Quantitative Trait Loci and Somatostatin

Abstract

The disclosure relates to the use of genetic traits in livestock for determining breeding characteristics of livestock progeny, and for optimizing the management and marketing of livestock for improving feedlot performance and meat quality. The disclosure specifically relates to genetic markers and single nucleotide polymorphisms (SNPs) in the bovine somatostatin locus, as well as haplotypes that include the somatostatin locus, which are associated with certain quantitative trait loci (QTLs), such as marbling, meat quality grade, and yield grade. In a preferred embodiment, the SNPs and haplotypes are predictive of the increased or decreased amount of tissue marbling in the animal.

1 . A method of predicting marbling in bovine, the method comprising identifying a haplotype that is predictive of marbling, wherein the haplotype comprises at least one single nucleotide polymorphism (SNP) at nucleotide position corresponding to nucleotide 244, at nucleotide position corresponding to nucleotide 575, or at both nucleotide positions corresponding to nucleotides 244 and 575 of a bovine somatostatin gene. 
     
     
         2 . The method of  claim 1 , wherein the haplotype further comprises at least one SNP selected from the group consisting of a SNP at nucleotide position corresponding to nucleotide 126, a SNP at nucleotide position corresponding to nucleotide 157, and a SNP at nucleotide position corresponding to nucleotide 981 of the somatostatin gene. 
     
     
         3 . The method of  claim 1 , wherein the haplotype comprises a T or C at nucleotide position corresponding to nucleotide 244 and a C at nucleotide position corresponding to nucleotide 575. 
     
     
         4 - 6 . (canceled) 
     
     
         7 . The method of  claim 1 , wherein the haplotype comprises a C at nucleotide position corresponding to nucleotide 244 and a T at nucleotide position corresponding to nucleotide 575. 
     
     
         8 . (canceled) 
     
     
         9 . The method of  claim 1 , wherein the bovine is Angus or Brahman. 
     
     
         10 . (canceled) 
     
     
         11 . A method of predicting a trait in bovine, the method comprising identifying a haplotype that is predictive of the trait, wherein:
 the haplotype comprises single nucleotide polymorphisms (SNPs) at nucleotide positions corresponding to nucleotides 244 and 575 of a bovine somatostatin gene; and   the trait is selected from the group consisting of yearling weight, actual fat thickness over the 10th and 11th rib, quality grade, connective tissue, flavor, and juiciness.   
     
     
         12 . The method of  claim 11 , wherein the haplotype further comprises at least one SNP selected from the group consisting of a SNP at nucleotide position corresponding to nucleotide 126, a SNP at nucleotide position corresponding to nucleotide 157, and a SNP at nucleotide position corresponding to nucleotide 981 of the somatostatin gene. 
     
     
         13 . The method of  claim 11 , wherein the haplotype comprises a T or C at nucleotide position corresponding to nucleotide 244 and a C at nucleotide position corresponding to nucleotide 575 of the somatostatin gene. 
     
     
         14 . (canceled) 
     
     
         15 . The method of  claim 11 , wherein the haplotype comprises a C at nucleotide position corresponding to nucleotide 244 and a T at nucleotide position corresponding to nucleotide 575 of the somatostatin gene. 
     
     
         16 . The method of  claim 11 , wherein the bovine is Angus or Brahman. 
     
     
         17 - 22 . (canceled) 
     
     
         23 . A method of predicting marbling in bovine, the method comprising:
 (a) obtaining a sample of nucleic acid from a bovine individual, wherein the sample comprises at least a portion of a bovine somatostatin gene;   (b) determining the identity of one or more single nucleotide polymorphisms (SNPs) located at nucleotide positions corresponding to nucleotides 126, 157, 244, 575, and 981 of the bovine somatostatin gene and;   (c) evaluating the identity of said one or more single nucleotide polymorphisms (SNPs) in order to predict marbling.   
     
     
         24 . The method of  claim 23 , wherein step (a) comprises amplifying at least a portion of the sample of nucleic acid. 
     
     
         25 . The method of  claim 23 , wherein step (b) comprises sequencing at least a portion of the sample of nucleic acid. 
     
     
         26 . The method of  claim 23 , wherein step (b) is performed through one or more methods selected from the group consisting of oligonucleotide ligation assay (OLA), doublecode OLA, mismatch hybridization, mass spectrometry, single base extensions assay, RFLP detection based on allele-specific restriction-endonuclease cleavage, hybridization with allele-specific oligonucleotide probes, hybridization with immobilized oligonucleotides, hybridization with oligonucleotide arrays, allele-specific PCR, mismatch repair detection (MRD), binding of MutS protein, single-strand-conformation-polymorphism detection, RNAse cleavage at mismatched base-pairs, chemical cleavage of heteroduplex DNA, enzymatic cleavage of heteroduplex DNA, allele specific primer extension, genetic bit analysis (GBA), radioactive DNA sequencing, fluorescent DNA sequencing and both radioactive and fluorescent DNA sequencing. 
     
     
         27 . A method of predicting marbling in an animal, the method comprising identifying a haplotype that is predictive of marbling, wherein the haplotype comprises an allele of a somatostatin gene associated with increased or decreased marbling in the animal. 
     
     
         28 . A method for selecting breeding bovines to produce offspring that exhibit increased marbling, the method comprising:
 (a) selecting a first parent bovine that has a haplotype predictive of increased marbling, wherein the haplotype comprises single nucleotide polymorphisms (SNPs) at nucleotide positions corresponding to nucleotides 244 and 575 of a bovine somatostatin gene; and   (b) mating the first parent bovine with a second parent bovine to produce offspring,   wherein the offspring demonstrating increased marbling compared to a bovine lacking predictive haplotype is selected.   
     
     
         29 . The method of  claim 28 , wherein the first parent bovine and the second parent bovine both have a haplotype predictive of marbling. 
     
     
         30 . The method of  claim 28 , wherein the haplotype further comprises at least one single nucleotide polymorphism (SNP) selected from the group of a SNP at nucleotide position corresponding to nucleotide 126, a SNP at nucleotide position corresponding to nucleotide 157, and a SNP at nucleotide position corresponding to nucleotide 981 of the somatostatin gene. 
     
     
         31 - 43 . (canceled) 
     
     
         44 . A method of predicting kidney, pelvic and heart fat percentage (KPH) in bovine, the method comprising identifying a haplotype that is predictive of KPH, wherein the haplotype comprises a single nucleotide polymorphism (SNP) at nucleotide position corresponding to nucleotide 981 or near nucleotide 981 of a bovine somatostatin gene that encodes amino acid lysine.