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Volume 9
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10.3390/plants9050596
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Article

Comparative Analysis of Root Transcriptome Reveals Candidate Genes and Expression Divergence of Homoeologous Genes in Response to Water Stress in Wheat

by
Behnam Derakhshani
1,2,
Habtamu Ayalew
3,
Kohei Mishina
4,
Tsuyoshi Tanaka
5,6,
Yoshihiro Kawahara
5,6,
Hossein Jafary
7 and
Youko Oono
2,*
1
Department of Agronomy & Plant Breeding, Faculty of Agriculture, University of Zanjan, Zanjan 45371-38791, Iran
2
Breeding Material Development Unit, Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba 305-8518, Japan
3
Small Grains Breeding Laboratory, Noble Research Institute LLC, Ardmore, OK 73401, USA
4
Plant Genome Research Unit, Institute of Crop Science, NARO, Tsukuba 305-8518, Japan
5
Breeding Informatics Research Unit, Institute of Crop Science, NARO, Tsukuba 305-8518, Japan
6
Bioinformatics Team, Advanced Analysis Center, NARO, Tsukuba 305-8518, Japan
7
Iranian Research Institute of Plant Protection, Agricultural Research, Education and Extension Organization (AREEO), Tehran 19395-1454, Iran
*
Author to whom correspondence should be addressed.
Plants 2020, 9(5), 596; https://doi.org/10.3390/plants9050596
Submission received: 1 March 2020 / Revised: 15 April 2020 / Accepted: 3 May 2020 / Published: 7 May 2020
(This article belongs to the Section Plant Molecular Biology)
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Abstract

Crop cultivars with larger root systems have an increased ability to absorb water and nutrients under conditions of water deficit. To unravel the molecular mechanism of water-stress tolerance in wheat, we performed RNA-seq analysis on the two genotypes, Colotana 296-52 (Colotana) and Tincurrin, contrasting the root growth under polyethylene-glycol-induced water-stress treatment. Out of a total of 35,047 differentially expressed genes, 3692 were specifically upregulated in drought-tolerant Colotana under water stress. Transcription factors, pyrroline-5-carboxylate reductase and late-embryogenesis-abundant proteins were among upregulated genes in Colotana. Variant calling between Colotana and Tincurrin detected 15,207 SNPs and Indels, which may affect protein function and mediate the contrasting root length phenotype. Finally, the expression patterns of five triads in response to water, high-salinity, heat, and cold stresses were analyzed using qRT-PCR to see if there were differences in homoeologous gene expression in response to those conditions. The five examined triads showed variation in the contribution of homoeologous genes to water, high-salinity, heat, and cold stresses in the two genotypes. The variation of homoeologous gene expression in response to environmental stresses may enable plants to better cope with stresses in their natural environments.
Keywords: wheat; water stress; abiotic stress; homoeolog gene expression; RNA-Seq wheat; water stress; abiotic stress; homoeolog gene expression; RNA-Seq

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MDPI and ACS Style

Derakhshani, B.; Ayalew, H.; Mishina, K.; Tanaka, T.; Kawahara, Y.; Jafary, H.; Oono, Y. Comparative Analysis of Root Transcriptome Reveals Candidate Genes and Expression Divergence of Homoeologous Genes in Response to Water Stress in Wheat. Plants 2020, 9, 596. https://doi.org/10.3390/plants9050596

AMA Style

Derakhshani B, Ayalew H, Mishina K, Tanaka T, Kawahara Y, Jafary H, Oono Y. Comparative Analysis of Root Transcriptome Reveals Candidate Genes and Expression Divergence of Homoeologous Genes in Response to Water Stress in Wheat. Plants. 2020; 9(5):596. https://doi.org/10.3390/plants9050596

Chicago/Turabian Style

Derakhshani, Behnam, Habtamu Ayalew, Kohei Mishina, Tsuyoshi Tanaka, Yoshihiro Kawahara, Hossein Jafary, and Youko Oono. 2020. "Comparative Analysis of Root Transcriptome Reveals Candidate Genes and Expression Divergence of Homoeologous Genes in Response to Water Stress in Wheat" Plants 9, no. 5: 596. https://doi.org/10.3390/plants9050596

APA Style

Derakhshani, B., Ayalew, H., Mishina, K., Tanaka, T., Kawahara, Y., Jafary, H., & Oono, Y. (2020). Comparative Analysis of Root Transcriptome Reveals Candidate Genes and Expression Divergence of Homoeologous Genes in Response to Water Stress in Wheat. Plants, 9(5), 596. https://doi.org/10.3390/plants9050596

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