI 
               
               
                 HP3 
                 ABS Global 
                 Hereford Polled 
                 MASTER DUTY 
               
               
                 HH1 
                 ABS Global 
                 Horned Hereford 
                 HR ROBIN HOOD 
               
               
                 HH3 
                 Charles Farber 
                 Horned Hereford 
                 CL 1 Domino 0144K 
               
               
                   
                   
                   
                 1ET 
               
               
                 HH4 
                 Charles Farber 
                 Horned Hereford 
                 HH Advance 249B 
               
               
                 SR1 
                 Select Sires 
                 Simmental Red 
                 Autobahn 
               
               
                 SR2 
                 Bovine Elite 
                 Simmental Red 
                 ER Americana 537B 
               
               
                 SR3 
                 Bovine Elite 
                 Simmental Red 
                 NLC Good A Nuff 33G 
               
               
                 ST1 
                 ABS Global 
                 Simmental 
                 FUTURE 
               
               
                   
                   
                 Traditional 
                 MODERATOR 
               
               
                 ST2 
                 Universalsemensales 
                 Simmental 
                 BEL DUTCH 89X 
               
               
                   
                   
                 Traditional 
               
               
                 ST3 
                 Bovine Elite 
                 Simmental 
                 Bar 5 Bernheim 405H 
               
               
                   
                   
                 Traditional 
               
               
                 CC1 
                 Select Sires 
                 Charolais Creme 
                 Choice Plus 
               
               
                 CC2 
                 Select Sires 
                 Charolais Creme 
                 Sir Prime Time 
               
               
                 CP1 
                 ABS Global 
                 Charolais Polled 
                 SILVER EDGE 
               
               
                 CS1 
                 ABS Global 
                 Charolais scurred 
                 SENTINAL RULER 
               
               
                 GR1 
                 ABS Global 
                 Gelbvieh Red 
                 TOP BRASS 
               
               
                 GR2 
                 ABS Global 
                 Gelbvieh Red 
                 TABASCO 
               
               
                 GR3 
                 ABS Global 
                 Gelbvieh Red 
                 SIR ARNOLD 
               
               
                 GR4 
                 ABS Global 
                 Gelbvieh Red 
                 MODERATOR 
               
               
                 LB1 
                 Select Sires 
                 Limousin Black 
                 Equity 
               
               
                 LR1 
                 ABS Global 
                 Limousin Red 
                 POLLED 
               
               
                   
                   
                   
                 MANHATTAN 
               
               
                 LR2 
                 ABS Global 
                 Limousin Red 
                 JUSTICE 
               
               
                 LR3 
                 Bovine Elite 
                 Limousin Red 
                 EXLR Latigo 029M 
               
               
                 WG1 
                 Universalsemensales 
                 Wagyu “A” 
                 BR Fukutsuru 0620 
               
               
                 WG2 
                 Universalsemensales 
                 Wagyu “B” 
                 BR Takazakura 0604 
               
               
                 WG3 
                 Universalsemensales 
                 Wagyu “C” 
                 BR Hirashigotayasu 9645 
               
               
                 BR1 
                 Select Sires 
                 Brangus 
                 Carrarra 
               
               
                 BR2 
                 Milton Thomas 
                 Brangus 
                 NMSU 830 
               
               
                 BR3 
                 Milton Thomas 
                 Brangus 
                 CCR INTEGRITY 
               
               
                   
                   
                   
                 F386F2 
               
               
                 BR4 
                 Milton Thomas 
                 Brangus 
                 John Wayne 44L 
               
               
                 BH1 
                 Select Sires 
                 Brahman 
                 852/5 
               
               
                 BH2 
                 Select Sires 
                 Brahman 
                 Rojo Bueno 
               
               
                 BH3 
                 Bovine Elite 
                 Brahman 
                 BB Mr Sting-Ray 10/0 
               
               
                 BH4 
                 Milton Thomas 
                 Brahman 
                 6X Sunland 874 
               
