Compositions and methods for determining likelihood of twinning

Abstract

Collections of polynucleotides useful for estimating breeding value or detecting likelihood of twinning are disclosed. The polynucleotides are used to detect genomic sequences quantitatively associated with the twinning trait. Also disclosed are methods and kits for using the collections to estimate breeding value or predict likelihood of twinning.

1 . A collection of one or more polynucleotides, each of which is at least partially complementary to a sequence in a bovine genome, the presence or absence of which such complementary sequences in the bovine genome is quantitatively associated with the trait of twinning in a cattle population, wherein the collection comprises at least one sequence that is quantitatively associated with twinning with statistical significance of at least p≦0.01. 
     
     
         2 . The collection of  claim 1  wherein the collection comprises at least one sequence that is quantitatively associated with twinning with statistical significance of at least p≦0.001. 
     
     
         3 . The collection of  claim 1  wherein each polynucleotide represents one allele of a SNP in the bovine genome. 
     
     
         4 . The collection of  claim 1  wherein in at least one of the polynucleotides is complementary to a sequence located on bovine chromosome 5 (BTA5). 
     
     
         5 . The collection of  claim 4  wherein at least one of the polynucleotides is complementary to a sequence located in a genomic sequence for Insulin-like Growth Factor 1 (IGF1). 
     
     
         6 . The collection of  claim 1  wherein at least one of the polynucleotides is complementary to a sequence in a genomic sequence for synapsin III (SYN3), synapsin III isoform A (SYN3A), collagen type X alpha-1 (COL10A1) precursor, eukaryotic translation initiation factor 3, subunit 7 (EIF3S7), insulin-like growth factor 1 (IGF1), inhibin beta-C (INHBC), cytoskeleton-associated protein 4 (CKAP4), or Alpha2-HS glycoprotein (AHSG.) 
     
     
         7 . The collection of  claim 1  comprising at least one polynucleotide useful for detecting one or more of the SNPs: NCBI ID Nos.: rs29012841, rs29013556, rs29010972, rs29009758, rs29016850, rs29012088, rs29014793, rs29010454, rs29017408, rs29010308, rs29018610, IGF1_SNP — 3, IGF1_SNP — 2, rs41257131, rs29024681, rs29024705, rs29015348, rs29018255, rs29024685, rs29024709, rs29014932, rs29027275, rs29011411, rs2901259, rs29015209, rs29020823, rs29018125, BTA — 146334, rs29019730, rs29025325, rs29010503, rs29010502, rs29021155, rs29026881, rs41257406, rs29025358, rs29023435, rs29023434, rs29021895, rs29025879, NGS — 74296, NGS — 25065, rs29010471, NGS — 28234, rs29020900, rs29010470, rs29014046, NGS — 70865, NGS — 38815, BAC — 17596, BTB — 005645, IBISS4snp1087, AffyID3519, rs29012557, BTB — 013878, rs41622614, rs29015662, rs290211.76, rs29022856, rs29020409, rs29022783, rs29015105, rs29010042, rs29010040, rs29015664, rs29021023, and rs29020955. 
     
     
         8 . The collection of  claim 7 , comprising one or more of SNPs: rs29010454, IGF1_SNP — 2, IGF1_SNP — 3, rs29015348, rs29024681, rs29012592, rs29011411, rs29020823, rs29015209, BTA — 146334, rs29010503, AffyID3519, IBISS4snp1087, BTB — 005645, NGS — 28234, rs29015662, rs29022783 and rs29020955. 
     
     
         9 . The collection of  claim 4 , comprising one or more of SNPs: ss38332405, ss38334594, ss38324419, ss38324418, ss38333537, ss38324813, ss46526664, 54966387, 54966493, 54977448, ss38322168, 58655362, 63551646, 63554840, 64273448, 65538715, ss46527005, ss46526677 and ss38322778. 
     
