Abstract
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.
Highlights
Porcine skeletal muscle is one of the main sources of protein for the Chinese people, and skeletal muscle accounts for 40% of the body weight [1]
Phenotype and ATAC-seq Quality Control of the Duroc and Luchuan Pig Muscle Tissues. It is well-known that the meat quality of Luchuan pigs is higher than that of Duroc pigs, partially because the diameter and area of muscle fiber of Luchuan pigs are smaller than those in Duroc pigs (Figure 1A)
In this study we present a novel method for identifying regions of open chromatin and predicting transcription factors (TFAP4, MAX, NHLH1, FRX5, and TGIF1), involved in the regulation of muscle development in different breeds of pigs
Summary
Porcine skeletal muscle is one of the main sources of protein for the Chinese people, and skeletal muscle accounts for 40% of the body weight [1]. One reason is that muscle fiber size affects the size of the muscle bundle, resulting in coarser muscle transverse sections [7, 8] Another reason is that the size of muscle fiber is related to tenderness; the smaller the muscle fiber, the lower the shear force, the better the tenderness and the better the meat quality [6]. The diameter and area of the longissimus dorsi muscle fibers are significantly smaller than those of Duroc pigs They are good models for studying the molecular mechanism underlying differences in meat quality. Studies on the differences between the longissimus dorsi muscle fibers of Luchuan and Duroc pigs can provide a direction for improving meat quality
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