Analysis of lncRNAs and Their Regulatory Network in Skeletal Muscle Development of the Yangtze River Delta White Goat.

Abstract

lncRNA (long non-coding RNA) has been confirmed to be associated with growth, development, cell proliferation, and other biological processes. This study explored the potential role and dynamic change process of lncRNAs and related ceRNA (competitive endogenous RNA) networks in skeletal muscle development of the Yangtze River Delta White (YDW) goat, and to analyze the differences in muscle fiber characteristics and meat quality levels of goats at different growth stages. In this study, we compared the expression profiles of lncRNAs in the M. Longissimus dorsi of the YDW goats at different stages of growth and development by RNA sequencing. The results revealed that, in terms of muscle fiber characteristics, muscle fiber diameter and muscle fiber area were significantly larger in 6-month-old and 10-month-old goats than those in 2-month-old goats (p < 0.01). In terms of muscle quality, a* and b* values of 6-month-old goats were significantly higher than those of 2-month-old goats (p < 0.01). Additionally, the a*, b*, and L* values of 6-month-old goats were significantly higher than those of 10-month-old goats (p < 0.01). The pH at 45 min post-mortem (pH_45min) in 10-month-old goats was significantly higher than that in 2-month-old goats (p = 0.006). However, the pH at 24 h post-mortem (pH_24h) in 10-month-old goats was significantly lower than that in both 2-month-old and 6-month-old goats (p < 0.01). Shear force increased gradually with age (p < 0.05), while there was no significant difference in drip loss among the different age groups (p > 0.05). Among the identified lncRNA expression profiles, a total of 3073 lncRNAs were found, including 2676 known lncRNAs and 397 novel lncRNAs. Of these, 110, 93, and 99 lncRNAs were specifically expressed in 2-month-old, 6-month-old, and 10-month-old goats, respectively. The lncRNA target gene enrichment analysis showed that they were mainly involved in actin binding, the actin cytoskeleton, the myocardin complex, as well as the AMPK, FoxO, and GnRH signaling pathways. When constructing the lncRNA-miRNA-mRNA ceRNA network, it was found that the ceRNA networks centered on chi-miR-758 and chi-miR-127-5p were involved in muscle development across all three periods, suggesting that they may play an important role in goat muscle growth and development.