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Balestrazzi A, Calvio C, Macovei A, Pagano A, Laux P, Moutahir H, Rajjou L, Tani E, Chachalis D, Katsis C, Ghaouti L, Gmouh S, Majid S, Elleuch A, Hanin M, Khemakhem B, El Abed H, Nunes J, Araújo S, Benhamrouche A, Bersi M. Seed quality as a proxy of climate-ready orphan legumes: the need for a multidisciplinary and multi-actor vision. FRONTIERS IN PLANT SCIENCE 2024; 15:1388866. [PMID: 39148611 PMCID: PMC11325182 DOI: 10.3389/fpls.2024.1388866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 07/12/2024] [Indexed: 08/17/2024]
Abstract
In developing countries, orphan legumes stand at the forefront in the struggle against climate change. Their high nutrient value is crucial in malnutrition and chronic diseases prevention. However, as the 'orphan' definition suggests, their seed systems are still underestimated and seed production is scanty. Seed priming is an effective, sustainable strategy to boost seed quality in orphan legumes for which up-to-date guidelines are required to guarantee reliable and reproducible results. How far are we along this path? What do we expect from seed priming? This brings to other relevant questions. What is the socio-economic relevance of orphan legumes in the Mediterranean Basin? How to potentiate a broader cultivation in specific regions? The case study of the BENEFIT-Med (Boosting technologies of orphan legumes towards resilient farming systems) project, developed by multidisciplinary research networks, envisions a roadmap for producing new knowledge and innovative technologies to improve seed productivity through priming, with the long-term objective of promoting sustainability and food security for/in the climate-sensitive regions. This review highlights the existing drawbacks that must be overcome before orphan legumes could reach the state of 'climate-ready crops'. Only by the integration of knowledge in seed biology, technology and agronomy, the barrier existing between research bench and local agricultural fields may be overcome, generating high-impact technical innovations for orphan legumes. We intend to provide a powerful message to encourage future research in line with the United Nations Agenda 2030 for Sustainable Development.
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Affiliation(s)
- Alma Balestrazzi
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Cinzia Calvio
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Anca Macovei
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Andrea Pagano
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Patrick Laux
- Institute of Meteorology and Climate Research (IMK-IFU), Karlsruhe Institute of Technology, Garmisch-Partenkirchen, Germany
| | - Hassane Moutahir
- Institute of Meteorology and Climate Research (IMK-IFU), Karlsruhe Institute of Technology, Garmisch-Partenkirchen, Germany
| | - Loїc Rajjou
- Université Paris-Saclay, National Research Institute for Agriculture, Food and the Environment (INRAE), AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
| | - Eleni Tani
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Athens, Greece
| | - Dimosthenis Chachalis
- Department of Pesticides' Control and Phytopharmacy, Benaki Phytopathological Institute, Athens, Greece
| | | | - Lamiae Ghaouti
- Department of Plant Production, Protection and Biotechnology, Hassan II Institute of Agronomy and Veterinary Medicine, Rabat, Morocco
| | - Said Gmouh
- Laboratory Laboratory of Engineering and Materials (LIMAT), Faculty of Sciences Ben M'sick, University Hassan II of Casablanca, Casablanca, Morocco
| | - Sanaa Majid
- Laboratory GeMEV, Faculty of Sciences Aïn Chock, University Hassan II of Casablanca, Casablanca, Morocco
| | - Amine Elleuch
- Higher Institute of Biotechnology, University of Sfax, Sfax, Tunisia
| | - Moez Hanin
- Higher Institute of Biotechnology, University of Sfax, Sfax, Tunisia
| | - Bassem Khemakhem
- Higher Institute of Biotechnology, University of Sfax, Sfax, Tunisia
| | - Hanen El Abed
- Higher Institute of Biotechnology, University of Sfax, Sfax, Tunisia
| | - Joao Nunes
- Center Bio R&D Unit, Association BLC3-Technology and Innovation Campus, Oliveira do Hospital, Portugal
| | - Susana Araújo
- Center Bio R&D Unit, Association BLC3-Technology and Innovation Campus, Oliveira do Hospital, Portugal
| | - Aziz Benhamrouche
- Institute of Architecture and Earth Science, University Ferhat Abbas-Setif 1, Setif, Algeria
| | - Mohand Bersi
- Institute of Architecture and Earth Science, University Ferhat Abbas-Setif 1, Setif, Algeria
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Kaur S, Seem K, Ali A, Jaiswal S, Gumachanamardi P, Kaur G, Singh N, Touthang L, Singh SK, Bhardwaj R, Singh BK, Mishra VK, Riar A. A comprehensive review on nutritional, nutraceutical, and industrial perspectives of perilla ( Perilla frutscens L.) seeds - An orphan oilseed crop. Heliyon 2024; 10:e33281. [PMID: 39022021 PMCID: PMC11252951 DOI: 10.1016/j.heliyon.2024.e33281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Revised: 06/18/2024] [Accepted: 06/18/2024] [Indexed: 07/20/2024] Open
Abstract
There is a growing need to mainstream orphan or underutilized crops to enhance nutritional security and sustainable agriculture. Among these, Perilla frutescens L. is an important crop due to its rich nutritional and phytochemical content which makes it significant in nutrition, medicine, and industrial sector. Perilla seeds are mainly rich in ω-3 fatty acids, dietary fiber, amino acids, vitamins, and minerals, high α-linolenic acid, which contributes to their health benefits. This review explores the nutritional profile of perilla seeds and highlights its unique composition compared to other oilseed crops. It also analyzes the phytochemical components of perilla seeds and their various biological activities, including antioxidant, antidiabetic, antiobesity, cardioprotective, anticancer, antimicrobial, neuroprotective, and anti-inflammatory effects. These activities demonstrate the potential of perilla seeds in both pharmaceutical and food sectors. The review also covers recent advancements in genomics and transgenic research discussing potential areas for crop improvement. Additionally, it explores the use of perilla seeds in functional foods, blending perilla oil with other oils, and their applications in enhancing product formulations. This review offers valuable insights for researchers, students, policymakers, environmentalists, and industry professionals by detailing the potential of perilla seeds across various sectors. The findings support sustainable agriculture, crop diversification, and innovative product development, thus contributing to the integration of perilla into mainstream agriculture.
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Affiliation(s)
- Simardeep Kaur
- ICAR-Research Complex for North Eastern Hill Region, Umiam, Meghalaya, 793103, India
| | - Karishma Seem
- ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Ansheef Ali
- ICAR-Indian Agricultural Research Institute, Assam, 734301, India
| | - Sandeep Jaiswal
- ICAR-Research Complex for North Eastern Hill Region, Umiam, Meghalaya, 793103, India
| | | | - Gurkanwal Kaur
- Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Naseeb Singh
- ICAR-Research Complex for North Eastern Hill Region, Umiam, Meghalaya, 793103, India
| | - Letngam Touthang
- ICAR-Research Complex for North Eastern Hill Region, Umiam, Meghalaya, 793103, India
| | | | - Rakesh Bhardwaj
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110012, India
| | - Binay K. Singh
- ICAR-Research Complex for North Eastern Hill Region, Umiam, Meghalaya, 793103, India
| | - Vinay Kumar Mishra
- ICAR-Research Complex for North Eastern Hill Region, Umiam, Meghalaya, 793103, India
| | - Amritbir Riar
- Department of International Cooperation, Research Institute of Organic Agriculture FiBL, Frick, Switzerland
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Bernal-Gallardo JJ, de Folter S. Plant genome information facilitates plant functional genomics. PLANTA 2024; 259:117. [PMID: 38592421 PMCID: PMC11004055 DOI: 10.1007/s00425-024-04397-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 03/20/2024] [Indexed: 04/10/2024]
Abstract
MAIN CONCLUSION In this review, we give an overview of plant sequencing efforts and how this impacts plant functional genomics research. Plant genome sequence information greatly facilitates the studies of plant biology, functional genomics, evolution of genomes and genes, domestication processes, phylogenetic relationships, among many others. More than two decades of sequencing efforts have boosted the number of available sequenced plant genomes. The first plant genome, of Arabidopsis, was published in the year 2000 and currently, 4604 plant genomes from 1482 plant species have been published. Various large sequence initiatives are running, which are planning to produce tens of thousands of sequenced plant genomes in the near future. In this review, we give an overview on the status of sequenced plant genomes and on the use of genome information in different research areas.
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Affiliation(s)
- Judith Jazmin Bernal-Gallardo
- Unidad de Genómica Avanzada (UGA-Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato, Mexico
| | - Stefan de Folter
- Unidad de Genómica Avanzada (UGA-Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato, Mexico.
