Abstract
Background: Pigs are one of the most important livestock species for providing meat products in the world. Deciphering the genetic architecture of feed efficiency-related traits is beneficial to improve the genetic progress of these traits and save the total cost of pork production. However, the genetic architecture of feed efficiency-related traits remains unclear. Methods: To address this problem, we collected 1301 genotyped Yorkshire pigs with three feed efficiency-related traits, including days at 100 kg (DAYS_100), backfat thickness at 100 kg (BFT_100), and feed conversion ratio from 30 to 100 kg (FCR_30_100), to explore the genetic parameters and genetic basis of these traits. Results: The heritability of DAYS_100, BFT_100, and FCR_30_100 was 0.25 ± 0.04, 0.40 ± 0.05, and 0.23 ± 0.04, respectively. Additionally, BFT_100 and DAYS_100 had a weak negative genetic correlation (−0.01 ± 0.12), while trait FCR_30_100 showed a positive genetic correlation with DAYS_100 (0.51 ± 0.11) and BFT_100 (0.28 ± 0.12). A genome-wide association study identified 7, 5, and 4 SNPs independently associated with BFT_100, DAYS_100, and FCR_30_100, respectively. Further analysis found that the candidate gene ETV4 was significantly associated with DAYS_100 and the candidate gene ENSSSCG00000045751 was associated with FCR_30_100. The functional annotation of candidate genes was enriched in the bile acid metabolic process and protein ubiquitination terms. Conclusions: This study discovered 16 quantitative trait loci associated with feed efficiency-related traits, providing a comprehensive insight for understanding the genetic basis of feed efficiency-related traits in pigs. The candidate genes, such as ETV4 gene in DAYS_100, CAMK1D gene for BFT_100, and ENSSSCG00000045751 gene for FCR_30_100, could be used for further investigation.