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Okemo PA, Njaci I, Kim YM, McClure RS, Peterson MJ, Beliaev AS, Hixson KK, Mundree S, Williams B. Tripogon loliiformis tolerates rapid desiccation after metabolic and transcriptional priming during initial drying. Sci Rep 2023; 13:20613. [PMID: 37996547 PMCID: PMC10667271 DOI: 10.1038/s41598-023-47456-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 11/14/2023] [Indexed: 11/25/2023] Open
Abstract
Crop plants and undomesticated resilient species employ different strategies to regulate their energy resources and growth. Most crop species are sensitive to stress and prioritise rapid growth to maximise yield or biomass production. In contrast, resilient plants grow slowly, are small, and allocate their resources for survival in challenging environments. One small group of plants, termed resurrection plants, survive desiccation of their vegetative tissue and regain full metabolic activity upon watering. However, the precise molecular mechanisms underlying this extreme tolerance remain unknown. In this study, we employed a transcriptomics and metabolomics approach, to investigate the mechanisms of desiccation tolerance in Tripogon loliiformis, a modified desiccation-tolerant plant, that survives gradual but not rapid drying. We show that T. loliiformis can survive rapid desiccation if it is gradually dried to 60% relative water content (RWC). Furthermore, the gene expression data showed that T. loliiformis is genetically predisposed for desiccation in the hydrated state, as evidenced by the accumulation of MYB, NAC, bZIP, WRKY transcription factors along with the phytohormones, abscisic acid, salicylic acid, amino acids (e.g., proline) and TCA cycle sugars during initial drying. Through network analysis of co-expressed genes, we observed differential responses to desiccation between T. loliiformis shoots and roots. Dehydrating shoots displayed global transcriptional changes across broad functional categories, although no enrichment was observed during drying. In contrast, dehydrating roots showed distinct network changes with the most significant differences occurring at 40% RWC. The cumulative effects of the early stress responses may indicate the minimum requirements of desiccation tolerance and enable T. loliiformis to survive rapid drying. These findings potentially hold promise for identifying biotechnological solutions aimed at developing drought-tolerant crops without growth and yield penalties.
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Affiliation(s)
- Pauline A Okemo
- School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD, Australia
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, QLD, Australia
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD, Australia
| | - Isaac Njaci
- School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD, Australia
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, QLD, Australia
| | - Young-Mo Kim
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Ryan S McClure
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | | | - Alexander S Beliaev
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, QLD, Australia
- Physical and Chemical Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Kim K Hixson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
- Physical and Chemical Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Sagadevan Mundree
- School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD, Australia
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, QLD, Australia
| | - Brett Williams
- School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD, Australia.
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, QLD, Australia.
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Edwards A, Njaci I, Sarkar A, Jiang Z, Kaithakottil GG, Moore C, Cheema J, Stevenson CEM, Rejzek M, Novák P, Vigouroux M, Vickers M, Wouters RHM, Paajanen P, Steuernagel B, Moore JD, Higgins J, Swarbreck D, Martens S, Kim CY, Weng JK, Mundree S, Kilian B, Kumar S, Loose M, Yant L, Macas J, Wang TL, Martin C, Emmrich PMF. Author Correction: Genomics and biochemical analyses reveal a metabolon key to β-L-ODAP biosynthesis in Lathyrus sativus. Nat Commun 2023; 14:5199. [PMID: 37626052 PMCID: PMC10457282 DOI: 10.1038/s41467-023-40984-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/27/2023] Open
Affiliation(s)
- Anne Edwards
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | - Isaac Njaci
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