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Yaqoob H, Tariq A, Bhat BA, Bhat KA, Nehvi IB, Raza A, Djalovic I, Prasad PVV, Mir RA. Integrating genomics and genome editing for orphan crop improvement: a bridge between orphan crops and modern agriculture system. GM CROPS & FOOD 2023; 14:1-20. [PMID: 36606637 PMCID: PMC9828793 DOI: 10.1080/21645698.2022.2146952] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Domestication of orphan crops could be explored by editing their genomes. Genome editing has a lot of promise for enhancing agricultural output, and there is a lot of interest in furthering breeding in orphan crops, which are sometimes plagued with unwanted traits that resemble wild cousins. Consequently, applying model crop knowledge to orphan crops allows for the rapid generation of targeted allelic diversity and innovative breeding germplasm. We explain how plant breeders could employ genome editing as a novel platform to accelerate the domestication of semi-domesticated or wild plants, resulting in a more diversified base for future food and fodder supplies. This review emphasizes both the practicality of the strategy and the need to invest in research that advances our understanding of plant genomes, genes, and cellular systems. Planting more of these abandoned orphan crops could help alleviate food scarcities in the challenge of future climate crises.
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Affiliation(s)
- Huwaida Yaqoob
- Department of Biotechnology, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Jammu and Kashmir, India
| | - Arooj Tariq
- Department of Biotechnology, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Jammu and Kashmir, India
| | - Basharat Ahmad Bhat
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar, Jammu and Kashmir, India
| | - Kaisar Ahmad Bhat
- Department of Biotechnology, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Jammu and Kashmir, India
| | - Iqra Bashir Nehvi
- Department of Clinical Biochemistry, SKIMS, Srinagar, Jammu and Kashmir, India
| | - Ali Raza
- College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China,Ali Raza College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Ivica Djalovic
- Institute of Field and Vegetable Crops, National Institute of the Republic of Serbia, Novi Sad, Serbia
| | - PV Vara Prasad
- Feed the Future Innovation Lab for Collaborative Research on Sustainable Intensification, Kansas State University, Manhattan, Kansas, USA
| | - Rakeeb Ahmad Mir
- Department of Biotechnology, School of Life Sciences, Central University of Kashmir, Jammu and Kashmir, India,CONTACT Rakeeb Ahmad MirDepartment of Biotechnology, School of Life Sciences, Central University of Kashmir, Jammu and Kashmir, India
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Ngigi PB, Termote C, Pallet D, Amiot MJ. Mainstreaming traditional fruits, vegetables and pulses for nutrition, income, and sustainability in sub-Saharan Africa: the case for Kenya and Ethiopia. Front Nutr 2023; 10:1197703. [PMID: 38146328 PMCID: PMC10749635 DOI: 10.3389/fnut.2023.1197703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 11/13/2023] [Indexed: 12/27/2023] Open
Abstract
This study documented existing knowledge on traditional fruits, vegetables and pulses in Kenya and Ethiopia. The aim was to identify neglected and underutilized species with high potential for food security, for their economic value and contribution to sustainable agriculture, based on a literature review and confirmation of existing data by local experts. In order of priority, the top 5 fruit species in Kenya are Tamarindus indica L., Adansonia digitata L., Sclerocarya birrea (A.Rich.) Hochst, Balanites aegyptiaca (L.) Delile, and Ziziphus mauritiana Lam., for vegetables are Amaranthus spp., Vigna unguiculata (L.) Walp., Solanum spp., and Cleome gynandra L. Top fruits in Ethiopia are Balanites aegyptiaca (L.) Delile, Ziziphus spina-christi (L.) Desf., Cordeauxia edulis Hemsl., Cordia africana Lam., and Mimusops kummel A. DC., for vegetables are Brassica carinata A. Braun, Cucurbita pepo L., and Amaranthus spp. In both countries, priority pulse species (no ranking) are Phaseolus lunatus L., Sphenostylis stenocarpa (A.Rich.) Harms, Mucuna pruriens (L.) DC., Lablab purpureus (L.) Sweet, and Cajanus cajan (L.) Millsp. Generally, these priority species are good sources of key nutrients known for their inadequate dietary intakes in sub-Saharan Africa, represent a safety net for household income, and contribute positively to ecosystem resilience in existing agricultural systems. Complete, accurate and reliable nutrient composition data are needed to raise consumer awareness about their nutritional and health benefits. Since women play a central role in traditional food systems, their empowerment, and hence resilience, increase the positive impact they can have on the households' dietary diversity. In particular, introducing small-scale processing techniques and marketing strategies could enhance their supply and consumption.
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Affiliation(s)
- Peter Biu Ngigi
- MoISA, Univ Montpellier, CIHEAM-IAMM, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
- UMR-Qualisud, CIRAD, Univ Montpellier, Avignon Université, Institut Agro, Université de La Réunion, Montpellier, France
| | - Céline Termote
- Alliance Bioversity International and CIAT (Nairobi), Nairobi, Kenya
| | - Dominique Pallet
- UMR-Qualisud, CIRAD, Univ Montpellier, Avignon Université, Institut Agro, Université de La Réunion, Montpellier, France
| | - Marie Josèphe Amiot
- MoISA, Univ Montpellier, CIHEAM-IAMM, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
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Naithani S, Deng CH, Sahu SK, Jaiswal P. Exploring Pan-Genomes: An Overview of Resources and Tools for Unraveling Structure, Function, and Evolution of Crop Genes and Genomes. Biomolecules 2023; 13:1403. [PMID: 37759803 PMCID: PMC10527062 DOI: 10.3390/biom13091403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/29/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
The availability of multiple sequenced genomes from a single species made it possible to explore intra- and inter-specific genomic comparisons at higher resolution and build clade-specific pan-genomes of several crops. The pan-genomes of crops constructed from various cultivars, accessions, landraces, and wild ancestral species represent a compendium of genes and structural variations and allow researchers to search for the novel genes and alleles that were inadvertently lost in domesticated crops during the historical process of crop domestication or in the process of extensive plant breeding. Fortunately, many valuable genes and alleles associated with desirable traits like disease resistance, abiotic stress tolerance, plant architecture, and nutrition qualities exist in landraces, ancestral species, and crop wild relatives. The novel genes from the wild ancestors and landraces can be introduced back to high-yielding varieties of modern crops by implementing classical plant breeding, genomic selection, and transgenic/gene editing approaches. Thus, pan-genomic represents a great leap in plant research and offers new avenues for targeted breeding to mitigate the impact of global climate change. Here, we summarize the tools used for pan-genome assembly and annotations, web-portals hosting plant pan-genomes, etc. Furthermore, we highlight a few discoveries made in crops using the pan-genomic approach and future potential of this emerging field of study.
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Affiliation(s)
- Sushma Naithani
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA;
| | - Cecilia H. Deng
- Molecular & Digital Breeing Group, New Cultivar Innovation, The New Zealand Institute for Plant and Food Research Limited, Private Bag 92169, Auckland 1142, New Zealand;
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China;
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA;
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Song B, Ning W, Wei D, Jiang M, Zhu K, Wang X, Edwards D, Odeny DA, Cheng S. Plant genome resequencing and population genomics: Current status and future prospects. MOLECULAR PLANT 2023; 16:1252-1268. [PMID: 37501370 DOI: 10.1016/j.molp.2023.07.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 05/30/2023] [Accepted: 07/25/2023] [Indexed: 07/29/2023]
Abstract
Advances in DNA sequencing technology have sparked a genomics revolution, driving breakthroughs in plant genetics and crop breeding. Recently, the focus has shifted from cataloging genetic diversity in plants to exploring their functional significance and delivering beneficial alleles for crop improvement. This transformation has been facilitated by the increasing adoption of whole-genome resequencing. In this review, we summarize the current progress of population-based genome resequencing studies and how these studies affect crop breeding. A total of 187 land plants from 163 countries have been resequenced, comprising 54 413 accessions. As part of resequencing efforts 367 traits have been surveyed and 86 genome-wide association studies have been conducted. Economically important crops, particularly cereals, vegetables, and legumes, have dominated the resequencing efforts, leaving a gap in 49 orders, including Lycopodiales, Liliales, Acorales, Austrobaileyales, and Commelinales. The resequenced germplasm is distributed across diverse geographic locations, providing a global perspective on plant genomics. We highlight genes that have been selected during domestication, or associated with agronomic traits, and form a repository of candidate genes for future research and application. Despite the opportunities for cross-species comparative genomics, many population genomic datasets are not accessible, impeding secondary analyses. We call for a more open and collaborative approach to population genomics that promotes data sharing and encourages contribution-based credit policy. The number of plant genome resequencing studies will continue to rise with the decreasing DNA sequencing costs, coupled with advances in analysis and computational technologies. This expansion, in terms of both scale and quality, holds promise for deeper insights into plant trait genetics and breeding design.
