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.

Differential fecundity in goats is a complex trait governed by coordinated molecular regulation across reproductive and endocrine tissues. In this study, we performed integrated metabolomic profiling of follicular fluid, serum, thyroid tissue, and uterine luminal fluid together with transcriptomic sequencing of follicular, thyroid, and uterine horn tissues from high-fecundity (HF) and low-fecundity (LF) Yangtze River Delta White goats. In addition, weighted gene co-expression network analysis (WGCNA) was conducted to elucidate the molecular mechanisms underlying differential litter size. High-fecundity goats exhibited enhanced follicular steroidogenesis, superior corpus luteum function, and more stable hypothalamic–pituitary–thyroid (HPT) axis activity, accompanied by increased uterine gland density and greater myometrial thickness. Metabolomic profiling identified 6640 metabolites displaying tissue-specific differential abundance patterns. Pathway enrichment analysis highlighted steroid hormone biosynthesis and energy metabolism in follicular fluid, PPAR signaling and tyrosine metabolism in thyroid tissue, and glycerophospholipid and one-carbon metabolism in uterine luminal fluid as major pathways associated with fecundity. Transcriptomic analysis identified 1596 differentially expressed genes (DEGs), including 20 genes shared across all examined tissues, constituting a systemic molecular signature associated with fecundity. WGCNA further revealed three functional tissue axes associated with follicular development (ELOVL4, INHA, NR5A2), thyroid endocrine regulation (GRHL2, NAPRT), and uterine receptivity (RSPO1, AGTR2, PTGER3). Low-fecundity-associated modules were predominantly concentrated in follicular and thyroid tissues, whereas the high-fecundity-specific module was mainly enriched in uterine horn. These findings provide a multi-tissue molecular framework underlying differential fecundity in goats and identify candidate hub genes and metabolites that may serve as candidate biomarkers for fecundity assessment and selective breeding programs.