Bovine polymorphisms and methods of predicting bovine traits

Abstract

Methods of predicting the phenotype of a trait in a bovine subject are provided. The methods include obtaining information about polynucleotide sequences specifically regarding the identity of the nucleotides present at one or more identified single nucleotide polymorphisms and using this information to make predictions regarding the trait in the subject. Also provided are kits for and methods of determining the nucleotide present in a bovine subject at a position in which a single nucleotide polymorphism is correlated with a trait.

1 - 36 . (canceled) 
     
     
         37 . A method of determining a nucleotide in a bovine subject at a position in which a single nucleotide polymorphism is correlated with a predicted occurrence of a trait comprising: detecting a target polynucleotide in a bovine sample with at least one oligonucleotide capable of binding the target polynucleotide, wherein the target polynucleotide comprises a nucleotide at a position corresponding to a position of SEQ ID NO: 7 selected from the group consisting of positions 895, 1045, 1117, 1125, 1128, 1134, and 1204 of the HSP70 promoter or corresponding to a position of SEQ ID NO: 3 selected from the group consisting of positions 1851, 1902, 1917, 1926, 2033, 2087, and 2098 of the HSP70 polynucleotide sequence; determining the nucleotide at the single nucleotide polymorphism in the bovine subject; and correlating
 presence or absence of a cytosine at a position of the target polynucleotide corresponding to position 895 of SEQ ID NO: 7,   a guanine or adenine at a position of the target polynucleotide corresponding to position 1045 of SEQ ID NO: 7,   a guanine or adenine at a position of the target polynucleotide corresponding to position 1117 of SEQ ID NO: 7,   an adenine or cytosine at a position of the target polynucleotide corresponding to position 1125 of SEQ ID NO: 7,   a guanine or thymine at a position of the target polynucleotide corresponding to position 1128 of SEQ ID NO: 7,   a thymine or cytosine at a position of the target polynucleotide corresponding to position 1134 of SEQ ID NO: 7,   a thymine or cytosine at a position of the target polynucleotide corresponding to position 1204 of SEQ ID NO: 7,   a guanine or adenine at a position of the target polynucleotide corresponding to position 1851 of SEQ ID NO: 3,   a cytosine or thymine at a position of the target polynucleotide corresponding to position 1902 of SEQ ID NO: 3,   a guanine or thymine at a position of the target polynucleotide corresponding to position 1917 of SEQ ID NO: 3,   a cytosine or guanine at a position of the target polynucleotide corresponding to position 1926 of SEQ ID NO: 3,   a guanine or cytosine at a position of the target polynucleotide corresponding to position 2033 of SEQ ID NO: 3,   a cytosine or guanine at a position of the target polynucleotide corresponding to position 2087 of SEQ ID NO: 3, or   a thymine or adenine at a position of the target polynucleotide corresponding to position 2098 of SEQ ID NO: 3   to the predicted occurrence of the trait, the trait selected from the group consisting of breed lineage, calf birth weight, calf weaning weight, calf weaning height, date of calving, calving rate, body condition, prolactin concentration, hormone concentrations, nonesterified fatty acid concentrations, LDH concentration, milk butterfat concentration, milk protein concentration, and milk somatic cell count.   
     
     
         38 . The method of  claim 37 , wherein the nucleotide at the single nucleotide polymorphism position is detected by analyzing the binding of the oligonucleotide to the target polynucleotide. 
     
     
         39 . The method of  claim 37 , wherein the target polynucleotide is detected by amplification. 
     
     
         40 . The method of  claim 39 , wherein the nucleotide at the SNP is determined by nucleotide sequencing or restriction fragment length polymorphism analysis. 
     
     
         41 .- 44 . (canceled) 
     
     
         45 . A method of predicting the occurrence of a trait in a bovine subject, comprising: analyzing a sample from the bovine subject to identify a nucleotide of the bovine subject at a position of the HSP70 promoter or nucleotide sequence corresponding to a position selected from the group consisting of position 895 of SEQ ID NO: 7, position 1045 of SEQ ID NO:7, position 1117 of SEQ ID NO:7, position 1125 of SEQ ID NO:7, position 1128 of SEQ ID NO:7, position 1128 of SEQ ID NO:7, position 1134 of SEQ ID NO:7, position 1204 of SEQ ID NO:7, position 1851 of SEQ ID NO:3, position 1902 of SEQ ID NO:3, position 1917 of SEQ ID NO:3, position 1926 of SEQ ID NO:3, position 2033 of SEQ ID NO:3, position 2087 of SEQ ID NO:3, and position 2098 of SEQ ID NO:3; and correlating presence or absence of a cytosine at a position of the target polynucleotide corresponding to position 895 of SEQ ID NO: 7,
 a guanine or adenine at a position of the target polynucleotide corresponding to position 1045 of SEQ ID NO: 7,   a guanine or adenine at a position of the target polynucleotide corresponding to position 1117 of SEQ ID NO: 7,   an adenine or cytosine at a position of the target polynucleotide corresponding to position 1125 of SEQ ID NO: 7,   a guanine or thymine at a position of the target polynucleotide corresponding to position 1128 of SEQ ID NO: 7,   a thymine or cytosine at a position of the target polynucleotide corresponding to position 1134 of SEQ ID NO: 7,   a thymine or cytosine at a position of the target polynucleotide corresponding to position 1204 of SEQ ID NO: 7,   a guanine or adenine at a position of the target polynucleotide corresponding to position 1851 of SEQ ID NO: 3,   a cytosine or thymine at a position of the target polynucleotide corresponding to position 1902 of SEQ ID NO: 3,   a guanine or thymine at a position of the target polynucleotide corresponding to position 1917 of SEQ ID NO: 3,   a cytosine or guanine at a position of the target polynucleotide corresponding to position 1926 of SEQ ID NO: 3,   a guanine or cytosine at a position of the target polynucleotide corresponding to position 2033 of SEQ ID NO: 3,   a cytosine or guanine at a position of the target polynucleotide corresponding to position 2087 of SEQ ID NO: 3, or   a thymine or adenine at a position of the target polynucleotide corresponding to position 2098 of SEQ ID NO: 3   to predict the occurrence of the trait in the bovine subject, the trait selected from the group consisting of breed lineage, calf birth weight, calf weaning weight, calf weaning height, date of calving, calving rate, pregnancy rate, body condition, prolactin concentration, hormone concentrations, nonesterified fatty acid concentrations, LDH concentration, milk butterfat concentration, milk protein concentration, and milk somatic cell count.   
     
