Identification of SNPs and Candidate Genes for Milk Produce Ability in Yorkshire Pig

Abstract

Background: Sow milk produce ability is an important limiting factor impacting suboptimal growth and survival of piglets. By pig genetic improvement, the litter size has been increased, and larger litters need more suckled mammary glands, that results in increased milk from lactating sow. Hence, it has much significance to explore the sow lactation performance. The aim of this study was to estimate genetic parameters and screen single nucleotide polymorphisms (SNPs) for milk produce ability trait in 985 Yorkshire pigs by a genome-wide association study (GWAS), and to further identify the candidate genes.Results: By ASReml, we estimated the heritability of sow milk produce ability: 0.18 ± 0.07. With the Fixed and random effect model Circulating Probability Unification (FarmCPU), we performed a GWAS, and detected seven genome-wide significant SNPs, namely, Sus scrofa Chromosome (SSC) 2: ASGA0010040 (P = 7.73E-11); SSC2:MARC0029355 (P = 1.30E-08), SSC6: WU_10.2_6_65751151 (P = 1.32E-10), SSC7: MARC0058875 (P = 4.99E-09), SSC10: WU_10.2_10_49571394 (P = 6.79E-08), SSC11: M1GA0014659 (P = 1.19E-07), and SSC15: MARC0042106 (P = 1.16E-07). We performed the distribution of phenotypes corresponding to genotypes of the seven SNPs, and showed that ASGA0010040, MARC0029355, MARC0058875, WU_10.2_10_49571394, M1GA0014659, and MARC0042106 have extreme phenotypic values corresponded to the homozygous genotypes, while the intermediate values corresponded to the heterozygous genotypes. Further, we screened for flanking regions ± 200 kb nearby seven significant SNPs, and identified 30 genes. Among of them, 24 as the candidates were involved in lactose metabolism, colostrum immunity, milk protein, and milk fat by the gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) analysis. Through the combined analysis between 24 candidate genes and differently expressed genes (DEGs) detected in transcriptome data (GSE101983), we found 11 commons (NAV2, ANO3, MUC15, DISP3, FBXO6, CLCN6, SLA-DQB1, PSMB8, PSMB9, TAP1, and KIF5C). Further, by comparing the chromosome positions of the candidate genes with the quantitative trait locus (QTLs) previously reported, a total of 13 genes were found to be within 0.86 Mb to 93.92 Mb of the reported QTLs for sow milk yield, in which, NAV2 was found to be located with 0.86 Mb of the QTL region ssc2: 40936355.Conclusions: In conclusion, we identified seven significant SNPs located on SSC2, 6, 7, 10, 11, and 15, and proposed 24 candidate genes for milk produce ability trait in Yorkshire pig. Among of them, 11 were the key candidates. These results contribute to the identification of variants and candidate genes for sow milk produce ability.