     
         10 . A method for estimating the likelihood of twinning in one or more members of a cattle population comprising the steps of
 a) providing a collection of one or more polynucleotides, each of which is at least partially complementary to a sequence in a bovine genome, comprising at least one sequence that is quantitatively associated with twinning with statistical significance of at least p≦0.01;   b) using the collection to determine the presence or absence of sequences complementary to one or more polynucleotides from the collection in one or more members of the cattle population genome, wherein the presence or absence of the complementary sequences is quantitatively associated with the trait of twinning in a cattle population;   c) estimating the likelihood of twinning based on the results of step b).   
     
     
         11 . The method of  claim 10  wherein the estimating step b) comprises a laboratory analysis or a field test, and step c) comprises a statistical calculation. 
     
     
         12 . The method of  claim 10  wherein the collection comprises at least one sequence that is quantitatively associated with twinning with statistical significance of at least p≦0.01. 
     
     
         13 . The method of  claim 10  wherein at least each polynucleotide in the collection is useful for detecting the presence or absence of one allele of a SNP in the bovine genome. 
     
     
         14 . The method of  claim 10  wherein in at least one of the polynucleotides in the collection is complementary to a sequence located on bovine chromosome 5 (BTA5). 
     
     
         15 . The method of  claim 14  wherein at least one of the polynucleotides in the collection is complementary to a sequence located in a genomic sequence for Insulin-like Growth Factor 1 (IGF1). 
     
     
         16 . The method of  claim 10  wherein at least one of the polynucleotides in the collection is complementary to a sequence in a genomic sequence for synapsin III (SYN3), synapsin III isoform A (SYN3A), collagen type X alpha-1 (COL10A1) precursor, eukaryotic translation initiation factor 3, subunit 0.7 (EIF3S7), insulin-like growth factor 1 (IGF1), inhibin beta-C (INHBC), cytoskeleton-associated protein 4 (CKAP4), or Alpha2-HS glycoprotein (AHSG.) 
     
     
         17 . The method of  claim 10 , wherein the collection comprises at least one polynucleotide useful for detecting one or more of the SNPs: NCBI ID Nos.: rs29012841, rs29013556, rs29010972, rs29009758, rs29016850, rs29012088, rs29014793, rs29010454, rs29017408, rs29010308, rs29018610, IGF1_SNP — 3, IGF1_SNP — 2, rs41257131, rs29024681, rs29024705, rs29015348, rs29018255, rs29024685, rs29024709, rs29014932, rs29027275, rs29011411, rs2901259, rs29015209, rs29020823, rs29018125, BTA — 146334, rs29019730, rs29025325, rs29010503, rs29010502, rs29021155, rs29026881, rs41257406, rs29025358, rs29023435, rs29023434, rs29021895, rs29025879, NGS — 74296, NGS — 25065, rs29010471, NGS — 28234, rs29020900, rs29010470, rs29014046, NGS — 70865, NGS — 38815, BAC — 17596, BTB — 005645, IBISS4snp1087, AffyID3519, rs29012557, BTB — 013878, rs41622614, rs29015662, rs29021176, rs29022856, rs29020409, rs29022783, rs29015105, rs29010042, rs29010040, rs29015664, rs29021023, and rs29020955. 
     
     
         18 . The method of  claim 17 , wherein the collection comprises comprising one or more of SNPs: rs29010454, IGF1_SNP — 2, IGF1_SNP — 3, rs29015348, rs29024681, rs29012592, rs29011411, rs29020823, rs29015209, BTA — 146334, rs29010503, AffyID3519, IBISS4snp1087, BTB — 005645, NGS — 28234, rs29015662, rs29022783 and rs29020955. 
     
     
         19 . The method of  claim 14 , wherein the collection comprises one or more of SNPs: ss38332405, ss38334594, ss38324419, ss38324418, ss38333537, ss38324813, ss46526664, 54966387, 54966493, 54977448, ss38322168, 58655362, 63551646, 63554840, 64273448, 65538715, ss46527005, ss46526677 and ss38322778. 
     
     
         20 . A kit for estimating breeding value or predicting the likelihood of twinning comprising: (1) a collection of polynucleotides according to  claim 1 ; and (2) instructions for using the collections for estimating breeding value or predicting the likelihood or genetic potential for twinning.