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Ho WK, Tanzi AS, Sang F, Tsoutsoura N, Shah N, Moore C, Bhosale R, Wright V, Massawe F, Mayes S. A genomic toolkit for winged bean Psophocarpus tetragonolobus. Nat Commun 2024; 15:1901. [PMID: 38429275 PMCID: PMC10907731 DOI: 10.1038/s41467-024-45048-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 01/12/2024] [Indexed: 03/03/2024] Open
Abstract
A sustainable supply of plant protein is critical for future generations and needs to be achieved while reducing green house gas emissions from agriculture and increasing agricultural resilience in the face of climate volatility. Agricultural diversification with more nutrient-rich and stress tolerant crops could provide the solution. However, this is often hampered by the limited availability of genomic resources and the lack of understanding of the genetic structure of breeding germplasm and the inheritance of important traits. One such crop with potential is winged bean (Psophocarpus tetragonolobus), a high seed protein tropical legume which has been termed 'the soybean for the tropics'. Here, we present a chromosome level winged bean genome assembly, an investigation of the genetic diversity of 130 worldwide accessions, together with two linked genetic maps and a trait QTL analysis (and expression studies) for regions of the genome with desirable ideotype traits for breeding, namely architecture, protein content and phytonutrients.
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Affiliation(s)
- Wai Kuan Ho
- Future Food Beacon, School of Biosciences, University of Nottingham Malaysia, Jalan Broga, 43500, Semenyih, Selangor, Malaysia
- Crops for the Future (UK) CIC, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Alberto Stefano Tanzi
- Future Food Beacon, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK
| | - Fei Sang
- Deep Seq, Centre for Genetics and Genomics, University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK
| | - Niki Tsoutsoura
- Future Food Beacon, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK
| | - Niraj Shah
- Digital and Technology Services, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK
| | - Christopher Moore
- Deep Seq, Centre for Genetics and Genomics, University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK
| | - Rahul Bhosale
- Future Food Beacon, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK
| | - Victoria Wright
- Deep Seq, Centre for Genetics and Genomics, University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK
| | - Festo Massawe
- Future Food Beacon, School of Biosciences, University of Nottingham Malaysia, Jalan Broga, 43500, Semenyih, Selangor, Malaysia
| | - Sean Mayes
- Crops for the Future (UK) CIC, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK.
- Future Food Beacon, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK.
- International Centre for Research in the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, 502324, India.
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Chankaew S, Sriwichai S, Rakvong T, Monkham T, Sanitchon J, Tangphatsornruang S, Kongkachana W, Sonthirod C, Pootakham W, Amkul K, Kaewwongwal A, Laosatit K, Somta P. The First Genetic Linkage Map of Winged Bean [Psophocarpus tetragonolobus (L.) DC.] and QTL Mapping for Flower-, Pod-, and Seed-Related Traits. PLANTS 2022; 11:plants11040500. [PMID: 35214834 PMCID: PMC8878720 DOI: 10.3390/plants11040500] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 02/10/2022] [Accepted: 02/10/2022] [Indexed: 11/16/2022]
Abstract
Winged bean [Psophocarpus tetragonolobus (L.) DC.] (2n = 2× = 18) is a tropical legume crop with multipurpose usages. Recently, the winged bean has regained attention from scientists as a food protein source. Currently, there is no breeding program for winged bean cultivars. All winged bean cultivars are landraces or selections from landraces. Molecular markers and genetic linkage maps are pre-requisites for molecular plant breeding. The aim of this study was to develop a high-density linkage map and identify quantitative trait loci (QTLs) for pod and seed-related traits of the winged bean. An F2 population of 86 plants was developed from a cross between winged bean accessions W054 and TPT9 showing contrasting pod length, and pod, flower and seed colors. A genetic linkage map of 1384 single nucleotide polymorphism (SNP) markers generated from restriction site-associated DNA sequencing was constructed. The map resolved nine haploid chromosomes of the winged bean and spanned the cumulative length of 4552.8 cM with the number of SNPs per linkage ranging from 36 to 218 with an average of 153.78. QTL analysis in the F2 population revealed 31 QTLs controlling pod length, pod color, pod anthocyanin content, flower color, and seed color. The number of QTLs per trait varied between 1 (seed length) to 7 (banner color). Interestingly, the major QTLs for pod color, anthocyanin content, and calyx color, and for seed color and flower wing color were located at the same position. The high-density linkage map QTLs reported in this study will be useful for molecular breeding of winged beans.
