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Plant Molecular Biology

, Volume 97, Issue 6, pp 489–506 | Cite as

Coexpression network revealing the plasticity and robustness of population transcriptome during the initial stage of domesticating energy crop Miscanthus lutarioriparius

  • Shilai Xing
  • Chengcheng Tao
  • Zhihong Song
  • Wei Liu
  • Juan Yan
  • Lifang Kang
  • Cong Lin
  • Tao Sang
Article

Abstract

Key message

Coexpression network revealing genes with Co-variation Expression pattern (CE) and those with Top rank of Expression fold change (TE) played different roles in responding to new environment of Miscanthus lutarioriparius.

Abstract

Variation in gene expression level, the product of genetic and/or environmental perturbation, determines the robustness-to-plasticity spectrum of a phenotype in plants. Understanding how expression variation of plant population response to a new field is crucial to domesticate energy crops. Weighted Gene Coexpression Network Analysis (WGCNA) was used to explore the patterns of expression variation based on 72 Miscanthus lutarioriparius transcriptomes from two contrasting environments, one near the native habitat and the other in one harsh domesticating region. The 932 genes with Co-variation Expression pattern (CE) and other 932 genes with Top rank of Expression fold change (TE) were identified and the former were strongly associated with the water use efficiency (r ≥ 0.55, P ≤ 10−7). Functional enrichment of CE genes were related to three organelles, which well matched the annotation of twelve motifs identified from their conserved noncoding sequence; while TE genes were mostly related to biotic and/or abiotic stress. The expression robustness of CE genes with high genetic diversity kept relatively stable between environments while the harsh environment reduced the expression robustness of TE genes with low genetic diversity. The expression plasticity of CE genes was increased less than that of TE genes. These results suggested that expression variation of CE genes and TE genes could account for the robustness and plasticity of acclimation ability of Miscanthus, respectively. The patterns of expression variation revealed by transcriptomic network would shed new light on breeding and domestication of energy crops.

Keywords

Miscanthus lutarioriparius Gene coexpression network Expression variation Genetic diversity Acclimation 

Abbreviations

WGCNA

Weighted gene coexpression network analysis

CE

Co-variation expression pattern

TE

Top rank of expression fold change

JH

Jiangxia in Hubei Province

QG

Qingyang in Gansu Province

WUE

Water use efficiency

A

CO2 assimilation rate

E

Transpiration rate

FPKM

Expected number of fragments per kilobase of transcript sequence per millions base pairs sequenced

ANOVA

Analysis of variance

TO

Topological overlap

ME

Module eigengene

GO

Gene ontology

KEGG

Kyoto encyclopedia of genes and genomes

SNPs

Single-nucleotide polymorphism

dS

The synonymous substitution rates

dN

Non-synonymous substitution rates

Ep

Average expression level

Ed

Expression diversity

π

Genetic diversity

NC

Non-differential change

Notes

Acknowledgements

This study was supported by the National Key Research and Development Program of China (No. 2016YFC0500905), the grants from the National Natural Science Foundation of China (31000147; 31400284), the Project for Autonomous Deployment of the Wuhan Botanical Garden (55Y755271G02) and the Science and Technology Service Network Initiative of the Chinese Academy of Sciences (KFJ-EW-STS-061).

Author contributions

TS conceived and designed the experiments. SX, ZS, JY, CL and LK performed the experiments. SX, ZS and WL performed data analysis. SX, CT, JY and TS wrote the manuscript. All authors read and approved the final manuscript.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

11103_2018_754_MOESM1_ESM.xls (46.1 mb)
Supplementary material 1 (XLS 47221 KB)
11103_2018_754_MOESM2_ESM.docx (445 kb)
Supplementary material 2 (DOCX 445 KB)

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Copyright information

© Springer Nature B.V. 2018

Authors and Affiliations

  1. 1.State Key Laboratory of Systematic and Evolutionary Botany, Institute of BotanyChinese Academy of SciencesBeijingChina
  2. 2.Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of BotanyChinese Academy of SciencesBeijingChina
  3. 3.Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical GardenChinese Academy of SciencesWuhanChina
  4. 4.University of Chinese Academy of SciencesBeijingChina

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