Transcriptome analysis of rice-seedling roots under soil–salt stress using RNA-Seq method

被引:1
作者
Anil Kumar Nalini Chandran
Jeong-Won Kim
Yo-Han Yoo
Hye Lin Park
Yeon-Ju Kim
Man-Ho Cho
Ki-Hong Jung
机构
[1] Kyung Hee University,Graduate School of Biotechnology and Crop Biotech Institute
[2] Kyung Hee University,Graduate School of Biotechnology and College of Life Science
[3] Kyung Hee University,Department of Oriental Medicinal Materials and Processing
来源
Plant Biotechnology Reports | 2019年 / 13卷
关键词
Gene ontology; MapMan; Rice; Root; RNA-Seq; Salt stress;
D O I
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中图分类号
学科分类号
摘要
Soil salinity is a major production constrain for agricultural crops, especially in Oryza sativa (rice). Analyzing physiological effect and molecular mechanism under salt stress is key for developing stress-tolerant plants. Roots system has a major role in coping with the osmotic change impacted by salinity and few salt-stress-related transcriptome studies in rice have been previously reported. However, transcriptome data sets using rice roots grown in soil condition are more relevant for further applications, but have not yet been available. The present work analyzed rice root and shoot physiological characteristics in response to salt stress using 250 mM NaCl for different timepoints. Subsequently, we identified that 5 day treatment is critical timepoint for stress response in the specific experimental design. We then generated RNA-Seq-based transcriptome data set with rice roots treated with 250 mM NaCl for 5 days along with untreated controls in soil condition using rice japonica cultivar Chilbo. We identified 447 upregulated genes under salt stress with more than fourfold changes (p value < 0.05, FDR < 0.05) and used qRT-PCR for six genes to confirm their salt-dependent induction patterns. GO-enrichment analysis indicated that carbohydrate and amino-acid metabolic process are significantly affected by the salt stress. MapMan overview analysis indicated that secondary metabolite-related genes are induced under salt stress. Metabolites profiling analysis confirmed that phenolics and flavonoids accumulate in root under salt stress. We further constructed a functional network consisting of regulatory genes based on predicted protein–protein interactions, suggesting useful regulatory molecular network for future applications.
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页码:567 / 578
页数:11
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