The RNA-Seq based high resolution gene expression atlas of chickpea (Cicer arietinum L.) reveals dynamic spatio-temporal changes associated with growth and development

Kudapa, H and Garg, V and Chitikineni, A and Varshney, R K (2018) The RNA-Seq based high resolution gene expression atlas of chickpea (Cicer arietinum L.) reveals dynamic spatio-temporal changes associated with growth and development. Plant, Cell & Environment (TSI). pp. 1-17. ISSN 0140-7791

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Abstract

Chickpea is one of the world's largest cultivated food legume and is an excellent source of high‐quality protein to the human diet. Plant growth and development are controlled by programmed expression of a suite of genes at the given time, stage and tissue. Understanding how the underlying genome sequence translates into specific plant phenotypes at key developmental stages, information on gene expression patterns is crucial. Here we present a comprehensive Cicer arietinum Gene Expression Atlas (CaGEA) across the plant developmental stages and organs covering the entire life cycle of chickpea. One of the widely used drought tolerant cultivar, ICC 4958 has been used to generate RNA‐Seq data from 27 samples at five major developmental stages of the plant. A total of 816 million raw reads were generated and of these, 794 million filtered reads after QC were subjected to downstream analysis. A total of 15,947 unique number of differentially expressed genes across different pairwise tissue combinations were identified. Significant differences in gene expression patterns contributing in the process of flowering, nodulation, seed and root development were inferred in this study. Furthermore, differentially expressed candidate genes from “QTL‐hotspot” region associated with drought stress response in chickpea were validated.

Item Type: Article
Divisions: Research Program : Genetic Gains
CRP: CGIAR Research Program on Grain Legumes and Dryland Cereals
Uncontrolled Keywords: chickpea, spatio‐temporal changes, gene expression patterns, QTL‐hotspot, drought stress response
Subjects: Others > Abiotic Stress
Others > Crop Improvement
Mandate crops > Chickpea
Others > Drought
Others > Genetics and Genomics
Others > Plant Growth
Depositing User: Mr Ramesh K
Date Deposited: 23 Apr 2018 04:07
Last Modified: 21 May 2018 04:36
URI: http://oar.icrisat.org/id/eprint/10623
Official URL: http://dx.doi.org/10.1111/pce.13210
Projects: UNSPECIFIED
Funders: UNSPECIFIED
Acknowledgement: The authors would like to thank Mr. Jaipal Goud and Poornima B forextending their support in this work. Thanks are due to GenotypicTechnology Pvt Ltd for generating partial sequence data in the presentstudy. Authors are grateful to the Bill & Melinda Gates Foundation forsupporting this study. VG acknowledges the award of research fellow-ship from Department of Science and Technology, Government ofIndia. This work has been undertaken as part of the CGIAR Research Program on Grain Legumes & Dryland Cereals. ICRISAT is a memberof CGIAR Consortium.
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