Investigating the hub genes and genetic basis regulating fatty acid metabolictraits in chicken breast muscle based on combined genomic and transcriptomic approaches

Background The composition of various fatty acids in meat plays a crucial role in the evaluation of the nutritional indicators of poultry and human health. Fatty acid metabolic indicators can more accurately reflect the nutritional status of meat and its acceptance by the general public. In this study, we utilized two analytical approaches, Genome-Wide Association Study (GWAS) and Weighted Gene Co-expression Network Analysis (WGCNA), to elucidate the genetic mechanisms underlying the fatty acid metabolic traits in chicken breast muscle.Initially, GWAS was conducted based on genotype data obtained by genotyping by sequencing (GBS) from 415 chickens of the Gushi-Anka F2 resource population and phenotypic data of 33 fatty acid metabolism traits in the breast muscle. Results We identified a total of 291 significant single nucleotide polymorphisms (SNPs) associated with the content of 12 types of fatty acids such as C14:0/C12:0, C18:0/C16:0, C18:1/C18:0, etc., which were mapped on chromosomes (Chr) 1, 2, 3, 4, 5, 7, 9, and 10. The most significant SNP was Chr2:102, 676, 165 ( P = 1.20E-06), which explained 2.33% of the phenotypic variation in the polyunsaturated fatty acids (PUFA)/mono-unsaturated fatty acids (MUFA) synthesis pathway. The SNP that explained the highest phenotypic variation was Chr4: 30, 150, 765 (5.85%). Interestingly, significant signals were identified for three fatty acid metabolic traits (C22:4/C18:3, C20:3/C18:3, C22:6/C18:3) within the same gene interval on Chr 9 (Chr9: 5.75 - 8.99Mb). Concurrently, WGCNA was conducted using the 613 candidate genes identified from the linkage disequilibrium regions of the aforementioned significant SNPs, as well as the transcriptome data and fatty acid content phenotypic values of the breast muscle of the Gujshi chicken from three periods, 13 hub genes ( FIG4 , METTL4 , PLD4 , IDH1 , FH , SDHA , EHHADH , AKT1 , PIK3CB , LPIN2 , FUT9 , PAK2 , and ACSL3 ) were finally determined. Further, we constructed the functional networks involving these candidate genes and deduced the potential fatty acid metabolic pathway. Conclusion These results enhance our understanding of the genetic regulation mechanisms of fatty acid composition in chicken muscle, providing a theoretical basis for future breeding practices targeting fatty acid composition traits.