               
                 BH5 
                 Milton Thomas 
                 Brahman 
                 SRW MR. FLYING W 
               
               
                   
                   
                   
                 831 
               
               
                 BH6 
                 Milton Thomas 
                 Brahman 
                 JDH MR. SALLUTO 
               
               
                   
                   
                   
                 MANSO 300/2 
               
               
                   
               
             
          
         
       
     
       Example 2  
     SNP Discovery Platform Using Resequencing Strategy 
       [0173]    A strategy for SNP discovery was developed for this project. SNPs were identified by resequencing candidate genes in panels of 48 animals (9 breeds) from the discovery panel. See, Table 2. A genomic reference sequence was assembled from GenBank sequences (genomic, mRNA and ESTs) and from Ensembl bovine genome sequences. The sequence was annotated to identify exons, introns, 2000 bp of the promoter and 1000 bp of the 3′ untranslated region. Repetitive and low-complexity sequences were masked with RepeatMasker to prevent sequencing repetitive regions of the genes. 
         [0174]    The sequencing project was outsourced to SeqWright (Houston, Tex.). SeqWright provided a full service of automated sequencing with a brief annotation and SNP discovery. Sequence traces were downloaded from SeqWright and resembled at UCDavis using software CodonCode Aligner to notate and discover SNPs. 
         [0175]    The genotype of the sequenced animals for each gene were analyzed using haploview software (on the worldwide web at broad.mit.edu/mpg/haploview/) to define haplotypes and to choose a minimal information subset of Tag SNPs for genotyping. In addition, computational algorithms were used, for example, SIFT and PolyPhen, to predict the impact of nucleotide or amino-acid substitutions on protein structure and function. These algorithms were useful to flag unique mutations of interest. 
       Example 3  
     Identify SNPs in STAT6  
       [0176]    Using a bioinformatics-based method to identify sequence homologies between bovine microsatellites (Farber and Medrano 2003, Animal Genetics 34, 11-18), and gene sequencing it was demonstrated that microsatellite ETH10 is located within the first exon of the bovine STAT6 gene. ETH10 has been strongly associated in earlier work with marbling in Wagyu cattle (Barendse, Australia), with a suggestion of RDH5 as being the causative gene. 
         [0177]    It was proposed that the association between ETH10 and marbling is either due to the repeat itself or polymorphisms with the STAT6 gene, which alter its function. Earlier, 3 SNPs between different breeds of dairy cattle were identified. 39 SNPs across the complete gene have been identified overall, in the 48 animals breed panel.  FIG. 1  shows an annotated sequence of the bovine STAT6 gene and the position of Tag SNPs statistically correlated with economically important traits in beef cattle. Table 3 shows flanking sequences of individual SNPs. 
         [0178]    After defining haplotypes and regions of linkage disequilibrium in the STAT6 genes of the selected animals, identified 15 Tag SNPs were identified. Tag SNPs are a minimal information subset of SNPs that capture all the variation of a gene in defined populations. Three of the SNPs, 14636, 16084 and 19597, are statistically correlated with economically important carcass and feedlot traits in beef cattle. See, Table 4. Four of the SNPs, 10922, 14257, 24000 and 25999, are fixed in  Bos taurus  and in  Bos indicus  and therefore find use in genotypically distinguishing these two species. 
         [0179]    The association analysis was performed using the Golden Helix Regression Analysis Module from Helixtree software. The Golden Helix Regression Module was used to test allelic associations with phenotypic variables. The Regression Module supports both linear and logistic regression. A stepwise regression was used to find confounding phenotypic variables, regressors were fixed, and then a search for significantly associated SNPs was performed. This regression approach is particularly powerful for overcoming the difficult challenges of population stratification. Permutation testing increased the flexibility of the analysis. Table 4 shows the significant results for the association analysis. 
         [0000]    
       
         
               
             
               
               
               
             
               
               
               
               
             
           
               
                 TABLE 3 
               
             
             
               
                   
               
               
                 Sequences Flanking SNPs in STAT6 Gene 
               
             
          