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Affiliation(s)
- Bo Song
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Weidong Ning
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; Huazhong Agricultural University, College of Informatics, Hubei Key Laboratory of Agricultural Bioinformatics, Wuhan, Hubei, China
| | - Di Wei
- Biotechnology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 53007, China
| | - Mengyun Jiang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China; Shenzhen Research Institute of Henan University, Shenzhen 518000, China
| | - Kun Zhu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China; Shenzhen Research Institute of Henan University, Shenzhen 518000, China
| | - Xingwei Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China; Shenzhen Research Institute of Henan University, Shenzhen 518000, China
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, Australia
| | - Damaris A Odeny
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) - Eastern and Southern Africa, Nairobi, Kenya
| | - Shifeng Cheng
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China.
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Machado IP, DoVale JC, Sabadin F, Fritsche-Neto R. On the usefulness of mock genomes to define heterotic pools, testers, and hybrid predictions in orphan crops. FRONTIERS IN PLANT SCIENCE 2023; 14:1164555. [PMID: 37332727 PMCID: PMC10272588 DOI: 10.3389/fpls.2023.1164555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 05/10/2023] [Indexed: 06/20/2023]
Abstract
The advances in genomics in recent years have increased the accuracy and efficiency of breeding programs for many crops. Nevertheless, the adoption of genomic enhancement for several other crops essential in developing countries is still limited, especially for those that do not have a reference genome. These crops are more often called orphans. This is the first report to show how the results provided by different platforms, including the use of a simulated genome, called the mock genome, can generate in population structure and genetic diversity studies, especially when the intention is to use this information to support the formation of heterotic groups, choice of testers, and genomic prediction of single crosses. For that, we used a method to assemble a reference genome to perform the single-nucleotide polymorphism (SNP) calling without needing an external genome. Thus, we compared the analysis results using the mock genome with the standard approaches (array and genotyping-by-sequencing (GBS)). The results showed that the GBS-Mock presented similar results to the standard methods of genetic diversity studies, division of heterotic groups, the definition of testers, and genomic prediction. These results showed that a mock genome constructed from the population's intrinsic polymorphisms to perform the SNP calling is an effective alternative for conducting genomic studies of this nature in orphan crops, especially those that do not have a reference genome.
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Affiliation(s)
| | - Júlio César DoVale
- Department of Crop Science, Federal University of Ceará, Fortaleza, Brazil
| | - Felipe Sabadin
- School of Plant and Environmental Sciences, Virginia Tech: Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Roberto Fritsche-Neto
- LSU AgCenter, Louisiana State University Agricultural Center, Baton Rouge, LA, United States
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Hoang NV, Sogbohossou EOD, Xiong W, Simpson CJC, Singh P, Walden N, van den Bergh E, Becker FFM, Li Z, Zhu XG, Brautigam A, Weber APM, van Haarst JC, Schijlen EGWM, Hendre PS, Van Deynze A, Achigan-Dako EG, Hibberd JM, Schranz ME. The Gynandropsis gynandra genome provides insights into whole-genome duplications and the evolution of C4 photosynthesis in Cleomaceae. THE PLANT CELL 2023; 35:1334-1359. [PMID: 36691724 PMCID: PMC10118270 DOI: 10.1093/plcell/koad018] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 01/18/2023] [Indexed: 06/17/2023]
Abstract
Gynandropsis gynandra (Cleomaceae) is a cosmopolitan leafy vegetable and medicinal plant, which has also been used as a model to study C4 photosynthesis due to its evolutionary proximity to C3 Arabidopsis (Arabidopsis thaliana). Here, we present the genome sequence of G. gynandra, anchored onto 17 main pseudomolecules with a total length of 740 Mb, an N50 of 42 Mb and 30,933 well-supported gene models. The G. gynandra genome and previously released genomes of C3 relatives in the Cleomaceae and Brassicaceae make an excellent model for studying the role of genome evolution in the transition from C3 to C4 photosynthesis. Our analyses revealed that G. gynandra and its C3 relative Tarenaya hassleriana shared a whole-genome duplication event (Gg-α), then an addition of a third genome (Th-α, +1×) took place in T. hassleriana but not in G. gynandra. Analysis of syntenic copy number of C4 photosynthesis-related gene families indicates that G. gynandra generally retained more duplicated copies of these genes than C3T. hassleriana, and also that the G. gynandra C4 genes might have been under positive selection pressure. Both whole-genome and single-gene duplication were found to contribute to the expansion of the aforementioned gene families in G. gynandra. Collectively, this study enhances our understanding of the polyploidy history, gene duplication and retention, as well as their impact on the evolution of C4 photosynthesis in Cleomaceae.
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Affiliation(s)
| | | | - Wei Xiong
- Biosystematics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Conor J C Simpson
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | - Pallavi Singh
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | - Nora Walden
- Biosystematics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Erik van den Bergh
- Biosystematics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Frank F M Becker
- Laboratory of Genetics, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Zheng Li
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Xin-Guang Zhu
- State Key Laboratory for Plant Molecular Genetics, Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Andrea Brautigam
- Faculty of Biology, Bielefeld University, 33501 Bielefeld, Germany
| | - Andreas P M Weber
- Cluster of Excellence on Plant Science (CEPLAS), Institute of Plant Biochemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Jan C van Haarst
- Business Unit Bioscience, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Elio G W M Schijlen
- Business Unit Bioscience, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Prasad S Hendre
- African Orphan Crops Consortium (AOCC), World Agroforestry (ICRAF), Nairobi 00100, Kenya
| | - Allen Van Deynze
- African Orphan Crops Consortium (AOCC), World Agroforestry (ICRAF), Nairobi 00100, Kenya
- Seed Biotechnology Center, University of California, Davis, California 95616, USA
| | - Enoch G Achigan-Dako
- Laboratory of Genetics, Biotechnology and Seed Science (GbioS), Faculty of Agronomic Sciences, University of Abomey-Calavi, BP 2549 Abomey-Calavi, Republic of Benin
| | - Julian M Hibberd
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
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Kumar B, Singh AK, Bahuguna RN, Pareek A, Singla‐Pareek SL. Orphan crops: A genetic treasure trove for hunting stress tolerance genes. Food Energy Secur 2022. [DOI: 10.1002/fes3.436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Brijesh Kumar
- Plant Stress Biology Group International Centre for Genetic Engineering and Biotechnology New Delhi India
| | - Anil Kumar Singh
- ICAR‐National Institute for Plant Biotechnology LBS Centre New Delhi India
| | - Rajeev Nayan Bahuguna
- Center for Advanced Studies on Climate Change Dr. Rajendra Prasad Central Agricultural University Bihar Pusa, Samastipur India
| | - Ashwani Pareek
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences Jawaharlal Nehru University New Delhi India
| | - Sneh L. Singla‐Pareek
- Plant Stress Biology Group International Centre for Genetic Engineering and Biotechnology New Delhi India
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11
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Dwyer W, Ibe CN, Rhee SY. Renaming Indigenous crops and addressing colonial bias in scientific language. TRENDS IN PLANT SCIENCE 2022; 27:1189-1192. [PMID: 36163314 DOI: 10.1016/j.tplants.2022.08.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 08/08/2022] [Accepted: 08/31/2022] [Indexed: 06/16/2023]
Abstract
Indigenous crops, commonly known as orphan, forgotten, or neglected crops, are understudied, but have important roles in the diet and economy of the communities that cultivate them. Here, we review potential benefits of Indigenous crop research and highlight the importance of an anticolonial framework to prevent exploitation of these unique resources.
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Affiliation(s)
- William Dwyer
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Carol N Ibe
- JR Biotek Foundation, Bowie, MD, USA; John Innes Centre, Department of Crop Genetics, John Innes Centre, Norwich, NR4 7UH, UK
| | - Seung Y Rhee
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA.
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12
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Jian L, Yan J, Liu J. De Novo Domestication in the Multi-Omics Era. PLANT & CELL PHYSIOLOGY 2022; 63:1592-1606. [PMID: 35762778 DOI: 10.1093/pcp/pcac077] [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: 01/14/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
Most cereal crops were domesticated within the last 12,000 years and subsequently spread around the world. These crops have been nourishing the world by supplying a primary energy and nutrient source, thereby playing a critical role in determining the status of human health and sustaining the global population. Here, we review the major challenges of future agriculture and emphasize the utilization of wild germplasm. De novo domestication is one of the most straightforward strategies to manipulate domestication-related and/or other genes with known function, and thereby introduce desired traits into wild plants. We also summarize known causal variations and their corresponding pathways in order to better understand the genetic basis of crop evolution, and how this knowledge could facilitate de novo domestication. Indeed knowledge-driven de novo domestication has great potential for the development of new sustainable crops that have climate-resilient high yield with low resource input and meet individual nutrient needs. Finally, we discuss current opportunities for and barriers to knowledge-driven de novo domestication.
