Methods and systems for inferring bovine traits

Abstract

Methods, compositions, and systems are provided for managing bovine subjects in order to maximize their individual potential performance and edible meat value, and to maximize profits obtained in marketing the bovine subjects. The methods and systems draw an inference of a trait of a bovine subject by determining the nucleotide occurrence of at least one bovine SNP that is identified herein as being associated with the trait. The inference is used in methods of the present invention to establish the economic value of a bovine subject, to improve profits related to selling beef from a bovine subject; to manage bovine subjects, to sort bovine subjects; to improve the genetics of a bovine population by selecting and breeding of bovine subjects, to clone a bovine subject with a specific trait, to track meat or another commercial product of a bovine subject; and to diagnose a health condition of a bovine subject. Methods are also disclosed for identifying additional SNPs associated with a trait, by using the associated SNPs identified herein.

What is claimed is: 
     
         1 . A method for inferring a trait of a bovine subject from a nucleic acid sample of the bovine subject, comprising identifying in the nucleic acid sample, at least one nucleotide occurrence of at least one single nucleotide polymorphism (SNP) corresponding to position 300 of any one of SEQ ID NOS:19473 to 21982, wherein the SNP is associated with the trait, thereby inferring the trait. 
     
     
         2 . The method of  claim 1 , wherein the nucleotide occurrence of at least 2 of the SNPs is determined to infer the trait. 
     
     
         3 . The method of  claim 2 , wherein the nucleotide occurrences of the at least 2 SNPs comprise a haplotype allele, and wherein the method infers the trait using the identified haplotype allele. 
     
     
         4 . The method of  claim 2 , wherein the at least 2 SNPs are related by dominance and/or epistasis. 
     
     
         5 . The method of  claim 4 , further comprising identifying a diploid pair of haplotype alleles and inferring the trait using the diploid pair of haplotype alleles. 
     
     
         6 . The method of  claim 1 , wherein the trait is marbling, tenderness, quality grade, muscle content, fat thickness, feed efficiency, red meat yield, average daily weight gain, disease resistance, disease susceptibility, feed intake, protein content, bone content, maintenance energy requirement, mature size, amino acid profile, fatty acid profile, milk production, a milk quality susceptibility to the buller syndrome, stress susceptibility and response, temperament, digestive capacity, production of calpain, caplastatin and myostatin, pattern of fat deposition, ribeye area, fertility, ovulation rate, conception rate, fertility, or susceptibility to infection with and shedding of pathogens. 
     
     
         7 . The method of  claim 6 , wherein the trait is fat thickness, retail yield, tenderness, marbling, or average daily gain. 
     
     
         8 . The method of  claim 7 , wherein the trait is fat thickness. 
     
     
         9 . The method of  claim 8 , wherein the at least one SNP and the at least one nucleotide occurrence are selected from at least one of the SNPs and nucleotide occurrences indicated in Table 1A as associated with high fat thickness. 
     
     
         10 . The method of  claim 8 , wherein the at least one SNP and the at least one nucleotide occurrence are selected from at least one of the SNPs and nucleotide occurrences indicated in Table 1A as associated with low fat thickness. 
     
     
         11 . The method of  claim 7 , wherein the trait is retail yield. 
     
     
         12 . The method of  claim 11 , wherein the at least one SNP and the at least one nucleotide occurrence are selected from at least one of the SNPs and nucleotide occurrences indicated in Table 1A as associated with high retail yield. 
     
     
         13 . The method of  claim 11 , wherein the at least one SNP and the at least one nucleotide occurrence are selected from at least one of the SNPs and nucleotide occurrences indicated in Table 1A as associated with low retail yield. 
     
     
         14 . The method of  claim 7 , wherein the trait is tenderness. 
     
     
         15 . The method of  claim 14 , wherein the at least one SNP and the at least one nucleotide occurrence are selected from at least one of the SNPs and nucleotide occurrences indicated in Table 1A as associated with high tenderness. 
     
     
         16 . The method of  claim 14 , wherein the at least one SNP and the at least one nucleotide occurrence are selected from at least one of the SNPs and nucleotide occurrences indicated in Table 1A as associated with low tenderness. 
     
     
         17 . The method of  claim 7 , wherein the trait is marbling. 
     
     
         18 . The method of  claim 17 , wherein the at least one SNP and the at least one nucleotide occurrence are selected from at least one of the SNPs and nucleotide occurrences indicated in Table 1A as associated with more abundant marbling. 
     
     
         19 . The method of  claim 17 , wherein the at least one SNP and the at least one nucleotide occurrence are selected from at least one of the SNPs and nucleotide occurrences indicated in Table 1A as associated with less abundant marbling. 
     
     
         20 . The method of  claim 7 , wherein the trait is average daily gain. 
     
     
         21 . The method of  claim 20 , wherein the at least one SNP and the at least one nucleotide occurrence are selected from at least one of the SNPs and nucleotide occurrences indicated in Table 1A as associated with a high daily gain. 
     
     
         22 . The method of  claim 20 , wherein the at least one SNP and the at least one nucleotide occurrence are selected from at least one of the SNPs and nucleotide occurrences indicated in Table 1A as associated with low daily gain. 
     
     
         23 . A method for determining a nucleotide occurrence of a polymorphism in a bovine sample, comprising:
 a) contacting a bovine polynucleotide in the sample with an oligonucleotide that binds to a target region of any one of SEQ ID NOS:24493 to 64886, wherein the target region comprises a position corresponding to position 300 of any one of