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Affiliation(s)
- Sompong Chankaew
- Department of Agronomy, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand; (S.C.); (S.S.); (T.R.); (T.M.); (J.S.)
| | - Sasiprapa Sriwichai
- Department of Agronomy, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand; (S.C.); (S.S.); (T.R.); (T.M.); (J.S.)
| | - Teppratan Rakvong
- Department of Agronomy, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand; (S.C.); (S.S.); (T.R.); (T.M.); (J.S.)
| | - Tidarat Monkham
- Department of Agronomy, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand; (S.C.); (S.S.); (T.R.); (T.M.); (J.S.)
| | - Jirawat Sanitchon
- Department of Agronomy, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand; (S.C.); (S.S.); (T.R.); (T.M.); (J.S.)
| | - Sithichoke Tangphatsornruang
- National Omics Center (NOC), National Science and Technology Development Agency, 111 Thailand Science Park, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand; (S.T.); (W.K.); (C.S.); (W.P.)
| | - Wasitthee Kongkachana
- National Omics Center (NOC), National Science and Technology Development Agency, 111 Thailand Science Park, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand; (S.T.); (W.K.); (C.S.); (W.P.)
| | - Chutima Sonthirod
- National Omics Center (NOC), National Science and Technology Development Agency, 111 Thailand Science Park, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand; (S.T.); (W.K.); (C.S.); (W.P.)
| | - Wirulda Pootakham
- National Omics Center (NOC), National Science and Technology Development Agency, 111 Thailand Science Park, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand; (S.T.); (W.K.); (C.S.); (W.P.)
| | - Kitiya Amkul
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom 73140, Thailand; (K.A.); (A.K.); (K.L.)
| | - Anochar Kaewwongwal
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom 73140, Thailand; (K.A.); (A.K.); (K.L.)
| | - Kularb Laosatit
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom 73140, Thailand; (K.A.); (A.K.); (K.L.)
| | - Prakit Somta
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom 73140, Thailand; (K.A.); (A.K.); (K.L.)
- Correspondence:
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Bassal H, Hijazi A, Farhan H, Trabolsi C, Ahmad BS, Khalil A, Maresca M, El Omar F. Study of the Antioxidant and Anti-Inflammatory Properties of the Biological Extracts of Psophocarpus tetragonolobus Using Two Extraction Methods. Molecules 2021; 26:molecules26154435. [PMID: 34361588 PMCID: PMC8347811 DOI: 10.3390/molecules26154435] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 07/05/2021] [Accepted: 07/12/2021] [Indexed: 11/16/2022] Open
Abstract
Psophocarpus tetragonolobus has long been used in traditional medicine and cuisine. In this study, Psophocarpus tetragonolobus extracts were isolated by maceration and ultrasound-assisted extraction and were evaluated for their antioxidant and anti-inflammatory effects in lipopolysaccharide (LPS)-stimulated RAW264.7 macrophages. The obtained results show that both extracts (maceration and ultrasound) were rich in bioactive molecules and exerted substantial antioxidant and anti-inflammatory effects. The P. tetragonolobus extracts’ treatment in LPS-stimulated RAW264.7 macrophages resulted in a significant downregulation of the expressions of tumor necrosis factor-α (TNF-α), interleukin-6 (IL-6), and IL-1β mRNA. In addition, the P. tetragonolobus extracts’ treatment attenuated inducible nitric oxide synthase (iNOS) and cyclooxygenase-2 (COX-2) protein expression. Our observations indicate that there is no significant difference between the two studied extracts of P. tetragonolobus in terms of biological properties (specifically, antioxidant and anti-inflammatory effects. Regardless of the extraction method, P. tetragonolobus could be used for treating diseases related to oxidative stress and inflammatory reactions.
