RNA-Seq Reveals Pathways Responsible for Meat Quality Characteristic Differences between Two Yunnan Indigenous...

Area of Science:

• Animal Science
• Genomics
• Biochemistry

Background:

• Poultry meat quality is crucial for global consumer demand.
• Indigenous chicken breeds offer unique genetic resources for meat improvement.
• Understanding genetic factors influencing meat quality is essential for breeding programs.

Purpose of the Study:

• To compare growth, meat quality, and muscle gene expression between indigenous Yunnan chicken breeds (Wuding chickens and Daweishan mini chickens) and commercial Cobb broilers.
• To identify differentially expressed genes (DEGs) and enriched pathways associated with meat quality traits.
• To explore the potential of identified genes as molecular markers for improving chicken meat quality.

Main Methods:

• Comparative analysis of growth and meat quality traits.
• RNA sequencing to profile muscle transcriptome and identify DEGs.
• Quantitative real-time PCR (qPCR) for validating gene expression.
• Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis.

Main Results:

• Wuding chickens showed significantly higher crude fat, inosine monophosphate, amino acid, and total fatty acid content compared to Cobb broilers and Daweishan mini chickens.
• 420 DEGs were found in Daweishan mini chicken pectoralis and 217 DEGs in Wuding chicken pectoralis relative to Cobb broilers, with 105 shared DEGs.
• Six KEGG pathways were enriched, including the PPAR signaling pathway, which is involved in fatty acid metabolism.
• Four genes (LPL, GK, SCD, FABP7) within the PPAR signaling pathway were upregulated in Wuding chicken muscles, correlating with higher fat and fatty acid content.

Conclusions:

• Indigenous Wuding chickens possess distinct meat quality characteristics, particularly higher fat and fatty acid content, attributed to specific gene expression patterns.
• The identified DEGs and enriched pathways, especially those in the PPAR signaling pathway, provide insights into the genetic basis of meat quality in Wuding chickens.
• This research provides a foundation for utilizing these identified genes as molecular markers in breeding programs to enhance meat quality traits in indigenous Yunnan chickens.