1
|
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.
Collapse
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.
| |
Collapse
|
2
|
Hu J, Duan Y, Yang J, Gan L, Chen W, Yang J, Xiao G, Guan L, Chen J. Transcriptome Analysis Reveals Genes Associated with Flooding Tolerance in Mulberry Plants. Life (Basel) 2023; 13:life13051087. [PMID: 37240733 DOI: 10.3390/life13051087] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/13/2023] [Accepted: 04/25/2023] [Indexed: 05/28/2023] Open
Abstract
Mulberry (Morus alba), a widely distributed economic plant, can withstand long-term flooding stress. However, the regulatory gene network underlying this tolerance is unknown. In the present study, mulberry plants were subjected to submergence stress. Subsequently, mulberry leaves were collected to perform quantitative reverse-transcription PCR (qRT-PCR) and transcriptome analysis. Genes encoding ascorbate peroxidase and glutathione S-transferase were significantly upregulated after submergence stress, indicating that they could protect the mulberry plant from flood damage by mediating ROS homeostasis. Genes that regulate starch and sucrose metabolism; genes encoding pyruvate kinase, alcohol dehydrogenase, and pyruvate decarboxylase (enzymes involved in glycolysis and ethanol fermentation); and genes encoding malate dehydrogenase and ATPase (enzymes involved in the TCA cycle) were also obviously upregulated. Hence, these genes likely played a key role in mitigating energy shortage during flooding stress. In addition, genes associated with ethylene, cytokinin, abscisic acid, and MAPK signaling; genes involved in phenylpropanoid biosynthesis; and transcription factor genes also showed upregulation under flooding stress in mulberry plants. These results provide further insights into the adaptation mechanisms and genetics of submergence tolerance in mulberry plants and could aid in the molecular breeding of these plants.
Collapse
Affiliation(s)
- Jingtao Hu
- College of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing 404100, China
| | - Yanyan Duan
- College of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing 404100, China
| | - Junnian Yang
- College of Teacher Education, Chongqing Three Gorges University, Chongqing 404100, China
| | - Liping Gan
- College of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing 404100, China
| | - Wenjing Chen
- College of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing 404100, China
| | - Jin Yang
- College of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing 404100, China
| | - Guosheng Xiao
- College of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing 404100, China
| | - Lingliang Guan
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Jingsheng Chen
- College of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing 404100, China
| |
Collapse
|
3
|
Ogbole OO, Akin-Ajani OD, Ajala TO, Ogunniyi QA, Fettke J, Odeku OA. Nutritional and pharmacological potentials of orphan legumes: Subfamily faboideae. Heliyon 2023; 9:e15493. [PMID: 37151618 PMCID: PMC10161725 DOI: 10.1016/j.heliyon.2023.e15493] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 04/05/2023] [Accepted: 04/11/2023] [Indexed: 05/09/2023] Open
Abstract
Legumes are a major food crop in many developing nations. However, orphan or underutilized legumes are domesticated legumes that have valuable properties but are less significant than main legumes due to use and supply restrictions. Compared to other major legumes, they are better suited to harsh soil and climate conditions, and their great tolerance to abiotic environmental circumstances like drought can help to lessen the strains brought on by climate change. Despite this, their economic significance in international markets is relatively minimal. This article is aimed at carrying out a comprehensive review of the nutritional and pharmacological benefits of orphan legumes from eight genera in the sub-family Faboidea, namely Psophocarpus Neck. ex DC., Tylosema (Schweinf.) Torre Hillc., Vigna Savi., Vicia L., Baphia Afzel. ex G. Lodd., Mucuna Adans, Indigofera L. and Macrotyloma (Wight & Arn.) Verdc, and the phytoconstituents that have been isolated and characterized from these plants. A literature search was conducted using PubMed, Google Scholar, and Science Direct for articles that have previously reported the relevance of underutilized legumes. The International Union for Conservation of Nature (IUCN) red list of threatened species was also conducted for the status of the species. References were scrutinized and citation searches were performed on the study. The review showed that many underutilized legumes have a lot of untapped potential in terms of their nutritional and pharmacological activities. The phytoconstituents from plants in the subfamily Faboideae could serve as lead compounds for drug discovery for the treatment of a variety of disorders, indicating the need to explore these plant species.
Collapse
Affiliation(s)
| | - Olufunke D. Akin-Ajani
- Department of Pharmaceutics and Industrial Pharmacy, University of Ibadan, Ibadan, Nigeria
| | - Tolulope O. Ajala
- Department of Pharmaceutics and Industrial Pharmacy, University of Ibadan, Ibadan, Nigeria
| | | | - Joerg Fettke
- Institute of Biochemistry and Biology, University of Potsdam, Golm, Germany
| | - Oluwatoyin A. Odeku
- Department of Pharmaceutics and Industrial Pharmacy, University of Ibadan, Ibadan, Nigeria
- Corresponding author.
| |
Collapse
|
4
|
Quintieri L, Nitride C, De Angelis E, Lamonaca A, Pilolli R, Russo F, Monaci L. Alternative Protein Sources and Novel Foods: Benefits, Food Applications and Safety Issues. Nutrients 2023; 15:nu15061509. [PMID: 36986239 PMCID: PMC10054669 DOI: 10.3390/nu15061509] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/16/2023] [Accepted: 03/19/2023] [Indexed: 03/30/2023] Open
Abstract
The increasing size of the human population and the shortage of highly valuable proteinaceous ingredients has prompted the international community to scout for new, sustainable, and natural protein resources from invertebrates (e.g., insects) and underutilized legume crops, unexploited terrestrial and aquatic weeds, and fungi. Insect proteins are known for their nutritional value, being rich in proteins with a good balance of essential amino acids and being a valuable source of essential fatty acids and trace elements. Unconventional legume crops were found rich in nutritional, phytochemical, and therapeutic properties, showing excellent abilities to survive extreme environmental conditions. This review evaluates the recent state of underutilized legume crops, aquatic weeds, fungi, and insects intended as alternative protein sources, from ingredient production to their incorporation in food products, including their food formulations and the functional characteristics of alternative plant-based proteins and edible insect proteins as novel foods. Emphasis is also placed on safety issues due to the presence of anti-nutritional factors and allergenic proteins in insects and/or underutilized legumes. The functional and biological activities of protein hydrolysates from different protein sources are reviewed, along with bioactive peptides displaying antihypertensive, antioxidant, antidiabetic, and/or antimicrobial activity. Due to the healthy properties of these foods for the high abundance of bioactive peptides and phytochemicals, more consumers are expected to turn to vegetarianism or veganism in the future, and the increasing demand for such products will be a challenge for the future.
Collapse
Affiliation(s)
- Laura Quintieri
- Institute of Sciences of Food Production, National Research Council of Italy (ISPA-CNR), Via Giovanni Amendola 122/O, 70126 Bari, Italy
| | - Chiara Nitride
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Portici, Italy
| | - Elisabetta De Angelis
- Institute of Sciences of Food Production, National Research Council of Italy (ISPA-CNR), Via Giovanni Amendola 122/O, 70126 Bari, Italy
| | - Antonella Lamonaca
- Institute of Sciences of Food Production, National Research Council of Italy (ISPA-CNR), Via Giovanni Amendola 122/O, 70126 Bari, Italy
| | - Rosa Pilolli
- Institute of Sciences of Food Production, National Research Council of Italy (ISPA-CNR), Via Giovanni Amendola 122/O, 70126 Bari, Italy
| | - Francesco Russo
- Functional Gastrointestinal Disorders Research Group, National Institute of Gastroenterology IRCCS "Saverio de Bellis", 70013 Castellana Grotte, Italy
| | - Linda Monaci
- Institute of Sciences of Food Production, National Research Council of Italy (ISPA-CNR), Via Giovanni Amendola 122/O, 70126 Bari, Italy
| |
Collapse
|
5
|
Muñoz-Espinoza C, Meneses M, Hinrichsen P. Transcriptomic Approach for Global Distribution of SNP/Indel and Plant Genotyping. Methods Mol Biol 2023; 2638:147-164. [PMID: 36781640 DOI: 10.1007/978-1-0716-3024-2_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Single Nucleotide Polymorphisms (SNPs) are the most common structural variants found in any genome. They have been used for different genetic studies, from the understanding of genetic structure of populations to the development of breeding selection markers. In this chapter we present the use of transcriptomic data obtained from contrasting phenotypes for a target trait, in searching of SNPs and insertions/deletions (InDels). This approach has the advantage that the identified markers are in or close to differentially expressed genes, and so they have higher chances to tag the genes underlying the phenotypic expression of a particular trait.