- Biosciences eastern and central Africa International Livestock Research Institute Hub, ILRI campus, Naivasha Road, P.O. 30709, Nairobi, 00100, Kenya
- Queensland University of Technology, 2 George St, Brisbane City, QLD, 4000, Australia
| | - Abhimanyu Sarkar
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
- National Institute of Agricultural Botany, 93 Laurence Weaver Road, Cambridge, CB3 0LE, UK
| | - Zhouqian Jiang
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
- School of Traditional Chinese Medicine, Capital Medical University, You An Men, Beijing, 100069, PR China
| | | | - Christopher Moore
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Jitender Cheema
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | | | - Martin Rejzek
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | - Petr Novák
- Institute of Plant Molecular Biology, Biology Centre CAS, Branisovska 31, Ceske Budejovice, CZ-37005, Czech Republic
| | - Marielle Vigouroux
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | - Martin Vickers
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | - Roland H M Wouters
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | - Pirita Paajanen
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | | | - Jonathan D Moore
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | - Janet Higgins
- Earlham Institute, Norwich Research Park, Colney Lane, Norwich, NR4 7UZ, UK
| | - David Swarbreck
- Earlham Institute, Norwich Research Park, Colney Lane, Norwich, NR4 7UZ, UK
| | - Stefan Martens
- Research and Innovation Centre, Fondazione Edmund Mach, Via Edmund Mach 1, 38098, San Michele all' Adige (TN), Italy
| | - Colin Y Kim
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Jing-Ke Weng
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Sagadevan Mundree
- Queensland University of Technology, 2 George St, Brisbane City, QLD, 4000, Australia
| | - Benjamin Kilian
- Global Crop Diversity Trust, Platz der Vereinten Nationen 7, 53113, Bonn, Germany
| | - Shiv Kumar
- International Center for Agricultural Research in the Dry Areas, Avenue Hafiane Cherkaoui, Rabat, Morocco
| | - Matt Loose
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Levi Yant
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
- Future Food Beacon of Excellence, University of Nottingham, NG7 2RD, Nottingham, UK
| | - Jiří Macas
- Institute of Plant Molecular Biology, Biology Centre CAS, Branisovska 31, Ceske Budejovice, CZ-37005, Czech Republic
| | - Trevor L Wang
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | - Cathie Martin
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | - Peter M F Emmrich
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK.
- Biosciences eastern and central Africa International Livestock Research Institute Hub, ILRI campus, Naivasha Road, P.O. 30709, Nairobi, 00100, Kenya.
- Norwich Institute for Sustainable Development, School of International Development, University of East Anglia, Norwich, NR4 7TJ, UK.
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Njaci I, Waweru B, Kamal N, Muktar MS, Fisher D, Gundlach H, Muli C, Muthui L, Maranga M, Kiambi D, Maass BL, Emmrich PMF, Domelevo Entfellner JB, Spannagl M, Chapman MA, Shorinola O, Jones CS. Chromosome-level genome assembly and population genomic resource to accelerate orphan crop lablab breeding. Nat Commun 2023; 14:1915. [PMID: 37069152 PMCID: PMC10110558 DOI: 10.1038/s41467-023-37489-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 03/17/2023] [Indexed: 04/19/2023] Open
Abstract
Under-utilised orphan crops hold the key to diversified and climate-resilient food systems. Here, we report on orphan crop genomics using the case of Lablab purpureus (L.) Sweet (lablab) - a legume native to Africa and cultivated throughout the tropics for food and forage. Our Africa-led plant genome collaboration produces a high-quality chromosome-scale assembly of the lablab genome. Our assembly highlights the genome organisation of the trypsin inhibitor genes - an important anti-nutritional factor in lablab. We also re-sequence cultivated and wild lablab accessions from Africa confirming two domestication events. Finally, we examine the genetic and phenotypic diversity in a comprehensive lablab germplasm collection and identify genomic loci underlying variation of important agronomic traits in lablab. The genomic data generated here provide a valuable resource for lablab improvement. Our inclusive collaborative approach also presents an example that can be explored by other researchers sequencing indigenous crops, particularly from low and middle-income countries (LMIC).
