Kiran Zahra

Cashmere production declines with age in Inner Mongolian cashmere goats, but the molecular mechanisms are unknown. This study employed a transcriptome-wide RNA-seq analysis to compare age-associated and breed-related gene expression profiles in goat skin, with particular emphasis on age-dependent AKT1 expression and its associated signaling pathways. Skin tissues from cashmere goats at 12 and 15 months and age-matched non-cashmere controls were analyzed by RNA-seq (BGIDNBSEQ platform). Differential expression and functional enrichment analyses were performed on skin transcriptomes of cashmere and control goats at 12 and 15 months. Age-specific functional profiles emerged: 12-month cashmere goats showed enrichment in GTPase activity, glucose transport, and ribosomal assembly, whereas 15-month goats were enriched for autophagosome assembly and apoptosis. FoxO signaling was commonly enriched across both ages, while the Hepatitis B pathway was unique to 12 months. AKT1 was significantly upregulated at 12 months coinciding with peak cashmere production with reduced expression at 15 months. This age-dependent pattern was supported by coordinated regulation of downstream effectors, including TSC2, PIK3R2, MAPK9, and FOXO3. Collectively, these transcriptomic data provide a mechanistic framework linking age-dependent AKT1 regulation to the decline in cashmere fiber production.

Background: Inter-species hybridization has been extensively used in breeding cervids to improve productive traits by hybrid vigor, but the genomic processes behind the process are not well studied. Methods: In this study, we investigated restriction-site-associated DNA sequencing (RAD-seq) to conduct a whole-genome analysis of Hua-Ma hybrid individuals (a cross of sika deer and Tianshan red deer). Results: A total of 571,835 SNPs were obtained and 427,121 high-quality SNPs were obtained from five individuals upon strict filtering. An analysis of genetic diversity has shown that the observed heterozygosity (Ho = 0.2130) was lower than expected heterozygosity (He = 0.3560). Although these estimates provide preliminary insights into the genetic diversity of the sampled Hua-Ma hybrids, they should be interpreted cautiously because of the limited sample size. After the pruning of linkage disequilibrium, 189,975 independent SNPs underwent principal component analysis (PCA). The first two principal components (PC1 = 32.6%, PC2 = 26.2%) indicate relative genomic clustering rather than definitive ancestry assignments. These patterns reflect relative genomic clustering rather than definitive ancestry assignments. Conclusions: The high polymorphic loci were functionally annotated and revealed the existence of synonymous and nonsynonymous variants, including a conserved locus adjacent to the BEND5 gene that exhibited a nonsynonymous mutation generating a valine-to-isoleucine amino acid substitution which may have potential functional relevance, although no phenotypic effects were evaluated in this study. On the whole, these results suggest heterozygosity and mixed ancestry in Hua-Ma hybrids. This exploratory study provides an initial SNP resource that may support future genomic selection, parentage analysis, and breeding optimization efforts.

Cashmere goats produce high-value fine fibers derived from secondary hair follicles; however, the molecular mechanisms underlying this trait remain incompletely understood. In this study, comparative transcriptome sequencing was performed on skin tissues from Inner Mongolian cashmere goats and normal goats to characterize gene expression differences associated with cashmere fiber production. High-quality RNA-seq data with strong mapping efficiency and reproducibility were obtained across all samples. Differential expression analysis identified 1543 significantly differentially expressed genes (DEGs) between cashmere and normal goats, including genes involved in hair follicle morphogenesis, epidermal differentiation, cell proliferation, and extracellular matrix organization. Multivariate analyses showed a clear transcriptomic separation between fleece types, indicating that fleece phenotype is the primary driver of variation in global gene expression. Functional enrichment revealed significant involvement of the Wnt, MAPK, and PI3K–Akt signaling pathways, and several biologically relevant regulators of hair follicle development and hair cycle control, including FGF5, SOX9, LHX2, and VDR, were differentially expressed. Gene fusion events were rare and showed no group specific patterns, whereas alternative splicing was widespread, with exon skipping as the predominant splicing event in goat skin. Overall, these results provide quantitative transcriptomic evidence linking signaling regulation, follicle development, and structural differentiation to secondary hair follicle activity and cashmere fiber formation, offering candidate genes and molecular pathways for functional validation and molecular breeding in cashmere goats.