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

Abstract

Objective: Growth traits are one of the most important economic traits of pigs, including body weight and average daily gain. However, the available genetic markers for these traits are limited, especially for Chinese indigenous pigs or Chinese indigenous pig hybrid breeds.

Methods: To discover SNP markers and candidate genes affecting body weight and average daily gain traits, we performed 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.

Results: The GWAS revealed 39 significant QTLs affecting body weight and average daily gain traits. Among these, 26 QTLs were significantly correlated with body weight traits. Thirteen QTLs were significantly correlated with average daily gain traits. Some candidate genes for body weight and average daily gain traits were identified, including MACROD2, ASB13, ATP12A, ZDHHC17, WDR37 and TENM4. Among the three single-locus models, only the GLM model identified significant SNPs, and the GLM model identified the largest number of 27 significant QTLs. The three multiple-locus models, MLMM, FarmCPU and BLINK, identified 4, 12 and 13 significant QTL loci, respectively.

Conclusion: We newly identified 18 QTLs 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.