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Affiliation(s)
- Isaac Njaci
- International Livestock Research Institute, PO Box 30709-00100, Nairobi, Kenya
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Bernice Waweru
- International Livestock Research Institute, PO Box 30709-00100, Nairobi, Kenya
| | - Nadia Kamal
- Helmholtz Zentrum München, Plant Genome and Systems Biology, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | | | - David Fisher
- University of Southampton, School of Biological Sciences, Southampton, SO17 1BJ, UK
| | - Heidrun Gundlach
- Helmholtz Zentrum München, Plant Genome and Systems Biology, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Collins Muli
- International Livestock Research Institute, PO Box 30709-00100, Nairobi, Kenya
| | - Lucy Muthui
- International Livestock Research Institute, PO Box 30709-00100, Nairobi, Kenya
| | - Mary Maranga
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, Nairobi, 00200, Kenya
| | - Davies Kiambi
- Bioscience Research Centre (PUBReC), Pwani University, P.O Box 195-80108, Kilifi, Kenya
| | - Brigitte L Maass
- Department of Crop Sciences, Georg-August-University Göttingen, Grisebachstr 6, 37077, Göttingen, Germany
| | - Peter M F Emmrich
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
- Department for International Development, University of East Anglia, Norwich, NR4 7TJ, UK
| | | | - Manuel Spannagl
- Helmholtz Zentrum München, Plant Genome and Systems Biology, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Mark A Chapman
- University of Southampton, School of Biological Sciences, Southampton, SO17 1BJ, UK.
| | - Oluwaseyi Shorinola
- International Livestock Research Institute, PO Box 30709-00100, Nairobi, Kenya.
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
| | - Chris S Jones
- International Livestock Research Institute, PO Box 30709-00100, Nairobi, Kenya.
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4
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Edwards A, Njaci I, Sarkar A, Jiang Z, Kaithakottil GG, Moore C, Cheema J, Stevenson CEM, Rejzek M, Novák P, Vigouroux M, Vickers M, Wouters RHM, Paajanen P, Steuernagel B, Moore JD, Higgins J, Swarbreck D, Martens S, Kim CY, Weng JK, Mundree S, Kilian B, Kumar S, Loose M, Yant L, Macas J, Wang TL, Martin C, Emmrich PMF. Genomics and biochemical analyses reveal a metabolon key to β-L-ODAP biosynthesis in Lathyrus sativus. Nat Commun 2023; 14:876. [PMID: 36797319 PMCID: PMC9935904 DOI: 10.1038/s41467-023-36503-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 02/03/2023] [Indexed: 02/18/2023] Open
Abstract
Grass pea (Lathyrus sativus L.) is a rich source of protein cultivated as an insurance crop in Ethiopia, Eritrea, India, Bangladesh, and Nepal. Its resilience to both drought and flooding makes it a promising crop for ensuring food security in a changing climate. The lack of genetic resources and the crop's association with the disease neurolathyrism have limited the cultivation of grass pea. Here, we present an annotated, long read-based assembly of the 6.5 Gbp L. sativus genome. Using this genome sequence, we have elucidated the biosynthetic pathway leading to the formation of the neurotoxin, β-L-oxalyl-2,3-diaminopropionic acid (β-L-ODAP). The final reaction of the pathway depends on an interaction between L. sativus acyl-activating enzyme 3 (LsAAE3) and a BAHD-acyltransferase (LsBOS) that form a metabolon activated by CoA to produce β-L-ODAP. This provides valuable insight into the best approaches for developing varieties which produce substantially less toxin.
