Whole-Genome Sequencing of Cashmere Goats Identify Genes Related to Fleece Traits

Inner Mongolia (including three subtypes: Erlangshan, Alashan, and Aerbasi) and Liaoning Cashmere goats are well-known indigenous breeds in China, characterized by superior fiber quality and high cashmere yield respectively. Here, we sequenced genomes of 54 Inner Mongolia and 19 Liaoning cashmere goats to identify the genes that related to fleece traits. A total of 4,356,754 SNPs and 194,273 Indels were identified in the Cashmere goats population by aligning the filtered reads against CHIR_2.0 of the goat genome. The expected heterozygosity (He), observed heterozygosity (Ho) and inbreeding coefficients (Fis) of each Cashmere goat breed were also obtained, respectively. Higher inbreeding coefficients were observed in Erlangshan and Alashan subtypes, the values are 0.2466 and 0.2507, respectively. An empirical genome-wide distribution of Fst (F-statistics) was constructed based on haplotype-based test to detect selective signals between Liaoning and Inner Mongolia cashmere goats. Interestingly, we highlighted several genes including BMP7, DVL1, KIF3A and CFDP that show signatures of selection are likely associated with fleece traits. All of these will provide a foundation for better understanding the genetic variation associated with fleece traits and aid in protection of native genetic resources.