Collapse
Affiliation(s)
| | - Marco Meneses
- Instituto de Investigaciones Agropecuarias, INIA La Platina, Santiago, Chile
| | - Patricio Hinrichsen
- Instituto de Investigaciones Agropecuarias, INIA La Platina, Santiago, Chile.
| |
Collapse
|
6
|
Chongtham SK, Devi EL, Samantara K, Yasin JK, Wani SH, Mukherjee S, Razzaq A, Bhupenchandra I, Jat AL, Singh LK, Kumar A. Orphan legumes: harnessing their potential for food, nutritional and health security through genetic approaches. PLANTA 2022; 256:24. [PMID: 35767119 DOI: 10.1007/s00425-022-03923-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 05/21/2022] [Indexed: 06/15/2023]
Abstract
Legumes, being angiosperm's third-largest family as well as the second major crop family, contributes beyond 33% of human dietary proteins. The advent of the global food crisis owing to major climatic concerns leads to nutritional deprivation, hunger and hidden hunger especially in developing and underdeveloped nations. Hence, in the wake of promoting sustainable agriculture and nutritional security, apart from the popular legumes, the inclusion of lesser-known and understudied local crop legumes called orphan legumes in the farming systems of various tropical and sub-tropical parts of the world is indeed a need of the hour. Despite possessing tremendous potentialities, wide adaptability under diverse environmental conditions, and rich in nutritional and nutraceutical values, these species are still in a neglected and devalued state. Therefore, a major re-focusing of legume genetics, genomics, and biology is much crucial in pursuance of understanding the yield constraints, and endorsing underutilized legume breeding programs. Varying degrees of importance to these crops do exist among researchers of developing countries in establishing the role of orphan legumes as future crops. Under such circumstances, this article assembles a comprehensive note on the necessity of promoting these crops for further investigations and sustainable legume production, the exploitation of various orphan legume species and their potencies. In addition, an attempt has been made to highlight various novel genetic, molecular, and omics approaches for the improvement of such legumes for enhancing yield, minimizing the level of several anti-nutritional factors, and imparting biotic and abiotic stress tolerance. A significant genetic enhancement through extensive research in 'omics' areas is the absolute necessity to transform them into befitting candidates for large-scale popularization around the globe.
Collapse
Affiliation(s)
- Sunil Kumar Chongtham
- Multi Technology Testing Centre and Vocational Training Centre, CAEPHT, CAU, Ranipool, Gangtok, Sikkim, 737135, India
| | | | - Kajal Samantara
- Department of Genetics and Plant Breeding, Centurion University of Technology and Management, Odisha, 761211, India
| | - Jeshima Khan Yasin
- Division of Genomic Resources, ICAR-National Bureau Plant Genetic Resources, PUSA Campus, New Delhi, 110012, India
| | - Shabir Hussain Wani
- Mountain Research Centre for Field Crops, Khudwani, Sher-E-Kashmir University of Agricultural Sciences and Technology, Srinagar, 192101, Jammu and Kashmir, India.
| | - Soumya Mukherjee
- Department of Botany, Jangipur College, University of Kalyani, West Bengal, 742213, India
| | - Ali Razzaq
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture Faisalabad, Faisalabad, 38040, Pakistan
| | - Ingudam Bhupenchandra
- ICAR-KVK Tamenglong, ICAR RC for NEH Region, Manipur Centre, Lamphelpat, Imphal, Manipur, 795 004, India
| | - Aanandi Lal Jat
- Castor-Mustard Research Station, SDAU, S.K. Nagar, Banaskantha, Gujarat, 385 506, India
| | - Laishram Kanta Singh
- ICAR-KVK Imphal West, ICAR RC for NEH region, Manipur Centre, Lamphelpat, Imphal, Manipur, 795 004, India
| | - Amit Kumar
- ICAR Research Complex for NEH Region, Tadong, Sikkim Centre, 737102, India
| |
Collapse
|
7
|
Jha UC, Nayyar H, Parida SK, Bakır M, von Wettberg EJB, Siddique KHM. Progress of Genomics-Driven Approaches for Sustaining Underutilized Legume Crops in the Post-Genomic Era. Front Genet 2022; 13:831656. [PMID: 35464848 PMCID: PMC9021634 DOI: 10.3389/fgene.2022.831656] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 02/24/2022] [Indexed: 12/22/2022] Open
Abstract
Legume crops, belonging to the Fabaceae family, are of immense importance for sustaining global food security. Many legumes are profitable crops for smallholder farmers due to their unique ability to fix atmospheric nitrogen and their intrinsic ability to thrive on marginal land with minimum inputs and low cultivation costs. Recent progress in genomics shows promise for future genetic gains in major grain legumes. Still it remains limited in minor legumes/underutilized legumes, including adzuki bean, cluster bean, horse gram, lathyrus, red clover, urd bean, and winged bean. In the last decade, unprecedented progress in completing genome assemblies of various legume crops and resequencing efforts of large germplasm collections has helped to identify the underlying gene(s) for various traits of breeding importance for enhancing genetic gain and contributing to developing climate-resilient cultivars. This review discusses the progress of genomic resource development, including genome-wide molecular markers, key breakthroughs in genome sequencing, genetic linkage maps, and trait mapping for facilitating yield improvement in underutilized legumes. We focus on 1) the progress in genomic-assisted breeding, 2) the role of whole-genome resequencing, pangenomes for underpinning the novel genomic variants underlying trait gene(s), 3) how adaptive traits of wild underutilized legumes could be harnessed to develop climate-resilient cultivars, 4) the progress and status of functional genomics resources, deciphering the underlying trait candidate genes with putative function in underutilized legumes 5) and prospects of novel breeding technologies, such as speed breeding, genomic selection, and genome editing. We conclude the review by discussing the scope for genomic resources developed in underutilized legumes to enhance their production and play a critical role in achieving the "zero hunger" sustainable development goal by 2030 set by the United Nations.
Collapse
Affiliation(s)
- Uday Chand Jha
- ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, India
| | | | - Swarup K Parida
- National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Melike Bakır
- Department of Agricultural Biotechnology, Faculty of Agriculture, Erciyes University, Kayseri, Turkey
| | - Eric J. B. von Wettberg
- Plant and Soil Science and Gund Institute for the Environment, The University of Vermont, Burlington, VT, United States
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
| | | |
Collapse
|
8
|
Talabi AO, Vikram P, Thushar S, Rahman H, Ahmadzai H, Nhamo N, Shahid M, Singh RK. Orphan Crops: A Best Fit for Dietary Enrichment and Diversification in Highly Deteriorated Marginal Environments. FRONTIERS IN PLANT SCIENCE 2022; 13:839704. [PMID: 35283935 PMCID: PMC8908242 DOI: 10.3389/fpls.2022.839704] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 01/31/2022] [Indexed: 05/23/2023]
Abstract
Orphan crops are indigenous and invariably grown by small and marginal farmers under subsistence farming systems. These crops, which are common and widely accepted by local farmers, are highly rich in nutritional profile, good for medicinal purposes, and well adapted to suboptimal growing conditions. However, these crops have suffered neglect and abandonment from the scientific community because of very low or no investments in research and genetic improvement. A plausible reason for this is that these crops are not traded internationally at a rate comparable to that of the major food crops such as wheat, rice, and maize. Furthermore, marginal environments have poor soils and are characterized by extreme weather conditions such as heat, erratic rainfall, water deficit, and soil and water salinity, among others. With more frequent extreme climatic events and continued land degradation, orphan crops are beginning to receive renewed attention as alternative crops for dietary diversification in marginal environments and, by extension, across the globe. Increased awareness of good health is also a major contributor to the revived attention accorded to orphan crops. Thus, the introduction, evaluation, and adaptation of outstanding varieties of orphan crops for dietary diversification will contribute not only to sustained food production but also to improved nutrition in marginal environments. In this review article, the concept of orphan crops vis-à-vis marginality and food and nutritional security is defined for a few orphan crops. We also examined recent advances in research involving orphan crops and the potential of these crops for dietary diversification within the context of harsh marginal environments. Recent advances in genomics coupled with molecular breeding will play a pivotal role in improving the genetic potential of orphan crops and help in developing sustainable food systems. We concluded by presenting a potential roadmap to future research engagement and a policy framework with recommendations aimed at facilitating and enhancing the adoption and sustainable production of orphan crops under agriculturally marginal conditions.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Rakesh Kumar Singh
- International Center for Biosaline Agriculture (ICBA), Dubai, United Arab Emirates
| |
Collapse
|
9
|
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 (BASEL, SWITZERLAND) 2022; 11:500. [PMID: 35214834 PMCID: PMC8878720 DOI: 10.3390/plants11040500] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [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.
