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Previous studies have concentrated on the periodic growth regulation of hair follicles in Inner Mongolia cashmere goats (IMCGs), identifying numerous candidate genes that influence cashmere traits. Research on the factors and regulatory mechanisms affecting cashmere fineness in different body parts is currently limited.Methods: The differences of cashmere fineness traits among different body parts or ages were determined by multiple comparison analysis testing in analysis of variance. RNA-seq and Gene Ontology (GO) &amp; Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were used to assess the differentially expressed genes (DEGs) across different body parts of IMCGs. The candidate genes were validated using quantitative realtime polymerase chain reaction techniques.Results: Ages and different body parts had significant effects on cashmere diameter of IMCGs (p&lt;0.05). Cashmere diameter was coarsest in the abdomen, but finest in the neck and back. A total of 2,178 DEGs were specifically screened among four body parts based on cashmere diameter. GO and KEGG analyses showed that these DEGs were mainly enriched in signaling pathways related to hair growth, such as MAPK signaling pathway and extracellular matrix-receptor interaction. The expression of MATN2 and CA12 were consistent with the phenotype of cashmere fineness in different body parts.Conclusion: The differences of cashmere fineness among different body parts of IMCGs were investigated through transcriptome and phenotype analysis, which provide a basis for understanding molecular regulation of cashmere growth in cashmere goats. ATN2 and CA12 have been validated as regulatory genes influencing the heterogeneity of cashmere fineness in various parts of IMCGs.<\/jats:p>","DOI":"10.5713\/ab.25.0119","type":"journal-article","created":{"date-parts":[[2025,7,11]],"date-time":"2025-07-11T05:37:33Z","timestamp":1752212253000},"page":"2612-2623","update-policy":"https:\/\/doi.org\/10.5713\/crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Comparative analysis of skin transcriptome reveals differences of cashmere fineness in different body parts of Inner Mongolia cashmere 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