           
               
                 PolyID 
                 Species 
                 Context 
               
               
                   
               
             
          
           
               
                 14636 
                 
                   Bos taurus 
                 
                 GGGTGGGAGTGGGGGAAAGTCTGGCCC 
                   
               
               
                 SEQ ID NO:2 
                   
                 CTCGCTGTCGGAGGATGGAGTAGGGGA 
               
               
                   
                   
                 GATTTGAAGGCAGGGCCATGCCAGGAA 
               
               
                   
                   
                 GCTGGTCACTCTTCCTAATCTAGGGGA 
               
               
                   
                   
                 TATGGAGGAAAGGGGAGCTGCCTCTGA 
               
               
                   
                   
                 CTTAGGGATCACCTC [C/G] GTCCCCG 
               
               
                   
                   
                 TAGGGTAGAGATAGAGGTCAAAGGTCT 
               
               
                   
                   
                 GAGCACCCTGAGAAACAGGAGAGAAAG 
               
               
                   
                   
                 AGGGAAGAGAGGAATGGAGTCCTCCCT 
               
               
                   
                   
                 TGAGTTTGAAACACAAACCAAAAGGTG 
               
               
                   
                   
                 CCCCACCCCAAGGTGGGTGTAGAGAAA 
               
               
                   
                   
                 GGTCTAT 
               
               
                   
               
               
                 16084 
                 
                   Bos taurus 
                 
                 ATTGGCAGCATGGAGTCTTAGCCACTG 
               
               
                 SEQ ID NO:3 
                   
                 GATCACCAGAGAAGTTCCGAGGGGAGG 
               
               
                   
                   
                 TTTCCTGCCAACAGAATCAGAGCTACA 
               
               
                   
                   
                 ACCCACATTCTCTGCCTTCTCTCAGAG 
               
               
                   
                   
                 AGCTTTCCCTACTGCCCCATTGCCCCT 
               
               
                   
                   
                 GTCTCTTACCCTCT [C/A] CCCTCCCC 
               
               
                   
                   
                 CAACTGGCTGCAGCTCAGCTCTTCCCA 
               
               
                   
                   
                 CTCCATTACCCCCATGCCTACTGTTGA 
               
               
                   
                   
                 AGAAAATACCTTGTTTCAGGCTTTGGC 
               
               
                   
                   
                 CAAAGAGGTTCCTGGTTTGATATAGTC 
               
               
                   
                   
                 TGRCTGAGAGTTGTGGTGCTGATGGTC 
               
               
                   
                   
                 TCTGAAA 
               
               
                   
               
               
                 19597 
                 
                   Bos taurus 
                 
                 TGTGAGAGCCTGGTGGACATTTATTCC 
               
               
                 SEQ ID NO:4 
                   
                 CAGCTGCAGCAGGAGGTGGGGGCAGCT 
               
               
                   
                   
                 GGTGGGGAGCTTGATCCCAAGACCCGG 
               
               
                   
                   
                 GCAGCGCTGATTAGCCGACTGGATGAA 
               
               
                   
                   
                 GTCCTGCGCACACTCGTCACCAGGTAT 
               
               
                   
                   
                 GAGCCCCCCTGCCTG [G/A] TGGAGAG 
               
               
                   
                   
                 CAGACCCCAAGGAAACAGGAGGGTCAG 
               
               
                   
                   
                 AGTTGTGGTGGGGGGAGGGGCAGTGGC 
               
               
                   
                   
                 GCCCAGAGGGACCCAGCTGTTCACTTC 
               
               
                   
                   
                 CCTGTGTCTTCCTTACTCCTCCCAGCT 
               
               
                   
                   
                 CTTTCCTGGTGGAAAAGCAGCCCCCCC 
               
               
                   
                   
                 AGGTTCTG 
               
               
                   
               
               
                 10922 
                   Bos taurus / 
                 AAGTGAAACAAATTTCATTAGACACTA 
               
               
                 SEQ ID NO:5 
                 
                   indicus 
                 
                 CTTATCCTTACTTTGTGTCATGCATTC 
               
               
                   