Collapse
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.)
| |
Collapse
|
10
|
Satyavathi CT, Tomar RS, Ambawat S, Kheni J, Padhiyar SM, Desai H, Bhatt SB, Shitap MS, Meena RC, Singhal T, Sankar SM, Singh SP, Khandelwal V. Stage specific comparative transcriptomic analysis to reveal gene networks regulating iron and zinc content in pearl millet [Pennisetum glaucum (L.) R. Br.]. Sci Rep 2022; 12:276. [PMID: 34997160 PMCID: PMC8742121 DOI: 10.1038/s41598-021-04388-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 12/13/2021] [Indexed: 12/13/2022] Open
Abstract
Pearl millet is an important staple food crop of poor people and excels all other cereals due to its unique features of resilience to adverse climatic conditions. It is rich in micronutrients like iron and zinc and amenable for focused breeding for these micronutrients along with high yield. Hence, this is a key to alleviate malnutrition and ensure nutritional security. This study was conducted to identify and validate candidate genes governing grain iron and zinc content enabling the desired modifications in the genotypes. Transcriptome sequencing using ION S5 Next Generation Sequencer generated 43.5 million sequence reads resulting in 83,721 transcripts with N50 of 597 bp and 84.35% of transcripts matched with the pearl millet genome assembly. The genotypes having high iron and zinc showed differential gene expression during different stages. Of which, 155 were up-regulated and 251 were down-regulated while during flowering stage and milking stage 349 and 378 transcripts were differentially expressed, respectively. Gene annotation and GO term showed the presence of transcripts involved in metabolic activities associated with uptake and transport of iron and zinc. Information generated will help in gaining insights into iron and zinc metabolism and develop genotypes with high yield, grain iron and zinc content.
Collapse
Affiliation(s)
- C Tara Satyavathi
- ICAR-AICRP on Pearl Millet, Agriculture University, Jodhpur, Rajasthan, 342 304, India.
| | - Rukam S Tomar
- Department of Biotechnology, Junagadh Agricultural University, Junagadh, Gujarat, India
| | - Supriya Ambawat
- ICAR-AICRP on Pearl Millet, Agriculture University, Jodhpur, Rajasthan, 342 304, India
| | - Jasminkumar Kheni
- Department of Biotechnology, Junagadh Agricultural University, Junagadh, Gujarat, India
| | - Shital M Padhiyar
- Department of Biotechnology, Junagadh Agricultural University, Junagadh, Gujarat, India
| | - Hiralben Desai
- Department of Biotechnology, Junagadh Agricultural University, Junagadh, Gujarat, India
| | - S B Bhatt
- Department of Biotechnology, Junagadh Agricultural University, Junagadh, Gujarat, India
| | - M S Shitap
- Department of Agricultural Statistics, Junagadh Agricultural University, Junagadh, Gujarat, India
| | - Ramesh Chand Meena
- ICAR-AICRP on Pearl Millet, Agriculture University, Jodhpur, Rajasthan, 342 304, India
| | - Tripti Singhal
- Division of Genetics, Indian Agricultural Research Institute, ICAR, New Delhi, India
| | - S Mukesh Sankar
- Division of Genetics, Indian Agricultural Research Institute, ICAR, New Delhi, India
| | - S P Singh
- Division of Genetics, Indian Agricultural Research Institute, ICAR, New Delhi, India
| | - Vikas Khandelwal
- ICAR-AICRP on Pearl Millet, Agriculture University, Jodhpur, Rajasthan, 342 304, India
| |
Collapse
|
11
|
Ikhajiagbe B, Ogwu MC, Ogochukwu OF, Odozi EB, Adekunle IJ, Omage ZE. The place of neglected and underutilized legumes in human nutrition and protein security in Nigeria. Crit Rev Food Sci Nutr 2021; 62:3930-3938. [PMID: 33455427 DOI: 10.1080/10408398.2020.1871319] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The enormous effects of food insecurity have worsened in Nigeria and are further heightened by internal conflicts combined with ongoing climate change impacts such as drought and floods. Moreover, food availability is affected by economic challenges especially a weakening of foreign exchange and fiscal revenues, which has reduced the rate of food importation and increased local prices. Furthermore, the geometric increase in population especially in the last five decades has placed enormous pressure on the limited food resources, making it more challenging for agricultural and food systems to sustainably meet local food needs. Put together, these indices are contributing significantly to undernourishment. The huge local legume resources if properly harnessed can contribute toward addressing food insecurity. However, most of the legumes are included in the United Nations' Food and Agriculture Organization list of underutilized crops. Also, there is an over-reliance on food high in calorie in Nigeria, which is discouraged by nutritionists worldwide. Plant-based protein from legumes is necessary for effective metabolism and human wellbeing. This work highlights the benefits of the sustainable utilization of neglected and underutilized legume resources in Nigeria. The work discusses potential solutions for food insecurity as well as avenues for improving human nutrition and wellbeing.
Collapse
Affiliation(s)
- Beckley Ikhajiagbe
- Department of Plant Biology and Biotechnology, Faculty of Life Sciences, University of Benin, Benin City, Nigeria
| | - Matthew Chidozie Ogwu
- Department of Plant Biology and Biotechnology, Faculty of Life Sciences, University of Benin, Benin City, Nigeria.,School of Biosciences and Veterinary Medicine, University of Camerino - Center for Floristic Research of the Apennine, Barisciano, L'Aquila, Italy
| | | | - Efeota Bright Odozi
- Department of Medical Laboratory Science, School of Basic Medical Sciences, University of Benin, Benin City, Nigeria
| | - Isaac Johnson Adekunle
- Department of Plant Biology and Biotechnology, Faculty of Life Sciences, University of Benin, Benin City, Nigeria
| | - Zipporah Emilomo Omage
- Department of Plant Biology and Biotechnology, Faculty of Life Sciences, University of Benin, Benin City, Nigeria
| |
Collapse
|
12
|
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.
Collapse
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
| |
Collapse
|
13
|
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.
Collapse
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;
| |
Collapse
|
14
|
Chai M, Ye H, Wang Z, Zhou Y, Wu J, Gao Y, Han W, Zang E, Zhang H, Ru W, Sun G, Wang Y. Genetic Divergence and Relationship Among Opisthopappus Species Identified by Development of EST-SSR Markers. Front Genet 2020; 11:177. [PMID: 32194635 PMCID: PMC7065708 DOI: 10.3389/fgene.2020.00177] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 02/13/2020] [Indexed: 12/16/2022] Open
Abstract
Opisthopappus Shih is an endemic and endangered genus restricted to the Taihang Mountains that has important ornamental and economic value. According to the Flora Reipublicae Popularis Sinicae (FRPS, Chinese version), this genus contains two species (Opisthopappus longilobus and Opisthopappus taihangensis), whereas in the Flora of China (English version) only one species O. taihangensis is present. The interspecific phylogenetic relationship remains unclear and undefined, which might primarily be due to the lack of specific molecular markers for phylogenetic analysis. For this study, 2644 expressed sequence tag-simple sequence repeats (EST-SSRs) from 33,974 unigenes using a de novo transcript assembly of Opisthopappus were identified with a distribution frequency of 7.78% total unigenes. Thereinto, mononucleotides (1200, 45.39%) were the dominant repeat motif, followed by trinucleotides (992, 37.52%), and dinucleotides (410, 15.51%). The most dominant trinucleotide repeat motif was ACC/GGT (207, 20.87%). Based on the identified EST-SSRs, 245 among 1444 designed EST-SSR primers were selected for the development of potential molecular markers. Among these markers, 63 pairs of primers (25.71%) generated clear and reproducible bands with expected sizes. Eventually, 11 primer pairs successfully amplified all individuals from the studied populations. Through the EST-SSR markers, a high level of genetic diversity was detected between Opisthopappus populations. A significant genetic differentiation between the O. longilobus and O. taihangensis populations was found. All studied populations were divided into two clusters by UPGMA, NJ, STRUCTURE, and PCoA. These results fully supported the view of the FRPS, namely, that O. longilobus and O. taihangensis should be regarded as two distinct species. Our study demonstrated that transcriptome sequences, as a valuable tool for the quick and cost-effective development of molecular markers, was helpful toward obtaining comprehensive EST-SSR markers that could contribute to an in-depth assessment of the genetic and phylogenetic relationships between Opisthopappus species.
