Meta-analysis of SNPs determining litter traits in pigs

Abstract Background: Nearly 2,000 SNPs associated with pig litter size traits were so far reported based on genome-wide association studies (GWAS). The aims of this study were to gather and integrate previously reported associations between SNPs and five litter traits: total number born (TNB), number born alive (NBA), number of stillborn (SB), litter birthweight (LWT), and corpus luteum number (CLN) to evaluate their common genetic background, and to perform the meta-analysis (MA) of GWAS for total number born (TNB) recorded on animals from five pig populations. Results: In this study, the genes with the largest number of associations with evaluated litter traits were GABRG3, RBP7, PRKD1, and STXBP6. Only 21 genes out of 233 associated with the evaluated litter traits were reported in more than one population or for more than one trait. Based on this evaluation the most interesting candidate gene is PRKD1, which has an association with SB and TNB. Based on GO term analysis, PRKD1 was shown to be involved in angiogenesis as well. As a result of the MA, two new genomic regions, that have not been previously reported, were found to be associated with TNB. One SNP was located on Sus scrofa chromosome (SSC) 14 in the intron of the FAM13C gene. The second SNP was located on SSC9 within the intron of the AGMO gene. Functional analysis revealed a strong candidate causal gene underlying the QTL on SSC9. The third best hit and the most promising candidate gene for litter size was found within the SOSTDC1 gene associated with lower male fertility in rats.Conclusions: We showed that litter traits studied across pig populations have only a few genomic regions in common based on candidate genes comparison. PRKD1 could be an interesting candidate gene with wider association with fertility. The MA identified new genomic regions on SSC9 and SSC14 associated with TNB. Further functional analysis indicated the most promising gene being SOSTDC1 that was confirmed to affect male fertility in other mammals. This is an important finding as litter traits are by default linked with females rather than males.