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

Siyu Yuan; Shaoqi Tian; Chuang Meng; Feng Ji; Bin Zhou; Hossam E Rushdi; Manhong Ye

doi:10.3390/ani13203256

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

Animals (Basel). 2023 Oct 19;13(20):3256. doi: 10.3390/ani13203256.

Authors

Siyu Yuan¹, Shaoqi Tian¹, Chuang Meng^{1

2}, Feng Ji³, Bin Zhou⁴, Hossam E Rushdi⁵, Manhong Ye^{1

5}

Affiliations

¹ College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China.
² Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China.
³ Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100089, China.
⁴ College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China.
⁵ Joint International Research Laboratory of Agricultural & Agri-Product Safety, Yangzhou University, Yangzhou 225009, China.

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.

Keywords: candidate genes; ddRAD sequencing; fatty acid; intramuscular fat; molecular docking analysis; squabs.

Abstract

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