Genome-wide association analysis of cashmere traits in Inner Mongolia Arbas cashmere goats

The aim of this study is to explore the important variation sites and candidate genes for the cashmere traits of Inner Mongolia Arbas cashmere goats through genome-wide association analysis (GWAS), and to provide important molecular markers for the genetic improvement of this breed. Four core cashmere-related phenotypic traits, including cashmere thickness (CT), cashmere fineness (CF), wool length (WL) and cashmere yield (CY), were measured from 2,299 Inner Mongolia Arbas cashmere goats. All individuals were genotyped using a goat 70 K SNP chip, and a mixed linear model was established for GWAS incorporating phenotypic data, environmental effects, and individual genotypes. The candidate genes were enriched by GO and KEGG pathways. Then, the significant sites were validated using Kompetitive Allele-Specific PCR (KASP). The results showed that a total of 66 candidate genes were identified on the whole genome, among which RUNX3 , RSRP1 , LDLRAP1 , TEC , LRPAP1 , RGS12 , PLCG1 , AFAP1 and NOP14 may be candidate genes affecting the cashmere traits of cashmere goats. The results of GO function and KEGG pathway enrichment analysis showed that regulation of transcription by RNA polymerase II, signal transduction and tissue regeneration are the key processes. The polymorphism of two significant SNPs were further verified using KASP. A statistically significant genotyping difference was identified at site 6:115473655_ A > T ( P < 0.01). The candidate genes and associated SNPs identified through GWAS in Inner Mongolia Arbas Cashmere Goats, which are related to cashmere traits, provide crucial molecular evidence to guide future breeding strategies for these economically important characteristics.