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. 2025 Jul 21;26(1):679.
doi: 10.1186/s12864-025-11803-7.

Identification of key candidate genes and marker metabolites of melanin synthesis in black-bone chicken

Ziyi Fang #  1 , Zhengxiao He #  1 , Weifang Yang  2 , Yongli Wang  1 , Yanji Chen  1 , Lilin Men  1 , Richun Cai  3 , Yang Yu  3 , Yaxiong Jia  4 , Guiping Zhao  5
Affiliations

Identification of key candidate genes and marker metabolites of melanin synthesis in black-bone chicken

Ziyi Fang et al. BMC Genomics. .

Abstract

Background: Blackness and growth traits are regarded as crucial economic traits in black-bone chicken production. In order to meet consumers' demand for black-bone chickens, it is necessary to study the mechanisms of body weight growth and melanin deposition in black-bone chickens. The genetic variations in growth traits, blackness traits, breast muscle transcriptome, and metabolism were compared between the Yanjin black-bone (YJ) chicken group (n = 20) and Jinling Partridge black-bone (JL) chicken group (n = 20). In addition, very high-melanin content (HB) individuals (n = 6) and very low-melanin content individuals (LB) (n = 6) were selected from the JL chicken group to investigate the melanin synthesis mechanism.

Results: Comparison between the breast muscle transcriptomes of YJ chickens and JL chickens, as well as between HB and LB of JL chickens, revealed that 81 common differentially expressed genes (DEGs) were significantly enriched in melanosomes, pigment particles, and melanogenesis pathways. Among them, four candidate genes, namely TYRP1, KIT, PRKCB and EDNRB2, may be significantly associated with melanin production in black-bone chicken breast muscle. Also, 2 of the marker metabolites among the 16 common differential metabolites (DMs) identified, namely tetrahydrobiopterin (BH4) and N-acetylneuraminic acid, significantly contribute to melanin synthesis in the breast muscle of black-bone chickens.

Conclusion: Our research presents complex regulatory networks of DEGs and DMs in melanin synthesis pathways. The results establish a basis for raising black-bone chickens with optimal melanin levels and offer a theoretical framework for investigating the mechanisms of melanin formation in these hens.

Keywords: Black-bone chicken; Melanin synthesis; Metabolomics; Transcriptomics.

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Conflict of interest statement

Declarations. Ethics approval and consent to participate: The experimental protocols were approved (No. IAS2024-136) by the Science Research Department of the Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS; Beijing, China). Consent for publication: Not applicable. Competing interests: The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
Volcano plot and Venn diagram of the DEGs. A Volcano plot of DEGs between YJ chicken vs. JL chicken groups (B) Volcano plot of DEGs between HB vs. LB groups (C) Venn diagram of the co-expressed DEGs in two comparisons (YJ chicken vs. JL chicken groups and HB vs. LB groups). Red dots indicate upregulated genes; blue dots indicate downregulated genes; Grey dots indicate DEGs that are not significant
Fig. 2
Fig. 2
The Gene Ontology (GO) terms in the two comparisons. A The 20 most significantly enriched GO pathway in the two comparisons; B GO term functional enrichment analysis of DEGs in the two comparisons
Fig. 3
Fig. 3
KEGG pathway enrichment in the two comparisons. A The 25 most significantly enriched KEGG pathways between the YJ chicken vs. JL chicken groups; B The 25 most significantly enriched KEGG pathways between the HB vs. LB groups; C The 25 most significantly enriched KEGG pathways of the co-expressed DEGs in the two comparisons
Fig. 4
Fig. 4
Volcano plot and Venn diagram of the DMs. A Volcano plot of DMs between the YJ chicken vs. JL chicken groups; B Volcano plot of DMs between the high-blackness (HB) vs. the low-blackness (LB) groups in JL chicken; C Venn diagram of the common DMs in two comparisons (YJ chicken vs. JL chicken groups and HB vs. LB groups). Red dots indicate upregulated DMs; blue dots indicate downregulated DMs;Grey dots indicate DMs that are not significant
Fig. 5
Fig. 5
KEGG pathway enrichment in two comparisons. A KEGG pathway enrichment analysis of DMs between the YJ chicken vs. JL chicken groups. B KEGG pathway enrichment analysis of DMs between the HB vs. LB groups
Fig. 6
Fig. 6
Pathway map of melanin regulation by identified candidate DEGs (TYRP1, EDNRB2, KIT, and PRKCB) and marker DMs (BH4, and N-acetylneuraminic acid)
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