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Affiliation(s)
- Hussein Bassal
- Doctoral School of Science and Technology, Research Platform for Environmental Science (PRASE), Lebanese University, Beirut P.O. Box 6573, Lebanon; (H.B.); (C.T.); (B.S.A.); (A.K.); (F.E.O.)
- Laboratory of Cancer Biology and Molecular Immunology, Faculty of Sciences, Lebanese University, Beirut P.O. Box 6573, Lebanon
| | - Akram Hijazi
- Doctoral School of Science and Technology, Research Platform for Environmental Science (PRASE), Lebanese University, Beirut P.O. Box 6573, Lebanon; (H.B.); (C.T.); (B.S.A.); (A.K.); (F.E.O.)
- Correspondence: (A.H.); (M.M.)
| | - Hussein Farhan
- Biotechnology Department, College of Science, University of Baghdad, Baghdad 10070, Iraq;
| | - Christine Trabolsi
- Doctoral School of Science and Technology, Research Platform for Environmental Science (PRASE), Lebanese University, Beirut P.O. Box 6573, Lebanon; (H.B.); (C.T.); (B.S.A.); (A.K.); (F.E.O.)
| | - Bouchra Sayed Ahmad
- Doctoral School of Science and Technology, Research Platform for Environmental Science (PRASE), Lebanese University, Beirut P.O. Box 6573, Lebanon; (H.B.); (C.T.); (B.S.A.); (A.K.); (F.E.O.)
| | - Alia Khalil
- Doctoral School of Science and Technology, Research Platform for Environmental Science (PRASE), Lebanese University, Beirut P.O. Box 6573, Lebanon; (H.B.); (C.T.); (B.S.A.); (A.K.); (F.E.O.)
| | - Marc Maresca
- CNRS, Centrale Marseille, iSm2, Aix Marseille University, 13397 Marseille, France
- Correspondence: (A.H.); (M.M.)
| | - Fawaz El Omar
- Doctoral School of Science and Technology, Research Platform for Environmental Science (PRASE), Lebanese University, Beirut P.O. Box 6573, Lebanon; (H.B.); (C.T.); (B.S.A.); (A.K.); (F.E.O.)
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Dhaliwal SK, Talukdar A, Gautam A, Sharma P, Sharma V, Kaushik P. Developments and Prospects in Imperative Underexploited Vegetable Legumes Breeding: A Review. Int J Mol Sci 2020; 21:E9615. [PMID: 33348635 PMCID: PMC7766301 DOI: 10.3390/ijms21249615] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/15/2020] [Accepted: 11/23/2020] [Indexed: 02/07/2023] Open
Abstract
Vegetable legumes are an essential source of carbohydrates, vitamins, and minerals, along with health-promoting bioactive chemicals. The demand for the use of either fresh or processed vegetable legumes is continually expanding on account of the growing consumer awareness about their well-balanced diet. Therefore, sustaining optimum yields of vegetable legumes is extremely important. Here we seek to present d etails of prospects of underexploited vegetable legumes for food availability, accessibility, and improved livelihood utilization. So far research attention was mainly focused on pulse legumes' performance as compared to vegetable legumes. Wild and cultivated vegetable legumes vary morphologically across diverse habitats. This could make them less known, underutilized, and underexploited, and make them a promising potential nutritional source in developing nations where malnutrition still exists. Research efforts are required to promote underexploited vegetable legumes, for improving their use to feed the ever-increasing population in the future. In view of all the above points, here we have discussed underexploited vegetable legumes with tremendous potential; namely, vegetable pigeon pea (Cajanus cajan), cluster bean (Cyamopsis tetragonoloba), winged bean (Psophocarpus tetragonolobus), dolichos bean (Lablab purpureus), and cowpea (Vigna unguiculata), thereby covering the progress related to various aspects such as pre-breeding, molecular markers, quantitative trait locus (QTLs), genomics, and genetic engineering. Overall, this review has summarized the information related to advancements in the breeding of vegetable legumes which will ultimately help in ensuring food and nutritional security in developing nations.
