Gene co-expression network analysis to identify critical modules and candidate genes of drought-resistance in wheat

Liangjie Lv; Wenying Zhang; Lijing Sun; Aiju Zhao; Yingjun Zhang; Limei Wang; Yuping Liu; Ziqian Li; Hui Li; Xiyong Chen

doi:10.1371/journal.pone.0236186

Gene co-expression network analysis to identify critical modules and candidate genes of drought-resistance in wheat

PLoS One. 2020 Aug 31;15(8):e0236186. doi: 10.1371/journal.pone.0236186. eCollection 2020.

Authors

Liangjie Lv¹, Wenying Zhang², Lijing Sun¹, Aiju Zhao¹, Yingjun Zhang¹, Limei Wang¹, Yuping Liu¹, Ziqian Li¹, Hui Li¹, Xiyong Chen¹

Affiliations

¹ Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Crop Genetics and Breeding Laboratory of Hebei, Shijiazhuang, China.
² Institute of Dryland Farming Hebei Academy of Agricultural and Forestry Sciences, Hengshui, China.

Abstract

Aim: To establish a gene co-expression network for identifying principal modules and hub genes that are associated with drought resistance mechanisms, analyzing their mechanisms, and exploring candidate genes.

Methods and findings: 42 data sets including PRJNA380841 and PRJNA369686 were used to construct the co-expression network through weighted gene co-expression network analysis (WGCNA). A total of 1,896,897,901 (284.30 Gb) clean reads and 35,021 differentially expressed genes (DEGs) were obtained from 42 samples. Functional enrichment analysis indicated that photosynthesis, DNA replication, glycolysis/gluconeogenesis, starch and sucrose metabolism, arginine and proline metabolism, and cell cycle were significantly influenced by drought stress. Furthermore, the DEGs with similar expression patterns, detected by K-means clustering, were grouped into 29 clusters. Genes involved in the modules, such as dark turquoise, yellow, and brown, were found to be appreciably linked with drought resistance. Twelve central, greatly correlated genes in stage-specific modules were subsequently confirmed and validated at the transcription levels, including TraesCS7D01G417600.1 (PP2C), TraesCS5B01G565300.1 (ERF), TraesCS4A01G068200.1 (HSP), TraesCS2D01G033200.1 (HSP90), TraesCS6B01G425300.1 (RBD), TraesCS7A01G499200.1 (P450), TraesCS4A01G118400.1 (MYB), TraesCS2B01G415500.1 (STK), TraesCS1A01G129300.1 (MYB), TraesCS2D01G326900.1 (ALDH), TraesCS3D01G227400.1 (WRKY), and TraesCS3B01G144800.1 (GT).

Conclusions: Analyzing the response of wheat to drought stress during different growth stages, we have detected three modules and 12 hub genes that are associated with drought resistance mechanisms, and five of those genes are newly identified for drought resistance. The references provided by these modules will promote the understanding of the drought-resistance mechanism. In addition, the candidate genes can be used as a basis of transgenic or molecular marker-assisted selection for improving the drought resistance and increasing the yields of wheat.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Acclimatization / genetics*
China
Cluster Analysis
Datasets as Topic
Droughts
Gene Expression Profiling
Gene Expression Regulation, Plant*
Gene Regulatory Networks*
Genes, Plant
Plant Breeding / methods
RNA-Seq
Selection, Genetic
Stress, Physiological / genetics*
Triticum / genetics*

Grants and funding

This study was financially supported by the HAAFS Agriculture Science and Technology Innovation Project (2019-4-6-02;4-09-04-01) to LL; Special Foundation of Hebei Academy of Agriculture and Forestry Sciences (2018060303) to LL; Earmarked Fund for Hebei Wheat Innovation Team of Modern Agro-industry Technology Research System (HBCT2018010201) to HL; Key Research and Development Program of china (CN) (2017YF00100603) to LL; Natural Science Foundation of Hebei Province (C2020301004) to LL. We have received funds for covering the costs to publish in open access. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.