Identification of key microRNAs affecting melanogenesis of breast muscle in Muchuan black-boned chickens by RNA sequencing

1. Melanin content is considered an important indicator of meat quality in black-boned chickens, which have a high market value. To understand the complex physiological processes underlying muscle melanogenesis in this chicken, differentially expressed miRNAs (DEMs) were detected between black muscle (BM) and white muscle (WM) of chickens using high-throughput sequencing technology. Six small RNA libraries were constructed, and more than 16.75 million clean reads were obtained for each library. 2. A total of 582 known miRNAs and 65 novel miRNAs were identified from the six chicken sequence libraries. A total of 19 DEMs were identified between the two groups, of which nine were upregulated and 10 were downregulated. Furthermore, the DEMs were predicted to target 572 genes. 3. Certain DEMs (such as miR-204, miR-133b, and miR-12 229-3p) and their target genes may play an important role in muscle melanogenesis of chickens. These findings provide a foundation for clarifying the miRNA regulatory mechanisms involved in muscle pigmentation in avian species.

Association of a novel SNP in the ASIP gene with skin color in black-bone chicken

The agouti signaling protein gene (ASIP) is a widely studied pigmentation gene that plays an important role in melanin synthesis. To determine the variety of ASIP expression in the Muchuan Black-Bone chicken, we examined genetic variation in the ASIP promoter region. A single nucleotide polymorphism (c.-1826A>T) was found to be associated with the skin color (dorsal and subalar) of black-bone chicken. Individuals with TT and AT genotypes had higher ASIP mRNA levels in the skin than did those with the AA genotype (P < 0.01). In addition, individuals with the TT genotype had higher ASIP mRNA levels than did those with the AT genotype (P < 0.05). Expression of melanogenesis-related genes (melanocortin 1 receptor and tyrosinase genes) was higher in the skin of chickens with the TT and AT genotypes than in those with the AA genotype (P < 0.01). A luciferase assay showed that promoter activity was higher in chickens with the TT genotype than in those with the AA genotype. Putative transcription factor prediction suggested that the c.-1826A>T mutation might shift the promoter binding affinity with differential transcription factors. In summary, we identified a novel mutation in the ASIP gene promoter that may affect chicken skin color by altering ASIP transcriptional activity.