Collapse
Affiliation(s)
- Min Chai
- School of Life Sciences, Shanxi Normal University, Linfen, China
| | - Hang Ye
- School of Life Sciences, Shanxi Normal University, Linfen, China
| | - Zhi Wang
- School of Life Sciences, Shanxi Normal University, Linfen, China
| | - Yuancheng Zhou
- Triticeae Research Institute, Shanxi Academy of Agricultural Science, Linfen, China
| | - Jiahui Wu
- School of Life Sciences, Shanxi Normal University, Linfen, China.,Changzhi University, Changzhi, China
| | - Yue Gao
- School of Life Sciences, Shanxi Normal University, Linfen, China
| | - Wei Han
- School of Life Sciences, Shanxi Normal University, Linfen, China
| | - En Zang
- School of Life Sciences, Shanxi Normal University, Linfen, China
| | - Hao Zhang
- School of Life Sciences, Shanxi Normal University, Linfen, China
| | | | - Genlou Sun
- Department of Biology, Saint Mary's University, Halifax, NS, Canada
| | - Yling Wang
- School of Life Sciences, Shanxi Normal University, Linfen, China
| |
Collapse
|
15
|
Afzal M, Alghamdi SS, Migdadi HH, Khan MA, Nurmansyah, Mirza SB, El-Harty E. Legume genomics and transcriptomics: From classic breeding to modern technologies. Saudi J Biol Sci 2019; 27:543-555. [PMID: 31889880 PMCID: PMC6933173 DOI: 10.1016/j.sjbs.2019.11.018] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 11/16/2019] [Accepted: 11/17/2019] [Indexed: 02/06/2023] Open
Abstract
Legumes are essential and play a significant role in maintaining food standards and augmenting physiochemical soil properties through the biological nitrogen fixation process. Biotic and abiotic factors are the main factors limiting legume production. Classical breeding methodologies have been explored extensively about the problem of truncated yield in legumes but have not succeeded at the desired rate. Conventional breeding improved legume genotypes but with more resources and time. Recently, the invention of next-generation sequencing (NGS) and high-throughput methods for genotyping have opened new avenues for research and developments in legume studies. During the last decade, genome sequencing for many legume crops documented. Sequencing and re-sequencing of important legume species have made structural variation and functional genomics conceivable. NGS and other molecular techniques such as the development of markers; genotyping; high density genetic linkage maps; quantitative trait loci (QTLs) identification, expressed sequence tags (ESTs), single nucleotide polymorphisms (SNPs); and transcription factors incorporated into existing breeding technologies have made possible the accurate and accelerated delivery of information for researchers. The application of genome sequencing, RNA sequencing (transcriptome sequencing), and DNA sequencing (re-sequencing) provide considerable insights for legume development and improvement programs. Moreover, RNA-Seq helps to characterize genes, including differentially expressed genes, and can be applied for functional genomics studies, especially when there is limited information available for the studied genomes. Genome-based crop development studies and the availability of genomics data as well as decision-making gears look be specific for breeding programs. This review mainly presents an overview of the path from classical breeding to new emerging genomics tools, which will trigger and accelerate genomics-assisted breeding for recognition of novel genes for yield and quality characters for sustainable legume crop production.
Collapse
Affiliation(s)
- Muhammad Afzal
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Salem S Alghamdi
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Hussein H Migdadi
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Muhammad Altaf Khan
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Nurmansyah
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Shaher Bano Mirza
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University (BAU), Istanbul, Turkey.,Department of Biosciences, COMSATS Institute of Information Technology (CIIT), Chak Shahzad, Islamabad, Pakistan
| | - Ehab El-Harty
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| |
Collapse
|
16
|
Cheng A, Raai MN, Zain NAM, Massawe F, Singh A, Wan-Mohtar WAAQI. In search of alternative proteins: unlocking the potential of underutilized tropical legumes. Food Secur 2019. [DOI: 10.1007/s12571-019-00977-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
17
|
Nutrient and Antinutrient Composition of Winged Bean (Psophocarpus tetragonolobus (L.) DC.) Seeds and Tubers. J FOOD QUALITY 2019. [DOI: 10.1155/2019/3075208] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Many people in sub-Saharan Africa suffer from protein malnutrition; this results in negative health and economic impacts. Winged bean (Psophocarpus tetragonolobus (L.) DC.) is a tropical underutilized legume with beneficial nutritional characteristics such as high protein content, which may help to alleviate these problems. The proximate composition (fat, moisture content, crude protein, ash, and carbohydrate) and antinutrient (tannin and phytate) level of winged bean seeds and tubers were determined using 50 accessions. In the processed seeds, accession Tpt17 had the highest protein content (40.30%) and Tpt48 the lowest (34.18%). In the unprocessed seeds, Tpt17 also recorded the highest crude protein (31.13%) with Tpt125 having the lowest (28.43%). In the tubers, protein content ranged from 19.07% (Tpt42) to 12.26% (Tpt10). The moisture content in the processed seeds ranged from 8.51% (Tpt42) to 6.72% (Tpt6); in the unprocessed seeds, it was between 8.53% (Tpt53) and 3.76% (Tpt14). In the processed seeds, the values of ash ranged from 4.93% (Tpt126) to 4.45% (Tpt15-4); in the unprocessed seeds, it ranged from 4.98% (Tpt17) to 4.55% (Tpt125). In the processed seeds, the fat content ranged from 18.91% (Tpt51) to 14.09% (Tp43) while in the unprocessed seeds, the values ranged from 19.01% (Tpt15) to 13.87% (Tpt3-B). The crude fiber in the processed samples ranged from 13.82% (Tpt6) to 10.40% (Tpt125) while in the unprocessed seeds, it ranged from 7.29% in Tpt51 to 4.83% in Tpt11. Carbohydrate content in the processed seeds ranged from 26.30% (Tpt3-B) to 20.94% (Tpt125) and 39.76% in Tpt3-B to 34.53% in Tpt18 in the unprocessed seeds. The tannin and phytate contents showed remarkably significant differences. In the tubers harvested, significant variation was observed in the parameters evaluated. Winged bean flour could be formulated into various meals for children and adults to reduce malnutrition in sub-Saharan Africa.
Collapse
|
18
|
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.
Collapse
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.
| |
Collapse
|
19
|
Raizada A, Souframanien J. Transcriptome sequencing, de novo assembly, characterisation of wild accession of blackgram (Vigna mungo var. silvestris) as a rich resource for development of molecular markers and validation of SNPs by high resolution melting (HRM) analysis. BMC PLANT BIOLOGY 2019; 19:358. [PMID: 31419947 PMCID: PMC6697964 DOI: 10.1186/s12870-019-1954-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 07/31/2019] [Indexed: 05/07/2023]
Abstract
BACKGROUND Blackgram [Vigna mungo (L.) Hepper], is an important legume crop of Asia with limited genomic resources. We report a comprehensive set of genic simple sequence repeat (SSR) and single nucleotide polymorphism (SNPs) markers using Illumina MiSeq sequencing of transcriptome and its application in genetic variation analysis and mapping. RESULTS Transcriptome sequencing of immature seeds of wild blackgram, V. mungo var. silvestris by Illumina MiSeq technology generated 1.9 × 107 reads, which were assembled into 40,178 transcripts (TCS) with an average length of 446 bp covering 2.97 GB of the genome. A total of 38,753 CDS (Coding sequences) were predicted from 40,178 TCS and 28,984 CDS were annotated through BLASTX and mapped to GO and KEGG database resulting in 140 unique pathways. The tri-nucleotides were most abundant (39.9%) followed by di-nucleotide (30.2%). About 60.3 and 37.6% of SSR motifs were present in the coding sequences (CDS) and untranslated regions (UTRs) respectively. Among SNPs, the most abundant substitution type were transitions (Ts) (61%) followed by transversions (Tv) type (39%), with a Ts/Tv ratio of 1.58. A total of 2306 DEGs were identified by RNA Seq between wild and cultivar and validation was done by quantitative reverse transcription polymerase chain reaction. In this study, we genotyped SNPs with a validation rate of 78.87% by High Resolution Melting (HRM) Assay. CONCLUSION In the present study, 1621genic-SSR and 1844 SNP markers were developed from immature seed transcriptome sequence of blackgram and 31 genic-SSR markers were used to study genetic variations among different blackgram accessions. Above developed markers contribute towards enriching available genomic resources for blackgram and aid in breeding programmes.
