Comparative Transcriptome Analyses of Longissimus thoracis Between Pig Breeds Differing in Muscle Characteristics

Cai, Chunbo; Li, Meng; Zhang, Yanwei; Meng, Shu; Yang, Yang; Gao, Pengfei; Guo, Xiaohong; Cao, Guoqing

doi:10.3389/fgene.2020.526309

Cited by 24 publications

(15 citation statements)

References 41 publications

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Section: Discussionmentioning

confidence: 99%

“…A better understanding of molecular biology of prenatal skeletal muscle development can help to improve animal health as well as meat production. Different pig breeds are commercially used for meat production that vary in feed efficiency, growth rate, fat content and distribution, as well as the transcriptomic profile [30,31]. Genes are master regulators of almost all biological processes and pathways [32], hence analysis of the transcriptomic profile can be useful to better understand the growth and performance of a particular animal species or breed.…”

Section: Discussionmentioning

confidence: 99%

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In Utero Fetal Weight in Pigs Is Regulated by microRNAs and Their Target Genes

Ali

Muráni

Hadlich

et al. 2021

Genes

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Impaired skeletal muscle growth in utero can result in reduced birth weight and poor carcass quality in pigs. Recently, we showed the role of microRNAs (miRNAs) and their target genes in prenatal skeletal muscle development and pathogenesis of intrauterine growth restriction (IUGR). In this study, we performed an integrative miRNA-mRNA transcriptomic analysis in longissimus dorsi muscle (LDM) of pig fetuses at 63 days post conception (dpc) to identify miRNAs and genes correlated to fetal weight. We found 13 miRNAs in LDM significantly correlated to fetal weight, including miR-140, miR-186, miR-101, miR-15, miR-24, miR-29, miR-449, miR-27, miR-142, miR-99, miR-181, miR-199, and miR-210. The expression of these miRNAs decreased with an increase in fetal weight. We also identified 1315 genes significantly correlated to fetal weight at 63 dpc, of which 135 genes were negatively correlated as well as identified as potential targets of the above-listed 13 miRNAs. These miRNAs and their target genes enriched pathways and biological processes important for fetal growth, development, and metabolism. These results indicate that the transcriptomic profile of skeletal muscle can be used to predict fetal weight, and miRNAs correlated to fetal weight can serve as potential biomarkers of prenatal fetal health and growth.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

In Utero Fetal Weight in Pigs Is Regulated by microRNAs and Their Target Genes

Ali

Muráni

Hadlich

et al. 2021

Genes

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“…In the biological process category of GO enrichment, mainly processes related to muscle cell differentiation and muscle development were enriched, among which actin cytoskeleton organization was the most significant ( Figure 3B ). Moreover, 74 KEGG pathways were significantly enriched ( P ≤ 0.05), many of which are involved in muscle development, such as the Wnt signaling pathway, the AMPK signaling pathway, and the Hippo signaling pathway ( 29 – 31 ). We showed 12 classical pathways associated with muscle development in Figure 3C .…”

Section: Resultsmentioning

confidence: 99%

“…( Figure 4D ). These downregulated DEmRNAs were enriched in protein digestion and absorption, starch and sucrose metabolism, the mTOR signaling pathway, ABC transporters, and the TGF-beta signaling pathway ( Figure 4E ) ( 29 – 31 ). This suggested that DEmRNAs may be involved in maintaining intramuscular homeostasis and muscle development.…”

Section: Resultsmentioning

confidence: 99%

Integrative ATAC-seq and RNA-seq Analysis of the Longissimus Muscle of Luchuan and Duroc Pigs

Miao

Tang

et al. 2021

Front. Nutr.

