影响藏猪与大约克夏猪肌肉品质的lncRNA的筛选及功能分析

doi:10.11843/j.issn.0366-6964.2022.01.006

Abstract

Abstract: This study aimed to identify the long non-coding RNAs (lncRNAs) and genes related to pork quality traits of the longissimus dorsi in Tibetan pigs and Yorkshire pigs (180 days old), and to further explore their molecular regulatory role, which could provide theoretical basis for the improvement breeding of pork quality traits. According to previously published data, 180-day-old healthy Tibetan boars (n=3) and Yorkshire boars (n=3) raised under the same conditions were used as the research objects to collect phenotype data of the quality of the longissimus dorsi and the transcriptome data of the longissimus dorsi of the same individual were used to screen differentially expressed lncRNAs and differentially expressed genes (DEGs). Cis- and trans-target DEGs were predicted based on the positional relationship and expression correlation of differentially expressed lncRNAs and DEGs, then trans-target DEGs were enriched by GO biological processes and KEGG pathway analysis. Subsequently, lncRNAs-DEGs-biological process regulatory network related to muscle growth and fat deposition was constructed. Then, association events between candidate target genes and meat quality traits were analyzed, which comprised of drip loss, pH, meat color, marbling, intramuscular fat content, muscle fiber cross-sectional area, loin muscle area and vitamin B₁ content. A total of 1 546 lncRNAs and 20 219 mRNAs were identified in the longissimus dorsi of Tibetan pigs and Yorkshire pigs,there were 49 differentially expressed lncRNAs and 154 DEGs of them based on statistical analysis. Of these, 7 cis and 138 trans regulatory DEGs targeted by differentially expressed lncRNAs were predicted. Functional enrichment analysis showed that a large number of candidate DEGs were significantly enriched in biological processes of muscle growth and fat deposition, including positive regulation of phosphatidylinositol 3-kinase signaling, muscle structure development, fat cell differentiation, positive regulation of JAK-STAT cascade, and positive regulation of MAPK cascade, etc. Evidence from regulatory network showed that MSTRG.34836.10 and MSTRG.151.1 had the most target DEGs, followed by MSTRG.21406.1, MSTRG.26709.1. Association analysis indicated that 11 candidate target DEGs were significantly related to the meat quality traits. Taken together, some differentially expressed lncRNAs identified in this study were related to muscle growth and fat deposition. It was also suggested that these differentially expressed lncRNAs had an effect on pork quality by regulating the expression of HES1, LEP, TGFB2, and PER2. This study laid the foundation for further analysis of the potential molecular mechanism of pork quality traits.

Key words: Tibetan pig, Yorkshire pig, RNA-seq, lncRNAs, meat quality traits

CLC Number:

S828.2

SONG Mingkun, XUE Mingming, ZHANG Lige, YAN Duo, XIA Ning, SHANG Peng, LI Xinjian, HAN Xuelei, QIAO Ruimin, LI Xiuling, LI Ming, WANG Kejun. Screening and Functional Analysis of lncRNA Affecting Muscle Quality in Tibetan and Yorkshire Pigs[J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(1): 53-65.

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Screening and Functional Analysis of lncRNA Affecting Muscle Quality in Tibetan and Yorkshire Pigs

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