Identification and functional prediction of long non-coding RNAs related to skeletal muscle development in Duroc pigs

Lixia Ma; Ming Qin; Yulun Zhang; Hui Xue; Shiyin Li; Wei Chen; Yongqing Zeng

doi:10.5713/ab.22.0020

Animal Bioscience (Oct 2022)

Identification and functional prediction of long non-coding RNAs related to skeletal muscle development in Duroc pigs

Lixia Ma,
Ming Qin,
Yulun Zhang,
Hui Xue,
Shiyin Li,
Wei Chen,
Yongqing Zeng

Affiliations

Lixia Ma: Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai’an, Shandong 271018, China
Ming Qin: Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai’an, Shandong 271018, China
Yulun Zhang: Shandong Ding Tai Animal Husbandry Co. Ltd., Jinan, Shandong 250300, China
Hui Xue: Shandong Ding Tai Animal Husbandry Co. Ltd., Jinan, Shandong 250300, China
Shiyin Li: Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai’an, Shandong 271018, China
Wei Chen: Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai’an, Shandong 271018, China
Yongqing Zeng: Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai’an, Shandong 271018, China

DOI: https://doi.org/10.5713/ab.22.0020
Journal volume & issue: Vol. 35, no. 10
pp. 1512 – 1523

Abstract

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Objective The growth of pigs involves multiple regulatory mechanisms, and modern molecular breeding techniques can be used to understand the skeletal muscle growth and development to promote the selection process of pigs. This study aims to explore candidate lncRNAs and mRNAs related to skeletal muscle growth and development among Duroc pigs with different average daily gain (ADG). Methods A total of 8 pigs were selected and divided into two groups: H group (high-ADG) and L group (low-ADG). And followed by whole transcriptome sequencing to identify differentially expressed (DE) lncRNAs and mRNAs. Results In RNA-seq, 703 DE mRNAs (263 up-regulated and 440 down-regulated) and 74 DE lncRNAs (45 up-regulated and 29 down-regulated) were identified. In addition, 1,418 Transcription factors (TFs) were found. Compared with mRNAs, lncRNAs had fewer exons, shorter transcript length and open reading frame length. DE mRNAs and DE lncRNAs can form 417 lncRNA-mRNA pairs (antisense, cis and trans). DE mRNAs and target genes of lncRNAs were enriched in cellular processes, biological regulation, and regulation of biological processes. In addition, quantitative trait locus (QTL) analysis was used to detect the functions of DE mRNAs and lncRNAs, the most of DE mRNAs and target genes of lncRNAs were enriched in QTLs related to growth traits and skeletal muscle development. In single-nucleotide polymorphism/insertion-deletion (SNP/INDEL) analysis, 1,081,182 SNP and 131,721 INDEL were found, and transition was more than transversion. Over 60% of percentage were skipped exon events among alternative splicing events. Conclusion The results showed that different ADG among Duroc pigs with the same diet maybe due to the DE mRNAs and DE lncRNAs related to skeletal muscle growth and development.

Published in Animal Bioscience

ISSN: 2765-0189 (Print); 2765-0235 (Online)
Publisher: Asian-Australasian Association of Animal Production Societies
Country of publisher: Korea, Republic of
LCC subjects: Science: Zoology
Website: https://www.animbiosci.org/index.php

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