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Affiliation(s)
- Anne Edwards
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | - Isaac Njaci
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
- Biosciences eastern and central Africa International Livestock Research Institute Hub, ILRI campus, Naivasha Road, P.O. 30709, Nairobi, 00100, Kenya
- Queensland University of Technology, 2 George St, Brisbane City, QLD, 4000, Australia
| | - Abhimanyu Sarkar
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
- National Institute of Agricultural Botany, 93 Laurence Weaver Road, Cambridge, CB3 0LE, UK
| | - Zhouqian Jiang
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
- School of Traditional Chinese Medicine, Capital Medical University, You An Men, Beijing, 100069, PR China
| | | | - Christopher Moore
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Jitender Cheema
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | | | - Martin Rejzek
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | - Petr Novák
- Institute of Plant Molecular Biology, Biology Centre CAS, Branisovska 31, Ceske Budejovice, CZ-37005, Czech Republic
| | - Marielle Vigouroux
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | - Martin Vickers
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | - Roland H M Wouters
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | - Pirita Paajanen
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | | | - Jonathan D Moore
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | - Janet Higgins
- Earlham Institute, Norwich Research Park, Colney Lane, Norwich, NR4 7UZ, UK
| | - David Swarbreck
- Earlham Institute, Norwich Research Park, Colney Lane, Norwich, NR4 7UZ, UK
| | - Stefan Martens
- Research and Innovation Centre, Fondazione Edmund Mach, Via Edmund Mach 1, 38098, San Michele all' Adige (TN), Italy
| | - Colin Y Kim
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Jing-Ke Weng
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Sagadevan Mundree
- Queensland University of Technology, 2 George St, Brisbane City, QLD, 4000, Australia
| | - Benjamin Kilian
- Global Crop Diversity Trust, Platz der Vereinten Nationen 7, 53113, Bonn, Germany
| | - Shiv Kumar
- International Center for Agricultural Research in the Dry Areas, Avenue Hafiane Cherkaoui, Rabat, Morocco
| | - Matt Loose
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Levi Yant
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
- Future Food Beacon of Excellence, University of Nottingham, NG7 2RD, Nottingham, UK
| | - Jiří Macas
- Institute of Plant Molecular Biology, Biology Centre CAS, Branisovska 31, Ceske Budejovice, CZ-37005, Czech Republic
| | - Trevor L Wang
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | - Cathie Martin
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | - Peter M F Emmrich
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK.
- Biosciences eastern and central Africa International Livestock Research Institute Hub, ILRI campus, Naivasha Road, P.O. 30709, Nairobi, 00100, Kenya.
- Norwich Institute for Sustainable Development, School of International Development, University of East Anglia, Norwich, NR4 7TJ, UK.
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Ngugi-Dawit A, Njaci I, Higgins TJV, Williams B, Ghimire SR, Mundree SG, Hoang LTM. Comparative TMT Proteomic Analysis Unveils Unique Insights into Helicoverpa armigera (Hübner) Resistance in Cajanus scarabaeoides (L.) Thouars. Int J Mol Sci 2021; 22:ijms22115941. [PMID: 34073052 PMCID: PMC8198728 DOI: 10.3390/ijms22115941] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/28/2021] [Accepted: 05/28/2021] [Indexed: 11/21/2022] Open
Abstract
Pigeonpea [Cajanus cajan (L.) Millspaugh] is an economically important legume playing a crucial role in the semi-arid tropics. Pigeonpea is susceptible to Helicoverpa armigera (Hübner), which causes devastating yield losses. This pest is developing resistance to many commercially available insecticides. Therefore, crop wild relatives of pigeonpea, are being considered as potential sources of genes to expand the genetic base of cultivated pigeonpea to improve traits such as host plant resistance to pests and pathogens. Quantitative proteomic analysis was conducted using the tandem mass tag platform to identify differentially abundant proteins between IBS 3471 and ICPL 87 tolerant accession and susceptible variety to H. armigera, respectively. Leaf proteome were analysed at the vegetative and flowering/podding growth stages. H. armigera tolerance in IBS 3471 appeared to be related to enhanced defence responses, such as changes in secondary metabolite precursors, antioxidants, and the phenylpropanoid pathway. The development of larvae fed on an artificial diet with IBS 3471 lyophilised leaves showed similar inhibition with those fed on an artificial diet with quercetin concentrations with 32 mg/25 g of artificial diet. DAB staining (3,3′-diaminobenzidine) revealed a rapid accumulation of reactive oxygen species in IBS 3471. We conclude that IBS 3471 is an ideal candidate for improving the genetic base of cultivated pigeonpea, including traits for host plant resistance.
