Genome-wide Association Studies For Female Reproductive Traits On Three Populations

Female reproductive traits play important roles in affecting the efficiency of pig industry. Here we performed genome-wide association studies(GWAS) to identify loci associated with the total number of born piglets(TNB), the number of born alive piglets(NBA), the number of corpus luteum(NCL) and the teat number.The populations in the study used included a White Duroc × Erhualian F2 resource population, Chinese Erhualian pig population and a Chinese Sutai pig population. 242 and 291 F2 sows of White Duroc × Erhualian F2 resource population were recorded for TNB,NBA and NCL, respectively. Teat number in three population including 1743 White Duroc × Erhualian F2, 320 Chinese Erhualian pigs and 383 Chinese Sutai pigs. The 60 K SNP dataset used for GWAS were delivered from directly genotyping on Illumina 60 K imputing from microsatellites. The SNPs quality control was conducted on Plink 1.07 and the GWAS were facilitated on the GenABEL package of R program with mixed linear model. The total of SNPs were identified to be associated with these 3 traits. The result showed that 3 SNPs on SSC7 were associated with TNB and 5 SNPs on the similar position on SSC7 were associated with NBA, 1 SNP on SSC8 was associated with NCL, 24 SNPs on SSC1, 7 and 12 with the teat number, respectively no significant associated SNPs were identified in a meta-analysis of GWAS. After searching plausible candidate genes within the associated region, we propose MEP1 A and SPINK2 as interesting candidate genes for TNB and NCL respectively, And we highlighted VRTN and KDM6 B at the loci on SSC7 and SSC12 as two candidate genes for the teat number.The result of this study provide new insight to decipher the mechanism of female reproductive traits in pig.