A genome-wide association study of reproductive traits in a Yorkshire pig population

Genome-wide association studies (GWASs) have been extensively utilized to identify economically important trait loci in livestock animals. We performed a GWAS on Yorkshire sows for reproduction traits (the number of piglets born alive;NBA, the total number of piglets born;TNB, the weight shortfall number, the total number of suckling piglets, and the number of pigs weaned). A total of 1061 sows were genotyped using the Illumina PorcineSNP60 BeadChip. Principal component analysis revealed no significant population stratification. We identified a total of 15 single nucleotide polymorphisms (SNPs) of which only one reached the Bonferroni level of significance (P < 2.33E-07) and the remaining fourteen SNPs were suggestive of association for the reproductive traits of interest (P < 5E-05). The heritability estimates obtained by all SNPs were 0.11 ± 0.04, 0.14 ± 0.05, 0.15 ± 0.05, 0.14 ± 0.05, and 0.02 ± 0.03 for NBA, TNB, weight shortfall number, total number of suckling piglets, and number of pigs weaned, respectively. The two most significant SNPs, rs81465399 (P = 8.05E-08) and rs80991683 (P = 1.55E-06) on SSC17, were associated with weight shortfall number. In addition, SNP rs81356596 (P = 1.20E-05) on SSC2 was associated with the total number of suckling piglets. Another two SNPs, rs81454514 (P = 1.07E-05) and rs81454465 (P = 1.56E-05) on SSC15 and associated with NBA, were located near the reported quantitative trait locus (QTL) region of both the NBA and TNB traits. The heritability estimate for the number of pigs weaned was the lowest among all five pig reproductive traits in our analysis. Overall, we found a number of significant SNPs, some of them belonging to an uncharacterized locus, LOC102165882, along with two important genes, ACSL3 and CD59, with various physiological functions relevant to reproduction.