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Affiliation(s)
- Liumei Jian
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Jie Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
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13
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Alavilli H, Poli Y, Verma KS, Kumar V, Gupta S, Chaudhary V, Jyoti A, Sahi SV, Kothari SL, Jain A. Miracle Tree Moringa oleifera: Status of the Genetic Diversity, Breeding, In Vitro Propagation, and a Cogent Source of Commercial Functional Food and Non-Food Products. PLANTS (BASEL, SWITZERLAND) 2022; 11:3132. [PMID: 36432862 PMCID: PMC9694164 DOI: 10.3390/plants11223132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 10/30/2022] [Accepted: 11/07/2022] [Indexed: 06/16/2023]
Abstract
Moringa oleifera Lam. (MO) is a fast-growing drought-resistant tree belonging to the family Moringaceae and native to the Indian subcontinent and cultivated and/or naturalized worldwide with a semi-arid climate. MO is also popularly known as a miracle tree for its repertoire of nutraceutical, pharmacological, and phytochemical properties. The MO germplasm is collected, conserved, and maintained by various institutions across the globe. Various morphological, biochemical, and molecular markers are used for determining the genetic diversity in MO accessions. A higher yield of leaves and pods is often desirable for making various products with commercial viability and amenable for trade in the international market. Therefore, breeding elite varieties adapted to local agroclimatic conditions and in vitro propagation are viable and sustainable approaches. Here, we provide a comprehensive overview of MO germplasm conservation and various markers that are employed for assessing the genetic diversity among them. Further, breeding and in vitro propagation of MO for various desirable agronomic traits are discussed. Finally, trade and commerce of various functional and biofortified foods and non-food products are enumerated albeit with a need for a rigorous and stringent toxicity evaluation.
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Affiliation(s)
- Hemasundar Alavilli
- Department of Bioresources Engineering, Sejong University, Seoul 05006, Republic of Korea
| | - Yugandhar Poli
- ICAR-Indian Institute of Rice Research, Hyderabad 500030, India
| | - Kumar Sambhav Verma
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur 303002, India
| | - Vikram Kumar
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur 303002, India
| | - Swati Gupta
- Department of Biosciences, Manipal University Jaipur, Jaipur 303007, India
| | - Vigi Chaudhary
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur 303002, India
| | - Anupam Jyoti
- Biotechnology Department, Chandigarh University, National Highway-95, Ludhiana-Chandigarh State Highway, Chandigarh 160055, India
| | - Shivendra V. Sahi
- Department of Biology, Saint Joseph’s University (University City Campus), 600 South 43rd Street, Philadelphia, PA 19104, USA
| | - Shanker Lal Kothari
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur 303002, India
| | - Ajay Jain
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur 303002, India
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14
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Naqvi RZ, Siddiqui HA, Mahmood MA, Najeebullah S, Ehsan A, Azhar M, Farooq M, Amin I, Asad S, Mukhtar Z, Mansoor S, Asif M. Smart breeding approaches in post-genomics era for developing climate-resilient food crops. FRONTIERS IN PLANT SCIENCE 2022; 13:972164. [PMID: 36186056 PMCID: PMC9523482 DOI: 10.3389/fpls.2022.972164] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 08/15/2022] [Indexed: 06/16/2023]
Abstract
Improving the crop traits is highly required for the development of superior crop varieties to deal with climate change and the associated abiotic and biotic stress challenges. Climate change-driven global warming can trigger higher insect pest pressures and plant diseases thus affecting crop production sternly. The traits controlling genes for stress or disease tolerance are economically imperative in crop plants. In this scenario, the extensive exploration of available wild, resistant or susceptible germplasms and unraveling the genetic diversity remains vital for breeding programs. The dawn of next-generation sequencing technologies and omics approaches has accelerated plant breeding by providing the genome sequences and transcriptomes of several plants. The availability of decoded plant genomes offers an opportunity at a glance to identify candidate genes, quantitative trait loci (QTLs), molecular markers, and genome-wide association studies that can potentially aid in high throughput marker-assisted breeding. In recent years genomics is coupled with marker-assisted breeding to unravel the mechanisms to harness better better crop yield and quality. In this review, we discuss the aspects of marker-assisted breeding and recent perspectives of breeding approaches in the era of genomics, bioinformatics, high-tech phonemics, genome editing, and new plant breeding technologies for crop improvement. In nutshell, the smart breeding toolkit in the post-genomics era can steadily help in developing climate-smart future food crops.
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15
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Adedeji-Badmus AN, Schramm S, Gigl M, Iwebema W, Albertos P, Dawid C, Sieberer T, Poppenberger B. Species-Specific Variation in Abscisic Acid Homeostasis and Responses Impacts Important Traits in Crassocephalum Orphan Crops. FRONTIERS IN PLANT SCIENCE 2022; 13:923421. [PMID: 35903235 PMCID: PMC9318166 DOI: 10.3389/fpls.2022.923421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 06/02/2022] [Indexed: 06/15/2023]
Abstract
Crassocephalum rubens and Crassocephalum crepidioides are plant species native to Africa, but grow in most tropical and subtropical regions of the world. They are rich in vitamins, minerals, and essential oils and are traditional leafy vegetables and medicinal plants in Sub-Saharan Africa. The plants are still mainly collected from the wild but shall be taken into cultivation and an important aim in the domestication of these species is to improve traits that are relevant for crop production. Here, seed formation and germination capacities in C. crepidioides and C. rubens were investigated, and it was found that C. crepidioides exhibits a higher level of seed dormancy, which could be broken with light, and was correlated with higher amounts of abscisic acid (ABA), a plant hormone that promotes seed dormancy. ABA is also very well-known for its role in abiotic stress tolerance, and it is shown that tetraploid C. crepidioides exhibits a higher level of resistance against drought and heat stress than diploid C. rubens, traits that will benefit the cultivation of these plants, particularly in rain-fed cropping systems. The potential of Crassocephalum to improve nutrition and increase the resilience of marginal cropping systems in Africa is discussed.
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Affiliation(s)
- Adebimpe N. Adedeji-Badmus
- Biotechnology of Horticultural Crops, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Sebastian Schramm
- Biotechnology of Horticultural Crops, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Michael Gigl
- Chair of Food Chemistry and Molecular Sensory Science, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Williams Iwebema
- Biotechnology of Horticultural Crops, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Pablo Albertos
- Biotechnology of Horticultural Crops, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Corinna Dawid
- Chair of Food Chemistry and Molecular Sensory Science, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Tobias Sieberer
- Research Group Plant Growth Regulation, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Brigitte Poppenberger
- Biotechnology of Horticultural Crops, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
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16
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Democratizing plant genomics to accelerate global food production. Nat Genet 2022; 54:911-913. [PMID: 35817968 DOI: 10.1038/s41588-022-01122-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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17
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Sarker U, Lin YP, Oba S, Yoshioka Y, Hoshikawa K. Prospects and potentials of underutilized leafy Amaranths as vegetable use for health-promotion. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 182:104-123. [PMID: 35487123 DOI: 10.1016/j.plaphy.2022.04.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 03/31/2022] [Accepted: 04/09/2022] [Indexed: 05/23/2023]
Abstract
Climate change causes environmental variation worldwide, which is one of the most serious threats to global food security. In addition, more than 2 billion people in the world are reported to suffer from serious malnutrition, referred to as 'hidden hunger.' Dependence on only a few crops could lead to the loss of genetic diversity and high fragility of crop breeding in systems adapting to global scale climate change. The exploitation of underutilized species and genetic resources, referred to as orphan crops, could be a useful approach for resolving the issue of adaptability to environmental alteration, biodiversity preservation, and improvement of nutrient quality and quantity to ensure food security. Moreover, the use of these alternative crops will help to increase the human health benefits and the income of farmers in developing countries. In this review, we highlight the potential of orphan crops, especially amaranths, for use as vegetables and health-promoting nutritional components. This review highlights promising diversified sources of amaranth germplasms, their tolerance to abiotic stresses, and their nutritional, phytochemical, and antioxidant values for vegetable purposes. Betalains (betacyanins and betaxanthins), unique antioxidant components in amaranth vegetables, are also highlighted regarding their chemodiversity across amaranth germplasms and their stability and degradation. In addition, we discuss the physiological functions, antioxidant, antilipidemic, anticancer, and antimicrobial activities, as well as the biosynthesis pathway, molecular, biochemical, genetics, and genomic mechanisms of betalains in detail.