                   
                 TGGTATTTTTTATTGTATTCTACTTTG 
               
               
                   
                   
                 TTTTTAAATACTGGTGGTCAAGGCTCA 
               
               
                   
                   
                 CTGTGATGGGTTGAACTCTGCCTCTCA 
               
               
                   
                   
                 AAAATTTATATATTA [A/G] TATGTTG 
               
               
                   
                   
                 AAATCACATATCCCTCAAAAATTCATA 
               
               
                   
                   
                 TTCATAGGAGGTACCCTCAGTCCCTCA 
               
               
                   
                   
                 GAATGTGACCTTATTCAGATATAGGGT 
               
               
                   
                   
                 CTTTACAGAGGAAATCTTTAGGGTGGG 
               
               
                   
                   
                 CCCTAATCCAATATGACTGATGTCTTT 
               
               
                   
                   
                 AGAAAAAG 
               
               
                   
               
               
                 14257 
                   Bos taurus / 
                 GCTGGTGGCTGGTGTTACTGAGTTTCG 
               
               
                 SEQ ID NO:6 
                 
                   indicus 
                 
                 GCAGTTTCGAAATATCAGAGGAATCTG 
               
               
                   
                   
                 GAGTGGGTACAGGCCCAGCACTTGCCC 
               
               
                   
                   
                 CGCTCCTCCCCAACATGGGTCACTTTT 
               
               
                   
                   
                 TCCACACACCCCATCCCCCGCAATCCA 
               
               
                   
                   
                 GGGACGTGTTAAGGC [C/A] GGGGAAG 
               
               
                   
                   
                 GAGGGCAAGGAGGTGCCCCTCTGCCCT 
               
               
                   
                   
                 CTGGGTTGGGGGGAAGTGGCCGCCCCT 
               
               
                   
                   
                 CCCTATAGAAAACTGATGGCAGGGGGC 
               
               
                   
                   
                 AGTGGATCCTCCACAGACCCCTATCCG 
               
               
                   
                   
                 GGCCCCCCACAAAGGTTCCTCTTCAAG 
               
               
                   
                   
                 GGTGTGGC 
               
               
                   
               
               
                 24000 
                   Bos taurus / 
                 CGGGGCTGGCAGCTCTGACTCCTTCTG 
               
               
                 SEQ ID NO:7 
                 
                   indicus 
                 
                 TGGTCCGCCTCCTCCCTGCTCCTGGTT 
               
               
                   
                   
                 GCCCCCACCCCACCTGCTGTGTGTCAT 
               
               
                   
                   
                 CCCTGACTTCTTCCTCCATTGTCATTT 
               
               
                   
                   
                 CCCTGCTTCTGGACCCTGCCCATCATC 
               
               
                   
                   
                 CATGCTCACCTTTTC [T/C] AGCTCCC 
               
               
                   
                   
                 TTCCTCCCTAACCCGGAAGCATTCCAT 
               
               
                   
                   
                 GGCTCTCCTTTCCTCCCCACAATAGCT 
               
               
                   
                   
                 GAGCAGATGGGTAAGGATGGCAGGGGT 
               
               
                   
                   
                 TATGTCCCAGCTACAATCAAGATGACT 
               
               
                   
                   
                 GTGGAAAGGTGAGTGTGCTGGTGTGGA 
               
               
                   
                   
                 TGGAGGGC 
               
               
                   
               
               
                 25999 
                   Bos taurus / 
                 TGAGCTCAAGCTCCTCATTCATYCCCR 
               
               
                 SEQ ID NO:8 
                 
                   indicus 
                 
                 GCCTCAACCCCACCCTGACCCCCCCCA 
               
               
                   
                   
                 CCACCTCATTTACTTCTCTGGGGCTGG 
               
               
                   
                   
                 CAGGGGCCTGCTGCCGTGCCCACCTCA 
               
               
                   
