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. 2020 Oct 18;10(10):1905.
doi: 10.3390/ani10101905.

Genetic Signatures of Selection for Cashmere Traits in Chinese Goats

Meilin Jin  1 , Jian Lu  2 , Xiaojuan Fei  1 , Zengkui Lu  3 , Kai Quan  4 , Yongbin Liu  5 , Mingxing Chu  1 , Ran Di  1 , Huihua Wang  1 , Caihong Wei  1
Affiliations

Genetic Signatures of Selection for Cashmere Traits in Chinese Goats

Meilin Jin et al. Animals (Basel). .

Abstract

Inner Mongolia and Liaoning cashmere goats in China are well-known for their cashmere quality and yield. Thus, they are great models for identifying genomic regions associated with cashmere traits. Herein, 53 Inner Mongolia cashmere goats, Liaoning cashmere goats and Huanghuai goats were genotyped, and 53,347 single-nucleotide polymorphisms (SNPs) were produced using the Illumina Caprine 50K SNP chip. Additionally, we identified some positively selected SNPs by analyzing Fst and XP-EHH. The top 5% of SNPs had selection signatures. After gene annotation, 222 and 173 candidate genes were identified in Inner Mongolia and Liaoning cashmere goats, respectively. Several genes were related to hair follicle development, such as TRPS1, WDR74, LRRC14, SPTLC3, IGF1R, PADI2, FOXP1, WNT10A and CSN3. Gene enrichment analysis of these cashmere trait-associated genes related 67 enriched signaling pathways that mainly participate in hair follicle development and stem cell pluripotency regulation. Furthermore, we identified 20 overlapping genes that were selected in both cashmere goat breeds. Among these overlapping genes, WNT10A and CSN3, which are associated with hair follicle development, are potentially involved in cashmere production. These findings may improve molecular breeding of cashmere goats in the future.

Keywords: Fst; XP-EHH; cashmere goat; cashmere trait.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
(a) Geographic map indicating the distribution of the Cashmere goats sampled in this study (Photographs were reference from Animal Genetic resources in China sheep and goats [8]). Map of sample locations in the present study. The map was created using the R package “map tools”, URL: http://rforge.r-project.org/projects/maptools/. (b) Neighbour-joining (NJ) phylogenetic tree for the six breeds based on pairwise Fst. Each population is represented by a different colour and symbol label: Liaoning Cashmere goats are indicated in red; Inner Mongolia Cashmere goats are indicated in orange and Huanghuai goats are yellow. (c) Plots for the first (Component 1) and second (Component 2) dimensions revealed the clustering of six breeds (Inner Mongolia Cashmere goat, Chengdu goat, Longlin goat, Liaoning Cashmere goat, Huanghuai goat and Daiyun goat). (d) Population structure of six goat breeds inferred by ADMIXTURE results from K = 2–3 are shown.
Figure 2
Figure 2
(a) Venn diagrams of each breed s selection genes from XP-EHH and Fst approaches; (b) Venn diagram of specific selection genes in three breeds.
Figure 3
Figure 3
Genome-wide distribution of FST and XP-EHH values. red dots represent sites showing significant signal in the Fst approach or XP-EHH approach. (a) Inner Mongolia Cashmere goat by Fst values. (b) Liaoning Cashmere goat breed by Fst values. (c) Inner Mongolia Cashmere goat by XP-EHH values. (d) Liaoning Cashmere goat breed by XP-EHH values.
See this image and copyright information in PMC

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