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Affiliation(s)
- Abigail Ngugi-Dawit
- Centre for Agriculture and the Bioeconomy (CAB), Queensland University of Technology (QUT), Brisbane 4001, Australia;
- Correspondence: (A.N.-D.); (S.G.M.); (L.T.M.H.); Tel.: +61-731-388-386 (S.G.M.)
| | - Isaac Njaci
- Biosciences Eastern and Central Africa—International Livestock Research Institute (BecA-ILRI) Hub, P.O. 30709, Nairobi 00100, Kenya; (I.N.); (S.R.G.)
| | - Thomas J. V. Higgins
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Agriculture and Food, Canberra 2601, Australia;
| | - Brett Williams
- Centre for Agriculture and the Bioeconomy (CAB), Queensland University of Technology (QUT), Brisbane 4001, Australia;
| | - Sita R. Ghimire
- Biosciences Eastern and Central Africa—International Livestock Research Institute (BecA-ILRI) Hub, P.O. 30709, Nairobi 00100, Kenya; (I.N.); (S.R.G.)
| | - Sagadevan G. Mundree
- Centre for Agriculture and the Bioeconomy (CAB), Queensland University of Technology (QUT), Brisbane 4001, Australia;
- Correspondence: (A.N.-D.); (S.G.M.); (L.T.M.H.); Tel.: +61-731-388-386 (S.G.M.)
| | - Linh Thi My Hoang
- Centre for Agriculture and the Bioeconomy (CAB), Queensland University of Technology (QUT), Brisbane 4001, Australia;
- Correspondence: (A.N.-D.); (S.G.M.); (L.T.M.H.); Tel.: +61-731-388-386 (S.G.M.)
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Njaci I, Ngugi-Dawit A, Oduor RO, Kago L, Williams B, Hoang LTM, Mundree SG, Ghimire SR. Comparative Analysis Delineates the Transcriptional Resistance Mechanisms for Pod Borer Resistance in the Pigeonpea Wild Relative Cajanus scarabaeoides (L.) Thouars. Int J Mol Sci 2020; 22:ijms22010309. [PMID: 33396747 PMCID: PMC7795875 DOI: 10.3390/ijms22010309] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/15/2020] [Accepted: 12/23/2020] [Indexed: 01/17/2023] Open
Abstract
Insect pests pose a serious threat to global food production. Pod borer (Helicoverpa armigera (Hübner)) is one of the most destructive pests of leguminous crops. The use of host resistance has been an effective, environmentally friendly and sustainable approach for controlling several agricultural pests. The exploitation of natural variations in crop wild relatives could yield pest-resistant crop varieties. In this study, we used a high-throughput transcriptome profiling approach to investigate the defense mechanisms of susceptible cultivated and tolerant wild pigeonpea genotypes against H. armigera infestation. The wild genotype displayed elevated pest-induced gene expression, including the enhanced induction of phytohormone and calcium/calmodulin signaling, transcription factors, plant volatiles and secondary metabolite genes compared to the cultivated control. The biosynthetic and regulatory processes associated with flavonoids, terpenes and glucosinolate secondary metabolites showed higher accumulations in the wild genotype, suggesting the existence of distinct tolerance mechanisms. This study provides insights into the molecular mechanisms underlying insect resistance in the wild pigeonpea genotype. This information highlights the indispensable role of crop wild relatives as a source of crucial genetic resources that could be important in devising strategies for crop improvement with enhanced pest resistance.
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Affiliation(s)
- Isaac Njaci
- Biosciences Eastern and Central Africa—International Livestock Research Institute (BecA-ILRI) Hub, Nairobi P.O. Box 30709-00100, Kenya; (I.N.); (L.K.)
| | - Abigail Ngugi-Dawit
- Centre for Agriculture and the Bioeconomy (CAB), Queensland University of Technology, Brisbane City, QLD 4000, Australia; (A.N.-D.); (B.W.); (L.T.M.H.)
| | - Richard O. Oduor
- Department of Biochemistry, Microbiology and Biotechnology, Kenyatta University, Nairobi P.O. Box 43844-00100, Kenya;
| | - Leah Kago
- Biosciences Eastern and Central Africa—International Livestock Research Institute (BecA-ILRI) Hub, Nairobi P.O. Box 30709-00100, Kenya; (I.N.); (L.K.)
