Single- and multiple-locus model genome-wide association study for growth traits in Dongliao black pigs.

Growth traits are one of the most important economic traits in pigs, including body weight and average daily gain. However, the available genetic markers for these traits are limited, especially concerning Chinese indigenous pigs and their hybrid breeds. To identify SNP markers and candidate genes affecting body weight and average daily gain traits, we performed a genome-wide association study (GWAS) for these traits in 358 Dongliao black pigs using three single-locus and three multiple-locus models. All pigs were genotyped using the China Chip-1 porcine SNP50K BeadChip. The GWAS revealed 39 significant quantitative trait loci (QTLs) affecting body weight and average daily gain traits. Among these, 26 QTLs were significantly correlated with body weight traits. Thirteen QTLs showed significant correlations with average daily gain traits. Some candidate genes associated with body weight and average daily gain traits include MACROD2, ASB13, ATP12A, ZDHHC17, WDR37 and TENM4. Of the three single-locus models examined, only the general linear model identified significant SNPs, identifying a total of 27 significant QTLs, which was the largest among the models assessed. The three multiple-locus models, multiple-locus mixed-model, FarmCPU and Bayesian-information and LD iteratively nested keyway, identified 4, 12 and 13 significant QTL loci, respectively. We newly identified 18 QTLs that are significantly correlated with body weight and average daily gain traits. Our results provided a foundation for biomarker breeding and enhancement of body weight and average daily gain traits in pigs.