Cross-cohort transcriptomic meta-analysis identifies conserved melanogenesis signatures and developmental background in black-boned chicken breast muscle

Objective: This study aimed to identify conserved transcriptomic signatures associated with melanin deposition in black-boned chicken breast muscle and to distinguish robust pigmentation signals from ordinary breast muscle developmental and breed-background effects. Methods: Public breast muscle RNA-seq datasets were integrated from three pigmentation-related cohorts comprising 53 samples and one ordinary breast muscle background cohort comprising 42 samples. Gene-level effects were estimated with Salmon, tximport, and DESeq2, followed by random-effects meta-analysis, leave-one-cohort-out analysis, background filtering, candidate layering, and exploratory signature score analysis. Results: Across the pigmentation-related cohorts, 14,139 genes were eligible for meta-analysis, and 257 genes reached meta false discovery rate <0.05. PMEL, TYRP1, DCT, and TYR showed strong and directionally consistent upregulation in black-boned chicken breast muscle. Among the 227 significant and direction-consistent meta-analysis genes, 156 were flagged by the background cohort at the prespecified threshold, including 145 background-development genes and 11 pigmentation-development background-overlap genes. KIT was the only melanogenesis-enriched gene not flagged by the background filter. The 11 muscle-phenotype-related candidates were consistently associated with pigmentation comparisons, whereas canonical myogenic regulators were not meta-significant. Conclusion: In addition to confirming conserved melanogenesis anchors, this study identified 11 muscle-phenotype-related genes, rather than canonical myogenic regulators, as the main reproducible muscle-context signals accompanying melanin deposition in black-boned chicken breast muscle.