Genome-wide association study of fleece traits in Inner Mongolia Cashmere goats

Abstract

Inner Mongolia Cashmere goat is a well-known local cashmere goat breed in China. It is famous for excellent fleece quality and a significant advantage in cashmere yield compared to other cashmere goat breeds. In this study, a genome-wide association study was used to investigate fiber length, fiber diameter, and cashmere yield of 192 Inner Mongolia Cashmere goats using the Illumina GoatSNP52K Beadchip panel. We discovered that four single nucleotide polymorphisms (SNPs) reached genome-wide significance levels. These SNPs were located in some genes, e.g. FGF12, SEMA3D, EVPL, and SOX5, possibly related to fleece traits in Inner Mongolia Cashmere goat. Gene ontology enrichment analysis revealed that these genes were enriched in several biological pathways that were involved in hair follicle development in cashmere goats. In summary, the identified significant SNPs and genes provide useful information to explore genetic mechanisms underlying the variation in fleece traits and genomic selection of Chinese cashmere goat.

Keywords: GoatSNP52K Beadchip; Inner Mongolia Cashmere goats; fleece traits; genome-wide association study.

Figure 1

Manhattan plots and quantile–quantile (Q‐Q) plots of fleece traits for Inner Mongolia Cashmere goats. Black and grey lines indicate the thresholds for genome‐wide significance levels and chromosome‐wide significance levels respectively. The Q‐Q plots show the observed vs expected log P‐values. (a) Fiber length; (b) fiber diameter; (c) cashmere yield.

Figure 2

Gene ontology (GO: a) and Kyoto Encyclopedia of Genes and Genomes (b) enrichment analysis for the regional candidate genes with chromosome‐wide significant association.