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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.Results: In the pigmentation-related cohorts, 14,139 genes were eligible for meta-analysis, with 257 genes reached meta false discovery rate &lt;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.Conclusion: The 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.<\/jats:p>","DOI":"10.5713\/ab.260430","type":"journal-article","created":{"date-parts":[[2026,6,24]],"date-time":"2026-06-24T00:20:27Z","timestamp":1782260427000},"page":"260430","update-policy":"https:\/\/doi.org\/10.5713\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Cross-cohort transcriptomic meta-analysis identifies conserved melanogenesis signatures and developmental background in black-boned chicken breast 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