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Ghodke P, Khandagale K, Thangasamy A, Kulkarni A, Narwade N, Shirsat D, Randive P, Roylawar P, Singh I, Gawande SJ, Mahajan V, Solanke A, Singh M. Comparative transcriptome analyses in contrasting onion (Allium cepa L.) genotypes for drought stress. PLoS One 2020; 15:e0237457. [PMID: 32780764 PMCID: PMC7418993 DOI: 10.1371/journal.pone.0237457] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 07/27/2020] [Indexed: 01/12/2023] Open
Abstract
Onion (Allium cepa L.) is an important vegetable crop widely grown for diverse culinary and nutraceutical properties. Being a shallow-rooted plant, it is prone to drought. In the present study, transcriptome sequencing of drought-tolerant (1656) and drought-sensitive (1627) onion genotypes was performed to elucidate the molecular basis of differential response to drought stress. A total of 123206 and 139252 transcripts (average transcript length: 690 bases) were generated after assembly for 1656 and 1627, respectively. Differential gene expression analyses revealed upregulation and downregulation of 1189 and 1180 genes, respectively, in 1656, whereas in 1627, upregulation and downregulation of 872 and 1292 genes, respectively, was observed. Genes encoding transcription factors, cytochrome P450, membrane transporters, and flavonoids, and those related to carbohydrate metabolism were found to exhibit a differential expression behavior in the tolerant and susceptible genotypes. The information generated can facilitate a better understanding of molecular mechanisms underlying drought response in onion.
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Affiliation(s)
- Pranjali Ghodke
- ICAR-Directorate of Onion and Garlic Research, Rajgurunagar, Pune, India
| | - Kiran Khandagale
- ICAR-Directorate of Onion and Garlic Research, Rajgurunagar, Pune, India
| | - A. Thangasamy
- ICAR-Directorate of Onion and Garlic Research, Rajgurunagar, Pune, India
| | - Abhijeet Kulkarni
- Department of Bioinformatics, Savitribai Phule Pune University, Pune, India
| | - Nitin Narwade
- Department of Bioinformatics, Savitribai Phule Pune University, Pune, India
| | - Dhananjay Shirsat
- ICAR-Directorate of Onion and Garlic Research, Rajgurunagar, Pune, India
| | - Pragati Randive
- ICAR-Directorate of Onion and Garlic Research, Rajgurunagar, Pune, India
| | - Praveen Roylawar
- S. N. Arts, D. J. M. Commerce and B. N. S. Science College, Sangamner, India
| | - Isha Singh
- School of Biomolecular Science, University College, Dublin, Ireland
| | - Suresh J. Gawande
- ICAR-Directorate of Onion and Garlic Research, Rajgurunagar, Pune, India
| | - Vijay Mahajan
- ICAR-Directorate of Onion and Garlic Research, Rajgurunagar, Pune, India
| | | | - Major Singh
- ICAR-Directorate of Onion and Garlic Research, Rajgurunagar, Pune, India
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Kumar S, Kanakachari M, Gurusamy D, Kumar K, Narayanasamy P, Kethireddy Venkata P, Solanke A, Gamanagatti S, Hiremath V, Katageri IS, Leelavathi S, Kumar PA, Reddy VS. Genome-wide transcriptomic and proteomic analyses of bollworm-infested developing cotton bolls revealed the genes and pathways involved in the insect pest defence mechanism. Plant Biotechnol J 2016; 14:1438-55. [PMID: 26799171 PMCID: PMC5066800 DOI: 10.1111/pbi.12508] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 11/02/2015] [Accepted: 11/06/2015] [Indexed: 05/31/2023]
Abstract
Cotton bollworm, Helicoverpa armigera, is a major insect pest that feeds on cotton bolls causing extensive damage leading to crop and productivity loss. In spite of such a major impact, cotton plant response to bollworm infection is yet to be witnessed. In this context, we have studied the genome-wide response of cotton bolls infested with bollworm using transcriptomic and proteomic approaches. Further, we have validated this data using semi-quantitative real-time PCR. Comparative analyses have revealed that 39% of the transcriptome and 35% of the proteome were differentially regulated during bollworm infestation. Around 36% of significantly regulated transcripts and 45% of differentially expressed proteins were found to be involved in signalling followed by redox regulation. Further analysis showed that defence-related stress hormones and their lipid precursors, transcription factors, signalling molecules, etc. were stimulated, whereas the growth-related counterparts were suppressed during bollworm infestation. Around 26% of the significantly up-regulated proteins were defence molecules, while >50% of the significantly down-regulated were related to photosynthesis and growth. Interestingly, the biosynthesis genes for synergistically regulated jasmonate, ethylene and suppressors of the antagonistic factor salicylate were found to be up-regulated, suggesting a choice among stress-responsive phytohormone regulation. Manual curation of the enzymes and TFs highlighted the components of retrograde signalling pathways. Our data suggest that a selective regulatory mechanism directs the reallocation of metabolic resources favouring defence over growth under bollworm infestation and these insights could be exploited to develop bollworm-resistant cotton varieties.
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Affiliation(s)
- Saravanan Kumar
- International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Mogilicherla Kanakachari
- National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute (IARI), New Delhi, India
| | - Dhandapani Gurusamy
- National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute (IARI), New Delhi, India
| | - Krishan Kumar
- International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Prabhakaran Narayanasamy
- National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute (IARI), New Delhi, India
| | | | - Amolkumar Solanke
- National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute (IARI), New Delhi, India
| | | | | | | | - Sadhu Leelavathi
- International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Polumetla Ananda Kumar
- National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute (IARI), New Delhi, India
| | - Vanga Siva Reddy
- International Centre for Genetic Engineering and Biotechnology, New Delhi, India
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