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Luchuan pig is a typical obese pig breed in China, and the diameter and area of its longissimus dorsi muscle fibers are significantly smaller than those of Duroc (lean) pig. Skeletal muscle fiber characteristics are related to meat quality of livestock. There is a significant correlation between the quality of different breeds of pork and the characteristics of muscle fiber, which is an important factor affecting the quality of pork. The diameter and area of muscle fibers are related to muscle growth and development. Therefore, we used the assay for transposase-accessible chromatin using sequencing (ATAC-seq) and RNA sequencing (RNA-seq) analysis to investigate the potential mechanism underlying the difference in skeletal muscle growth and development between the two types of pigs. First, transposase-accessible chromatin was analyzed to map the landscape of open chromatin regions and transcription factor binding sites. We identified several transcription factors that potentially affected muscle growth and development, including TFAP4, MAX, NHLH1, FRX5, and TGIF1. We also found that transcription factors with basic helix-loop-helix structures had a preference for binding to genes involved in muscle development. Then, by integrating ATAC-seq and RNA-seq, we found that the Wnt signaling pathway, the mTOR signaling pathway, and other classical pathways regulate skeletal muscle development. In addition, some pathways that might regulate skeletal muscle growth, such as parathyroid hormone synthesis, secretion, and action, synthesis and degradation of ketone bodies, and the thyroid hormone signaling pathway, which were significantly enriched. After further study, we identified a number of candidate genes (ASNS, CARNS1, G0S2, PPP1R14C, and SH3BP5) that might be associated with muscle development. We also found that the differential regulation of chromatin openness at the level of some genes was contrary to the differential regulation at the level of transcription, suggesting that transcription factors and transcriptional repressors may be involved in the regulation of gene expression. Our study provided an in-depth understanding of the mechanism behind the differences in muscle fibers from two species of pig and provided an important foundation for further research on improving the quality of pork.

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“…Therefore, the pork with high IMF content and good eating quality is generally favored by consumers (1,2). There are considerable variations in IMF contents among different pig breeds, especially between western commercial pig breeds and Chinese native pig breeds (3)(4)(5), which suggests that heredity is a major determinant of IMF. In fact, a large number of quantitative trait loci (QTL) or candidate genes for IMF have been identified by linkage and genomewide association (GWA) studies.…”

Section: Introductionmentioning

confidence: 99%

Evidence Against the Causal Relationship Between a Putative Cis-Regulatory Variant of MYH3 and Intramuscular Fat Content in Pigs

et al. 2021

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Improving meat quality has become the main goal of modern pig breeding. Intramuscular fat content (IMF) is an important trait influencing meat quality of livestock, but the molecular mechanism behind this trait is still unclear. Recently, Cho et al. reported the discovery of the first causal mutation affecting IMF and red flesh color (a*) in pigs, namely XM_013981330.2:g.−1805_−1810del, a 6-bp deletion variant in the porcine MYH3 promoter region. The objective of this study was to reassess the causality of this mutation for its potential commercial application. By Sanger sequencing, we firstly identified several new variants (including a 4-bp deletion) at or near the 6-bp deletion site, which formed four haplotypes in multiple breeds. Unexpectedly, the 6-bp deletion allele, previously determined as the MYH3 Q allele because of its significantly positive effect on IMF and a*, was found not only in Chinese indigenous breeds, but also in four western commercial breeds with relatively lower IMF levels, including Duroc, Large White, Landrace and Pietrain. More surprisingly, we found that the MYH3 Q allele and the haplotypes harboring it had no significant effects on IMF, marbling and color score in three large-scale divergent pig populations: the heterogeneous F6 and F7 pigs and commercial crossbred Duroc × (Landrace × Yorkshire) pigs. Transient transfection analysis in porcine satellite cells showed that the 6-bp deletion variants had a negligible effect on transcription of reporter gene, but could attenuate the MRF (myogenesis regulatory factors)-induced increase in luciferase activity of the MYH3 promoter vector. The MYH3 protein level in muscle did not differ significantly among the haplotype groups. Therefore, our results cannot support the causal relationship between the 6-bp deletion in MYH3 and IMF trait, suggesting that the causal mutation for the IMF QTL on SSC12 needs to be further identified.

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Comparative Transcriptome Analyses of Longissimus thoracis Between Pig Breeds Differing in Muscle Characteristics

Cited by 24 publications

References 41 publications

In Utero Fetal Weight in Pigs Is Regulated by microRNAs and Their Target Genes

In Utero Fetal Weight in Pigs Is Regulated by microRNAs and Their Target Genes

Integrative ATAC-seq and RNA-seq Analysis of the Longissimus Muscle of Luchuan and Duroc Pigs

Evidence Against the Causal Relationship Between a Putative Cis-Regulatory Variant of MYH3 and Intramuscular Fat Content in Pigs

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