Transcriptomic Architecture of Meat Quality Traits in Nigerian Indigenous Cattle: From Gene Expression to Phenotype

This study characterises the transcriptomic architecture underlying meat quality variation in Nigerian indigenous cattle breeds, establishing connections between gene expression profiles in muscle tissue and phenotypic meat quality outcomes, and identifying molecular markers for quality prediction and breeding. Beef quality is increasingly important for Nigeria's domestic and potential export markets, but the biological determinants of quality variation in indigenous breeds adapted to tropical conditions remain poorly characterised. This study uses a systems genetics approach, collecting skeletal muscle biopsies from the longissimus dorsi of 240 Bunaji, Sokoto Gudali, and N'Dama steers at NAPRI and abattoir sampling, followed by RNA sequencing for transcriptome profiling. Meat quality phenotypes measured include shear force, cooking loss, pH decline, colour stability, intramuscular fat percentage, water holding capacity, and trained panel sensory scores. eQTL analysis integrating transcriptomic and SNP genotyping data identifies genetic variants controlling gene expression relevant to meat quality. Co-expression network analysis using WGCNA identifies gene modules associated with quality traits. Pathway enrichment analysis characterises biological processes underlying quality trait variation. Findings reveal 1,247 differentially expressed genes between high and low meat quality animals, with calcium signalling, ubiquitin-proteasome proteolysis, and lipid metabolism pathways most enriched in quality-associated gene modules. Troponin I and Calpastatin expression levels are the strongest individual gene predictors of Warner-Bratzler shear force values. N'Dama cattle show a distinctive intramuscular fat gene expression profile associated with superior eating quality despite lower yield. The study contributes an original meat quality transcriptome reference for Nigerian cattle and recommends RNA-based biomarker development for quality prediction.

Keywords: transcriptomics, meat quality, Nigerian cattle, gene expression, eQTL analysis.