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Affiliation(s)
- Sandeep Kaur Dhaliwal
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana 141004, India; (S.K.D.); (P.S.)
| | - Akshay Talukdar
- Division of Genetics, Indian Agricultural Research Institute, New Delhi 110012, India;
| | - Ashish Gautam
- Department of Genetics and Plant Breeding, G.B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145, India;
| | - Pankaj Sharma
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana 141004, India; (S.K.D.); (P.S.)
| | - Vinay Sharma
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India;
| | - Prashant Kaushik
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, 46022 Valencia, Spain
- Nagano University, Ueda 386-0031, Japan
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5
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Bassal H, Merah O, Ali AM, Hijazi A, El Omar F. Psophocarpus tetragonolobus: An Underused Species with Multiple Potential Uses. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1730. [PMID: 33302439 PMCID: PMC7762608 DOI: 10.3390/plants9121730] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/30/2020] [Accepted: 12/06/2020] [Indexed: 11/17/2022]
Abstract
Natural products, particularly those extracted from plants, have been used as therapy for different diseases for thousands of years. The first written records on the plants used in natural medicine, referred to as "medicinal plants", go back to about 2600 BC. A thorough and complete understanding of medicinal plants encompasses a multiplex of overlapping and integrated sciences such as botany, pharmacognosy, chemistry, enzymology and genetics. Psophocarpus tetragonolobus, a member of Fabaceae family also called winged bean, is a perennial herbaceous plant characterized by its tuberous roots and its winged pod twinning and a perennial legume rich in proteins, oils, vitamins and carbohydrates. Besides nutrients, winged bean also contains bioactive compounds that have therapeutic activities like anti-oxidant, anti-inflammatory, antinociceptive, antibacterial, antifungal, antiproliferative and cytotoxic activity, a few of which already been reported. This plant can also be used as a medicinal plant for future benefits. With this concept in mind, the present review is designed to shed the light on the interests in the various phytochemicals and pharmacological pharmacognostical aspects of Psophocarpus tetragonolobus.
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Affiliation(s)
- Hussein Bassal
- Doctoral School of Science and Technology, Research Platform for Environmental Science (PRASE), Lebanese University, Beirut, Lebanon;
- Laboratory of Cancer Biology and Molecular Immunology, Faculty of Sciences, Lebanese University, Hadath-Beirut, Beirut, Lebanon
| | - Othmane Merah
- Laboratoire de Chimie Agro-industrielle, LCA, Université de Toulouse, INRA, 31030 Toulouse, France
- Département Génie Biologique, Université Paul Sabatier, IUT A, 32000 Auch, France
| | - Aqeel M. Ali
- Department of Biology, College of Science, Al Mustansiriya University, Baghdad, Iraq;
| | - Akram Hijazi
- Doctoral School of Science and Technology, Research Platform for Environmental Science (PRASE), Lebanese University, Beirut, Lebanon;
| | - Fawaz El Omar
- Doctoral School of Science and Technology, Lebanese University, EDST, Hadath, Beirut, Lebanon;
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Tian R, Zhang C, Huang Y, Guo X, Chen M. A Novel Software and Method for the Efficient Development of Polymorphic SSR Loci Based on Transcriptome Data. Genes (Basel) 2019; 10:E917. [PMID: 31717904 PMCID: PMC6895799 DOI: 10.3390/genes10110917] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 11/04/2019] [Accepted: 11/05/2019] [Indexed: 11/25/2022] Open
Abstract
Traditional methods for developing polymorphic microsatellite loci without reference sequences are time-consuming and labor-intensive, and the polymorphisms of simple sequence repeat (SSR) loci developed from expressed sequence tag (EST) databases are generally poor. To address this issue, in this study, we developed a new software (PSSRdt) and established an effective method for directly obtaining polymorphism details of SSR loci by analyzing diverse transcriptome data. The new method includes three steps, raw data processing, PSSRdt application, and loci extraction and verification. To test the practicality of the method, we successfully obtained 1940 potential polymorphic SSRs from the transcript dataset combined with 44 pea aphid transcriptomes. Fifty-two SSR loci obtained by the new method were selected for validating the polymorphic characteristics by genotyping in pea aphid individuals. The results showed that over 92% of SSR loci were polymorphic and 73.1% of loci were highly polymorphic. Our new software and method provide an innovative approach to microsatellite development based on RNA-seq data, and open a new path for the rapid mining of numerous loci with polymorphism to add to the body of research on microsatellites.
