# Integrated miRNAs, Transcriptome, and Metabolome Uncover Underlying Mechanisms for Breast Muscle Metabolic Regulation in Liancheng White and Cherry Valley Ducks

## TL;DR

This study uses multi-omics to uncover genes and miRNAs linked to meat quality differences in two duck breeds, offering insights for improving poultry meat traits.

## Contribution

The study integrates metabolomics, transcriptomics, and miRNA data to identify breed-specific molecular mechanisms affecting duck meat quality.

## Key findings

- Liancheng ducks had higher amino and bile acids, while Cherry Valley ducks had higher carbohydrates.
- SLC6A9, SLC7A6, and SOCS3 were differentially expressed and linked to metabolic traits.
- oan-miR-1386 was identified as a key miRNA regulating these genes.

## Abstract

This study aimed to identify specific metabolites, genes, and regulatory miRNAs associated with differences in meat quality and nutritional value between two duck breeds: the Liancheng white duck (LD) and a common meat-type Cherry Valley duck (CD). Using metabolomics, RNA-seq, and miRNA-seq, we compared the composition differences between their breast muscles. The results show that LD contained higher levels of amino and bile acids, while CD was richer in carbohydrates. Transcriptome analysis revealed differentially expressed genes (FDR < 0.05, |log2(Fold Change)| > 1) linked to these metabolic differences, including amino acid transporters (SLC6A9, SLC7A6), a carbohydrate metabolism regulator (SOCS3), and a bile acid synthesis gene (CH25H). Key regulatory miRNAs, such as oan-miR-1386 (which is predicted to target SLC6A9 and SOCS3), were also identified. These findings provide a molecular foundation for improved meat quality and nutritional value from breeding ducks and offer candidate targets for future functional validation and marker-assisted selection.

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.