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 2 cashmere goat breeds and 6 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–κB and Wnt signaling pathways. Of them, LHX2, regulating hair follicle development, was evident from the strongest selection signal when comparing the Uhumqin cashmere goat and ordinary goat. Interestingly, we identified a 582-bp deletion at 367 kb upstream of LHX2 with higher frequency in cashmere goats and their ancient relatives. This mutation probably arose along with breeding procedures and is putatively responsible for cashmere production and diameter, as revealed by association studies. Luciferase assay showed that the 582-bp sequence, which acts as an insulator, restrains the expression of LHX2 by interfering with its upstream enhancers. Our findings provide new insights into the genetic formation of cashmere and facilitate subsequent molecular breeding for cashmere goat improvement.