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Affiliation(s)
| | | | | | | | - Maohua Chen
- Northwest A&F University, State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Integrated Pest Management on Crops in Northwestern Loess Plateau, Ministry of Agriculture and Rural Affairs, Yangling 712100, China; (R.T.); (C.Z.); (Y.H.); (X.G.)
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Tanzi AS, Eagleton GE, Ho WK, Wong QN, Mayes S, Massawe F. Winged bean (Psophocarpus tetragonolobus (L.) DC.) for food and nutritional security: synthesis of past research and future direction. PLANTA 2019; 250:911-931. [PMID: 30911885 DOI: 10.1007/s00425-019-03141-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Accepted: 03/15/2019] [Indexed: 06/09/2023]
Abstract
Winged bean is popularly known as "One Species Supermarket" for its nutrient-dense green pods, immature seeds, tubers, leaves, and mature seeds. This underutilised crop has potential beneficial traits related to its biological nitrogen-fixation to support low-input farming. Drawing from past knowledge, and based on current technologies, we propose a roadmap for research and development of winged bean for sustainable food systems. Reliance on a handful of "major" crops has led to decreased diversity in crop species, agricultural systems and human diets. To reverse this trend, we need to encourage the greater use of minor, "orphan", underutilised species. These could contribute to an increase in crop diversity within agricultural systems, to improve human diets, and to support more sustainable and resilient food production systems. Among these underutilised species, winged bean (Psophocarpus tetragonolobus) has long been proposed as a crop for expanded use particularly in the humid tropics. It is an herbaceous perennial legume of equatorial environments and has been identified as a rich source of protein, with most parts of the plant being edible when appropriately prepared. However, to date, limited progress in structured improvement programmes has restricted the expansion of winged bean beyond its traditional confines. In this paper, we discuss the reasons for this and recommend approaches for better use of its genetic resources and related Psophocarpus species in developing improved varieties. We review studies on the growth, phenology, nodulation and nitrogen-fixation activity, breeding programmes, and molecular analyses. We then discuss prospects for the crop based on the greater understanding that these studies have provided and considering modern plant-breeding technologies and approaches. We propose a more targeted and structured research approach to fulfil the potential of winged bean to contribute to food security.
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Affiliation(s)
- Alberto Stefano Tanzi
- School of Biosciences, University of Nottingham Malaysia, Jalan Broga, 43500, Semenyih, Selangor Darul Ehsan, Malaysia
- Crops for the Future, Jalan Broga, 43500, Semenyih, Selangor Darul Ehsan, Malaysia
| | - Graham Ewen Eagleton
- Department of Planning, Ministry of Agriculture, Livestock and Irrigation, Nay Pyi Taw, 15011, Myanmar
| | - Wai Kuan Ho
- School of Biosciences, University of Nottingham Malaysia, Jalan Broga, 43500, Semenyih, Selangor Darul Ehsan, Malaysia
- Crops for the Future, Jalan Broga, 43500, Semenyih, Selangor Darul Ehsan, Malaysia
| | - Quin Nee Wong
- School of Biosciences, University of Nottingham Malaysia, Jalan Broga, 43500, Semenyih, Selangor Darul Ehsan, Malaysia
| | - Sean Mayes
- Crops for the Future, Jalan Broga, 43500, Semenyih, Selangor Darul Ehsan, Malaysia
- School of Biosciences, Faculty of Science, University of Nottingham Sutton Bonington Campus, Sutton Bonington, Leicestershire, LE12 5RD, UK
| | - Festo Massawe
- School of Biosciences, University of Nottingham Malaysia, Jalan Broga, 43500, Semenyih, Selangor Darul Ehsan, Malaysia.