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Affiliation(s)
- Umakanta Sarker
- Department of Genetics and Plant Breeding, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, 1706, Bangladesh.
| | - Ya-Ping Lin
- World Vegetable Center, P.O. Box 42, Shanhua, Tainan, 74199, Taiwan
| | - Shinya Oba
- Faculty of Applied Biological Science, Gifu University, Gifu, 501-1193, Japan
| | - Yosuke Yoshioka
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba, 305-8572, Ibaraki, Japan; Tsukuba-Plant Innovation Research Center, University of Tsukuba, Tsukuba, 305-8572, Japan
| | - Ken Hoshikawa
- World Vegetable Center, P.O. Box 42, Shanhua, Tainan, 74199, Taiwan; Tsukuba-Plant Innovation Research Center, University of Tsukuba, Tsukuba, 305-8572, Japan; Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences, Ohwashi 1-1, Tsukuba, Ibaraki, 305-8686, Japan.
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18
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Abberton M, Paliwal R, Faloye B, Marimagne T, Moriam A, Oyatomi O. Indigenous African Orphan Legumes: Potential for Food and Nutrition Security in SSA. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2022. [DOI: 10.3389/fsufs.2022.708124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In Sub-Saharan Africa (SSA), both crop production and the hidden hunger index (HHI, a combination of zinc, iron, and vitamin A deficiency), continue to be worse than the rest of the world. Currently, 31 out of 36 countries of SSA show the highest HHI. At the same time, several studies show climate change as a major constraint to agriculture productivity and a significant threat to SSA food security without significant action regarding adaptation. The food security of SSA is dependent on a few major crops, with many of them providing largely only an energy source in the diet. To address this, crop diversification and climate-resilient crops that have adaptation to climate change can be used and one route toward this is promoting the cultivation of African orphan (neglected or underutilized) crops. These crops, particularly legumes, have the potential to improve food and nutrition security in SSA due to their cultural linkage with the regional food habits of the communities, nutritionally rich food, untapped genetic diversity, and adaptation to harsh climate conditions and poor marginal soils. Despite the wide distribution of orphan legumes across the landscape of SSA, these important crop species are characterized by low yield and decreasing utilization due in part to a lack of improved varieties and a lack of adequate research attention. Genomic-assisted breeding (GAB) can contribute to developing improved varieties that yield more, have improved resilience, and high nutritional value. The availability of large and diverse collections of germplasm is an essential resource for crop improvement. In the Genetic Resources Center of the International Institute of Tropical Agriculture, the collections of orphan legumes, particularly the Bambara groundnut, African yambean, and Kersting's groundnut, have been characterized and evaluated for their key traits, and new collections are being undertaken to fill gaps and to widen the genetic diversity available to underpin breeding that can be further utilized with GAB tools to develop faster and cost-effective climate-resilient cultivars with a high nutrition value for SSA farmers. However, a greater investment of resources is required for applying modern breeding to orphan legume crops if their full potential is to be realized.
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19
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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.
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Affiliation(s)
| | | | | | | | | | | | | | - Rakesh Kumar Singh
- International Center for Biosaline Agriculture (ICBA), Dubai, United Arab Emirates
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20
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The Future of Food: Domestication and Commercialization of Indigenous Food Crops in Africa over the Third Decade (2012–2021). SUSTAINABILITY 2022. [DOI: 10.3390/su14042355] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
This paper follows the transition from ethnobotany to a deeper scientific understanding of the food and medicinal properties of African agroforestry tree products as inputs into the start of domestication activities. It progresses on to the integration of these indigenous trees as new crops within diversified farming systems for multiple social, economic and environmental benefits. From its advent in the 1990s, the domestication of indigenous food and non-food tree species has become a global programme with a strong African focus. This review of progress in the third decade is restricted to progress in Africa, where multi-disciplinary research on over 59 species has been reported in 759 research papers in 318 science publications by scientists from over 833 research teams in 70 countries around the world (532 in Africa). The review spans 23 research topics presenting the recent research literature for tree species of high priority across the continent, as well as that in each of the four main ecological regions: the humid zone of West and Central Africa; the Sahel and North Africa; the East African highlands and drylands; and the woody savannas of Southern Africa. The main areas of growth have been the nutritional/medicinal value of non-timber forest products; the evaluation of the state of natural resources and their importance to local people; and the characterization of useful traits. However, the testing of putative cultivars; the implementation of participatory principles; the protection of traditional knowledge and intellectual property rights; and the selection of elite trees and ideotypes remain under-researched. To the probable detriment of the upscaling and impact in tropical agriculture, there has been, at the international level, a move away from decentralized, community-based tree domestication towards a laboratory-based, centralized approach. However, the rapid uptake of research by university departments and national agricultural research centres in Africa indicates a recognition of the importance of the indigenous crops for both the livelihoods of rural communities and the revitalization and enhanced outputs from agriculture in Africa, especially in West Africa. Thus, on a continental scale, there has been an uptake of research with policy relevance for the integration of indigenous trees in agroecosystems and their importance for the attainment of the UN Sustainable Development Goals. To progress this in the fourth decade, there will need to be a dedicated Centre in Africa to test and develop cultivars of indigenous crops. Finally, this review underpins a holistic approach to mitigating climate change, as well as other big global issues such as hunger, poverty and loss of wildlife habitat by reaping the benefits, or ‘profits’, from investment in the five forms of Capital, described as ‘land maxing’. However, policy and decision makers are not yet recognizing the potential for holistic and transformational adoption of these new indigenous food crop opportunities for African agriculture. Is ‘political will’ the missing sixth capital for sustainable development?
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Mir RA, Nazir M, Naik S, Mukhtar S, Ganai BA, Zargar SM. Utilizing the underutilized plant resources for development of life style foods: Putting nutrigenomics to use. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 171:128-138. [PMID: 34998100 DOI: 10.1016/j.plaphy.2021.12.038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 12/26/2021] [Accepted: 12/30/2021] [Indexed: 06/14/2023]
Abstract
Sufficient amount of minerals, vitamins, and proteins in human diet play indispensable role in maintaining the active metabolism for better human health. All the essential nutrients that are requisite for an individual's survival are acquired from plants as well as animals. Micronutrients and macronutrients directly influence the metabolic pathways and their deficiencies play a substantial role in development of manifold disorders. In addition to environmental factors, quality and quantity of foods are key factors in maintaining the human health. Transition from healthy to diseased state is concurrent with the pattern of gene expression that is largely influenced by nutrition and environment. A combined approach to study the influence of nutrition on expression of numerous genes can be well explored through nutrigenomic studies. Nutrigenomics includes studies wherein applied genomics is used to investigate nutritional science to understand the compartmentalization of genes that influence the cause of diet-related complications. This review describes the role of underutilized crops as frontline foods to circumvent the health complications through the nutrigenomic studies. Further dynamics of nutrigenomic tools to study the impact of nutrition on the changing pattern of genome stability and gene expression for developing precise safety measures against wide range of health ailments linked to metabolic networks. Additionally, this review provides detailed information on nutrigenomic studies undertaken to unravel the potential of underutilized crops to augment the human health and to carry the agronomic/genomic approaches to enhance nutritional profile of underutilized crops to overcome diet-related disorders.
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Affiliation(s)
- Rakeeb Ahmad Mir
- Department of Biotechnology, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, Jammu and Kashmir, 185131, India
| | - Muslima Nazir
- Centre of Research for Development, University of Kashmir, Hazratbal, Srinagar, Jammu and Kashmir, 190006, India
| | - Samiullah Naik
- Proteomics Laboratory, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Jammu and Kashmir, 190025, India
| | - Shazia Mukhtar
- Proteomics Laboratory, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Jammu and Kashmir, 190025, India
| | - Bashir Ahmad Ganai
- Centre of Research for Development, University of Kashmir, Hazratbal, Srinagar, Jammu and Kashmir, 190006, India
| | - Sajad Majeed Zargar
- Proteomics Laboratory, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Jammu and Kashmir, 190025, India.
