Integrated Transcriptomics Profiling in Chahua and Digao Chickens’ Breast for Assessment Molecular Mechanism of Meat Quality Traits

Meat quality traits are an important economic trait and remain a major argument, from the producer to the consumer. However, there are a few candidate genes and pathways of chicken meat quality traits that were reported for chicken molecular breeding. The purpose of the present study is to identify the candidate genes and pathways associated with meat quality underlying variations in meat quality. Hence, transcriptome profiles of breast tissue in commercial Digao (DG, 5 male) and Chahua (CH, 5 male) native chicken breeds were analyzed at the age of 100 days. The results found 3525 differentially expressed genes (DEGs) in CH compared to DG with adjusted p-values of ≤0.05 and log2FC ≥ 0.1 FDR ≤ 0.05. Functional analysis of GO showed that the DEGs are mainly involved in the two types of processes of meat quality, such as positive regulation of the metabolic process, extracellular structure organization, collagen trimer, cellular amino acid metabolic process, cellular amino acid catabolic process, and heme binding. Functional analysis of KEGG showed that the DEGs are mainly involved in the two types of processes of meat quality, such as oxidative phosphorylation, carbon metabolism, valine, leucine, and isoleucine degradation, and fatty acid degradation. Many of the DEGs are well known to be related to meat quality, such as COL28A1, COL1A2, MB, HBAD, HBA1, ACACA, ACADL, ACSL1, ATP8A1, CAV1, FADS2, FASN, DCN, CHCHD10, AGXT2, ALDH3A2, and MORN4. Therefore, the current study detected multiple pathways and genes that could be involved in the control of the meat quality traits of chickens. These findings should be used as an essential resource to improve the accuracy of selection for meat traits in chickens using marker-assisted selection based on differentially expressed genes.