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A genome‐wide association study reveals a quantitative trait locus for days open on chromosome 2 in J apanese B lack cattle
Author(s) -
Sasaki Shinji,
Ibi Takayuki,
Kojima Takatoshi,
Sugimoto Yoshikazu
Publication year - 2016
Publication title -
animal genetics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.756
H-Index - 81
eISSN - 1365-2052
pISSN - 0268-9146
DOI - 10.1111/age.12360
Subject(s) - biology , single nucleotide polymorphism , linkage disequilibrium , genetics , quantitative trait locus , genome wide association study , locus (genetics) , genetic association , allele , haplotype , snp , minor allele frequency , population , allele frequency , imputation (statistics) , gene , genotype , demography , machine learning , sociology , missing data , computer science
Summary Days open ( DO ), which is the interval from calving to conception, is an important trait related to reproductive performance in cattle. To identify quantitative trait loci for DO in Japanese Black cattle, we conducted a genome‐wide association study with 33 303 single nucleotide polymorphisms ( SNP s) using 459 animals with extreme DO values selected from a larger group of 15 488 animals. We identified a SNP on bovine chromosome 2 ( BTA 2) that was associated with DO . After imputation using phased haplotype data inferred from 586 812 SNP s of 1041 Japanese Black cattle, six SNP s associated with DO were located in an 8.5‐kb region of high linkage disequilibrium on BTA 2. These SNP s were located on the telomeric side at a distance of 177 kb from the parathyroid hormone 2 receptor ( PTH 2R ) gene. The association was replicated in a sample of 1778 animals. In the replicated population, the frequency of the reduced‐ DO allele ( Q ) was 0.63, and it accounted for 1.72% of the total genetic variance. The effect of a Q ‐to‐ q allele substitution on DO was a decrease of 3.74 days. The results suggest that the Q allele could serve as a marker in Japanese Black cattle to select animals with superior DO performance.