Animal skeletal muscle growth is regulated by a complex molecular network including some non-coding RNAs (ncRNAs). In this paper, we review the non-coding RNAs related to the growth and development of common animal skeletal muscles, aiming to provide a reference for the in-depth study of the role of ncRNAs in the development of animal skeletal muscles, and to provide new ideas for the improvement of animal production performance.

Copy number variations (CNV) are important genetic variations. The endogenous factors cobalamin receptor (CUBN) and MIA SH3 domain ER-derived factor 3 (MIA3) are associated with bone/muscle development and intramuscular fat deposition. There have been no reports on the effects of CUBN and MIA3 CNVs on growth traits of Chinese cattle. This study aimed to determine the correlation between the CUBN and MIA3 CNVs and growth traits in Chinese cattle. qRT-PCR was used to detect the distribution of CUBN and MIA3 CNV and the expression levels of their mRNA, and correlation analysis was conducted between CNV and growth traits. The CUBN was differentially expressed in different breeds of cattle, and CUBN CNV correlated significantly with body height, hip height, body slanting length, and hip width of Grassland Red cattle (CYH); eye muscle area of Yanbian cattle (YB) and Yan Yellow cattle (YH). MIA3 showed no CNV in CYH and YB cattle, and only one deletion type occurred in YH cattle. CUBN and MIA3 mRNA have different expression patterns in different cattle breeds and tissues. In conclusion, CUBN CNV is correlated significantly with growth traits in Chinese cattle and is a novel molecular marker that could be exploited in cattle breeding.

Intramuscular fat (IMF) deposition drives premium beef value, but phenotypic selection is costly and slow. Although genome-wide studies have linked the KIRREL3 region to meat quality, whether intronic variants directly affect carcass traits and retain predictive power across physiological stages remains unproven. We genotyped two intronic SNPs (g.29756010C>T and g.29756149C>T) in Woking cattle, a high-quality beef breed developed in Jilin Province, China (n = 473; 226 and 206 heifers at 36 and 48 months, respectively, plus an independent validation cohort of n = 41), assessed for fatty acid composition, meat quality, and multi-tissue gene expression. Both loci were polymorphic and in Hardy–Weinberg equilibrium. At 36 months, TT individuals showed higher dressing percentage, rib thickness, and meat grade than CC at both loci. By 48 months, the 63-bp locus retained broader associations with carcass traits, whereas the 203-bp locus effects weakened. In the validation group, CC animals had higher IMF and muscle KIRREL3 expression than TT, yet received lower meat grades. Five fatty acids differed significantly among genotypes after Benjamini–Hochberg correction (q < 0.05), whereas the dominant fatty acids (C16:0, C18:1n9c, C18:0, C18:2n6c) showed no proportional differences. KIRREL3 was most highly expressed in the kidney among eight tissues examined. These findings identify the 63-bp site as a candidate marker for meat quality in local Chinese cattle, with potential for marker-assisted selection pending confirmation in larger cohorts and functional studies.

Intramuscular fat (IMF) deposition is the primary economic driver of premium beef production, yet conventional phenotypic selection requires costly rearing to slaughter age. Although whole-genome sequencing has repeatedly flagged the KIRREL3 region on BTA29 as a candidate interval for meat quality in beef cattle, whether intronic polymorphisms within this gene are directly associated with carcass or meat-quality traits--and whether such marker effects remain stable across physiological stages--has not been validated. To address these gaps, we genotyped two intronic SNPs in KIRREL3 (g.30324329C>T, 63-bp site; g.30324473C>T, 203-bp site) in two age cohorts of Woking heifers (n = 226 at 36 months; n = 206 at 48 months), together with an independent validation cohort (n = 41) for fatty-acid profiling, meat-quality phenotyping, and multi-tissue expression analysis. Both loci were moderately polymorphic (PIC = 0.37) and in Hardy-Weinberg equilibrium. At 36 months, the TT genotype was associated with significantly higher dressing percentage, rib thickness, and meat grade than CC at both loci. By 48 months, associations at the 63-bp site persisted and the T allele showed complete dominance (CT and TT both exceeded CC in grade and rib thickness), whereas associations at the 203-bp site dissipated with age, showing no significant effect on intermuscular fat thickness or grade. In the validation cohort, palmitic acid (C16:0), linolenic acid (C18:3n3), and arachidonic acid (C20:4) followed a CC > TC >= TT trend (P < 0.05). Notably, CC animals displayed higher IMF and muscle KIRREL3 mRNA levels than TT animals, yet received lower meat grades--a pattern that awaits functional clarification. These findings identify KIRREL3 g.30324329C>T as a robust age-stable marker, providing a concrete target for early marker-assisted selection in Woking cattle.