Collapse
Affiliation(s)
- Avi Raizada
- Nuclear Agriculture and Biotechnology Division, BARC, Trombay, Mumbai, Trombay, 400085, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Anushakti Nagar, 400094, India
| | - J Souframanien
- Nuclear Agriculture and Biotechnology Division, BARC, Trombay, Mumbai, Trombay, 400085, India.
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Anushakti Nagar, 400094, India.
| |
Collapse
|
20
|
Kumar J, Choudhary AK, Gupta DS, Kumar S. Towards Exploitation of Adaptive Traits for Climate-Resilient Smart Pulses. Int J Mol Sci 2019; 20:E2971. [PMID: 31216660 PMCID: PMC6627977 DOI: 10.3390/ijms20122971] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/18/2019] [Accepted: 05/28/2019] [Indexed: 12/20/2022] Open
Abstract
Pulses are the main source of protein and minerals in the vegetarian diet. These are primarily cultivated on marginal lands with few inputs in several resource-poor countries of the world, including several in South Asia. Their cultivation in resource-scarce conditions exposes them to various abiotic and biotic stresses, leading to significant yield losses. Furthermore, climate change due to global warming has increased their vulnerability to emerging new insect pests and abiotic stresses that can become even more serious in the coming years. The changing climate scenario has made it more challenging to breed and develop climate-resilient smart pulses. Although pulses are climate smart, as they simultaneously adapt to and mitigate the effects of climate change, their narrow genetic diversity has always been a major constraint to their improvement for adaptability. However, existing genetic diversity still provides opportunities to exploit novel attributes for developing climate-resilient cultivars. The mining and exploitation of adaptive traits imparting tolerance/resistance to climate-smart pulses can be accelerated further by using cutting-edge approaches of biotechnology such as transgenics, genome editing, and epigenetics. This review discusses various classical and molecular approaches and strategies to exploit adaptive traits for breeding climate-smart pulses.
Collapse
Affiliation(s)
- Jitendra Kumar
- Indian Institute of Pulses Research, Kalyanpur, Kanpur 208 024, Uttar Pradesh, India.
| | | | - Debjyoti Sen Gupta
- Indian Institute of Pulses Research, Kalyanpur, Kanpur 208 024, Uttar Pradesh, India.
| | - Shiv Kumar
- Biodiversity and Integrated Gene Management Program, International Centre for Agricultural Research in the Dry Areas (ICARDA), P.O. Box 6299, Rabat-Institute, Rabat, Morocco.
| |
Collapse
|
21
|
Expanding Phaseolus coccineus Genomic Resources: De Novo Transcriptome Assembly and Analysis of Landraces 'Gigantes' and 'Elephantes' Reveals Rich Functional Variation. Biochem Genet 2019; 57:747-766. [PMID: 30997627 DOI: 10.1007/s10528-019-09920-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 04/01/2019] [Indexed: 10/27/2022]
Abstract
Beans are one of the most important staple crops in the world. Runner bean (Phaseolus coccineus L.) is a small-scale agriculture crop compared to common bean (Phaseolusvulgaris). Beans have been introduced to Europe from the Central America to Europe and since then they have been scattered to different geographical regions. This has resulted in the generation of numerous local cultivars and landraces with distinguished characters and adaptive potential. To identify and characterize the underlying genomic variation of two very closely related runner bean cultivars, we performed RNA-Seq with de novo transcriptome assembly in two landraces of P. coccineus, 'Gigantes' and 'Elephantes' phenotypically distinct, differing in seed size and shape. The cleaned reads generated 37,379 and 37,774 transcripts for 'Gigantes' and 'Elephantes,' respectively. A total of 1896 DEGs were identified between the two cultivars, 1248 upregulated in 'Elephantes' and 648 upregulated in 'Gigantes.' A significant upregulation of defense-related genes was observed in 'Elephantes,' among those, numerous members of the AP2-EREBP, WRKY, NAC, and bHLH transcription factor families. In total, 3956 and 4322 SSRs were identified in 'Gigantes' and 'Elephantes,' respectively. Trinucleotide repeats were the most dominant repeat motif, accounting for 41.9% in 'Gigantes' and 40.1% in 'Elephantes' of the SSRs identified, followed by dinucleotide repeats (29.1% in both cultivars). Additionally, 19,281 putative SNPs were identified, among those 3161 were non-synonymous, thus having potential functional implications. High-confidence non-synonymous SNPs were successfully validated with an HRM assay, which can be directly adopted for P. coccineus molecular breeding. These results significantly expand the number of polymorphic markers within P. coccineus genus, enabling the robust identification of runner bean cultivars, the construction of high-resolution genetic maps, potentiating genome-wide association studies. They finally contribute to the genetic reservoir for the improvement of the closely related and intercrossable Phaseolus vulgaris.
Collapse
|
22
|
Ravindran SP, Herrmann M, Cordellier M. Contrasting patterns of divergence at the regulatory and sequence level in European Daphnia galeata natural populations. Ecol Evol 2019; 9:2487-2504. [PMID: 30891195 PMCID: PMC6405927 DOI: 10.1002/ece3.4894] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 12/05/2018] [Accepted: 12/13/2018] [Indexed: 12/30/2022] Open
Abstract
Understanding the genetic basis of local adaptation has long been a focus of evolutionary biology. Recently, there has been increased interest in deciphering the evolutionary role of Daphnia's plasticity and the molecular mechanisms of local adaptation. Using transcriptome data, we assessed the differences in gene expression profiles and sequences in four European Daphnia galeata populations. In total, ~33% of 32,903 transcripts were differentially expressed between populations. Among 10,280 differentially expressed transcripts, 5,209 transcripts deviated from neutral expectations and their population-specific expression pattern is likely the result of local adaptation processes. Furthermore, a SNP analysis allowed inferring population structure and distribution of genetic variation. The population divergence at the sequence level was comparatively higher than the gene expression level by several orders of magnitude consistent with strong founder effects and lack of gene flow between populations. Using sequence homology, the candidate transcripts were annotated using a comparative genomics approach. Additionally, we also performed a weighted gene co-expression analysis to identify population-specific regulatory patterns of transcripts in D. galeata. Thus, we identified candidate transcriptomic regions for local adaptation in this key species of aquatic ecosystems in the absence of any laboratory-induced stressor.
Collapse
Affiliation(s)
| | - Maike Herrmann
- Department of Veterinary MedicinePaul‐Ehrlich‐InstitutLangenGermany
| | | |
Collapse
|
23
|
De Novo Transcriptomic Analysis and Development of EST–SSRs for Styrax japonicus. FORESTS 2018. [DOI: 10.3390/f9120748] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Styrax japonicus sieb. et Zucc. is widely distributed in China with ornamental and medicinal values. However, the transcriptome of S. japonicus has not yet been reported. In this study, we carried out the first transcriptome analysis of S. japonicus and developed a set of expressed sequence tag–simple sequence repeats (EST–SSRs). We obtained 338,570,222 clean reads in total, of which the mean GC content was 41.58%. In total, 136,071 unigenes were obtained having an average length of 611 bp and 71,226 unigenes were favorably annotated in the database. In total, we identified 55,977 potential EST–SSRs from 38,611 unigenes, of which there was 1 SSR per 6.73 kb. The di-nucleotide repeats (40.40%) were the most identified SSRs. One set of 60 primer pairs was randomly selected, and the amplified products in S. japonicus were validated; 28 primer pairs successfully produced clear amplicons. A total of 21 (35%) polymorphic genic SSR markers were identified between two populations. In total, 15 alleles were detected and the average number was 6. The average of observed heterozygosity and expected heterozygosity was 0.614 and 0.552, respectively. The polymorphism information content (PIC) value fluctuated between 0.074 and 0.855, with a mean value of 0.504, which was also the middle level. This study provides useful information for diversity studies and resource assessments of S. japonicus.