     
         46 . The method of  claim 45 , wherein a cytosine at the position of the target polynucleotide corresponding to position 895 of SEQ ID NO: 7 correlates to the bovine subject having a trait selected from later calving date or decreased calving rate. 
     
     
         47 . The method of  claim 45 , wherein an adenine at the position of the target polynucleotide corresponding to position 1045 of SEQ ID NO: 7 or position 1117 of SEQ ID NO: 7 correlates to the bovine subject having a trait selected from higher hormone concentrations in subjects with low body condition, higher prolactin concentrations, higher nonesterified fatty acid concentrations in subjects with low body condition and increased calving rate as compared to bovine subjects with a guanine at the same positions. 
     
     
         48 . The method of  claim 45 , wherein an adenine at the position of the target polynucleotide corresponding to position 1125 of SEQ ID NO: 7 or a guanine at the position of the target polynucleotide corresponding to position 1128 of SEQ ID NO: 7 correlates to the bovine subject having a trait selected from later calving date, higher calving rate, higher pregnancy rate as compared to bovine subjects with a cytosine at position 1125 of SEQ ID NO:7 or a thymine at position 1128 of SEQ ID NO:7. 
     
     
         49 . The method of  claim 45 , wherein a cytosine at the position of the target polynucleotide corresponding to position 1134 of SEQ ID NO: 7 correlates to the bovine subject having a trait selected from higher hormone concentrations in subjects with low body condition, higher prolactin concentrations, higher nonesterified fatty acid concentrations in subjects with low body condition and increased calving rate as compared to bovine subjects with a thymine at the same position. 
     
     
         50 . The method of  claim 45 , wherein a cytosine at the position of the target polynucleotide corresponding to position 1204 of SEQ ID NO: 7 correlates to the bovine subject having a trait selected from higher nonesterified fatty acid concentrations and increased LDH levels in subjects having low body condition as compared to bovine subjects with a thymine at the same position. 
     
     
         51 . The method of  claim 45 , wherein an adenine at the position of the target polynucleotide corresponding to position 1851 of SEQ ID NO: 3 correlates to the bovine subject having Angus ancestry as compared to bovine subjects with a guanine at the same position. 
     
     
         52 . The method of  claim 45 , wherein a thymine at the position of the target polynucleotide corresponding to position 1902 of SEQ ID NO: 3, a thymine at the position of the target polynucleotide corresponding to position 1917 of SEQ ID NO: 3, a guanine at the position of the target polynucleotide corresponding to position 1926 of SEQ ID NO: 3, or an adenine at the position of the target polynucleotide corresponding to position 2098 of SEQ ID NO: 3 correlates to the bovine subject having a trait selected from Brahman ancestry, increased calf birth weight, increased calf weight at weaning, increased calf height at weaning, increased milk protein concentration, and increased milk butterfat concentrations as compared to bovine subjects without the indicated base at the same position. 
     
     
         53 . The method of  claim 45 , wherein a cytosine at the position of the target polynucleotide corresponding to position 1902 of SEQ ID NO: 3, a guanine at the position of the target polynucleotide corresponding to position 1917 of SEQ ID NO: 3, a cytosine at the position of the target polynucleotide corresponding to position 1926 of SEQ ID NO: 3, or a thymine at the position of the target polynucleotide corresponding to position 2098 of SEQ ID NO: 3 correlates to the bovine subject having a trait selected from Angus ancestry, decreased calf birth weight, decreased calf weight at weaning, decreased calf height at weaning, decreased milk protein concentration, and decreased milk butterfat concentrations as compared to bovine subjects without the indicated base at the same position. 
     
     
         54 . The method of  claim 45 , wherein a guanine at the position of the target polynucleotide corresponding to position 2033 of SEQ ID NO: 3 correlates to the bovine subject having a trait selected from increased somatic cell counts in the milk and increased calf weaning weight when raised on tall fescue as compared to bovine subjects with a cytosine at the same position. 
     
     
         55 . The method of  claim 45 , wherein an adenine at the position of the target polynucleotide corresponding to position 2087 of SEQ ID NO: 3 correlates to the bovine subject having Brahman ancestry as compared to bovine subjects with a thymine at the same position.