Melanin Deposition and Screening of Melanogenesis-Related Differential RNAs and Construction of ceRNA Regulatory Network in Liancheng White Ducks

Liancheng white ducks have a distinctive “white feathers, black beak, and green feet” phenotype, making them a useful model for studying pigmentation traits in waterfowl. The previous study found that the F1 generation of Liancheng white ducks crossed with white-feathered ducks and hemp-feathered ducks were all gray-black in color. This indicates the specificity and complexity of melanin deposition in Liancheng white ducks, which makes the selection and breeding of pigment traits through phenotyping difficult. The aim of this study was to investigate the candidate transcriptomic regulatory signals of melanogenesis in Liancheng white ducks. Skin, mouth skin, foot skin, liver, and muscle samples were collected from 130-day-old Liancheng white ducks. Morphological differences were observed via histological analysis, and extraction-based pigment levels were determined. The results showed that melanin granules were clearly observed in tissues other than the liver and were distributed mainly in the basal layer of the epidermis and around feather follicles; the pigment values in the tissues decreased in the order mouth skin > liver > foot skin > muscle and skin. However, the relatively high liver value should be interpreted cautiously because obvious melanin granule deposition was not observed histologically. Whole-transcriptome sequencing was performed on mouth skin and skin samples. In total, 3074 differentially expressed genes (DEGs) were screened; upregulated genes associated with melanogenesis included melanocyte inducing transcription factor (MITF) and tyrosinase (TYR); downregulated genes included agouti signaling protein (ASIP) and adenylate cyclase 2 (ADCY2). Eighteen differentially expressed microRNAs (DEmiRNAs) were identified. Based on target prediction and pathway enrichment analysis, novel_290 and apl-miR-11588-3p were identified as candidate miRNAs potentially associated with melanogenesis-related pathways, and their predicted target genes included phosphatidylinositol 3-kinase (PI3K) and Janus kinase 1 (JAK1). Additionally, 364 differentially expressed long noncoding RNAs (DElncRNAs) were identified; TCONS_00063335 and TCONS_00019814 were identified as candidate lncRNAs potentially associated with melanogenesis-related genes, including TYR and TYRP1. A putative ceRNA network was constructed based on the predicted miRNA–mRNA and miRNA–lncRNA relationships, and ENSAPLT00000025522–apl-miR-11588-3p–MAPK8IP3 was identified as a candidate network relationship associated with MAPK-related pigmentation pathways. However, because this relationship was inferred mainly from bioinformatic prediction and expression association analysis, further functional validation is required to confirm whether it contributes to melanogenesis regulation. These findings provide candidate transcriptomic and noncoding RNA information for the further investigation of tissue-specific pigmentation in Liancheng white ducks.