Phenotypic, transcriptomic, and genomic analyses reveal the spatiotemporal patterns and associated genes of coarse hair density in goats

The genetic regulation of hair density in animals remains poorly understood. The Dazu black goat, characterized by its black coarse hair and white skin, provides a unique model for dissecting coarse hair density (CHD). Using high-resolution micro-camera imaging, this study analyzed 905 skin images, 33 skin transcriptomes, 272 whole-genome sequences, and 182 downloaded transcriptomes. Morphological assessment from juvenile to adult stages revealed the thickening of hair shafts accompanied by a progressive decline in density, largely attributable to rapid surface expansion of the trunk skin. Transcriptomic comparison between high- and low-CHD individuals identified 572 differentially expressed genes (DEGs). A genome-wide association study detected 25 significant single nucleotide polymorphisms ( <i>P</i><9.07e-8) and mapped 48 annotated genes, with the most prominent association signal located near <i>GJA1</i> on chr9.15931585-18621011. Literature review and Venn analysis highlighted six genes ( <i>GJA1</i>, <i>GPRC5D</i>, <i>CD1D</i>, <i>CD207</i>, <i>TFAM</i>, and <i>CXCL12</i>) with documented roles in skin and hair biology, and three genes ( <i>GJA1</i>, <i>GPRC5D</i>, and <i>ATP6V1B1</i>) overlapped with DEGs. Multiple-tissue transcriptomic profiling, western blotting, immunohistochemical staining, and skin single-cell RNA sequencing confirmed that <i>GJA1</i> and <i>GPRC5D</i> were highly and specifically expressed in skin, particularly within hair follicles. Expression was localized predominantly to follicular stem cells and dermal papilla cells, suggesting a significant role in folliculogenesis and structural maintenance. Cross-validation using four public datasets further demonstrated positive correlations between <i>GJA1</i> and <i>GPRC5D</i> expression and hair follicle density. The innovative micro-camera application allowed the elucidation of spatiotemporal patterns and genes associated with CHD, thereby addressing a significant knowledge gap in animal hair density.