Method and Markers for Determining the Genotype of Horned/Polled Cattle

Abstract

Provided herein are methods to discover and use single nucleotide polymorphisms (SNP) for determining the genotype of a horned/polled ruminant subject. The present invention further provides specific nucleic acid sequences, SNPs, and SNP patterns that can be used for determining the genotype of a horned/polled ruminant subject.

1 . A method for identifying the polled phenotype in a bovine subject, comprising detecting a dominant polled haplotype allele in a nucleic acid sample from the subject selected from: 
       
         
           
                 
                 
               
                     
                   GCTCAC, 
                 
                     
                     
                 
                     
                   GCTCGC, 
                 
                     
                     
                 
                     
                   GATGGG, 
                 
                     
                     
                 
                     
                   AATGGG, 
                 
                     
                     
                 
                     
                   AATGGC, 
                 
                     
                     
                 
                     
                   AATCAC, 
                 
                     
                     
                 
                     
                   AATCGG, 
                 
                     
                   and 
                 
                     
                     
                 
                     
                   AATCGC 
                 
             
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
               
            
           
         
         wherein the sequence of letters of the haplotype allele represent the nucleotide occurrence of a single nucleotide polymorphism corresponding to nucleotide position 300 of SEQ ID NOs: 53 (marker MMBT25287), 59 (marker MMBT25303), 52 (marker MMBT25281), 63 (marker MMBT25316), 62 (marker MMBT25314), and 61 (marker MMBT25313) respectively. 
       
     
     
         2 . The method of  claim 1 , comprising detecting a diploid pair of haplotype alleles. 
     
     
         3 . The method of  claim 1 , wherein the bovine subject is a member of a breed selected from Angus, Charolais, Gelbvieh, Hereford, Limousin, or Simmental. 
     
     
         4 . The method of  claim 1 , wherein the bovine subject is a member of a breed raised for beef production. 
     
     
         5 . The method of  claim 4 , wherein the bovine subject is a member of a breed raised for beef and milk production. 
     
     
         6 . A method for identifying the horned phenotype in a bovine subject, comprising:
 detecting a pair of recessive horned haplotype alleles in a nucleic acid sample from the subject, wherein each haplotype allele is independently selected from:   
       
         
           
                 
                 
               
                     
                   GCGCGC, 
                 
                     
                     
                 
                     
                   GAGCGG, 
                 
                     
                     
                 
                     
                   GAGCGC, 
                 
                     
                     
                 
                     
                   GATGGC, 
                 
                     
                     
                 
                     
                   GATCAC, 
                 
                     
                   and 
                 
                     
                     
                 
                     
                   GATCGC 
                 
             
                
                
                
                
                
                
                
                
                
                
                
                
               
            
           
         
       
       wherein the sequence of letters of the haplotype allele represent the nucleotide occurrence of a single nucleotide polymorphism corresponding to nucleotide position 300 of SEQ ID NOs: 53 (marker MMBT25287), 59 (marker MMBT25303), 52 (marker MMBT25281), 63 (marker MMBT25316), 62 (marker MMBT25314), and 61 (marker MMBT25313) respectively. 
     
     
         7 . The method of  claim 6 , wherein the bovine subject is a member of a breed selected from Charolais, Gelbvieh, Hereford, Limousin, or Simmental. 
     
     
         8 . The method of  claim 6 , wherein the bovine subject is a member of a breed raised for beef production. 
     
     
         9 . The method of  claim 8 , wherein the bovine subject is a member of a breed raised for beef and milk production. 
     
     
         10 . A method for identifying the polled phenotype in a bovine subject:
 a. detecting a GATCGG haplotype allele in a nucleic acid sample from the subject, wherein the sequence of letters of the haplotype allele represent the nucleotide occurrence of a single nucleotide polymorphism corresponding to nucleotide position 300 of SEQ ID NOs: 53 (marker MMBT25287), 59 (marker MMBT25303), 52 (marker MMBT25281), 63 (marker MMBT25316), 62 (marker MMBT25314), and 61 (marker MMBT25313) respectively; and   b. detecting the GATCGG haplotype in a nucleic acid sample from at least one polled parent of the subject.   
     
     
         11 . The method of  claim 10 , wherein the bovine subject is a dairy animal. 
     
     
         12 . The method of  claim 10 , where the bovine subject is a member of a breed selected from Limousin, Jersey, or Holstein. 
     
     
         13 . The method of  claim 1 ,  6 , or  10 , wherein the nucleic acid sample is isolated from a tissue or bodily fluid. 
     
     
         14 . The method of  claim 1 , 6 , or  10 , wherein the nucleic acid sample comprises DNA. 
     
     
         15 . The method of  claim 14 , wherein the DNA is genomic DNA. 
     
     
         16 . A method for identifying a haplotype allele associated with a horned phenotype in a bovine subject comprising
 a. determining a haplotype in at least one allele of at least one horned bovine subject, wherein the haplotype allele comprises the nucleotide occurrence of a nucleotide polymorphism corresponding to nucleotide position 300 of each of SEQ ID NOs: 53, 59, 52, 63, 62, and 61,   b. thereby, identifying a haplotype allele associated the horned phenotype in a bovine subject.   
     
     
         17 . The method of  claim 16 , wherein the haplotype of both alleles is detected. 
     
     
         18 . The method of  claim 17 , wherein the haplotypes of each allele of the bovine subject is different, and thereby two haplotype alleles associated with the horned phenotype are detected 
     
     
         19 . A method for identifying a haplotype allele associated with a polled phenotype in a bovine subject comprising:
 a. detecting the nucleotide occurrence of single nucleotide polymorphisms corresponding to nucleotide position 300 of each of SEQ ID NOs: 53, 59, 52, 63, 62, and 61, in both first and second alleles of a first bovine subject, wherein the first subject displays the polled phenotype;   b. identifying the horned or polled phenotype of a second bovine subject, wherein the second subject is homozygous for the first haplotype allele identified in step a., wherein a polled phenotype of the second subject identifies the first haplotype allele as a haplotype allele associated with the polled phenotype, and wherein a horned phenotype of the second subject identifies the second haplotype allele as a haplotype allele associated with the polled phenotype,   thereby, identifying a haplotype allele associated the polled phenotype in a bovine subject.   
     
     
         20 . The method of  claim 19 , wherein the first and second alleles of the first bovine subject are the same.