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Journal article
Integrated transcriptome, small RNA and degradome sequencing approaches provide insights into Ascochyta blight resistance in chickpea
Plant Biotechnology Journal, Vol.17(5), pp.914-931
2019
Abstract
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 post‐transcriptionally 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.
Details
- Title
- Integrated transcriptome, small RNA and degradome sequencing approaches provide insights into Ascochyta blight resistance in chickpea
- Authors/Creators
- V. Garg (Author/Creator)A.W. Khan (Author/Creator)H. Kudapa (Author/Creator)S.M. Kale (Author/Creator)A. Chitikineni (Author/Creator)S. Qiwei (Author/Creator)M. Sharma (Author/Creator)C. Li (Author/Creator)B. Zhang (Author/Creator)L. Xin (Author/Creator)P.B.K. Kishor (Author/Creator)R.K. Varshney (Author/Creator)
- Publication Details
- Plant Biotechnology Journal, Vol.17(5), pp.914-931
- Publisher
- Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.
- Identifiers
- 991005540602807891
- Copyright
- © 2018 The Authors.
- Murdoch Affiliation
- State Agricultural Biotechnology Centre; Murdoch University; Centre for Crop and Food Innovation
- Language
- English
- Resource Type
- Journal article
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- Collaboration types
- Domestic collaboration
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- Citation topics
- 3 Agriculture, Environment & Ecology
- 3.4 Crop Science
- 3.4.159 Arabidopsis
- Web Of Science research areas
- Biotechnology & Applied Microbiology
- Plant Sciences
- ESI research areas
- Plant & Animal Science