Genome sequence-based genome-wide association study of feed efficiency in Pacific abalone

The Pacific abalone (Haliotis discus hannai) is the most commonly farmed abalone species in China. Seaweed, which is the feed for abalone, accounts for the highest costs in commercial farming. Genetic improvement of feed efficiency (FE) related traits in abalone could result in significant cost and energy savings. We performed a genome-wide association study (GWAS) of the FE traits in Pacific abalone. A total of 25 significant single -nucleotide polymorphisms (SNPs) were detected as being associated with the feed efficiency ratio (FER), and 30 significant SNPs were associated with residual feed intake (RFI). A total of 64 genes, including copb1, megf10, prxs, prdx4, myo19, ptp, ggt, aps, perlucin, and nimul, were identified as candidate genes that may affect FER or RFI traits through biological processes such as cell proliferation, nutrition metabolism, and the immune system. Furthermore, an overlapped gene (apol3) was identified as being associated with RFI by combining the results of GWAS and comparative transcriptomic analyses between the high-FE and low-FE groups. This study will not only improve our understanding of the genetics of abalone FE but will also provide valuable SNPs for molecular marker selection and breeding in the Pacific abalone.