The Identification of Functional Genes Affecting Fat-Related Meat Traits in Meat-Type Pigeons Using Double-Digest Restriction-Associated DNA Sequencing and Molecular Docking Analysis

SIMPLE SUMMARY: Fat-related traits, such as intramuscular fat content and fatty acid compositions, are important factors affecting meat quality. In this study, we aimed to identify candidate genes affecting fat-related traits in meat-type pigeons. Double-digest restriction-associated DNA sequencing was employed to screen genomic single nucleotide polymorphisms in two meat-type pigeon breeds (the Chinese indigenous Shiqi pigeon and the imported White King pigeon) which demonstrated significant differences in fat-related meat traits. Gene ontology enrichment analysis and pathway analysis were performed on genes harboring genetic variants, and with clear annotations. Nineteen functional genes involved in lipid metabolism were identified as candidate genes that may affect fat-related traits in squabs. A molecular docking analysis further revealed that three non-synonymous amino acid mutations, resulting from the polymorphic sites in three functional genes, could influence the binding properties between the enzymatic proteins and their substrates, which may subsequently alter the catalytic efficiency of enzymes. We suggested that these three genes (acetyl-CoA acyltransferase 1 and 2, acetyl-CoA carboxylase beta), which encode rate-limiting enzymes in fatty acid synthesis and degradation, were worthy of further investigation to explore their contributions to the discrepancies in fat-related traits in squabs. ABSTRACT: The Chinese indigenous Shiqi (SQ) pigeon and the imported White King (WK) pigeon are two meat-type pigeon breeds of economical and nutritional importance in China. They displayed significant differences in such meat quality traits as intramuscular fat (IMF) content and fatty acid (FA) compositions in the breast muscles. In this study, we aimed to screen candidate genes that could affect fat-related meat quality traits in meat-type pigeons. We investigated the polymorphic variations at the genomic level using double-digest restriction-associated DNA (ddRAD) sequencing in 12 squabs of SQ and WK pigeons that exhibited significant inter-breed differences in IMF content as well as FA and amino acid compositions in the breast muscles, and screened candidate genes influencing fat-related traits in squabs through gene ontology analysis and pathway analysis. By focusing on 6019 SNPs, which were located in genes with correct annotations and had the potential to induce changes in the encoded proteins, we identified 19 genes (ACAA1, ACAA2, ACACB, ACADS, ACAT1, ACOX3, ACSBG1, ACSBG2, ACSL1, ACSL4, ELOVL6, FADS1, FADS2, HACD4, HADH, HADHA, HADHB, MECR, OXSM) as candidate genes that could affect fat-related traits in squabs. They were significantly enriched in the pathways of FA metabolism, degradation, and biosynthesis (p < 0.05). Results from molecular docking analysis further revealed that three non-synonymous amino acid alterations, ACAA1(S357N), ACAA2(T234I), and ACACB(H1418N), could alter the non-bonding interactions between the enzymatic proteins and their substrates. Since ACAA1, ACAA2, and ACACB encode rate-limiting enzymes in FA synthesis and degradation, alterations in the enzyme–substrate binding affinity may subsequently affect the catalytic efficiency of enzymes. We suggested that SNPs in these three genes were worthy of further investigation into their roles in explaining the disparities in fat-related traits in squabs.