Integrated transcriptome, small RNA and degradome sequencing approaches provide insights into Ascochyta blight resistance in chickpea

Garg, V and Khan, A W and Kudapa, H and Kale, S M and Chitikineni, A and Qiwei, S and Sharma, M and Li, C and Zhang, B and Xin, L and Kavi Kishor, P B and Varshney, R K (2019) Integrated transcriptome, small RNA and degradome sequencing approaches provide insights into Ascochyta blight resistance in chickpea. Plant Biotechnology Journal (TSI), 17 (5). pp. 914-931. ISSN 1467-7644

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Ascochyta blight (AB) is one of the major biotic stresses known to limit the chickpea production worldwide. To dissect the complex mechanisms of AB resistance in chickpea, three approaches,namely, transcriptome, small RNA and degradome sequencing were used. The transcriptome sequencing of 20 samples including two resistant genotypes, two susceptible genotypes and one introgression line under control and stress conditions at two time points (3rd and 7th day post inoculation) identified a total of 6767 differentially expressed genes (DEGs). These DEGs were mainly related to pathogenesis-related proteins, disease resistance genes like NBS-LRR, cell wall biosynthesis and various secondary metabolite synthesis genes. The small RNA sequencing of the samples resulted in the identification of 651 miRNAs which included 478 known and 173 novel miRNAs. A total of 297 miRNAs were differentially expressed between different genotypes, conditions and time points. Using degradome sequencing and in silico approaches, 2131 targets were predicted for 629 miRNAs. The combined analysis of both small RNA and transcriptome datasets identified 12 miRNA-mRNA interaction pairs that exhibited contrasting expression in resistant and susceptible genotypes and also, a subset of genes that might be posttranscriptionally silenced during AB infection. The comprehensive integrated analysis in the study provides better insights into the transcriptome dynamics and regulatory network components associated with AB stress in chickpea and, also offers candidate genes for chickpea improvement.

Item Type: Article
Divisions: Research Program : Asia
Research Program : Genetic Gains
CRP: CGIAR Research Program on Grain Legumes and Dryland Cereals (GLDC)
Uncontrolled Keywords: miRNA, differentially expressed genes, fungal stress, mRNA targets, Ascochyta blight resistance, miRNA-mRNA, cleavage, Chickpea, Ascochyta blight, biotic stress
Subjects: Others > Biotic Stress
Mandate crops > Chickpea
Others > Genetics and Genomics
Depositing User: Mr Ramesh K
Date Deposited: 28 Aug 2019 06:36
Last Modified: 12 Dec 2019 08:17
Official URL:
Funders: Bill & Melinda Gates Foundation
Acknowledgement: Vanika Garg acknowledges the award of Research Fellowship from Department of Science and Technology, Government of India. The authors are thankful to Mr. Jaipal Goud for technical assistance. Authors are also grateful to the Bill & Melinda Gates Foundation for partially supporting the study. This work has been undertaken as part of the CGIAR Research Program on Grain Legumes & Dryland Cereals. ICRISAT is a member of CGIAR Consortium.
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