                   
                 GGATCATGCTGTGTCCAGCCCTGAGCC 
               
               
                   
                   
                 CTTGCTCTGCTCAGA [T/C] GTGACCA 
               
               
                   
                   
                 TGGCAGAAGACAGCTGCCTGAACCAGC 
               
               
                   
                   
                 CGGTGGGAGGGTTCCCTCAAGGCACCT 
               
               
                   
                   
                 GGTGAGTGTCAGCCTGGGGGTGGAGGC 
               
               
                   
                   
                 TGGGTGGGGGGTTGCGGTGTGGGTACC 
               
               
                   
                   
                 ATGCCTATCCCACTGCTTCTCCACTCC 
               
               
                   
                   
                 TCTCTGCA 
               
               
                   
               
             
          
         
       
     
         [0000]    
       
         
               
             
               
               
               
               
               
               
               
               
             
           
               
                 TABLE 4 
               
               
                   
               
               
                 EFFECT OF STAT6 GENOTYPES ON PERFORMANCE AND CARCASS TRAITS IN BEEF CATTLE 
               
               
                   
               
             
             
               
                   
               
             
          
           
               
                 STAT6 SNP 
                   
                   
                   
                   
                   
                   
                 Allele Subs. 
               
               
                 16084 
                 AA 
                 AC 
                 CC 
                 P-value b   
                 Additive Effect 
                 Dominace Effect 
                 Effect a   
               
               
                   
               
               
                 Back Fat 
                 0.59 ± 0.07 
                 0.51 ± 0.01 
                  0.47 ± 0.005 
                 0.00030 
                 0.12 ± 0.06 
                 −0.02 ± 0.04   
                 0.08 
               
               
                   
                   
                   
                   
                   
                 P = 0.0004 
                 P = 0.001 
                 P = 0.0002 
               
               
                 Calculated 
                 3.1 ± 0.2 
                 2.82 ± 0.05 
                 2.66 ± 0.02 
                 0.0031 
                 0.44 ± 0.1  
                 −0.06 ± 0.02   
                 0.32 
               
               
                 yield grade 
                   
                   
                   
                   
                 P = 0.011 
                 P = 0.013 
                 P = 0.0009 
               
               
                 Cutability 
                 49.5 ± 0.6  
                 50.1 ± 0.1  
                 50.46 ± 0.05  
                 0.0029 
                 −0.96 ± 0.3    
                 0.12 ± 0.1  
                 −0.76 
               
               
                   
                   
                   
                   
                   
                 P = 0.011 
                 P = 0.013 
                 P = 0.0087 
               
               
                   
               
               
                 STAT6 SNP 
                   
                   
                   
                   
                   
                   
                 Allele Subs. 
               
               
                 19597 
                 AA 
                 AG 
                 GG 
                 P-value b   
                 Additive Effect 
                 Dominace Effect 
                 Effect a   
               
               
                   
               
               
                 Hot carcass 
                 762 ± 4  
                 754 ± 3  
                 744 ± 4  
                 0.0019 
                 18 ± 4  
                 1 ± 4 
                 18.26 
               
               
                 weight 
                   
                   
                   
                   
                 P = 0.002 
                 P = 0.008 
                 P = 0.002 
               
               
                 Dry matter 
                 2945 ± 29  
                 2909 ± 19  
                 2825 ± 23  
                 0.0018 
                 120 ± 24  
                 24 ± 22 
                 120.45 
               
               
                 intake 
                   
                   
                   
                   
                 P = 0.00013 
                 P = 0.0016 
                 P = 0.001 
               
               
                 Days on feed 
                 138 ± 1  
                 141.5 ± 1    
                 144 ± 1  
                 0.00088 
                 −6 ± 1   
                 0.5 ± 1   
                 6.12 
               
               
                   
                   
                   
                   
                   
                 P = 0.0007 
                 P = 0.003 
                 P = 0.0007 
               
               
                   
               
               
                 STAT6 SNP 
                   
                   
                   
                   
                   
                   
                 Allele Subs. 
               