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22
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Nayak SP, Lone RA, Fakhrah S, Chauhan A, Sarvendra K, Mohanty CS. Mainstreaming underutilized legumes for providing nutritional security. FUTURE FOODS 2022. [DOI: 10.1016/b978-0-323-91001-9.00023-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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23
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Woldetsadik D, Llorent-Martínez EJ, Gebrezgabher S, Njenga M, Mendum R, Castillo-López R, Fernández-de Córdova ML, Hailu H, Evans CT, Madani N, Mafika TP, Fleming DEB. Okra ( Abelmoschus esculentus) in a refugee context in East Africa: Kitchen gardening helps with mineral provision. SN APPLIED SCIENCES 2021; 4:32. [PMID: 34957376 PMCID: PMC8689287 DOI: 10.1007/s42452-021-04898-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 11/23/2021] [Indexed: 02/07/2023] Open
Abstract
Kitchen gardening is considered a way to reconnect with agriculture and complement the cereal-based relief food offered to refugees in East Africa. This work aimed at profiling mineral content of okra in four refugee camps and settlements located in Ethiopia and Uganda and its contribution to adequate intake (AIs) or recommended dietary allowances (RDAs) for young children and pregnant and lactating women (PLW). The study also evaluated the applicability of portable X-ray fluorescence (PXRF) as compared with inductively coupled plasma mass spectrometry (ICP-MS) for mineral profiling of okra powder samples. The contents of minerals (mg kg-1) from the ICP-MS readings were in the following ranges: K (14,385-33,294), Ca (2610-14,090), P (3178-13,248), Mg (3896-7986), Cu (3.81-19.3), Fe (75.7-1243), Zn (33-141) and Mn (23.1-261). Regardless of geographic origin, at low-end consumption probability (17 g day-1 for young children and 68 g day-1 for PLW), okra could contribute ˂ 15% (2.7-12.9%) AI for macro-minerals (K and Ca). In addition, the contributions to RDA values for Fe and Zn, elements of known public health interest, ranged from 4.5 to 34.7% for young children. Interestingly, regression lines revealed strong agreement between ICP-MS and PXRF readings for Mn and Zn, with R2 values > 0.91. This information is useful in support of nutrition-sensitive kitchen gardening programs through scaling culturally important crops in refugee settings. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s42452-021-04898-6.
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Affiliation(s)
- Desta Woldetsadik
- Department of Soil and Water Resources Management, Wollo University, Dessie, Ethiopia
| | - Eulogio J. Llorent-Martínez
- Department of Physical and Analytical Chemistry, Faculty of Experimental Sciences, University of Jaén, Campus Las Lagunillas, 23071 Jaén, Spain
| | | | - Mary Njenga
- World Agroforestry (ICRAF), Nairobi, Kenya
- Wangari Maathai Institute for Peace and Environmental Studies, University of Nairobi, Nairobi, Kenya
| | - Ruth Mendum
- Office of International Programs, College of Agricultural Sciences, Pennsylvania State University, State College, USA
| | - Roxana Castillo-López
- Department of Physical and Analytical Chemistry, Faculty of Experimental Sciences, University of Jaén, Campus Las Lagunillas, 23071 Jaén, Spain
| | - Maria L. Fernández-de Córdova
- Department of Physical and Analytical Chemistry, Faculty of Experimental Sciences, University of Jaén, Campus Las Lagunillas, 23071 Jaén, Spain
| | - Hillette Hailu
- Department of Soil and Water Resources Management, Wollo University, Dessie, Ethiopia
| | - Colby T. Evans
- Physics Department, Mount Allison University, Sackville, NB Canada
| | - Nelly Madani
- Physics Department, Mount Allison University, Sackville, NB Canada
| | - Tamlyn P. Mafika
- Physics Department, Mount Allison University, Sackville, NB Canada
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Daszkowska-Golec A. The landscape of plant genomics after 20 years. Trends Genet 2021; 38:310-311. [PMID: 34949464 DOI: 10.1016/j.tig.2021.12.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 12/12/2021] [Indexed: 12/01/2022]
Abstract
Many letters of the plant genetic code have been read since the first plant genome was published in 2000 for Arabidopsis. In a recent paper, Marks et al. examined 798 plant genomes and provide a current view of plant genomics in terms of the quality of the assemblies, coupled with their taxonomical and geographical distribution.
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Affiliation(s)
- Agata Daszkowska-Golec
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland.
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Sabadin F, Carvalho HF, Galli G, Fritsche-Neto R. Population-tailored mock genome enables genomic studies in species without a reference genome. Mol Genet Genomics 2021; 297:33-46. [PMID: 34755217 DOI: 10.1007/s00438-021-01831-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 10/28/2021] [Indexed: 11/26/2022]
Abstract
Based on molecular markers, genomic prediction enables us to speed up breeding schemes and increase the response to selection. There are several high-throughput genotyping platforms able to deliver thousands of molecular markers for genomic study purposes. However, even though its widely applied in plant breeding, species without a reference genome cannot fully benefit from genomic tools and modern breeding schemes. We used a method to assemble a population-tailored mock genome to call single-nucleotide polymorphism (SNP) markers without an available reference genome, and for the first time, we compared the results with standard genotyping platforms (array and genotyping-by-sequencing (GBS) using a reference genome) for performance in genomic prediction models. Our results indicate that using a population-tailored mock genome to call SNP delivers reliable estimates for the genomic relationship between genotypes. Furthermore, genomic prediction estimates were comparable to standard approaches, especially when considering only additive effects. However, mock genomes were slightly worse than arrays at predicting traits influenced by dominance effects, but still performed as well as standard GBS methods that use a reference genome. Nevertheless, the array-based SNP markers methods achieved the best predictive ability and reliability to estimate variance components. Overall, the mock genomes can be a worthy alternative for genomic selection studies, especially for those species where the reference genome is not available.
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Affiliation(s)
- Felipe Sabadin
- Department of Genetics, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil.
| | - Humberto Fanelli Carvalho
- Department of Genetics, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Giovanni Galli
- Department of Genetics, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Roberto Fritsche-Neto
- Department of Genetics, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
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Venezia M, Creasey Krainer KM. Current Advancements and Limitations of Gene Editing in Orphan Crops. FRONTIERS IN PLANT SCIENCE 2021; 12:742932. [PMID: 34630494 PMCID: PMC8493294 DOI: 10.3389/fpls.2021.742932] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 08/20/2021] [Indexed: 05/23/2023]
Abstract
Gene editing provides precise, heritable genome mutagenesis without permanent transgenesis, and has been widely demonstrated and applied in planta. In the past decade, clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated proteins (Cas) has revolutionized the application of gene editing in crops, with mechanistic advances expanding its potential, including prime editing and base editing. To date, CRISPR/Cas has been utilized in over a dozen orphan crops with diverse genetic backgrounds, leading to novel alleles and beneficial phenotypes for breeders, growers, and consumers. In conjunction with the adoption of science-based regulatory practices, there is potential for CRISPR/Cas-mediated gene editing in orphan crop improvement programs to solve a plethora of agricultural problems, especially impacting developing countries. Genome sequencing has progressed, becoming more affordable and applicable to orphan crops. Open-access resources allow for target gene identification and guide RNA (gRNA) design and evaluation, with modular cloning systems and enzyme screening methods providing experimental feasibility. While the genomic and mechanistic limitations are being overcome, crop transformation and regeneration continue to be the bottleneck for gene editing applications. International collaboration between all stakeholders involved in crop improvement is vital to provide equitable access and bridge the scientific gap between the world's most economically important crops and the most under-researched crops. This review describes the mechanisms and workflow of CRISPR/Cas in planta and addresses the challenges, current applications, and future prospects in orphan crops.
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Paliwal R, Adegboyega TT, Abberton M, Faloye B, Oyatomi O. Potential of genomics for the improvement of underutilized legumes in sub‐Saharan Africa. LEGUME SCIENCE 2021; 3. [PMID: 0 DOI: 10.1002/leg3.69] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Affiliation(s)
- Rajneesh Paliwal
- Genetic Resources Center International Institute of Tropical Agriculture Ibadan Nigeria
| | | | - Michael Abberton
- Genetic Resources Center International Institute of Tropical Agriculture Ibadan Nigeria
| | - Ben Faloye
- Genetic Resources Center International Institute of Tropical Agriculture Ibadan Nigeria
| | - Olaniyi Oyatomi
- Genetic Resources Center International Institute of Tropical Agriculture Ibadan Nigeria
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Schramm S, Rozhon W, Adedeji-Badmus AN, Liang Y, Nayem S, Winkelmann T, Poppenberger B. The Orphan Crop Crassocephalum crepidioides Accumulates the Pyrrolizidine Alkaloid Jacobine in Response to Nitrogen Starvation. FRONTIERS IN PLANT SCIENCE 2021; 12:702985. [PMID: 34394157 PMCID: PMC8355542 DOI: 10.3389/fpls.2021.702985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 06/30/2021] [Indexed: 06/13/2023]
Abstract
Crassocephalum crepidioides is an African orphan crop that is used as a leafy vegetable and medicinal plant. Although it is of high regional importance in Sub-Saharan Africa, the plant is still mainly collected from the wild and therefore efforts are made to promote its domestication. However, in addition to beneficial properties, there was first evidence that C. crepidioides can accumulate the highly toxic pyrrolizidine alkaloid (PA) jacobine and here it was investigated, how jacobine production is controlled. Using ecotypes from Africa and Asia that were characterized in terms of their PA profiles, it is shown that the tetraploid C. crepidioides forms jacobine, an ability that its diploid close relative Crassocephalum rubens appears to lack. Evidence is provided that nitrogen (N) deficiency strongly increases jacobine in the leaves of C. crepidioides, that this capacity depends more strongly on the shoot than the root system, and that homospermidine synthase (HSS) activity is not rate-limiting for this reaction. A characterization of HSS gene representation and transcription showed that C. crepidioides and C. rubens possess two functional versions, one of which is conserved, that the HSS transcript is mainly present in roots and that its abundance is not controlled by N deficiency. In summary, this work improves our understanding of how environmental cues impact PA biosynthesis in plants and provides a basis for the development of PA-free C. crepidioides cultivars, which will aid its domestication and safe use.
