Comparative RNA-Seq analysis of the root revealed transcriptional regulation system for aluminum tolerance in contrastin
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ORIGINAL ARTICLE
Comparative RNA-Seq analysis of the root revealed transcriptional regulation system for aluminum tolerance in contrasting indica rice of North East India Jay Prakash Awasthi 1 & Kazutaka Kusunoki 2 & Bedabrata Saha 1,3 Sanjib Kumar Panda 1,4
&
Yuriko Kobayashi 2 & Hiroyuki Koyama 2 &
Received: 22 July 2020 / Accepted: 28 October 2020 # Springer-Verlag GmbH Austria, part of Springer Nature 2020
Abstract Expression pattern of aluminum (Al) tolerance genes is one of the major determinants of Al avoidance/tolerance within plant cultivars. We have performed transcriptome analysis of two contrasting (Al-tolerant, Disang; Al-sensitive, Joymati) cultivars of India’s North Eastern region, an indica rice diversity hotspot, on exposure to excess Al3+ treatment in acidic condition. Coexpression analysis and SNPs enrichment analysis proposed the role of both trans-acting and cis-acting polymorphisms in Al signaling in the Al-tolerant cultivar. We proposed ten major genes, including arginine decarboxylase, phytase, and betaglucosidase aggregating factor as candidates responsible for Al tolerance based on transcriptome analysis. Al3+ stress led to changes in the alternative splicing profile of the Al-tolerant cultivar. These studies demonstrated the transcriptional variations affiliated to Al avoidance/tolerance in contrasting indica rice of North East India and provided us with several candidate genes responsible for Al tolerance. Keywords RNA-Seq . Rice . Aluminum toxicity . Co-expression . SNPs enrichment . Differentially expressed gene
Introduction Rice is the utmost crucial cereal crop for more than one-half of the world populace. Although rice is relatively tolerant to Al Jay Prakash Awasthi and Kazutaka Kusunoki contributed equally to this work. Handling Editor: Néstor Carrillo Supplementary Information The online version contains supplementary material available at https://doi.org/10.1007/s00709-02001581-2. * Sanjib Kumar Panda [email protected] 1
Plant Molecular Biotechnology Laboratory, Department of Life Science and Bioinformatics, Assam University, Silchar, Assam 788011, India
2
Plant Cell Technology Laboratory, Faculty of Applied Biological Sciences, Gifu University, Gifu 5011193, Japan
3
Present address: School of Biological Sciences, National Institute of Science Education and Research, Jatni, Odisha 752050, India
4
Present address: Department of Biochemistry, Central University of Rajasthan, Bandarsindri, Ajmer 305817, India
rhizotoxiciy caused by solubilized Al3+ in acid soil (constitutes one-third of total arable land worldwide), indica rice is comparatively Al-sensitive to japonica rice (Famoso et al. 2011). Therefore, there is large potential for improvement in its yield through biotechnological approaches. Meanwhile, Al3+ interacts with a number of extracellular as well as intracellular cellular components, leading to the occurrence of toxicity symptoms which include alteration of cell wall properties, membrane ion flux, excess synthesis of reactive oxygen species (ROS), and a
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