| | - Brett Williams
- Centre for Agriculture and the Bioeconomy (CAB), Queensland University of Technology, Brisbane City, QLD 4000, Australia; (A.N.-D.); (B.W.); (L.T.M.H.)
| | - Linh Thi My Hoang
- Centre for Agriculture and the Bioeconomy (CAB), Queensland University of Technology, Brisbane City, QLD 4000, Australia; (A.N.-D.); (B.W.); (L.T.M.H.)
| | - Sagadevan G. Mundree
- Centre for Agriculture and the Bioeconomy (CAB), Queensland University of Technology, Brisbane City, QLD 4000, Australia; (A.N.-D.); (B.W.); (L.T.M.H.)
- Correspondence: (S.G.M.); (S.R.G.)
| | - Sita R. Ghimire
- Biosciences Eastern and Central Africa—International Livestock Research Institute (BecA-ILRI) Hub, Nairobi P.O. Box 30709-00100, Kenya; (I.N.); (L.K.)
- Correspondence: (S.G.M.); (S.R.G.)
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7
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Asami P, Rupasinghe T, Moghaddam L, Njaci I, Roessner U, Mundree S, Williams B. Roots of the Resurrection Plant Tripogon loliiformis Survive Desiccation Without the Activation of Autophagy Pathways by Maintaining Energy Reserves. Front Plant Sci 2019; 10:459. [PMID: 31105716 PMCID: PMC6494956 DOI: 10.3389/fpls.2019.00459] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 03/27/2019] [Indexed: 05/18/2023]
Abstract
Being sessile, plants must regulate energy balance, potentially via source-sink relations, to compromise growth with survival in stressful conditions. Crops are sensitive, possibly because they allocate their energy resources toward growth and yield rather than stress tolerance. In contrast, resurrection plants tightly regulate sugar metabolism and use a series of physiological adaptations to suppress cell death in their vegetative tissue to regain full metabolic capacity from a desiccated state within 72 h of watering. Previously, we showed that shoots of the resurrection plant Tripogon loliiformis, initiate autophagy upon dehydration as one strategy to reinstate homeostasis and suppress cell death. Here, we describe the relationship between energy status, sugar metabolism, trehalose-mediated activation of autophagy pathways and investigate whether shoots and roots utilize similar desiccation tolerance strategies. We show that despite containing high levels of trehalose, dehydrated Tripogon roots do not display elevated activation of autophagy pathways. Using targeted and non-targeted metabolomics, transmission electron microscopy (TEM) and transcriptomics we show that T. loliiformis engages a strategy similar to the long-term drought responses of sensitive plants and continues to use the roots as a sink even during sustained stress. Dehydrating T. loliiformis roots contained more sucrose and trehalose-6-phosphate compared to shoots at an equivalent water content. The increased resources in the roots provides sufficient energy to cope with stress and thus autophagy is not required. These results were confirmed by the absence of autophagosomes in roots by TEM. Upregulation of sweet genes in both shoots and roots show transcriptional regulation of sucrose translocation from leaves to roots and within roots during dehydration. Differences in the cell's metabolic status caused starkly different cell death responses between shoots and roots. These findings show how shoots and roots utilize different stress response strategies and may provide candidate targets that can be used as tools for the improvement of stress tolerance in crops.
