Integrative metabolome and transcriptome analyses provide insights into skeletal muscle development of two duck breeds during embryonic stage

Zhigang Hu; Yingjie Cai; Zhuo Zhi; Mengmeng Cui; Huiya Zhang; Jie Zhou; Jianqin Zhang; Xiaolin Liu

doi:10.1016/j.psj.2026.106444

Integrative metabolome and transcriptome analyses provide insights into skeletal muscle development of two duck breeds during embryonic stage

Poult Sci. 2026 Jan 14;105(4):106444. doi: 10.1016/j.psj.2026.106444. Online ahead of print.

Authors

Zhigang Hu¹, Yingjie Cai¹, Zhuo Zhi¹, Mengmeng Cui¹, Huiya Zhang¹, Jie Zhou¹, Jianqin Zhang¹, Xiaolin Liu²

Affiliations

¹ College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.
² College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China. Electronic address: liuxiaolin@nwsuaf.edu.cn.

Abstract

Yulin black duck with an all black body, is a native duck breed from Guangxi Province, China, and people like to use the duck to make soup because its meat is considered as a nutritious food and medicinal herb. At present, the molecular mechanisms related to its meat characteristics are still unclear. Furthermore, the differences in muscle development between Yulin black duck and Pekin duck need to be thoroughly investigated. This study aims to elucidate the disparities in muscle development between the two duck breeds and provide foundational data to enhance our understanding of the meat production mechanisms in Yulin black duck. In this study, three embryonic developmental stages (E15, E21 and E27) of Pekin duck and Yulin black duck were selected to investigate muscle development. Integrated transcriptomics and metabolomics were jointly analyzed to compare the significantly different metabolites (SDMs) and differentially expressed genes (DEGs) associated with muscle development between the two duck breeds at identical embryonic stages. The RNA-seq results were further validated using qRT-PCR. The results revealed a total of 106 DEGs in BME 15 vs. PME 15 (BM: the muscle of Yulin black duck, PM: the muscle of Pekin duck), with 57 genes up-regulated and 49 genes down-regulated. A total of 135 DEGs were identified in BME 21 vs. PME 21, including 74 up-regulated and 84 down-regulated genes. In BME 27 vs. PME 27, 65 DEGs were up-regulated, and 70 were down-regulated. As important DEGs about muscle development, CLDN18, PRKAR2B, PHGDH, GPT2, ASL, WIF1, CHRM5, NTNG1, and LOC101804261 were identified. Significant metabolic pathways included the Wnt signaling pathway (apla04310), regulation of the actin cytoskeleton (apla04810), biosynthesis of amino acids (apla01230), cell adhesion molecules (apla04514), and the insulin signaling pathway (apla04910). Meanwhile, 68, 80, and 69 differential metabolites were identified at three embryonic development stages (E15, E21, and E27), primarily involving the glycerophospholipid category: PE(22:4/0:0), PE(P-16:0/22:6(4Z,7Z,10Z,13Z,16Z,19Z)), PE(15:0/0:0), and PG 38:5. Combined analysis demonstrated that ETNPPL exhibited a negative correlation with the expression of differential metabolites such as PG and PI in the glycerophospholipid metabolism pathway. In contrast, HDC and acetylhistamine showed a positive correlation in the histidine metabolism pathway. Additionally, GAD1, which was involved in the alanine, aspartate, and glutamate metabolism pathway, displayed a negative correlation with specific metabolites. In conclusions, CLDN18, PRKAR2B, PHGDH, GPT2, ASL, WIF1, CHRM5, NTNG1, and LOC101804261 were important DEGs in the breast muscles of the Pekin duck and Yulin black duck at the same period of the embryonic stage, and the SDMs of the two duck species were mainly glycerophospholipids. Significant metabolic pathways included the Wnt signaling pathway, regulation of the actin cytoskeleton, biosynthesis of amino acids, cell adhesion molecules, and the insulin signaling pathway. These results will provide effective information and more evidence for further exploring the regulatory mechanisms of skeletal muscle development in duck breeds.

Keywords: Duck; Metabolome; Regulatory mechanism; Skeletal muscle; Transcriptome.