Supporting data for "Selection signatures in goats reveal a novel deletion mutant underlying cashmere yield and diameter"

Cashmere traits were deployed for fiber yield and quality during the domestication of goats. However, the genetic alterations underlying cashmere trait selection are still unclear. We sequenced 120 Chinese native goats including two cashmere goat breeds and six ordinary goat breeds. The genome-wide selective sweep of cashmere goat and ordinary goat revealed a novel set of candidate genes as well as pathways, such as Nuclear factor kappa-B and Wnt Signaling pathways. Of them, the <i>LHX2</i> gene regulating hair follicle development, was evident from the strongest selection signal when comparing the Uhumqin cashmere goat and ordinary goat. Interestingly, we identified a 582bp deletion at 367 kb upstream of <i>LHX2</i> with higher frequency in cashmere goats and their ancient relatives. This mutation probably rises along the breeding procedures, and is putatively responsible for cashmere production and diameter, as revealed by association studies. Luciferase assay shows that the deletion, which acts as an insulator, restrains the expression of <i>LHX2</i> by interfering its upstream enhancers. Our study discovers a novel insulator of the <i>LHX2</i> involved in regulating cashmere production and diameter. Our findings also provide new insights into the genetic formation of cashmere, and facilitate subsequent molecular breeding for cashmere goat improvement.