Genome-wide association analysis identifies quantitative trait loci for growth and fatness in Diannan small-ear (DSE) pigs

Abstract Background: In the livestock industry, the growth and fatness traits are directly related to production efficiency and economic profits. As for Diannan small-ear (DSE) pigs, a unique indigenous breed, the genetic architecture of growth and fatness traits are still elusive. The aim of this study was to search the genetic loci and candidate genes associated with phenotypic traits in DSE pigs using GWAS based on the Geneseek Porcine 50K SNP Chip data. Results: A total of 30,648 single nucleotide polymorphisms (SNPs) were detected in 265 DSE pigs. After filtering, 22,146 SNPs were used for Genome-wide association studies (GWAS) analysis. The significant phenotypic correlations among eight important growth traits (body weight, back-fat thickness, and six body measurement traits) were observed. Seven SNPs surpassing the suggestively significant threshold for back height, backfat thickness, chest circumference and cannon bone circumference. Based on gene annotation results, these seven SNPs were mapped to the following candidate genes, VIPR2, SLC10A2, NUCKS1, MCT1, CHCHD3, SMOX and GPR1, which are mainly involved with adipocyte differentiation, lipid metabolism, skeletal muscle development, and average daily weight gain. Conclusions: Our work offers novel insights into the genetic architecture of swine important economic traits and may play an important role in molecular markers breeding for DSE pig.