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Affiliation(s)
- Pauline Asami
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD, Australia
| | - Thusitha Rupasinghe
- Metabolomics Australia, School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Lalehvash Moghaddam
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD, Australia
| | - Isaac Njaci
- Biosciences Eastern and Central Africa-International Livestock Research Institute, Nairobi, Kenya
| | - Ute Roessner
- Metabolomics Australia, School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Sagadevan Mundree
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD, Australia
| | - Brett Williams
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD, Australia
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Njaci I, Williams B, Castillo-González C, Dickman MB, Zhang X, Mundree S. Genome-Wide Investigation of the Role of MicroRNAs in Desiccation Tolerance in the Resurrection Grass Tripogon loliiformis. Plants (Basel) 2018; 7:E68. [PMID: 30200279 PMCID: PMC6161015 DOI: 10.3390/plants7030068] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 08/24/2018] [Accepted: 08/29/2018] [Indexed: 12/15/2022]
Abstract
Drought causes approximately two-thirds of crop and yield loss worldwide. To sustain future generations, there is a need to develop robust crops with enhanced water use efficiency. Resurrection plants are naturally resilient and tolerate up to 95% water loss with the ability to revive upon watering. Stress is genetically encoded and resilient species may garner tolerance by tightly regulating the expression of stress-related genes. MicroRNAs (miRNAs) post-transcriptionally regulate development and other stress response processes in eukaryotes. However, their role in resurrection plant desiccation tolerance is poorly understood. In this study, small RNA sequencing and miRNA expression profiling was conducted using Tripogon loliiformis plants subjected to extreme water deficit conditions. Differentially expressed miRNA profiles, target mRNAs, and their regulatory processes were elucidated. Gene ontology enrichment analysis revealed that development, stress response, and regulation of programmed cell death biological processes; Oxidoreductase and hydrolyase molecular activities; and SPL, MYB, and WRKY transcription factors were targeted by miRNAs during dehydration stress, indicating the indispensable regulatory role of miRNAs in desiccation tolerance. This study provides insights into the molecular mechanisms of desiccation tolerance in the resurrection plant T. loliiformis. This information will be useful in devising strategies for crop improvement on enhanced drought tolerance and water use efficiency.
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Affiliation(s)
- Isaac Njaci
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD 4000, Australia.
| | - Brett Williams
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD 4000, Australia.
| | - Claudia Castillo-González
- Department of Biochemistry and Biophysics, Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843, USA.
| | - Martin B Dickman
- Department of Plant Pathology and Microbiology, Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843, USA.
| | - Xiuren Zhang
- Department of Biochemistry and Biophysics, Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843, USA.
| | - Sagadevan Mundree
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD 4000, Australia.
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Williams B, Njaci I, Moghaddam L, Long H, Dickman MB, Zhang X, Mundree S. Trehalose Accumulation Triggers Autophagy during Plant Desiccation. PLoS Genet 2015; 11:e1005705. [PMID: 26633550 PMCID: PMC4669190 DOI: 10.1371/journal.pgen.1005705] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [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: 04/06/2015] [Accepted: 11/06/2015] [Indexed: 12/19/2022] Open
Abstract
Global climate change, increasingly erratic weather and a burgeoning global population are significant threats to the sustainability of future crop production. There is an urgent need for the development of robust measures that enable crops to withstand the uncertainty of climate change whilst still producing maximum yields. Resurrection plants possess the unique ability to withstand desiccation for prolonged periods, can be restored upon watering and represent great potential for the development of stress tolerant crops. Here, we describe the remarkable stress characteristics of Tripogon loliiformis, an uncharacterised resurrection grass and close relative of the economically important cereals, rice, sorghum, and maize. We show that T. loliiformis survives extreme environmental stress by implementing autophagy to prevent Programmed Cell Death. Notably, we identified a novel role for trehalose in the regulation of autophagy in T.loliiformis. Transcriptome, Gas Chromatography Mass Spectrometry, immunoblotting and confocal microscopy analyses directly linked the accumulation of trehalose with the onset of autophagy in dehydrating and desiccated T. loliiformis shoots. These results were supported in vitro with the observation of autophagosomes in trehalose treated T. loliiformis leaves; autophagosomes were not detected in untreated samples. Presumably, once induced, autophagy promotes desiccation tolerance in T.loliiformis, by removal of cellular toxins to suppress programmed cell death and the recycling of nutrients to delay the onset of senescence. These findings illustrate how resurrection plants manipulate sugar metabolism to promote desiccation tolerance and may provide candidate genes that are potentially useful for the development of stress tolerant crops.