- Crops for the Future, Jalan Broga, 43500, Semenyih, Selangor Darul Ehsan, Malaysia.
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Gregory PJ, Mayes S, Hui CH, Jahanshiri E, Julkifle A, Kuppusamy G, Kuan HW, Lin TX, Massawe F, Suhairi TASTM, Azam-Ali SN. Crops For the Future (CFF): an overview of research efforts in the adoption of underutilised species. PLANTA 2019; 250:979-988. [PMID: 31250097 DOI: 10.1007/s00425-019-03179-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 04/30/2019] [Indexed: 05/28/2023]
Abstract
Crops For the Future (CFF), as an entity, has established a broad range of research activities to promote the improvement and adoption of currently underutilised crops. This paper summarises selected research activities at Crops For the Future (CFF) in pursuit of its mission 'to develop solutions for diversifying future agriculture using underutilised crops'. CFF is a research company focussed on the improvement of underutilised crops, so that they might be grown and consumed more widely with benefits to human food and nutritional security; its founding guarantors were the Government of Malaysia and the University of Nottingham. From its base in Malaysia, it engages in research around the world with a focus on species and system diversification. CFF has adopted a food system approach that adds value by delivering prototype food, feed and knowledge products. Bambara groundnut (Vigna subterranea) was adopted as an exemplar crop around which to develop CFF's food system approach with emphasis on the short-day photoperiod requirement for pod-filling and the hard-to-cook trait. Selective breeding has allowed the development of lines that are less susceptible to photoperiod but also provided a range of tools and approaches that are now being exploited in other crops such as winged bean (Psophocarpus tetragonolobus), amaranth (Amaranthus spp.), moringa (Moringa oleifera) and proso (Panicum miliaceum) and foxtail (Setaria italica) millets. CFF has developed and tested new food products and demonstrated that several crops can be used as feed for black soldier fly which can, in turn, be used to feed fish thereby reducing the need for fishmeal. Information about underutilised crops is widely dispersed; so, a major effort has been made to develop a knowledge base that can be interrogated and used to answer practical questions about potential exploitation of plant and nutritional characteristics. Future research will build on the success with Bambara groundnut and include topics such as urban agriculture, rural development and diversification, and the development of novel foods.
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Affiliation(s)
- Peter J Gregory
- Crops for the Future, Jalan Broga, 43500, Semenyih, Selangor Darul Ehsan, Malaysia.
- School of Agriculture, Policy and Development, University of Reading, Earley Gate, Reading, RG6 6AR, UK.
| | - Sean Mayes
- Crops for the Future, Jalan Broga, 43500, Semenyih, Selangor Darul Ehsan, Malaysia
- School of Biosciences, University of Nottingham, Sutton Bonington, Loughborough, LE12 5RD, UK
| | - Chai Hui Hui
- Crops for the Future, Jalan Broga, 43500, Semenyih, Selangor Darul Ehsan, Malaysia
| | - Ebrahim Jahanshiri
- Crops for the Future, Jalan Broga, 43500, Semenyih, Selangor Darul Ehsan, Malaysia
| | - Advina Julkifle
- Crops for the Future, Jalan Broga, 43500, Semenyih, Selangor Darul Ehsan, Malaysia
| | - Giva Kuppusamy
- Crops for the Future, Jalan Broga, 43500, Semenyih, Selangor Darul Ehsan, Malaysia
| | - Ho Wai Kuan
- Crops for the Future, Jalan Broga, 43500, Semenyih, Selangor Darul Ehsan, Malaysia
- School of Biosciences, University of Nottingham Malaysia Campus, Jalan Broga, 43500, Semenyih, Selangor Darul Ehsan, Malaysia
| | - Tan Xin Lin
- Crops for the Future, Jalan Broga, 43500, Semenyih, Selangor Darul Ehsan, Malaysia
| | - Festo Massawe
- School of Biosciences, University of Nottingham Malaysia Campus, Jalan Broga, 43500, Semenyih, Selangor Darul Ehsan, Malaysia
| | - T A S T M Suhairi
- Crops for the Future, Jalan Broga, 43500, Semenyih, Selangor Darul Ehsan, Malaysia
| | - Sayed N Azam-Ali
- Crops for the Future, Jalan Broga, 43500, Semenyih, Selangor Darul Ehsan, Malaysia
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Yang S, Grall A, Chapman MA. Origin and diversification of winged bean (Psophocarpus tetragonolobus (L.) DC.), a multipurpose underutilized legume. AMERICAN JOURNAL OF BOTANY 2018; 105:888-897. [PMID: 29874397 DOI: 10.1002/ajb2.1093] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 02/21/2018] [Indexed: 06/08/2023]
