ORIGINAL RESEARCH article
Front. Mol. Biosci.
Sec. Protein Biochemistry for Basic and Applied Sciences
Deciphering Skeletal Muscle Trait Differences Between Chinese a nd Western Pig Breeds Based on 4D-label Ubiquitin-Proteomics
Yunlei Li 1
Zikai AI 1
Yun Zhang 1
Mingfu Xiong 1
Jingyang DONG 1
Yilong YAO 1
Yaxing LIU 1
Jian LI 1
Yongjin ZHANG 1,2
Xinhao FAN 1,2
Mengjuan WEI 1
Yongsheng ZHANG 1
Tao HUANG 1
1. Shihezi University, Shihezi, China
2. Chinese Academy of Agricultural Sciences, Beijing, China
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Abstract
To decipher post-transcriptional regulatory mechanisms underlying skeletal muscle trait differences between Chinese and W estern pig breeds, this study analyzed 30-day-old Duroc (Western) and Tibetan minipigs, as well as Bama minipigs (Chinese i ndigenous), using 4D-label ubiquitin proteomics of anterior tibialis muscles. It identified 762 ubiquitinated proteins, 1786 peptid es, and 2414 ubiquitination sites. Through differential and functional analyses, three core differentially ubiquitinated proteins (Z FC3H1, ATP2A1, and RAD23B) were found, associated with 21, 23, and 70 meat-quality QTLs, respectively. Bioinformatics a nalysis revealed that all proteins possessed intrinsically disordered regions, exhibit liquid-liquid phase separation (LLPS) capabili ty, and are expressed in skeletal muscle. Phosphorylation experiments confirmed higher RAD23B phosphorylation in Bama Fra grant pigs than in Duroc, verifying the negative regulation of phosphorylation on RAD23B ubiquitination. The study hypothesiz es that differences in ubiquitination of these proteins may affect LLPS and interact with phosphorylation to regulate myofibril formation, differentiation, and metabolism, thereby causing breed-specific differences in muscle growth and meat quality (this h ypothesis needs further verification). It provides new insights into the genetic mechanisms underlying porcine muscle and theor etical support for genetic improvement in pig meat production.
Summary
Keywords
ATP2A1, Phase Separation, pig, RAD23b, skeletal muscle, Ubiquitination, ZFC3H1
Received
04 November 2025
Accepted
22 January 2026
Copyright
© 2026 Li, AI, Zhang, Xiong, DONG, YAO, LIU, LI, ZHANG, FAN, WEI, ZHANG and HUANG. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
*Correspondence: Yongsheng ZHANG
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