Integrated GWAS and transcriptome analysis reveals key genes associated with muscle fibre and fat traits in Gushi chicken

1. In the following experiment meat quality traits of a Gushi-Anka F2 resource population were measured, and their heritability estimated. Intramuscular fat (IMF) had medium heritability (0.35) but leg muscle fibre density (LMD), leg muscle fibre diameter (LMF), breast muscle fibre density (BMD), fresh fat content (FFA), and absolute dry fat content (AFC) had low heritability (0–0.2). The IMF presented the most important genetic additive effect among the poultry meat quality-related traits studied. 2. The phenotypic data of meat quality traits in the Gushi-Anka F2 resource population were combined with genotyping by sequencing (GBS) data to obtain genotype data. Six meat quality traits in 734 birds were analysed by GWAS. Based on these variants, 83 significant (–log₁₀(p) &gt; 4.42) single nucleotide polymorphisms and four quantitative trait loci (QTL) regions corresponding to 175 genes were identified. Further linkage disequilibrium (LD) analysis was conducted on chromosome 13 (Chr13) and chromosome 27 (Chr27) QTL regions. 3. Based on the transcriptome data and GWAS results, 12 shared genes - <i>ITGB3</i>, <i>DNAJC27</i>, <i>ETV4</i>, <i>C7orf50</i>, <i>FKBP1B</i>, <i>G3BP1</i>, <i>IGF2BP1</i>, <i>KCNH6</i>, <i>LOC416263</i>, <i>SCARA5</i>, <i>SMIM5</i> and <i>TBL1XR1</i> were identified as candidate genes influencing muscle fibre and fat traits.