Single-step genome-wide association study reveals candidate genes for body mass index trait in Yunong-black pigs.

Abstract

Body mass index (BMI) can serve as a reasonable indicator of overall body fat content in pigs. This study aimed to identify underlying variants and candidate genes associated with BMI in Yunong-black pigs. A single-step genome-wide association analysis (GWAS) was performed on 1405 BMI records and 924 Yunong-black pigs genotyped using a 50 K SNP Chip. De-regressed estimated breeding values were taken as the response variable in the GWAS. The estimated heritability for BMI was 0.157. Nine significant regions were associated with BMI, accounting for 12.828% of genetic variance, with the highest region explaining 1.969% of the genetic variance. Linkage disequilibrium analysis of the nine significant regions revealed that SNPs in six single-step GWAS-identified genomic regions were all located in the linkage disequilibrium blocks. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses of the 29 protein-coding genes annotated to these regions revealed that FABP2, a key gene associated with BMI in human, was enriched in the fatty acid binding term and the fat digestion and absorption pathway. This study provides a better insight into the genetic architecture of the BMI trait, and offers potential molecular markers for the breeding of Yunong-black pigs.