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Affiliation(s)
- Brett Williams
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Isaac Njaci
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Lalehvash Moghaddam
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Hao Long
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Martin B Dickman
- Department of Plant Pathology and Microbiology, Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, Texas, United States of America
| | - Xiuren Zhang
- Department of Biochemistry and Biophysics, Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, Texas, United States of America
| | - Sagadevan Mundree
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, Queensland, Australia
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Thanh NM, Jung H, Lyons RE, Njaci I, Yoon BH, Chand V, Tuan NV, Thu VTM, Mather P. Optimizing de novo transcriptome assembly and extending genomic resources for striped catfish (Pangasianodon hypophthalmus). Mar Genomics 2015; 23:87-97. [PMID: 25979246 DOI: 10.1016/j.margen.2015.05.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 05/03/2015] [Accepted: 05/03/2015] [Indexed: 12/17/2022]
Abstract
Striped catfish (Pangasianodon hypophthalmus) is a commercially important freshwater fish used in inland aquaculture in the Mekong Delta, Vietnam. The culture industry is facing a significant challenge however from saltwater intrusion into many low topographical coastal provinces across the Mekong Delta as a result of predicted climate change impacts. Developing genomic resources for this species can facilitate the production of improved culture lines that can withstand raised salinity conditions, and so we have applied high-throughput Ion Torrent sequencing of transcriptome libraries from six target osmoregulatory organs from striped catfish as a genomic resource for use in future selection strategies. We obtained 12,177,770 reads after trimming and processing with an average length of 97bp. De novo assemblies were generated using CLC Genomic Workbench, Trinity and Velvet/Oases with the best overall contig performance resulting from the CLC assembly. De novo assembly using CLC yielded 66,451 contigs with an average length of 478bp and N50 length of 506bp. A total of 37,969 contigs (57%) possessed significant similarity with proteins in the non-redundant database. Comparative analyses revealed that a significant number of contigs matched sequences reported in other teleost fishes, ranging in similarity from 45.2% with Atlantic cod to 52% with zebrafish. In addition, 28,879 simple sequence repeats (SSRs) and 55,721 single nucleotide polymorphisms (SNPs) were detected in the striped catfish transcriptome. The sequence collection generated in the current study represents the most comprehensive genomic resource for P. hypophthalmus available to date. Our results illustrate the utility of next-generation sequencing as an efficient tool for constructing a large genomic database for marker development in non-model species.
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Affiliation(s)
- Nguyen Minh Thanh
- International University - VNU HCMC, Quarter 6, Linh Trung Ward, Thu Duc District, Ho Chi Minh City, Viet Nam.
| | - Hyungtaek Jung
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, GPO Box 2434, Brisbane, QLD 4001, Australia; Science and Engineering Faculty, Queensland University of Technology, GPO Box 2434, Brisbane, QLD 4001, Australia.
| | - Russell E Lyons
- Animal Genetics Laboratory, School of Veterinary Science, University of Queensland, Gatton, QLD 4343, Australia.
| | - Isaac Njaci
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, GPO Box 2434, Brisbane, QLD 4001, Australia.
| | - Byoung-Ha Yoon
- Medical Genomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Republic of Korea; Department of Functional Genomics, Korea University of Science and Technology, Daejoen 305-333, Republic of Korea.
| | - Vincent Chand
- Science and Engineering Faculty, Queensland University of Technology, GPO Box 2434, Brisbane, QLD 4001, Australia.
| | - Nguyen Viet Tuan
- Science and Engineering Faculty, Queensland University of Technology, GPO Box 2434, Brisbane, QLD 4001, Australia.
| | - Vo Thi Minh Thu
- International University - VNU HCMC, Quarter 6, Linh Trung Ward, Thu Duc District, Ho Chi Minh City, Viet Nam.
| | - Peter Mather
- Science and Engineering Faculty, Queensland University of Technology, GPO Box 2434, Brisbane, QLD 4001, Australia.
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Ommeh S, Budd A, Ngara MV, Njaci I, de Villiers EP. Basic Molecular Evolution Workshop - A trans-African virtual training course. Bioessays 2011; 33:243-7. [DOI: 10.1002/bies.201000139] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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