Gene expression atlas of pigeonpea and its application to gain insights into genes associated with pollen fertility implicated in seed formation

Pazhamala, L T and Purohit, S and Saxena, R K and Garg, V and Krishnamurthy, L and Verdier, J and Varshney, R K (2017) Gene expression atlas of pigeonpea and its application to gain insights into genes associated with pollen fertility implicated in seed formation. Journal of Experimental Botany, 68 (8). pp. 2037-2054. ISSN 0022-0957

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Pigeonpea (Cajanus cajan) is an important grain legume of the semi-arid tropics, mainly used for its protein rich seeds. To link the genome sequence information with agronomic traits resulting from specific developmental processes, a Cajanus cajan gene expression atlas (CcGEA) was developed using the Asha genotype. Thirty tissues/organs representing developmental stages from germination to senescence were used to generate 590.84 million paired-end RNA-Seq data. The CcGEA revealed a compendium of 28 793 genes with differential, specific, spatio-temporal and constitutive expression during various stages of development in different tissues. As an example to demonstrate the application of the CcGEA, a network of 28 flower-related genes analysed for cis-regulatory elements and splicing variants has been identified. In addition, expression analysis of these candidate genes in male sterile and male fertile genotypes suggested their critical role in normal pollen development leading to seed formation. Gene network analysis also identified two regulatory genes, a pollen-specific SF3 and a sucrose-proton symporter, that could have implications for improvement of agronomic traits such as seed production and yield. In conclusion, the CcGEA provides a valuable resource for pigeonpea to identify candidate genes involved in specific developmental processes and to understand the well-orchestrated growth and developmental process in this resilient crop.

Item Type: Article
Divisions: Research Program : Genetic Gains
CRP: CGIAR Research Program on Grain Legumes
Uncontrolled Keywords: Cajanus cajan, CcGEA, gene clustering, gene expression atlas, gene networking, legume genomics, male sterile genotype, pigeonpea, pollen-specific SF3, sucrose–proton symporter
Subjects: Mandate crops > Pigeonpea
Others > Genetics and Genomics
Depositing User: Mr Ramesh K
Date Deposited: 13 Apr 2017 03:52
Last Modified: 05 Sep 2017 04:26
Official URL:
Acknowledgement: This work has been undertaken as part of the CGIAR Research Program on Genetic Gains. ICRISAT is a member of CGIAR Consortium. Special thanks are due to Dr Vinay Kumar, Ms Anu Chitikineni of ICRISAT and Genotypic Technology Pvt Ltd for generating sequence data. We also acknowledge Ms Akanksha Kulshreshtha and Mr M. Manikyam for extending assistance with tissue collection and sample preparation.
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