Abstract
PREMISE OF THE STUDY For many crops, research into the origin and partitioning of genetic variation is limited and this can slow or prevent crop improvement programs. Many of these underutilized crops have traits that could be of benefit in a changing climate due to stress tolerance or nutritional properties. Winged bean (Psophocarpus tetragonolobus (L.) DC.) is one such crop. All parts of the plant can be eaten, from the roots to the seeds, and is high in protein as well as other micronutrients. The goal of our study was to identify the wild progenitor and analyze the partitioning of genetic variation in the crop. METHODS We used molecular phylogenetic analyses (cpDNA and nuclear ITS sequencing) to resolve relationships between all species in the genus, and population genetics (utilizing microsatellites) to identify genetic clusters of winged bean accessions and compare this to geography. KEY RESULTS We find that winged bean is genetically distinct from all other members of the genus. We also provide support for four groups of species in the genus, largely, but not completely, corresponding to the results of previous morphological analyses. Within winged bean, population genetic analysis using 10 polymorphic microsatellite markers suggests four genetic groups; however, there is little correspondence between the genetic variation and the geography of the accessions. CONCLUSIONS The true wild progenitor of winged bean remains unknown (or is extinct). There has likely been large-scale cross-breeding, trade, and transport of winged bean and/or multiple origins of the crop.
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Affiliation(s)
- Shuyi Yang
- Biological Sciences, University of Southampton, Life Sciences Building 85, Highfield Campus, Southampton, SO17 1BJ, UK
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangdong, 510642, China
| | - Aurélie Grall
- Africa & Madagascar Team, Identification & Naming Department, Royal Botanic Gardens, Kew, TW9 3AE, UK
| | - Mark A Chapman
- Biological Sciences, University of Southampton, Life Sciences Building 85, Highfield Campus, Southampton, SO17 1BJ, UK
- Centre for Underutilised Crops, University of Southampton, Highfield Campus, Southampton, SO17 1BJ, UK
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10
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Jo IH, Lee J, Hong CE, Lee DJ, Bae W, Park SG, Ahn YJ, Kim YC, Kim JU, Lee JW, Hyun DY, Rhee SK, Hong CP, Bang KH, Ryu H. Isoform Sequencing Provides a More Comprehensive View of the Panax ginseng Transcriptome. Genes (Basel) 2017; 8:E228. [PMID: 28914759 PMCID: PMC5615361 DOI: 10.3390/genes8090228] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 08/17/2017] [Accepted: 09/12/2017] [Indexed: 11/17/2022] Open
Abstract
Korean ginseng (Panax ginseng C.A. Meyer) has been widely used for medicinal purposes and contains potent plant secondary metabolites, including ginsenosides. To obtain transcriptomic data that offers a more comprehensive view of functional genomics in P. ginseng, we generated genome-wide transcriptome data from four different P. ginseng tissues using PacBio isoform sequencing (Iso-Seq) technology. A total of 135,317 assembled transcripts were generated with an average length of 3.2 kb and high assembly completeness. Of those unigenes, 67.5% were predicted to be complete full-length (FL) open reading frames (ORFs) and exhibited a high gene annotation rate. Furthermore, we successfully identified unique full-length genes involved in triterpenoid saponin synthesis and plant hormonal signaling pathways, including auxin and cytokinin. Studies on the functional genomics of P. ginseng seedlings have confirmed the rapid upregulation of negative feed-back loops by auxin and cytokinin signaling cues. The conserved evolutionary mechanisms in the auxin and cytokinin canonical signaling pathways of P. ginseng are more complex than those in Arabidopsis thaliana. Our analysis also revealed a more detailed view of transcriptome-wide alternative isoforms for 88 genes. Finally, transposable elements (TEs) were also identified, suggesting transcriptional activity of TEs in P. ginseng. In conclusion, our results suggest that long-read, full-length or partial-unigene data with high-quality assemblies are invaluable resources as transcriptomic references in P. ginseng and can be used for comparative analyses in closely related medicinal plants.