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Affiliation(s)
- Sebastian Schramm
- Biotechnology of Horticultural Crops, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Wilfried Rozhon
- Biotechnology of Horticultural Crops, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Adebimpe N. Adedeji-Badmus
- Biotechnology of Horticultural Crops, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Yuanyuan Liang
- Biotechnology of Horticultural Crops, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Shahran Nayem
- Biotechnology of Horticultural Crops, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Traud Winkelmann
- Woody Plant and Propagation Physiology Section, Institute of Horticultural Production Systems, Gottfried Wilhelm Leibniz University Hannover, Hanover, Germany
| | - Brigitte Poppenberger
- Biotechnology of Horticultural Crops, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
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Ghazal H, Adam Y, Idrissi Azami A, Sehli S, Nyarko HN, Chaouni B, Olasehinde G, Isewon I, Adebiyi M, Ajani O, Matovu E, Obembe O, Ajamma Y, Kuzamunu G, Pandam Salifu S, Kayondo J, Benkahla A, Adebiyi E. Plant genomics in Africa: present and prospects. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:21-36. [PMID: 33837593 DOI: 10.1111/tpj.15272] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 03/29/2021] [Accepted: 04/01/2021] [Indexed: 06/12/2023]
Abstract
Plants are the world's most consumed goods. They are of high economic value and bring many health benefits. In most countries in Africa, the supply and quality of food will rise to meet the growing population's increasing demand. Genomics and other biotechnology tools offer the opportunity to improve subsistence crops and medicinal herbs in the continent. Significant advances have been made in plant genomics, which have enhanced our knowledge of the molecular processes underlying both plant quality and yield. The sequencing of complex genomes of African plant species, facilitated by the continuously evolving next-generation sequencing technologies and advanced bioinformatics approaches, has provided new opportunities for crop improvement. This review summarizes the achievements of genome sequencing projects of endemic African plants in the last two decades. We also present perspectives and challenges for future plant genomic studies that will accelerate important plant breeding programs for African communities. These challenges include a lack of basic facilities, a lack of sequencing and bioinformatics facilities, and a lack of skills to design genomics studies. However, it is imperative to state that African countries have become key players in the plant genome revolution and genome derived-biotechnology. Therefore, African governments should invest in public plant genomics research and applications, establish bioinformatics platforms and training programs, and stimulate university and industry partnerships to fully deploy plant genomics, particularly in the fields of agriculture and medicine.
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Affiliation(s)
- Hassan Ghazal
- National Center for Scientific and Technical Research, Rabat, Morocco
- Mohammed VI University of Health Sciences, Casablanca, Morocco
| | - Yagoub Adam
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ogun State, Km 10 Idiroko Road, P.M.B. 1023, Nigeria
| | | | - Sofia Sehli
- Mohammed VI University of Health Sciences, Casablanca, Morocco
| | - Hannah N Nyarko
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana
| | - Bouchra Chaouni
- Laboratory of Plant and Microbial Biotechnology, Biodiversity and Environment, Faculty of Sciences, University Mohammed V, Rabat, Morocco
| | - Grace Olasehinde
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ogun State, Km 10 Idiroko Road, P.M.B. 1023, Nigeria
- Department of Biological Sciences, Covenant University, Ogun State, Km 10 Idiroko Road, P.M.B. 1023, Ota, Nigeria
| | - Itunuoluwa Isewon
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ogun State, Km 10 Idiroko Road, P.M.B. 1023, Nigeria
- Department of Computer and Information Sciences, Covenant University, Ogun State, Km 10 Idiroko Road, P.M.B. 1023, Ota, Nigeria
| | - Marion Adebiyi
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ogun State, Km 10 Idiroko Road, P.M.B. 1023, Nigeria
- Department of Computer Science, Landmark University, Kwara-State, Omu-Aran, Nigeria
| | - Olayinka Ajani
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ogun State, Km 10 Idiroko Road, P.M.B. 1023, Nigeria
- Department of Chemistry, Covenant University, Ogun State, Km 10 Idiroko Road, P.M.B. 1023, Ota, Nigeria
| | - Enock Matovu
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, P. O. Box 7062, Kampala, Uganda
| | - Olawole Obembe
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ogun State, Km 10 Idiroko Road, P.M.B. 1023, Nigeria
- Department of Biological Sciences, Covenant University, Ogun State, Km 10 Idiroko Road, P.M.B. 1023, Ota, Nigeria
| | - Yvonne Ajamma
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ogun State, Km 10 Idiroko Road, P.M.B. 1023, Nigeria
| | - Gaston Kuzamunu
- African Institute for Mathematical Sciences, Cape Town, 7945, South Africa
- Department of Pathology, Division of Human Genetics, University of Cape Town, IDM, Cape Town, South Africa
- Department of Integrative Biomedical Sciences, Computational Biology Division, University of Cape Town, Observatory, 7925, South Africa
| | - Samson Pandam Salifu
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana
| | - Jonathan Kayondo
- Uganda Virus Research Institute (UVRI), Uganda Research Unit on AIDS, Entebbe, Uganda
| | - Alia Benkahla
- Bioinformatics and Biostatistics Laboratory (LR16IPT09), Pasteur Institute of Tunis, Tunis, Tunisia
| | - Ezekiel Adebiyi
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ogun State, Km 10 Idiroko Road, P.M.B. 1023, Nigeria
- Department of Computer and Information Sciences, Covenant University, Ogun State, Km 10 Idiroko Road, P.M.B. 1023, Ota, Nigeria
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), G200, Im Neuenheimer Feld 280, Heidelberg, 69120, Germany
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African Lives Matter: Wild Food Plants Matter for Livelihoods, Justice, and the Environment—A Policy Brief for Agricultural Reform and New Crops. SUSTAINABILITY 2021. [DOI: 10.3390/su13137252] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
International agricultural policies to address hunger and malnutrition in the tropics and sub-tropics have typically been based on approaches to the intensification of farming systems effective in industrialised economies where the social, economic, and environmental conditions and the infrastructure are very different to those in Africa. The consequence of this short-sightedness has been that agricultural productivity, dependent on ecosystem services from natural capital, has declined in Africa due to ecological and environmental collapse. This has undermined the livelihoods of the millions of smallholder farmers living on the brink of the cash economy, leading to severe social injustice. This review summarises advances in smallholder agriculture’s sustainable intensification in the tropics and sub-tropics, leveraging the domestication and commercialisation of wild indigenous tree species that produce nutritious, marketable, and useful food and non-food products. These are grown within diversified and multifunctional farming systems together with conventional food staples and local orphan crops to reduce land degradation, pollution, water extraction, and nutrient mining while promoting services such as pollination and other ecological functions. The benefits arising from this approach simultaneously address hunger, malnutrition, poverty, social injustice, and a stagnant economy, as well as important global issues such as climate change, loss of biodiversity and environmental degradation. Addressing these issues may also reduce the risk of future pandemics of zoonotic diseases, such as COVID-19. This set of serious global issues epitomise our divided and dysfunctional world and calls out for action. Enhancing sustainable smallholder productivity using indigenous and wild foods is an important international policy and business intervention, vital for achieving the 2030 Sustainable Development Goals and the rebalancing of the global economy by restoring natural capital within new African indigenous food industries.
