Background: The cashmere goat is a biological resource that mainly produces cashmere. Cashmere has a soft hand feel and good luster, with high economic value. The quality and yield of cashmere are determined by the process of hair follicle development during the embryonic period. Methods: In this study, the skin of the Inner Mongolia cashmere goat at different embryonic stages (45, 55, 65, and 75d) was collected, and the differentially expressed lncRNA MSTRG.20890.1 at 75d was obtained by screening. Dual luciferase reporter gene system, qRT-PCR, and EDU experiments were used to verify further the regulatory role and molecular mechanism of the lncRNA in dermal fibroblasts. Results: Based on the transcriptome database of Inner Mongolia cashmere goat skin at different embryonic stages, which was previously constructed by our group, according to the characteristics of hair follicle development in the embryonic stage, we screened out the lncRNA MSTRG.20890.1 that was down-expressed on the 75-SHFINI day of the embryonic stage. We found that lncRNA MSTRG.20890.1 was mainly located in the cytoplasm of cells, and it could inhibit the proliferation and directional migration of dermal fibroblasts through the chi-miR-24-3p/ADAMTS3 signaling axis, thereby inhibiting the formation of dermal papilla structure at embryonic stage. Conclusions: This study revealed that lncRNA MSTRG.20890.1 regulated secondary hair follicle morphogenesis and development in cashmere goats through the chi-miR-24-3p/ADAMTS3 signaling axis.

In this study, genome-wide association analysis was performed on the growth traits (body height, body length, chest circumference, chest depth, chest width, tube circumference, and body weight) of Inner Mongolian cashmere goats (Erlangshan type) based on resequencing data. The population genetic parameters were estimated, haplotypes were constructed for the significant sites, and association analysis was conducted between the haplotypes and phenotypes. A total of two hundred and eighty-four SNPs and eight candidate genes were identified by genome-wide association analysis, gene annotation, and enrichment analysis. The phenotypes of 16 haplotype combinations were significantly different by haplotype analysis. Combined with the above results, the TGFB2, BAG3, ZEB2, KCNJ12, MIF, MAP2K3, HACD3, and MEGF11 functional candidate genes and the haplotype combinations A2A2, C2C2, E2E2, F2F2, I2I2, J2J2, K2K2, N2N2, O2O2, P2P2, R1R1, T1T1, W1W1, X1X1, Y1Y1, and Z1Z1 affected the growth traits of the cashmere goats and could be used as molecular markers to improve the accuracy of early selection and the economic benefits of breeding.

The Inner Mongolia cashmere goat is a local breed valued for both its cashmere and meat production. Early growth traits include birth weight and weaning weight. Generally, cashmere goats with higher birth and weaning weights tend to exhibit a higher carcass weight at slaughter. Consequently, exploring the genetic variation associated with these early growth traits is crucial in enhancing the meat production performance of Inner Mongolia cashmere goats. For this study, we performed genome-wide association analysis and haplotype analysis on the early growth traits of 212 Inner Mongolia cashmere goats (72 rams, 140 ewes) to identify molecular markers and haplotypes significantly associated with birth and weaning weights. Through genome-wide association analysis and gene annotation, we identified 21 SNPs and 117 candidate genes linked to early growth traits. Notably, genes such as RUNX1T1, ERBIN, MYO15B, NT5C, GRB2, ITGB4, and GALK emerged as significant factors influencing the early growth of Inner Mongolia cashmere goats. Additionally, nine haplotype blocks related to early growth traits were constructed, resulting in eight haplotype combinations. In conclusion, the haplotype combinations A1A1, C1C1, and D1D1 were found to be beneficial for the genetic improvement of early growth traits in Inner Mongolia cashmere goats.