Collapse
|
24
|
Palumbo F, Vannozzi A, Vitulo N, Lucchin M, Barcaccia G. The leaf transcriptome of fennel (Foeniculum vulgare Mill.) enables characterization of the t-anethole pathway and the discovery of microsatellites and single-nucleotide variants. Sci Rep 2018; 8:10459. [PMID: 29993007 PMCID: PMC6041299 DOI: 10.1038/s41598-018-28775-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 06/29/2018] [Indexed: 02/06/2023] Open
Abstract
Fennel is a plant species of both agronomic and pharmaceutical interest that is characterized by a shortage of genetic and molecular data. Taking advantage of NGS technology, we sequenced and annotated the first fennel leaf transcriptome using material from four different lines and two different bioinformatic approaches: de novo and genome-guided transcriptome assembly. A reference transcriptome for assembly was produced by combining these two approaches. Among the 79,263 transcripts obtained, 47,775 were annotated using BLASTX analysis performed against the NR protein database subset with 11,853 transcripts representing putative full-length CDS. Bioinformatic analyses revealed 1,011 transcripts encoding transcription factors, mainly from the BHLH, MYB-related, C2H2, MYB, and ERF families, and 6,411 EST-SSR regions. Single-nucleotide variants of SNPs and indels were identified among the 8 samples at a frequency of 0.5 and 0.04 variants per Kb, respectively. Finally, the assembled transcripts were screened to identify genes related to the biosynthesis of t-anethole, a compound well-known for its nutraceutical and medical properties. For each of the 11 genes encoding structural enzymes in the t-anethole biosynthetic pathway, we identified at least one transcript showing a significant match. Overall, our work represents a treasure trove of information exploitable both for marker-assisted breeding and for in-depth studies on thousands of genes, including those involved in t-anethole biosynthesis.
Collapse
Affiliation(s)
- Fabio Palumbo
- Department of Agronomy, Food, Natural resources, Animals, Environment, University of Padova - Campus di Agripolis, Viale dell'università 16, 35020, Legnaro (PD), Italy
| | - Alessandro Vannozzi
- Department of Agronomy, Food, Natural resources, Animals, Environment, University of Padova - Campus di Agripolis, Viale dell'università 16, 35020, Legnaro (PD), Italy
| | - Nicola Vitulo
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | - Margherita Lucchin
- Department of Agronomy, Food, Natural resources, Animals, Environment, University of Padova - Campus di Agripolis, Viale dell'università 16, 35020, Legnaro (PD), Italy
| | - Gianni Barcaccia
- Department of Agronomy, Food, Natural resources, Animals, Environment, University of Padova - Campus di Agripolis, Viale dell'università 16, 35020, Legnaro (PD), Italy.
| |
Collapse
|
25
|
Haynsen MS, Vatanparast M, Mahadwar G, Zhu D, Moger-Reischer RZ, Doyle JJ, Crandall KA, Egan AN. De novo transcriptome assembly of Pueraria montana var. lobata and Neustanthus phaseoloides for the development of eSSR and SNP markers: narrowing the US origin(s) of the invasive kudzu. BMC Genomics 2018; 19:439. [PMID: 29871589 PMCID: PMC5989403 DOI: 10.1186/s12864-018-4798-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 05/15/2018] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Kudzu, Pueraria montana var. lobata, is a woody vine native to Southeast Asia that has been introduced globally for cattle forage and erosion control. The vine is highly invasive in its introduced areas, including the southeastern US. Modern molecular marker resources are limited for the species, despite its importance. Transcriptomes for P. montana var. lobata and a second phaseoloid legume taxon previously ascribed to genus Pueraria, Neustanthus phaseoloides, were generated and mined for microsatellites and single nucleotide polymorphisms. RESULTS Roche 454 sequencing of P. montana var. lobata and N. phaseoloides transcriptomes produced read numbers ranging from ~ 280,000 to ~ 420,000. Trinity assemblies produced an average of 17,491 contigs with mean lengths ranging from 639 bp to 994 bp. Transcriptome completeness, according to BUSCO, ranged between 64 and 77%. After vetting for primer design, there were 1646 expressed simple sequence repeats (eSSRs) identified in P. montana var. lobata and 1459 in N. phaseoloides. From these eSSRs, 17 identical primer pairs, representing inter-generic phaseoloid eSSRs, were created. Additionally, 13 primer pairs specific to P. montana var. lobata were also created. From these 30 primer pairs, a final set of seven primer pairs were used on 68 individuals of P. montana var. lobata for characterization across the US, China, and Japan. The populations exhibited from 20 to 43 alleles across the seven loci. We also conducted pairwise tests for high-confidence SNP discovery from the kudzu transcriptomes we sequenced and two previously sequenced P. montana var. lobata transcriptomes. Pairwise comparisons between P. montana var. lobata ranged from 358 to 24,475 SNPs, while comparisons between P. montana var. lobata and N. phaseoloides ranged from 5185 to 30,143 SNPs. CONCLUSIONS The discovered molecular markers for kudzu provide a starting point for comparative genetic studies within phaseoloid legumes. This study both adds to the current genetic resources and presents the first available genomic resources for the invasive kudzu vine. Additionally, this study is the first to provide molecular evidence to support the hypothesis of Japan as a source of US kudzu and begins to narrow the origin of US kudzu to the central Japanese island of Honshu.
Collapse
Affiliation(s)
- Matthew S. Haynsen
- Department of Biology, George Washington University, Washington, DC USA
- Computational Biology Institute, Milken Institute School of Public Health, George Washington University, Washington, DC USA
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC USA
| | - Mohammad Vatanparast
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC USA
| | - Gouri Mahadwar
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC USA
- Present address: College of Engineering, Oregon State University, Corvallis, OR USA
| | - Dennis Zhu
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC USA
- Present address: Department of Biology, Washington University in St. Louis, St. Louis, MO USA
| | - Roy Z. Moger-Reischer
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC USA
- Present address: Department of Biology, Indiana University Bloomington, Bloomington, IN USA
| | - Jeff J. Doyle
- School of Integrated Plant Science, Plant Breeding and Genetics Section, Cornell University, Ithaca, NY USA
| | - Keith A. Crandall
- Computational Biology Institute, Milken Institute School of Public Health, George Washington University, Washington, DC USA
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC USA
| | - Ashley N. Egan
- Computational Biology Institute, Milken Institute School of Public Health, George Washington University, Washington, DC USA
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC USA
| |
Collapse
|
26
|
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.
Collapse
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
| |
Collapse
|
27
|
Han Z, Ma X, Wei M, Zhao T, Zhan R, Chen W. SSR marker development and intraspecific genetic divergence exploration of Chrysanthemum indicum based on transcriptome analysis. BMC Genomics 2018; 19:291. [PMID: 29695227 PMCID: PMC5918905 DOI: 10.1186/s12864-018-4702-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 04/18/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Chrysanthemum indicum L., an important ancestral species of the flowering plant chrysanthemum, can be used as medicine and for functional food development. Due to the lack of hereditary information for this species and the difficulty of germplasm identification, we herein provide new genetic insight from the perspective of intraspecific transcriptome comparison and present single sequence repeat (SSR) molecular marker recognition technology. RESULTS Through the study of a diploid germplasm (DIWNT) and a tetraploid germplasm (DIWT), the following outcome were obtained. (1) A significant difference in Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations for specific homologous genes was observed using the OrthoMCL method for the identification of homologous gene families between the two cytotypes. Ka/Ks analysis of common, single-copy homologous family members also revealed a greater difference among genes that experienced positive selection than among those experiencing positive selection. (2) Of more practical value, 2575 SSR markers were predicted and partly verified. We used TaxonGap as a visual tool to inspect genotype uniqueness and screen for high-performance molecular loci; we recommend four primers of 65 randomly selected primers with a combined identification success rate of 88.6% as priorities for further development of DNA fingerprinting of C. indicum germplasm. CONCLUSIONS The SSR technology based on next-generation sequencing was proved to be successful in the identification of C. indicum germplasms. And the information on the intraspecfic genetic divergence generated by transcriptome comparison deepened the understanding of this complex species' nature.
Collapse
Affiliation(s)
- Zhengzhou Han
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine; Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education; Joint Laboratory of National Engineering Research Center for the Pharmaceutics of Traditional Chinese Medicines, Guangzhou, 510006, People's Republic of China.,China Resources Sanjiu Medical & Pharmaceutical Co., Ltd, Shenzhen, 518110, Guangdong, China
| | - Xinye Ma
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine; Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education; Joint Laboratory of National Engineering Research Center for the Pharmaceutics of Traditional Chinese Medicines, Guangzhou, 510006, People's Republic of China.
| | - Min Wei
- China Resources Sanjiu Medical & Pharmaceutical Co., Ltd, Shenzhen, 518110, Guangdong, China
| | - Tong Zhao
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine; Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education; Joint Laboratory of National Engineering Research Center for the Pharmaceutics of Traditional Chinese Medicines, Guangzhou, 510006, People's Republic of China
| | - Ruoting Zhan
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine; Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education; Joint Laboratory of National Engineering Research Center for the Pharmaceutics of Traditional Chinese Medicines, Guangzhou, 510006, People's Republic of China
| | - Weiwen Chen
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine; Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education; Joint Laboratory of National Engineering Research Center for the Pharmaceutics of Traditional Chinese Medicines, Guangzhou, 510006, People's Republic of China.
