Background Average backfat thickness (BFT) is a critical complex trait in pig and an important indicator for fat deposition and lean rate. Usually, genome-wide association study (GWAS) was used to discover quantitative trait loci (QTLs) of BFT in a single population. However, the power of GWAS is limited by sample size in a single population. Alternatively, meta-analysis of GWAS (metaGWAS) is an attractive method to increase the statistical power by integrating data from multiple breeds and populations. The aim of this study is to identify shared genetic characterization of BFT across breeds in pigs via metaGWAS.  Results In this study, we performed metaGWAS on BFT using 15,353 pigs (5,143 Duroc, 7,275 Yorkshire, and 2,935 Landrace) from 19 populations. We detected 40 genome-wide significant SNPs (Bonferroni corrected P < 0.05) and defined five breed-shared QTLs in across-breed metaGWAS. Markers within the five QTL regions explained 7 ~ 9% additive genetic variance and showed strong heritability enrichment. Furthermore, by integrating information from multiple bioinformatics databases, we annotated 46 candidate genes located in the five QTLs. Among them, three important (MC4R, PPARD, and SLC27A1) and seven suggestive candidate genes (PHLPP1, NUDT3, ILRUN, RELCH, KCNQ5, ITPR3, and U3) were identified. Conclusion QTLs and candidate genes underlying BFT across breeds were identified via metaGWAS from multiple populations. Our findings contribute to the understanding of the genetic architecture of BFT and the regulating mechanism underlying fat deposition in pigs.

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The domestic pig (Sus scrofa) and subfamilies have a long-term and extensive gene flow, especially in Southeast Asia. Demographically, as a gateway of southern China, Yunnan province with unique geographical location and complex climate system, but genomic, genetic introgression of Yunnan indigenous pigs is insufficient. Here, we analyzed population structure, differentiation, gene flow, adaptive introgression, signature selection and gene function of Yunnan indigenous pigs, European commercial and other Southeast Asia pigs using a pig genomics reference panel (PGRP v1) from pig Genotype-Tissue Expression project (PigGTEx). In this study, we clarified that the Diannan small-ear pig owned particular genetic information in the whole genome; we provided evidence of the introgression events from the Vietnam pig to the Diannan small-ear pig. We also outlined at least two conceptual routes of gene flow to Diannan small-ear in Southeast Asia. Three introgressed loci with similar chromosome positions and strong signature selection harbored the NAF1, NPY1R and NPY5R genes, which related to fat mass, immunity, and litter weight of pig complex trait using multiple bio-functionalization databases. Conclusively, these results laid the foundation for understanding introgression from Southeast Asia pigs to Yunnan indigenous pigs and provided a new insight into explaining the biological function of genes through multiple databases.