Insights into the architecture of human-induced polygenic selection in Duroc pigs

Abstract

Background As one of the most utilized commercial composite boar lines, Duroc pigs have been introduced to China and undergone strongly human-induced selection over the past decades. However, the efficiencies and limitations of previous breeding of Chinese Duroc pigs are largely understudied. The objective of this study was to uncover directional polygenic selection in the Duroc pig genome, and investigate points overlooked in the past breeding process. Results Here, we utilized the Generation Proxy Selection Mapping (GPSM) on a dataset of 1067 Duroc pigs with 8,766,074 imputed SNPs. GPSM detected a total of 5649 putative SNPs actively under selection in the Chinese Duroc pig population, and the potential functions of the selection regions were mainly related to production, meat and carcass traits. Meanwhile, we observed that the allele frequency of variants related to teat number (NT) relevant traits was also changed, which might be influenced by genes that had pleiotropic effects. First, we identified the direction of selection on NT traits by $$\hat{G}$$ G ^ , and further pinpointed large-effect genomic regions associated with NT relevant traits by selection signature and GWAS. Combining results of NT relevant traits-specific selection signatures and GWAS, we found three common genome regions, which were overlapped with QTLs related to production, meat and carcass traits besides “teat number” QTLs. This implied that there were some pleiotropic variants underlying NT and economic traits. We further found that rs346331089 has pleiotropic effects on NT and economic traits, e.g., litter size at weaning (LSW), litter weight at weaning (LWW), days to 100 kg (D100), backfat thickness at 100 kg (B100), and loin muscle area at 100 kg (L100) traits. Conclusions The selected loci that we identified across methods displayed the past breeding process of Chinese Duroc pigs, and our findings could be used to inform future breeding decision.

Genome-Wide Association Study Meta-Analysis Elucidates Genetic Structure and Identifies Candidate Genes of Teat Number Traits in Pigs

“…Additionally, teat number and backfat thickness displayed noteworthy loci, such as 7_97614602, with a genetic correlation of −0.3068. This indicated that these SNPs possess the potential to influence a multitude of intricate traits [ 22 ]. Consequently, these SNPs warrant further scrutiny in the context of breeding programs.…”

“…Different breeds each possess distinct features, and there exists a discrepancy in breeding goals. Specifically, the Duroc breed exhibits rapid growth, efficient feed utilization, and a high percentage of lean meat in the carcass, making it commonly used for terminal sires [ 22 ]. On the other hand, Landrace pigs are known for their excellent reproductive performance and have a high number of piglets per litter; this breed is commonly employed as the maternal line in commercial herds [ 23 ].…”

Molecular Design-Based Breeding: A Kinship Index-Based Selection Method for Complex Traits in Small Livestock Populations

“…The first step in building the ideal individual is to identify the advantageous traits in the parent breed. Different pig breeds have specific advantages; the advantageous traits of Chinese indigenous pigs are mainly in meat quality, roughage tolerance, and disease resistance, while that of the introduced breeds has better leanness, growth rate, and feed conversion ratio [ 15 ]. The beneficial genotype corresponding to the desired trait is identified after the determination of the advantageous trait.…”