| |
Collapse
|
28
|
Vatanparast M, Powell A, Doyle JJ, Egan AN. Targeting legume loci: A comparison of three methods for target enrichment bait design in Leguminosae phylogenomics. APPLICATIONS IN PLANT SCIENCES 2018; 6:e1036. [PMID: 29732266 PMCID: PMC5895186 DOI: 10.1002/aps3.1036] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 02/22/2018] [Indexed: 05/19/2023]
Abstract
PREMISE OF THE STUDY The development of pipelines for locus discovery has spurred the use of target enrichment for plant phylogenomics. However, few studies have compared pipelines from locus discovery and bait design, through validation, to tree inference. We compared three methods within Leguminosae (Fabaceae) and present a workflow for future efforts. METHODS Using 30 transcriptomes, we compared Hyb-Seq, MarkerMiner, and the Yang and Smith (Y&S) pipelines for locus discovery, validated 7501 baits targeting 507 loci across 25 genera via Illumina sequencing, and inferred gene and species trees via concatenation- and coalescent-based methods. RESULTS Hyb-Seq discovered loci with the longest mean length. MarkerMiner discovered the most conserved loci with the least flagged as paralogous. Y&S offered the most parsimony-informative sites and putative orthologs. Target recovery averaged 93% across taxa. We optimized our targeted locus set based on a workflow designed to minimize paralog/ortholog conflation and thus present 423 loci for legume phylogenomics. CONCLUSIONS Methods differed across criteria important for phylogenetic marker development. We recommend Hyb-Seq as a method that may be useful for most phylogenomic projects. Our targeted locus set is a resource for future, community-driven efforts to reconstruct the legume tree of life.
Collapse
Affiliation(s)
- Mohammad Vatanparast
- Department of BotanyNational Museum of Natural HistorySmithsonian InstitutionP.O. Box 37012, MRC 166WashingtonDC20560USA
- Present address:
Forest, Nature, and Biomass SectionDepartment of Geosciences and Natural Resource ManagementRolighedsvej 23, 1958 Frederiksberg C., University of CopenhagenDenmark
| | - Adrian Powell
- Section of Plant Breeding and GeneticsSchool of Integrated Plant SciencesCornell University512 Mann LibraryIthacaNew York14853USA
- Present address:
Boyce Thompson Institute533 Tower RoadIthacaNew York14853USA
| | - Jeff J. Doyle
- Section of Plant Breeding and GeneticsSchool of Integrated Plant SciencesCornell University512 Mann LibraryIthacaNew York14853USA
| | - Ashley N. Egan
- Department of BotanyNational Museum of Natural HistorySmithsonian InstitutionP.O. Box 37012, MRC 166WashingtonDC20560USA
| |
Collapse
|
29
|
Taheri S, Lee Abdullah T, Yusop MR, Hanafi MM, Sahebi M, Azizi P, Shamshiri RR. Mining and Development of Novel SSR Markers Using Next Generation Sequencing (NGS) Data in Plants. Molecules 2018; 23:E399. [PMID: 29438290 PMCID: PMC6017569 DOI: 10.3390/molecules23020399] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 01/11/2018] [Accepted: 01/13/2018] [Indexed: 11/17/2022] Open
Abstract
Microsatellites, or simple sequence repeats (SSRs), are one of the most informative and multi-purpose genetic markers exploited in plant functional genomics. However, the discovery of SSRs and development using traditional methods are laborious, time-consuming, and costly. Recently, the availability of high-throughput sequencing technologies has enabled researchers to identify a substantial number of microsatellites at less cost and effort than traditional approaches. Illumina is a noteworthy transcriptome sequencing technology that is currently used in SSR marker development. Although 454 pyrosequencing datasets can be used for SSR development, this type of sequencing is no longer supported. This review aims to present an overview of the next generation sequencing, with a focus on the efficient use of de novo transcriptome sequencing (RNA-Seq) and related tools for mining and development of microsatellites in plants.
Collapse
Affiliation(s)
- Sima Taheri
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Thohirah Lee Abdullah
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Mohd Rafii Yusop
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Mohamed Musa Hanafi
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
- Laboratory of Plantation Science and Technology, Institute of Plantation Studies, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
- Department of Land Management, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Mahbod Sahebi
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Parisa Azizi
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Redmond Ramin Shamshiri
- Smart Farming Technology Research Center, Department of Biological and Agricultural Engineering, Faculty of Engineering, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
| |
Collapse
|
30
|
Dai Y, Su W, Yang C, Song B, Li Y, Fu Y. Development of Novel Polymorphic EST-SSR Markers in Bailinggu (Pleurotus tuoliensis) for Crossbreeding. Genes (Basel) 2017; 8:genes8110325. [PMID: 29149037 PMCID: PMC5704238 DOI: 10.3390/genes8110325] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 10/16/2017] [Accepted: 11/08/2017] [Indexed: 01/02/2023] Open
Abstract
Identification of monokaryons and their mating types and discrimination of hybrid offspring are key steps for the crossbreeding of Pleurotus tuoliensis (Bailinggu). However, conventional crossbreeding methods are troublesome and time consuming. Using RNA-seq technology, we developed new expressed sequence tag-simple sequence repeat (EST-SSR) markers for Bailinggu to easily and rapidly identify monokaryons and their mating types, genetic diversity and hybrid offspring. We identified 1110 potential EST-based SSR loci from a newly-sequenced Bailinggu transcriptome and then randomly selected 100 EST-SSRs for further validation. Results showed that 39, 43 and 34 novel EST-SSR markers successfully identified monokaryons from their parent dikaryons, differentiated two different mating types and discriminated F1 and F2 hybrid offspring, respectively. Furthermore, a total of 86 alleles were detected in 37 monokaryons using 18 highly informative EST-SSRs. The observed number of alleles per locus ranged from three to seven. Cluster analysis revealed that these monokaryons have a relatively high level of genetic diversity. Transfer rates of the EST-SSRs in the monokaryons of closely-related species Pleurotuseryngii var. ferulae and Pleurotus ostreatus were 72% and 64%, respectively. Therefore, our study provides new SSR markers and an efficient method to enhance the crossbreeding of Bailinggu and closely-related species.
Collapse
Affiliation(s)
- Yueting Dai
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China.
| | - Wenying Su
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China.
| | - Chentao Yang
- China National GeneBank, Environmental Genomics, Beijing Genomics Institute, Shenzhen 518083, China.
| | - Bing Song
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China.
| | - Yu Li
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China.
| | - Yongping Fu
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China.
| |
Collapse
|
31
|
Zhou S, Yan B, Li F, Zhang J, Zhang J, Ma H, Liu W, Lu Y, Yang X, Li X, Liu X, Li L. RNA-Seq Analysis Provides the First Insights into the Phylogenetic Relationship and Interspecific Variation between Agropyron cristatum and Wheat. FRONTIERS IN PLANT SCIENCE 2017; 8:1644. [PMID: 28983310 PMCID: PMC5613732 DOI: 10.3389/fpls.2017.01644] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Accepted: 09/07/2017] [Indexed: 05/30/2023]
Abstract
Agropyron cristatum, which is a wild grass of the tribe Triticeae, grows widely in harsh environments and provides many desirable genetic resources for wheat improvement. However, unclear interspecific phylogeny and genome-wide variation has limited the utilization of A. cristatum in the production of superior wheat varieties. In this study, by sequencing the transcriptome of the representative tetraploid A. cristatum Z559 and the common wheat variety Fukuhokomugi (Fukuho), which are often used as parents in a wide cross, their phylogenetic relationship and interspecific variation were dissected. First, 214,854 transcript sequences were assembled, and 3,457 orthologous genes related to traits of interest were identified in A. cristatum. Second, a total of 72 putative orthologous gene clusters were used to construct phylogenetic relationships among A. cristatum, Triticeae and other genomes. A clear division between A. cristatum and the other Triticeae species was revealed. Third, the sequence similarity of most genes related to traits of interest is greater than 95% between A. cristatum and wheat. Therefore, using the 5% mismatch parameter for A. cristatum, we mapped the transcriptome sequencing data to wheat reference sequences to discover the variations between A. cristatum and wheat and 862,340 high-quality variants were identified. Additionally, compared with the wheat A and B genomes, the P and D genomes displayed an obviously larger variant density and a longer evolutionary distance, suggesting that A. cristatum is more distantly related to the wheat D genome. Finally, by using Kompetitive Allele Specific PCR array (KASPar) technology, 37 of 53 (69.8%) SNPs were shown to be genuine in Z559, Fukuho, and additional lines with seven different P chromosomes, and function of the genes in which these SNPs are located were also determined. This study provides not only the first insights into the phylogenetic relationships between the P genome and Triticeae but also genetic resources for gene discovery and specific marker development in A. cristatum, and this information will be vital for future wheat-breeding efforts. The sequence data have been deposited in the Sequence Read Archive (SRA) database at the NCBI under accession number SRP090613.