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Affiliation(s)
- Ick-Hyun Jo
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science (NIHHS), Rural development administration (RDA), Eumseong 27709, Korea.
| | - Jinsu Lee
- Department of Biology, Chungbuk National University, Cheongju 28644, Korea.
| | - Chi Eun Hong
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science (NIHHS), Rural development administration (RDA), Eumseong 27709, Korea.
| | | | - Wonsil Bae
- Department of Biology, Chungbuk National University, Cheongju 28644, Korea.
| | - Sin-Gi Park
- TheragenEtex Bio Institute, Suwon 16229, Korea.
| | - Yong Ju Ahn
- TheragenEtex Bio Institute, Suwon 16229, Korea.
| | - Young Chang Kim
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science (NIHHS), Rural development administration (RDA), Eumseong 27709, Korea.
| | - Jang Uk Kim
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science (NIHHS), Rural development administration (RDA), Eumseong 27709, Korea.
| | - Jung Woo Lee
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science (NIHHS), Rural development administration (RDA), Eumseong 27709, Korea.
| | - Dong Yun Hyun
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science (NIHHS), Rural development administration (RDA), Eumseong 27709, Korea.
| | - Sung-Keun Rhee
- Department of Microbiology, Chungbuk National University, Cheongju 28644, Korea.
| | | | - Kyong Hwan Bang
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science (NIHHS), Rural development administration (RDA), Eumseong 27709, Korea.
| | - Hojin Ryu
- Department of Biology, Chungbuk National University, Cheongju 28644, Korea.
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11
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Lepcha P, Egan AN, Doyle JJ, Sathyanarayana N. A Review on Current Status and Future Prospects of Winged Bean (Psophocarpus tetragonolobus) in Tropical Agriculture. PLANT FOODS FOR HUMAN NUTRITION (DORDRECHT, NETHERLANDS) 2017; 72:225-235. [PMID: 28866817 DOI: 10.1007/s11130-017-0627-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Winged bean, Psophocarpus tetragonolobus (L.) DC., is analogous to soybean in yield and nutritional quality, proving a valuable alternative to soybean in tropical regions of the world. The presence of anti-nutritional factors and high costs associated with indeterminate plant habit have been major concerns in this crop. But occurrence of good genetic variability in germplasm collections offers precious resources for winged bean breeding. However, lack of germplasm characterization is hindering such efforts. From a genomic standpoint, winged bean has been little studied despite rapid advancement in legume genomics in the last decade. Exploiting modern genomics/breeding approaches for genetic resource characterization and the breeding of early maturing, high yielding, determinate varieties which are disease resistant and free of anti-nutritional factors along with developing consumer friendly value-added products of local significance are great challenges and opportunities in the future that would boost cultivation of winged bean in the tropics. We review past efforts and future prospects towards winged bean improvement.
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Affiliation(s)
- Patrush Lepcha
- Department of Botany, Sikkim University, 6th Mile, Tadong, Gangtok, Sikkim, 737102, India
| | - Ashley N Egan
- US National Herbarium (US), Department of Botany, Smithsonian Institution - NMNH, 10th and Constitution Ave NW, Washington DC, 20013, USA
| | - Jeff J Doyle
- Section of Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, 412 Mann Library, Ithaca, NY, 14853, USA
| | - N Sathyanarayana
- Department of Botany, Sikkim University, 6th Mile, Tadong, Gangtok, Sikkim, 737102, India.
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