Novel insight into the wooden breast defect from revisiting RNA-seq data

The present research aimed at providing new insights into the biological mechanisms underlying the wooden breast defect (WB) and identifying novel genes likely involved in its occurrence. To do this, a differential gene expression analysis has been performed using the newest reference genome assembly for Gallus gallus (bGalGal1.mat.broiler.GRCg7). The WB mainly affects the Pectoralis major muscle (PM) of modern fast-growing broilers and is characterized by the presence of stiffened and pale areas having detrimental effects on meat quality. Considering its high prevalence and consequential economic losses, several studies were performed to elucidate the mechanisms underlying its occurrence. Nevertheless, the precise initial causes remain to be clarified. In the present research, we used RNA-seq data obtained in a previous study to identify differentially expressed genes (DEGs) between 6 affected (WB) and 5 unaffected (NORM) broilers’ PM muscles. The quality of raw RNA-seq reads was checked using FastQC v0.11.9 and MultiQC v1.13. Trimmomatric v.0.39 was used to filter low-quality reads and remove adaptor sequences. Clean reads were aligned to the latest chicken reference genome GRCg7 using the HISAT2 v2.2.1 aligner. After read counting using HTseq v0.11.2, the differential expression analysis was performed in the R environment using the “edgeR” package. An FDR-adjusted P-value of 0.01 was considered as the significance threshold. To identify functional categories significantly enriched by the DEGs, the gene list was analyzed using DAVID tool v.2021. We identified 2441 DEGs between WB and NORM (FDR<.01). Functional analysis evidenced DEGs involved in the glycolytic process (p<.0001), intracellular signal transduction (p<.0001), carbohydrate metabolism (p<.01), and protein serine/threonine kinase activity (p<.05.). Among the genes not yet reported in previous studies, the present study detected genes involved in mitochondrial biogenesis and function (i.e., PPARGC1B, ND2, COX2, and COX3) as downregulated in WB (FDR<.01). Besides, genes related to insulin signaling pathway and carbohydrate metabolism (i.e., G6PC1, PPP1R1A, PPP1R3D, and UGP2) were found lower expressed in WB (FDR<.01). In conclusion, our results corroborate the evidence concerning the impaired glucose metabolism and mitochondrial dysfunction in WB muscles and identify genes potentially involved in those mechanisms. Notably, the PPARGC1B gene, encoding for the peroxisome proliferator-activated receptor co-activator 1 (PGC1-β), has pivotal roles in maintaining glucose homeostasis and regulating mitochondrial biogenesis. Therefore, its involvement in the biological mechanisms underlying WB occurrence may be hypothesized.