The development of secondary hair follicles in cashmere goats directly influences the yield and quality of cashmere, and hair follicle morphogenesis is a complex biological process involving multiple signaling pathways and regulatory factors. In recent years, the regulatory role of long non-coding RNAs in hair follicle development has gradually been uncovered. Based on a previously established transcriptome database of embryonic skin tissue from cashmere goats, this study ultimately identified lncRNA MRPS28, which exhibits significant differential expression during the morphogenesis of secondary hair follicles. Our results indicate that lncRNA MRPS28 is a non-coding RNA transcribed from the intron region of the MRPS28 gene. Additionally, it can inhibit the proliferation and migration of dermal fibroblasts while promoting their apoptosis. Further mechanistic studies have shown that lncRNA MRPS28 acts as a competing endogenous RNA, sponging chi-miR-145-5p, thereby relieving its inhibitory effect on the target gene NUAK1. This, in turn, inhibits the formation of dermal papilla structures and ultimately affects the morphogenesis of secondary hair follicles during the embryonic period. This study provides a novel perspective on dissecting the regulatory network of hair follicle development in cashmere goats and offers potential theoretical insights for breeding new strains of cashmere goats.

Non-coding negative regulation is an important but incompletely resolved component of gene-expression control in livestock. We conducted a narrative review using PubMed, Web of Science Core Collection, and Scopus, prioritizing primary studies in pigs, cattle, sheep, goats, and poultry and using model-organism studies only for directly relevant mechanistic or methodological evidence. We distinguish sequence-defined silencers, context-dependent enhancer-silencer elements, functional microRNA-binding sites, long non-coding RNA-associated regulation, and candidate repressive chromatin regions, and evaluate representative livestock studies using a four-tier framework comprising candidate annotation, molecular functional evidence, endogenous causal evidence, and animal-level validation. Current evidence is strongest for a small number of loci, whereas many of the livestock candidates reviewed here are supported primarily by association, chromatin state, or in vitro assays. We further assess how multi-omics data can prioritize candidates and assign target genes, while emphasizing that reporter activity, repressive chromatin marks, and population association do not establish endogenous causality. Progress will depend on locus-specific perturbation, rescue experiments, relevant animal phenotyping, and inheritance testing. This evidence-centered framework provides a focused basis for interpreting negative regulatory variation in livestock and identifying robust targets for future genetic improvement.

Background: Long non-coding RNAs (lncRNAs) are important regulators of developmental gene expression, but their roles during key windows of embryonic hair follicle morphogenesis in cashmere goats remain unclear. This study aimed to identify temporally specific lncRNAs associated with early hair follicle development and to evaluate a candidate cytoplasmic lncRNA and its potential regulatory relationship in an in vitro dermal fibroblast model. Results: Temporal screening identified 32 candidate lncRNAs with transient, stage-specific expression changes at embryonic day 55, suggesting that this stage may represent an important window of transcriptional regulation associated with embryonic hair follicle morphogenesis. Enrichment analysis showed positive enrichment of Wnt-related gene sets in the day 55 vs. day 45 and day 65 vs. day 55 comparisons; however, this finding does not constitute a direct measurement of Wnt pathway activity. Among the prioritized candidates, MSTRG.18075.2 showed relatively high expression at day 55 and was predominantly localized to the cytoplasm. In a heterologous 293T-cell reporter system, chi-miR-145-5p reduced the activity of wild-type reporters containing the predicted MSTRG.18075.2 or WNT16 3’ UTR site, whereas the corresponding mutant reporters did not show the same changes, supporting sequence-specific reporter responses mediated by these predicted sites. In cashmere goat dermal fibroblasts, MSTRG.18075.2 knockdown was associated with reduced apoptosis, slower cell-cycle progression, impaired proliferation and migration, and increased intracellular reactive oxygen species (ROS). Combined knockdown of chi-miR-145-5p partially reversed some phenotypes induced by MSTRG.18075.2 or WNT16 knockdown. These results are consistent with a candidate MSTRG.18075.2/chi-miR-145-5p/WNT16 regulatory model. Conclusions: This study provides supporting evidence for a relationship between MSTRG.18075.2 and the candidate chi-miR-145-5p/WNT16 regulatory axis at the levels of temporal expression, cytoplasmic localization, sequence-specific reporter responses, and in vitro cellular phenotypes. Because endogenous RNA complexes, downstream Wnt activity, and effects on hair follicle morphogenesis in vivo were not examined, the current findings do not directly establish an endogenous ceRNA mechanism or a causal relationship in vivo.