Integrative skin phenotypic and transcriptomic analyses reveal candidate genes for coat color and fiber length in four Chinese goat breeds (Capra hircus)

Coat color and fiber length are key traits for breed improvement and fiber production in goats. In this study, fiber samples and skin tissues were collected from four Chinese goat breeds: The solid black group (Dazu black goat and Yudong black goat) and the solid white group (Banjiao goat and Inner Mongolian cashmere goat). Fiber and skin color was evaluated, fiber length was measured, and skin transcriptome sequencing was performed using these samples. Our results showed that skin pigmentation was predominant in the epidermis, hair papilla, hair shaft, and outer root sheath of black goats. Specifically, the melanin content of the black goats' hair was approximately 22.2 times greater than that of the white goats (p < 0.05). Inner Mongolian cashmere goats had longer hair/cashmere length compared with the other breeds (p < 0.05). After reads mapping and gene quantification, differentially expressed genes (DEG) were identified. The Venn analysis between the black and white goats revealed seven overlapping upregulated genes and eight overlapping downregulated genes. Among these, melanogenesis-related genes including TYR, TYRP1, DCT, PMEL, SLC24A5, SLC45A2, and ASIP were validated using quantitative polymerase chain reaction (qPCR). Furthermore, 176 DEGs were identified between cashmere and non-cashmere goat breeds. Among them, fiber length-related genes (FOXQ1, HOXA10, and EDA2R) were differentially expressed, as found by qPCR. In conclusion, the comparative analyses of phenotypes and transcriptomes provide valuable insights into the genetic regulation of coat color and fiber length in goats and establish a foundation for future breeding programs and genetic selection strategies.