Genetic architecture and key regulatory genes of fatty acid composition in Gushi chicken breast muscle determined by GWAS and WGCNA

Abstract

Background Fatty acids composition in poultry muscle is directly related to its tenderness, flavour, and juiciness, whereas its genetic mechanisms have not been elucidated. In this study, the genetic structure and key regulatory genes of the breast muscle fatty acid composition of local Chinese chicken, Gushi-Anka F2 resource population by integrating genome-wide association study (GWAS) and weighted gene co-expression network analysis (WGCNA) strategies. GWAS was performed based on 323,306 single nucleotide polymorphisms (SNPs) obtained by genotyping by sequencing (GBS) method and 721 chickens from the Gushi-Anka F2 resource population with highly variable fatty acid composition traits in the breast muscle. And then, according to the transcriptome data of the candidate genes that were obtained and phenotypic data of fatty acid composition traits in breast muscle of Gushi chickens at 14, 22, and 30 weeks of age, we conducted a WGCNA. Results A total of 128 suggestive significantly associated SNPs for 11 fatty acid composition traits were identified and mapped on chromosomes (Chr) 2, 3, 4, 5, 13, 17, 21, and 27. Of these, the two most significant SNPs were Chr13:5,100,140 (P = 4.56423e-10) and Chr13:5,100,173 (P = 4.56423e-10), which explained 5.6% of the phenotypic variation in polyunsaturated fatty acids (PUFA). In addition, six fatty acid composition traits, including C20:1, C22:6, saturated fatty acid (SFA), unsaturated fatty acids (UFA), PUFA, and average chain length (ACL), were located in the same QTL intervals on Chr13. We obtained 505 genes by scanning the linkage disequilibrium (LD) regions of all significant SNPs and performed a WGCNA based on the transcriptome data of the above 505 genes. Combining two strategies, 9 hub genes (ENO1, ADH1, ASAH1, ADH1C, PIK3CD, WISP1, AKT1, PANK3, and C1QTNF2) were finally identified, which could be the potential candidate genes regulating fatty acid composition traits in chicken breast muscle. Conclusion The results of this study deepen our understanding of the genetic mechanisms underlying the regulation of fatty acid composition traits, which is helpful in the design of breeding strategies for the subsequent improvement of fatty acid composition in poultry muscle.

Transcriptome and Weighted Gene Co-Expression Network Analysis for Feather Follicle Density in a Chinese Indigenous Breed

“…In recent studies, transcriptomics has been used to discover differentially expressed genes related to target traits from a large amount of genomic information in chickens, thereby revealing the inherent relationship between gene expression and important economic traits [ 19 , 20 ]. Weighted gene co-expression network analysis (WGCNA) combines phenotypic data analysis of chicken transcriptome profiles and is used to find key module and hub gene networks [ 21 , 22 ]. Thus, the primary aim of this study was to conduct a transcriptome and weighted gene co-expression network analysis (WGCNA) to assess feather follicle density in Wannan male chickens.…”

Identification of key modules and hub genes involved in regulating the feather follicle development of Wannan chickens using WGCNA

“…In recent years, transcriptome analysis has been employed extensively applied to study of various species and traits ( Choi, et al, 2020 ; Cassar-Malek, et al, 2022 ; Jin, et al, 2022 ), Furthermore, it has been successfully employed in the study of poultry traits ( Ren, et al, 2021 ; Pham, et al, 2022 ; Sun, et al, 2023 ). Weighted gene co-expression network analysis ( WGCNA ) has also been widely used to identify key modules of traits and important genes in a multitude of species ( Fan, et al, 2023 ; Yu, et al, 2023 ). With the transition of live poultry markets to the sale of chilled products.…”