Li Li

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.

Meat quality characteristics are important economic traits of ducks. To identify the molecular bases of these traits, we performed an integrated multi-omics analysis (metabolomics, transcriptomics, and miRNAomics) that compared the breast muscle of 300-day-old Liancheng white duck (LD), which is a lean-type breed prized for its soup flavor, and traditional meat duck Cherry Valley duck (CD), which is a fast-growing fat-type breed used for roasting. The results show that LD had higher levels of amino and bile acids, while CD had higher levels of carbohydrates. Integration analysis revealed key breed-specific molecular signatures. In LD, upregulation of the amino acid transporters SLC7A6 and SLC6A9 related to amino acid transport was consistent with elevated intramuscular amino acids. For carbohydrate metabolism, SOCS3—a well-established negative regulator of glucose uptake in mammalian skeletal muscle—was significantly upregulated in LD, consistent with their lower intramuscular carbohydrate levels. SLC6A9 and SOCS3 were predicted to be negatively regulated by oan-miR-1386. In LD, upregulation of the bile acid biosynthesis gene CH25H paralleled the higher bile acid content, suggesting complex, tissue-specific regulation of these pathways. This integrated analysis provides a resource for candidate genes, miRNAs, and metabolic pathways underlying breed-specific meat quality traits in ducks. The findings generate testable hypotheses for future functional studies and offer potential molecular targets for breeding strategies aimed at improving poultry meat quality.