Whole-genome selection signatures identified candidate genes associated with cashmere traits in Inner Mongolia Cashmere Goats.

Abstract

Objective: Inner Mongolia cashmere goats are superior indigenous breeds developed through long-term natural selection and systematic artificial selection, which have experienced a certain intensity of selection pressure during the breeding process, leading to bipolar differentiation trends in cashmere traits. Therefore, identifying genomic selection signatures associated with cashmere traits in Inner Mongolia cashmere goats is crucial for breeding high-quality cashmere-producing goats.

Methods: To unravel the genetic basis of cashmere traits, this study stratified 375 Inner Mongolia cashmere goats into eight subgroups based on breeding values for cashmere traits: high-yield vs low-yield cashmere types (HYCG vs LYCG), fine vs coarse cashmere types (FCG vs CCG), long vs short cashmere types (LCG vs SCG), and long vs short fleece types (LFCG vs SFCG). Whole-genome resequencing was performed for genotyping, followed by detection of selection signatures.

Results: Results revealed 144, 158, 147, and 147 high-frequency ROH regions in HYCG, FCG, LCG, and LFCG subgroups, respectively, annotating to 515, 565, 510, and 521 genes. Additionally, genomic regions under positive selection were identified using FST, θπ ratios, and XP-EHH methods, with overlapping regions detected by ≥2 methods defined as candidate regions. Gene annotation identified 777, 660, 712, and 726 candidate genes in HYCG vs LYCG, FCG vs CCG, LCG vs SCG, and LFCG vs SFCG comparisons, respectively. These genes were enriched in 3,051 GO terms and 318 KEGG pathways, including Hippo, MAPK, Wnt, PI3K-Akt, and mTOR signaling pathways associated with cashmere growth and development, involving genes such as LGR6, RUNX2,IGF1R, CCNE2, and SEH1L.

Conclusion: In this study, we employed four complementary approaches, including ROHs, FST, θπ ratios, and XP-EHH, to identify genomic signatures of selection for cashmere traits in Inner Mongolia cashmere goats. These findings provide valuable insights for improving cashmere production performance and developing novel strains with high-quality cashmere in Inner Mongolia cashmere goats.