Identification of the Key Genes Associated with Different Hair Types in the Inner Mongolia Cashmere Goat

Abstract

The Inner Mongolia cashmere goat is an excellent local breed in China. According to the characteristics of wool quilts, the Inner Mongolia cashmere goat can be divided into three types: a long-hair type (hair length of >22 cm), a short-hair type (hair length of ≤13 cm), and an intermediate type (hair length of >13 cm and ≤22 cm). It is found that hair length has a certain reference value for the indirect selection of other important economic traits of cashmere. In order to explore the molecular mechanisms and related regulatory genes of the different hair types, a weighted gene coexpression network analysis (WGCNA) was carried out on the gene expression data and phenotypic data of 12-month-old Inner Mongolia cashmere goats with a long-hair type (LHG) and a short-hair type (SHG) to explore the coexpression modules related to different coat types and nine candidate genes, and detect the relative expression of key candidate genes. The results showed that the WGCNA divided these genes into 19 coexpression modules and found that there was a strong correlation between one module and different hair types. The expression trends of this module’s genes were different in the two hair types, with high expression in the LHG and low expression in the SHG. GO functions are mainly concentrated in cellular components, including intermediate filaments (GO:0005882), intermediate filament cytoskeletons (GO:0045111), and cytoskeletal parts (GO:0044430). The KEGG pathway is mainly enriched in arginine as well as proline metabolism (chx00330) and the MAPK signaling pathway (chx04010). The candidate genes of the different hair types, including the KRT39, KRT74, LOC100861184, LOC102177231, LOC102178767, LOC102179881, LOC106503203, LOC108638293, and LOC108638298 genes, were screened. Through qRT-PCR, it was found that there were significant differences in these candidate genes between the two hair types, and most of them had a significant positive correlation with hair length. It was preliminarily inferred that these candidate genes could regulate the different hair types of cashmere goats and provide molecular markers for hair growth.

Keywords: Inner Mongolia cashmere goats; KRT; WGCNA; different hair types; hair growth.

Figure 1

Photographs of long-hair-type and short-hair-type cashmere goats. (A) Long-hair-type cashmere goat, (B) short-hair-type cashmere goat.

Figure 2

Construction of the weighted gene coexpression network. (A) Hierarchical clustering information of samples, (B) soft threshold filtering, the red line is β = 0.8, and the red number represents the β value, (C) gene coexpression network gene clustering number, and (D) network heatmap of gene–gene, different colors represent different gene modules.

Figure 3

Module–properties relationships. Abscissa is the properties and the ordinate is the module name. The number in the grid indicates the Pearson correlation coefficient between the module and the character. The closer the value is to ± 1, the stronger the correlation between the module and the character is, and the number in parentheses represents a significant p-value. The Pearson correlation coefficient judged the correlation between module genes and phenotypic traits, and the p-value judged the significant degree of correlation.

Figure 4

Magenta module function analysis. (A) Heatmap of the magenta module’s gene expression patterns, (B) GO analysis of the magenta module, and (C) KEGG enrichment analysis of the magenta module.

Figure 5

Gene coexpression network in the magenta module. The genes framed in red are the genes of the intermediate filaments (GO:0005882), the genes framed in yellow are arginine and proline metabolism (chx00330), the genes framed in green are the MAPK signaling pathway (chx04010), and the genes with a yellow background are the candidate genes.

Figure 6

Gene expression trends of the candidate genes. (A–N) Abscissa is month, anagen (April to November), catagen (December to January), and telogen (February to March); ordinate is the FPKM.

Figure 7

The relative expressions of the candidate genes. (A–K) Abscissa indicates period, anagen (September), catagen (December), and telogen (March); ordinate was relative expression quantity F = 2^−ΔΔCT, ** indicates extremely significant difference, * indicates significant difference, and ns indicates no significant difference.