Collapse
|
32
|
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.
Collapse
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.
| |
Collapse
|
33
|
Sathyanarayana N, Pittala RK, Tripathi PK, Chopra R, Singh HR, Belamkar V, Bhardwaj PK, Doyle JJ, Egan AN. Transcriptomic resources for the medicinal legume Mucuna pruriens: de novo transcriptome assembly, annotation, identification and validation of EST-SSR markers. BMC Genomics 2017; 18:409. [PMID: 28545396 PMCID: PMC5445377 DOI: 10.1186/s12864-017-3780-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 05/10/2017] [Indexed: 12/14/2022] Open
Abstract
Background The medicinal legume Mucuna pruriens (L.) DC. has attracted attention worldwide as a source of the anti-Parkinson’s drug L-Dopa. It is also a popular green manure cover crop that offers many agronomic benefits including high protein content, nitrogen fixation and soil nutrients. The plant currently lacks genomic resources and there is limited knowledge on gene expression, metabolic pathways, and genetics of secondary metabolite production. Here, we present transcriptomic resources for M. pruriens, including a de novo transcriptome assembly and annotation, as well as differential transcript expression analyses between root, leaf, and pod tissues. We also develop microsatellite markers and analyze genetic diversity and population structure within a set of Indian germplasm accessions. Results One-hundred ninety-one million two hundred thirty-three thousand two hundred forty-two bp cleaned reads were assembled into 67,561 transcripts with mean length of 626 bp and N50 of 987 bp. Assembled sequences were annotated using BLASTX against public databases with over 80% of transcripts annotated. We identified 7,493 simple sequence repeat (SSR) motifs, including 787 polymorphic repeats between the parents of a mapping population. 134 SSRs from expressed sequenced tags (ESTs) were screened against 23 M. pruriens accessions from India, with 52 EST-SSRs retained after quality control. Population structure analysis using a Bayesian framework implemented in fastSTRUCTURE showed nearly similar groupings as with distance-based (neighbor-joining) and principal component analyses, with most of the accessions clustering per geographical origins. Pair-wise comparison of transcript expression in leaves, roots and pods identified 4,387 differentially expressed transcripts with the highest number occurring between roots and leaves. Differentially expressed transcripts were enriched with transcription factors and transcripts annotated as belonging to secondary metabolite pathways. Conclusions The M. pruriens transcriptomic resources generated in this study provide foundational resources for gene discovery and development of molecular markers. Polymorphic SSRs identified can be used for genetic diversity, marker-trait analyses, and development of functional markers for crop improvement. The results of differential expression studies can be used to investigate genes involved in L-Dopa synthesis and other key metabolic pathways in M. pruriens. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3780-9) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- N Sathyanarayana
- Department of Botany, Sikkim University, 6th Mile, Tadong-737102, Gangtok, Sikkim, India.
| | - Ranjith Kumar Pittala
- Department of Botany, Sikkim University, 6th Mile, Tadong-737102, Gangtok, Sikkim, India
| | - Pankaj Kumar Tripathi
- Department of Botany, Sikkim University, 6th Mile, Tadong-737102, Gangtok, Sikkim, India
| | - Ratan Chopra
- United States Department of Agriculture, Agriculture Research Service, 3810 4th St., Lubbock, TX, 79415, USA
| | - Heikham Russiachand Singh
- Department of Plant Science, McGill University, Raymond Building, 21111 Lakeshore Road, Ste. Anne de Bellevue, Quebec, H9X 3V9, Canada
| | - Vikas Belamkar
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
| | - Pardeep Kumar Bhardwaj
- Institute of Bioresources and Sustainable Development, ikkim Centre, Tadong-737102, Gangtok, Sikkim, India
| | - Jeff J Doyle
- Section of Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, 412 Mann Library, Ithaca, NY, 14853, USA
| | - Ashley N Egan
- Department of Botany, Smithsonian Institution, National Museum of Natural History, US National Herbarium, 10th and Constitution Ave NW, Washington, DC, 20013, USA.
| |
Collapse
|
34
|
Singh V, Goel R, Pande V, Asif MH, Mohanty CS. De novo sequencing and comparative analysis of leaf transcriptomes of diverse condensed tannin-containing lines of underutilized Psophocarpus tetragonolobus (L.) DC. Sci Rep 2017; 7:44733. [PMID: 28322296 PMCID: PMC5359716 DOI: 10.1038/srep44733] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 02/13/2017] [Indexed: 11/09/2022] Open
Abstract
Condensed tannin (CT) or proanthocyanidin (PA) is a unique group of phenolic metabolite with high molecular weight with specific structure. It is reported that, the presence of high-CT in the legumes adversely affect the nutrients in the plant and impairs the digestibility upon consumption by animals. Winged bean (Psophocarpus tetragonolobus (L.) DC.) is one of the promising underutilized legume with high protein and oil-content. One of the reasons for its underutilization is due to the presence of CT. Transcriptome sequencing of leaves of two diverse CT-containing lines of P. tetragonolobus was carried out on Illumina Nextseq 500 sequencer to identify the underlying genes and contigs responsible for CT-biosynthesis. RNA-Seq data generated 102586 and 88433 contigs for high (HCTW) and low CT (LCTW) lines of P. tetragonolobus, respectively. Based on the similarity searches against gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) database revealed 5210 contigs involved in 229 different pathways. A total of 1235 contigs were detected to differentially express between HCTW and LCTW lines. This study along with its findings will be helpful in providing information for functional and comparative genomic analysis of condensed tannin biosynthesis in this plant in specific and legumes in general.
Collapse
Affiliation(s)
- Vinayak Singh
- Plant Molecular Biology and Genetic Engineering Division, CSIR-National Botanical Research Institute, Lucknow-226 001 Uttar Pradesh, India.,Department of Biotechnology, Kumaun University, Nainital, Uttarakhand, 263001 India
| | - Ridhi Goel
- Plant Molecular Biology and Genetic Engineering Division, CSIR-National Botanical Research Institute, Lucknow-226 001 Uttar Pradesh, India
| | - Veena Pande
- Department of Biotechnology, Kumaun University, Nainital, Uttarakhand, 263001 India
| | - Mehar Hasan Asif
- Plant Molecular Biology and Genetic Engineering Division, CSIR-National Botanical Research Institute, Lucknow-226 001 Uttar Pradesh, India
| | - Chandra Sekhar Mohanty
- Plant Molecular Biology and Genetic Engineering Division, CSIR-National Botanical Research Institute, Lucknow-226 001 Uttar Pradesh, India
| |
Collapse
|
35
|
Development of Gene-Based SSR Markers in Winged Bean (Psophocarpus tetragonolobus (L.) DC.) for Diversity Assessment. Genes (Basel) 2017; 8:genes8030100. [PMID: 28282950 PMCID: PMC5368704 DOI: 10.3390/genes8030100] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 03/03/2017] [Indexed: 11/16/2022] Open
Abstract
Winged bean (Psophocarpus tetragonolobus) is an herbaceous multipurpose legume grown in hot and humid countries as a pulse, vegetable (leaves and pods), or root tuber crop depending on local consumption preferences. In addition to its different nutrient-rich edible parts which could contribute to food and nutritional security, it is an efficient nitrogen fixer as a component of sustainable agricultural systems. Generating genetic resources and improved lines would help to accelerate the breeding improvement of this crop, as the lack of improved cultivars adapted to specific environments has been one of the limitations preventing wider use. A transcriptomic de novo assembly was constructed from four tissues: leaf, root, pod, and reproductive tissues from Malaysian accessions, comprising of 198,554 contigs with a N50 of 1462 bp. Of these, 138,958 (70.0%) could be annotated. Among 9682 genic simple sequence repeat (SSR) motifs identified (excluding monomer repeats), trinucleotide-repeats were the most abundant (4855), followed by di-nucleotide (4500) repeats. A total of 18 SSR markers targeting di- and tri-nucleotide repeats have been validated as polymorphic markers based on an initial assessment of nine genotypes originated from five countries. A cluster analysis revealed provisional clusters among this limited, yet diverse selection of germplasm. The developed assembly and validated genic SSRs in this study provide a foundation for a better understanding of the plant breeding system for the genetic improvement of winged bean.
Collapse
|