Genome-wide association study identifies novel loci associated with feed efficiency traits in Hu lambs

Feed efficiency (FE) is a crucial economic trait that significantly impacts profitability in intensive sheep production, and can be evaluated by the residual feed intake (RFI) and feed conversion ratio (FCR). However, the underlying genetic mechanisms that underlie FE-related traits in sheep are not fully understood. Herein, we measured the FE-related traits of 1,280 Hu sheep and conducted the phenotype statistics and correlation analysis, the result showcase that there was a large variation for FE-related traits, and RFI was significant positive correlation with average daily feed intake (ADFI) and FCR. Moreover, a genome-wide association study (GWAS) was conducted using whole-genome resequencing data to investigate the genetic associations of ADFI, FCR and RFI. For ADFI and FCR traits, 2 and one single nucleotide polymorphisms (SNPs) exceeded the genome-wide significance threshold, whereas ten and 5 SNPs exceeded the suggestive significance threshold. For RFI traits, only 4 SNPs exceeded the suggestive significance threshold. Finally, a total of 8 genes (LOC101121953, LOC101110202, CTNNA3, IZUMO3, PPM1E, YIPF7, ZSCAN12 and LOC105603808) were identified as potential candidate genes for FE-related traits. Simultaneously, we further analyzed the effects of 2 candidate SNPs associated with RFI on growth and FE traits in enlarged experimental population, the results demonstrated that these 2 SNPs was not significantly associated with growth traits (P>0.05), but significantly related to RFI traits (P<0.05). These findings will provide valuable reference data and key genetic variants that can be used to effectively select feed-efficient individual in sheep breeding programs.