Transcriptome Profile Analysis Identifies Candidate Genes for the Melanin Pigmentation of Skin in Tengchong Snow Chickens

SIMPLE SUMMARY: Chicken meat with high melanin content in black-boned chickens is considered a highly nutritious food with potential medicinal value. Tengchong Snow chicken is one of the valuable poultry resources in Yunnan Province, and this chicken is usually dominated by dark meat. However, during the rearing process, we found that a small number of white meat traits still existed in this chicken population. The purpose of this study was to investigate the deposition pattern and molecular mechanism of melanin formation in Tengchong Snow chickens. We selected Tengchong Snow black meat chicken (Bc) and white meat chicken (Wc) as the study subjects to determine differences in the luminance value (L value) and melanin content in their skin tissues at 1, 42 and 90 days; the L value and melanin content of the skin were measured using color chromatography, ELISA kits, and enzyme markers. We found that age had an effect on skin L values and melanin content. The L value gradually increased with age, while melanin content showed the opposite trend. Moreover, the L value of the skin tissue was negatively correlated with melanin content. Finally, we identified the TYR, DCT and EDNRB2 genes as being the possible main effector genes affecting skin pigmentation using transcriptome profiling; the expression of the TYR, DCT, MC1R, EDNRB2, GPR143, MITF, and TYRP1 genes also gradually decreased with increasing day age. In conclusion, this study describes and reveals the differences in L values and melanin content in chicken skin tissues. The results of the study provide a valuable theoretical basis for future breeding programs of Tengchong Snow chickens, as well as a foundation for studies on skin tone deposition and a theoretical reference for the future conservation and utilization of black-boned chickens. ABSTRACT: Tengchong Snow chickens are one of the most precious, black-boned chickens in Yunnan province and usually produce black meat. However, we found a small number of white meat traits in the chicken population during feeding. In order to determine the pattern of melanin deposition and the molecular mechanism of formation in the Tengchong Snow chicken, we measured the luminance value (L value) and melanin content in the skin of black meat chickens (Bc) and white meat chickens (Wc) using a color colorimeter, ELISA kit, and enzyme marker. The results showed that the L value of skin tissues in black meat chickens was significantly lower than that of white meat chickens, and the L value of skin tissues gradually increased with an increase in age. The melanin content of skin tissues in black meat chickens was higher than that of white meat chickens, and melanin content in the skin tissues gradually decreased with an increase in age, but this difference was not significant (p > 0.05); the L value of skin tissues in black meat chickens was negatively correlated with melanin content, and the correlation coefficient was mostly above −0.6. In addition, based on the phenotypic results, we chose to perform the comparative transcriptome profiling of skin tissues at 90 days of age. We screened a total of 44 differential genes, of which 32 were upregulated and 12 were downregulated. These DEGs were mainly involved in melanogenesis, tyrosine metabolism and RNA transport. We identified TYR, DCT, and EDNRB2 as possible master effector genes for skin pigmentation in Tengchong Snow black meat chickens through DEGs analysis. Finally, we measured the mRNA of TYR, DCT, MC1R, EDNRB2, GPR143, MITF, and TYRP1 genes through a quantitative real-time polymerase chain reaction (qPCR) and found that the mRNA of all the above seven genes decreased with increasing age. In conclusion, our study initially constructed an evaluation system for the black-boned traits of Tengchong Snow chickens and found key candidate genes regulating melanin deposition, which could provide an important theoretical basis for the selection and breeding of black-boned chickens.