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ORIGINAL RESEARCH article

Front. Vet. Sci.
Sec. Livestock Genomics
Volume 11 - 2024 | doi: 10.3389/fvets.2024.1431248

Muscle Growth Differences in Lijiang Pigs Revealed by ATAC-seq Multi-omics

Provisionally accepted
Yi LAN Yi LAN 1*Dawei YAN Dawei YAN 1*Xinpeng LI Xinpeng LI 1*Chunlu ZHOU Chunlu ZHOU 1*Ying BAI Ying BAI 2*Xinxing DONG Xinxing DONG 1*
  • 1 Yunnan Agricultural University, Kunming, China
  • 2 College of Life Sciences and Food Engineering, Hebei University of Engineering, Handan, Hebei Province, China

The final, formatted version of the article will be published soon.

    As one of the largest tissues in the animal body, skeletal muscle plays a pivotal role in the production and quality of pork. Consequently, it is of paramount importance to investigate the growth and developmental processes of skeletal muscle.Lijiang pigs, which naturally have two subtypes, fast-growing and slow-growing, provide an ideal model for such studies by eliminating breed-related influences. In this study, we selected 3 fast-growing and 3 slow-growing 6-month-old Lijiang pigs as subjects. We utilized assay for transposase-accessible chromatin with sequencing (ATAC-seq) combined with genomics, RNA sequencing, and proteomics to screen for differentially expressed genes and transcription factors linked to increased longissimus dorsi muscle volume in Lijiang pigs. We identified 126 genes through ATAC-seq, including PPARA, TNRC6B, NEDD1, and FKBP5, that exhibited differential expression patterns during muscle growth . Additionally, we identified 59 transcription factors, including Foxh1, JunB, Mef2 family members (Mef2a/b/c/d), NeuroD1, and TEAD4. By examining open chromatin regions (OCRs) with significant genetic differentiation, genes such as SAV1, CACNA1H, PRKCG, and FGFR4 were found. Integrating ATAC-seq with transcriptomics and transcriptomics with proteomics, we identified differences in open chromatin regions, transcription, and protein levels of FKBP5 and SCARB2 genes in fast-growing and slow-growing Lijiang pigs. Utilizing multi-omics analysis with R packages, we jointed ATAC-seq, transcriptome, and proteome datasets, identifying enriched pathways related to glycogen metabolism and skeletal muscle cell differentiation. We pinpointed genes such as MYF6 and HABP2 that exhibit strong correlations across these diverse data types. This study provides a multi-faceted understanding of the molecular mechanisms that lead to differences in pig muscle fiber growth.

    Keywords: ATAC-seq, multi-omics, Growth, Muscle, Lijiang pigs

    Received: 11 May 2024; Accepted: 07 Aug 2024.

    Copyright: © 2024 LAN, YAN, LI, ZHOU, BAI and DONG. 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:
    Yi LAN, Yunnan Agricultural University, Kunming, China
    Dawei YAN, Yunnan Agricultural University, Kunming, China
    Xinpeng LI, Yunnan Agricultural University, Kunming, China
    Chunlu ZHOU, Yunnan Agricultural University, Kunming, China
    Ying BAI, College of Life Sciences and Food Engineering, Hebei University of Engineering, Handan, 056021, Hebei Province, China
    Xinxing DONG, Yunnan Agricultural University, Kunming, China

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