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

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    Author
    Garg, Vanika; Khan, Aamir W.; Kudapa, Himabindu; Kale, Sandip M.; Chitikineni, Annapurna; Qiwei, Sun; Sharma, Mamta; Li, Chuanying; Zhang, Baohong; Xin, Liu; Kishor, P.B. Kavi; Varshney, Rajeev K.
    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.
    URI
    http://hdl.handle.net/10342/8121
    Subject
    miRNA, differentially expressed genes, fungal stress, mRNA targets, Ascochyta blight resistance, miRNA-mRNA, cleavage
    Date
    2018-10-16
    Citation:
    APA:
    Garg, Vanika, & Khan, Aamir W., & Kudapa, Himabindu, & Kale, Sandip M., & Chitikineni, Annapurna, & Qiwei, Sun, & Sharma, Mamta, & Li, Chuanying, & Zhang, Baohong, & Xin, Liu, & Kishor, P.B. Kavi, & Varshney, Rajeev K.. (October 2018). Integrated transcriptome, small RNA and degradome sequencing approaches provide insights into Ascochyta blight resistance in chickpea. Plant Biotechnology Journal, (914–931. Retrieved from http://hdl.handle.net/10342/8121

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    MLA:
    Garg, Vanika, and Khan, Aamir W., and Kudapa, Himabindu, and Kale, Sandip M., and Chitikineni, Annapurna, and Qiwei, Sun, and Sharma, Mamta, and Li, Chuanying, and Zhang, Baohong, and Xin, Liu, and Kishor, P.B. Kavi, and Varshney, Rajeev K.. "Integrated transcriptome, small RNA and degradome sequencing approaches provide insights into Ascochyta blight resistance in chickpea". Plant Biotechnology Journal. . (914–931.), October 2018. August 17, 2022. http://hdl.handle.net/10342/8121.
    Chicago:
    Garg, Vanika and Khan, Aamir W. and Kudapa, Himabindu and Kale, Sandip M. and Chitikineni, Annapurna and Qiwei, Sun and Sharma, Mamta and Li, Chuanying and Zhang, Baohong and Xin, Liu and Kishor, P.B. Kavi and Varshney, Rajeev K., "Integrated transcriptome, small RNA and degradome sequencing approaches provide insights into Ascochyta blight resistance in chickpea," Plant Biotechnology Journal 17, no. (October 2018), http://hdl.handle.net/10342/8121 (accessed August 17, 2022).
    AMA:
    Garg, Vanika, Khan, Aamir W., Kudapa, Himabindu, Kale, Sandip M., Chitikineni, Annapurna, Qiwei, Sun, Sharma, Mamta, Li, Chuanying, Zhang, Baohong, Xin, Liu, Kishor, P.B. Kavi, Varshney, Rajeev K.. Integrated transcriptome, small RNA and degradome sequencing approaches provide insights into Ascochyta blight resistance in chickpea. Plant Biotechnology Journal. October 2018; 17() 914–931. http://hdl.handle.net/10342/8121. Accessed August 17, 2022.
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