               
                 14636 
                 CC 
                 CG 
                 GG 
                 P-value b   
                 Additive Effect 
                 Dominace Effect 
                 Effect a   
               
               
                   
               
               
                 BFAT RATE 
                 0.0131 ± 0.0004 
                 0.0126 ± 0.0002 
                 0.0117 ± 0.0001 
                 2.34E−07 
                 0.0014 ± 0.0002 
                 0.0002 ± 0.0001 
                 0.0015 
               
               
                   
                   
                   
                   
                   
                 P = 0.0032 
                 P = 0.0076 
                 P = 1.6E−6 
               
               
                 Days on feed 
                 136 ± 1  
                 139.8 ± 1    
                 144 ± 1  
                 1.51E−05 
                 −8 ± 1   
                 −0.2 ± 1     
                 −8.2 
               
               
                   
                   
                   
                   
                   
                 P = 2.6E−5 
                 P = 0.0001 
                 P = 2.6E−5 
               
               
                 Average daily 
                 3.83 ± 0.02 
                 3.70 ± 0.03 
                 3.61 ± 0.02 
                 4.52E−05 
                 0.22 ± 0.02 
                 −0.02 ± 0.02   
                 0.19 
               
               
                 gain 
                   
                   
                   
                   
                 P = 0.002 
                 P = 0.01 
                 P = 0.0001 
               
               
                   
               
               
                   a Allele substitution effect estimated by regression of phenotype on genotype dummy variables. The effect represents the regression coefficient (equal to the absolute effect) of genotype. 
               
               
                   b P value from overall F-test. 
               
             
          
         
       
     
       Example 4  
     Detection of SNP ID 14257 Using PCR-RFLP Protocol 
       [0180]    This example shows a PCR/RFLP genotyping assay for STAT6 SNP ID 14257. Detecting polymorphisms at SNP ID 14257 differentiates between  Bos taurus  and  Bos indicus  species. 
         [0181]    The nucleotide at SNP ID 14257 of the bovine STAT6 gene is PCR amplified from bovine genomic DNA template using forward primer 5′-GGGCCTCTGACTACCAATGT-3′ (SEQ ID NO:9) and reverse primer 5′-CCACACCCTTGAAGAGGAAC-3′ (SEQ ID NO: 10). 
         [0182]    The PCR amplification conditions are as follows: 
         [0000]    
       
         
               
               
               
               
             
           
               
                   
                   
               
             
             
               
                   
                 dH 2 O 
                 17.3 
                 μl 
               
               
                   
                 10x PCR buffer 
                 2.5 
                 μl 
               
               
                   
                 50 mM MgCl 2   
                 1.5 
                 μl 
               
               
                   
                 10 mM dNTPs 
                 0.5 
                 μl 
               
               
                   
                 10 pmol/μl Primers 
                 1 
                 μl each 
               
               
                   
                 Taq polymerase 5U 
                 0.2 
                 μl 
               
               
                   
                 DNA 50 ng 
                 1 
                 μl 
               
               
                   
                 Total Volume 
                 25 
                 μl 
               
               
                   
                   
               
             
          
         
       
     
         [0183]    The PCR reaction is run for 35 cycles: 30 sec. at 94° C.; 30 sec. at 60° C.; and 30 sec. at 72° C. The amplified PCR amplicons (397 bp when uncut) are then subject to restriction endonuclease digestion with MspI. If the bovine is a  Bos taurus , then the restriction endonuclease digestion produces fragments of 36 bp, 114 bp and 247 bp. If the bovine is a  Bos indicus , then the restriction endonuclease digestion produces fragments of 361 bp and 36 bp. A representative result is shown in  FIG. 3 . 
         [0184]    It is understood that the examples and embodiments described herein are for illustrative purposes only and that various modifications or changes in light thereof will be suggested to persons skilled in the art and are to be included within the spirit and purview of this application and scope of the appended claims. All publications, patents, and patent applications cited herein are hereby incorporated by reference in their entirety for all purposes.