ArticleAnimal bioscience2026
Cross-cohort transcriptomic meta-analysis identifies conserved melanogenesis signatures and developmental background in black-boned chicken breast muscle.
Article in Animal bioscience, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
objectiveThe purpose of this study was to identify conserved transcriptomic signatures associated with melanin deposition in black-boned chicken breast muscle and to distinguish robust pigmentation signals from normal breast muscle developmental and breedbackground effects.
methodsRNA-seq datasets of public breast muscle were integrated from three pigmentation-related cohorts, comprising 53 samples alongside one ordinary breast muscle background cohort, which included 42 samples. Gene-level effects were estimated using Salmon, tximport, and DESeq2, followed by random-effects meta-analysis, leave-one-cohortout analysis, background filtering, candidate layering, and exploratory signature score analysis.
resultsIn the pigmentation-related cohorts, 14,139 genes were eligible for meta-analysis, with 257 genes reached meta false discovery rate <0.05. Notably, PMEL, TYRP1, DCT, and TYR showed significant and directionally consistent upregulation in the breast muscle of black-boned chicken. Among the 227 significant and direction-consistent meta-analysis genes, 156 were identified by the background cohort at the prespecified threshold, including 145 background-development genes and 11 pigmentation-development backgroundoverlap genes. KIT was the only melanogenesis-enriched gene not identified by the background filter. The 11 candidates related to muscle phenotype showed consistent association with pigmentation comparisons, whereas canonical myogenic regulators did not achieve meta-significant.
conclusionThe present study confirmed conserved melanogenesis anchors and identified 11 muscle-phenotype-related genes, rather than canonical myogenic regulators, as the primary reproducible muscle-context signals associated with melanin deposition in blackboned chicken breast muscle.
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