Compositions, methods, and systems for inferring bovine breed

Abstract

Provided herein are methods to discover and use single nucleotide polymorphisms (SNP) for identifying breed, or line and breed, or line composition of a bovine subject. The present invention further provides specific nucleic acid sequences, SNPs, and SNP patterns that can be used for identifying breed or breed combinations for Angus, Holstein, Limousin, Brahman, Hereford, Simmental, Gelbvieh, Charolais and Beefmaster breeds. These patterns can be utilized to manage animals in a feedlot to obtain optimum performance based on known characteristics of specific breeds and identify animals for breeding in selection programs. In another aspect, these patterns can be used to ensure labeling on breed specific branded products.

1 - 55 . (canceled) 
     
     
         56 . A method for providing labeling accuracy for breed identified meat products, comprising:
 inferring the breed of a bovine subject from a nucleic acid sample from the bovine subject by identifying a haplotype allele associated with a breed; and,   determining whether to brand the harvested meat product based on the inferred breed.   
     
     
         57 . The method  claim 56 , wherein the haplotype allele comprises a nucleotide occurrence of at least one single nucleotide polymorphism (SNP) listed in Table, 3A, Table 3B, or Table 5. 
     
     
         58 . The method  claim 56 , wherein the haplotype allele comprises a nucleotide occurrence of at least one single nucleotide polymorphism (SNP) corresponding to position 300 of at least any one of SEQ ID NOs: 1-4868 or SEQ ID NOs: 64887-64895. 
     
     
         59 . The method of  claim 56 , wherein the step of inferring a breed comprises identifying in the nucleic acid sample a nucleotide occurrence of at least one single nucleotide polymorphism (SNP) that is in linkage disequilibrium with at least one SNP corresponding to position 300 of at least any one of SEQ ID NOs: 1-4868 or SEQ ID Nos: 64887-64895. 
     
     
         60 . The method of  claim 56 , wherein the step of inferring a breed comprises identifying in the nucleic acid sample a nucleotide occurrence of at least one single nucleotide polymorphism (SNP) corresponding to position 300 of at least any one of SEQ ID NOs: 1-4868 or SEQ ID Nos: 64887-64895. 
     
     
         61 . The method of  claim 56 , wherein the step of inferring the breed comprises identifying a diploid pair of haplotype alleles, and inferring the breed using the diploid pair of haplotype alleles. 
     
     
         62 . The method of  claim 56 , wherein identifying a haplotype comprises identifying the occurrence of at least two single nucleotide polymorphisms (SNPs) in more than one gene, wherein the SNPs are associated with a breed. 
     
     
         63 . The method of  claim 56 , wherein the identified haplotype allele is associated with Angus, Holstein, Limousin, Brahman, Simmental, Hereford, Gelbvieh, or Charolais cattle. 
     
     
         64 . The method of  claim 56 , comprising branding harvested meat product from the bovine subject based on the inferred breed. 
     
     
         65 . A method of breeding a bovine, comprising:
 a. inferring the breed of a bovine subject from a nucleic acid sample from the bovine subject by identifying a haplotype allele associated with a breed; and,   b. determining whether to select the bovine subject for use in a breeding program, thereby breeding the bovine subject.   
     
     
         66 . The method  claim 65 , wherein the haplotype allele comprises a nucleotide occurrence of at least one single nucleotide polymorphism (SNP) listed in Table, 3A, Table 3B, or Table 5. 
     
     
         67 . The method  claim 65 , wherein the haplotype allele comprises a nucleotide occurrence of at least one single nucleotide polymorphism (SNP) corresponding to position 300 of at least any one of SEQ ID NOs: 1-4868 or SEQ ID NOs: 64887-64895. 
     
     
         68 . The method of  claim 65 , wherein the step of inferring a breed comprises identifying in the nucleic acid sample a nucleotide occurrence of at least one single nucleotide polymorphism (SNP) that is in linkage disequilibrium with at least one SNP corresponding to position 300 of at least any one of SEQ ID NOs: 1-4868 or SEQ ID Nos: 64887-64895. 
     
     
         69 . The method of  claim 65 , wherein the step of inferring a breed comprises identifying in the nucleic acid sample a nucleotide occurrence of at least one single nucleotide polymorphism (SNP) corresponding to position 300 of at least any one of SEQ ID NOs: 1-4868 or SEQ ID Nos:
 64887-64895.   
     
     
         70 . The method of  claim 65 , wherein the step of inferring the breed comprises identifying a diploid pair of haplotype alleles, and inferring the breed using the diploid pair of haplotype alleles. 
     
     
         71 . The method of  claim 65 , wherein identifying a haplotype comprises identifying the occurrence of at least two single nucleotide polymorphisms (SNPs) in more than one gene, wherein the SNPs are associated with a breed. 
     
     
         72 . The method of  claim 65 , wherein the identified haplotype allele is associated with Angus, Holstein, Limousin, Brahman, Simmental, Hereford, Gelbvieh, or Charolais cattle.