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Kamenya SN, Mikwa EO, Song B, Odeny DA. Genetics and breeding for climate change in Orphan crops. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1787-1815. [PMID: 33486565 PMCID: PMC8205878 DOI: 10.1007/s00122-020-03755-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 12/16/2020] [Indexed: 05/17/2023]
Abstract
Climate change is rapidly changing how we live, what we eat and produce, the crops we breed and the target traits. Previously underutilized orphan crops that are climate resilient are receiving much attention from the crops research community, as they are often the only crops left in the field after periods of extreme weather conditions. There are several orphan crops with incredible resilience to biotic and abiotic stresses. Some are nutritious, while others provide good sources of biofuel, medicine and other industrial raw materials. Despite these benefits, orphan crops are still lacking in important genetic and genomic resources that could be used to fast track their improvement and make their production profitable. Progress has been made in generating draft genomes of at least 28 orphan crops over the last decade, thanks to the reducing cost of sequencing. The implementation of a structured breeding program that takes advantage of additional modern crop improvement tools such as genomic selection, speed breeding, genome editing, high throughput phenotyping and breeding digitization would make rapid improvement of these orphan crops possible, but would require coordinated research investment. Other production challenges such as lack of adequate germplasm conservation, poor/non-existent seed systems and agricultural extension services, as well as poor marketing channels will also need to be improved if orphan crops were to be profitable. We review the importance of breeding orphan crops under the increasing effects of climate change, highlight existing gaps that need to be addressed and share some lessons to be learned from major crops.
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Affiliation(s)
- Sandra Ndagire Kamenya
- African Center of Excellence in Agroecology and Livelihood Systems, Uganda Martyrs University, Kampala, Uganda
| | - Erick Owuor Mikwa
- The International Crops Research Institute for the Semi-Arid Tropics - Eastern and Southern Africa, Nairobi, Kenya
| | - Bo Song
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute At Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518060, People's Republic of China.
| | - Damaris Achieng Odeny
- The International Crops Research Institute for the Semi-Arid Tropics - Eastern and Southern Africa, Nairobi, Kenya.
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Zenda T, Liu S, Dong A, Duan H. Advances in Cereal Crop Genomics for Resilience under Climate Change. Life (Basel) 2021; 11:502. [PMID: 34072447 PMCID: PMC8228855 DOI: 10.3390/life11060502] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 05/21/2021] [Accepted: 05/25/2021] [Indexed: 12/12/2022] Open
Abstract
Adapting to climate change, providing sufficient human food and nutritional needs, and securing sufficient energy supplies will call for a radical transformation from the current conventional adaptation approaches to more broad-based and transformative alternatives. This entails diversifying the agricultural system and boosting productivity of major cereal crops through development of climate-resilient cultivars that can sustainably maintain higher yields under climate change conditions, expanding our focus to crop wild relatives, and better exploitation of underutilized crop species. This is facilitated by the recent developments in plant genomics, such as advances in genome sequencing, assembly, and annotation, as well as gene editing technologies, which have increased the availability of high-quality reference genomes for various model and non-model plant species. This has necessitated genomics-assisted breeding of crops, including underutilized species, consequently broadening genetic variation of the available germplasm; improving the discovery of novel alleles controlling important agronomic traits; and enhancing creation of new crop cultivars with improved tolerance to biotic and abiotic stresses and superior nutritive quality. Here, therefore, we summarize these recent developments in plant genomics and their application, with particular reference to cereal crops (including underutilized species). Particularly, we discuss genome sequencing approaches, quantitative trait loci (QTL) mapping and genome-wide association (GWAS) studies, directed mutagenesis, plant non-coding RNAs, precise gene editing technologies such as CRISPR-Cas9, and complementation of crop genotyping by crop phenotyping. We then conclude by providing an outlook that, as we step into the future, high-throughput phenotyping, pan-genomics, transposable elements analysis, and machine learning hold much promise for crop improvements related to climate resilience and nutritional superiority.
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Affiliation(s)
- Tinashe Zenda
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding 071001, China; (S.L.); (A.D.)
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China
- Department of Crop Science, Faculty of Agriculture and Environmental Science, Bindura University of Science Education, Bindura P. Bag 1020, Zimbabwe
| | - Songtao Liu
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding 071001, China; (S.L.); (A.D.)
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China
| | - Anyi Dong
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding 071001, China; (S.L.); (A.D.)
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China
| | - Huijun Duan
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding 071001, China; (S.L.); (A.D.)
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China
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Bambara Groundnut (Vigna subterranea L. Verdc): A Crop for the New Millennium, Its Genetic Diversity, and Improvements to Mitigate Future Food and Nutritional Challenges. SUSTAINABILITY 2021. [DOI: 10.3390/su13105530] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The world’s food and agricultural schemes have gradually fallen into an alarming state due to challenges such as high population birth rates, diverse agro-climatic zones, a lack of measures to counter global warming, severe practices of sole-culture cultivation, and asset reduction. A very high dependency on limited staple food crops is associated with repetitious diets, deprivation of food, and shortages of trace minerals, which often causes dietary sicknesses. To ensure nutritious diets worldwide, a real-world and justifiable scheme is provided to garner extra attention towards variation in both agriculture/farming approaches and food habits. The EAT-Lancet statement emphasized an increase in agri-based diets as a way of attaining global generational health. Enlarging neglected crops with plenty of genomic stocks and potentially profitable attributes is a solution that could address food and nutritional security concerns. Bambara groundnut is one such imperative and neglected legume crop that contributes positively to improving global food and nutrient safety. As a “complete food”, this crop has recently been treated as a new millennium crop, and furthermore, it is more adjusted to poor soil and climatic conditions than other dominant crops. Bambara groundnut is a repository of vital nutrients that provides carbohydrates, crucial amino acids, proteins, and energy as well as minerals and vitamins to developed and low-income countries where animal proteins are not readily available. This review explores the potential of Bambara groundnut in ensuring food and nutrient security; its variables, production, processing, nutrient values, role in reducing the nutritional gap, and diverse uses; and attempts in improving its traits. To strengthen food production, an agricultural revolution is required for underutilized crop species to feed the ever-expanding population in the world. Henceforth, advanced plant-breeding procedures, such as next-generation breeding techniques, various molecular tools, TILLING, Eco-TILLING, proteomics, genomics, and transcriptomics (which has been used for major crops), also need to be practiced to intensify production. To boost productivity and to feed the most starved and malnourished populations of the world, it is assumed that the application of modern techniques will play a vital role in the advancement of the underutilized Bambara groundnut.
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He S, Creasey Krainer KM. The Inequity of Biotechnological Impact. MOLECULAR PLANT 2021; 14:1-2. [PMID: 33340688 DOI: 10.1016/j.molp.2020.12.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 12/11/2020] [Accepted: 12/14/2020] [Indexed: 05/06/2023]
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35
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Ye CY, Fan L. Orphan Crops and their Wild Relatives in the Genomic Era. MOLECULAR PLANT 2021; 14:27-39. [PMID: 33346062 DOI: 10.1016/j.molp.2020.12.013] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 12/01/2020] [Accepted: 12/15/2020] [Indexed: 05/06/2023]
Abstract
More than half of the calories consumed by humans are provided by three major cereal crops (rice, maize, and wheat). Orphan crops are usually well adapted to low-input agricultural conditions, and they not only play vital roles in local areas but can also contribute to food and nutritional needs worldwide. Interestingly, many wild relatives of orphan crops are important weeds of major crops. Although orphan crops and their wild relatives have received little attentions from researchers for many years, genomic studies have recently been performed on these plants. Here, we provide an overview of genomic studies on orphan crops, with a focus on orphan cereals and their wild relatives. The genomes of at least 12 orphan cereals and/or their wild relatives have been sequenced. In addition to genomic benefits for orphan crop breeding, we discuss the potential ways for mutual utilization of genomic data from major crops, orphan crops, and their wild relatives (including weeds) and provide perspectives on genetic improvement of both orphan and major crops (including de novo domestication of orphan crops) in the coming genomic era.
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Affiliation(s)
- Chu-Yu Ye
- Institute of Crop Sciences & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Longjiang Fan
- Institute of Crop Sciences & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China; Hainan Institute of Zhejiang University, Sanya 572024, China.
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36
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Letting FK, Venkataramana PB, Ndakidemi PA. Breeding potential of lablab [ Lablab purpureus (L.) Sweet]: a review on characterization and bruchid studies towards improved production and utilization in Africa. GENETIC RESOURCES AND CROP EVOLUTION 2021; 68:3081-3101. [PMID: 34580565 PMCID: PMC8457029 DOI: 10.1007/s10722-021-01271-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 09/14/2021] [Indexed: 05/15/2023]
Abstract
Lablab (Lablab purpureus) [Lablab purpureus (L.) Sweet] is termed a lost, underutilized and neglected crop in Africa. Despite the multipurpose use, production, consumption and research are still limited. Wide genetic diversity of lablab germplasm exists in Africa. Diversity studies provide significant information for subsequent research programs and improvement. The advent of genotyping and sequencing technologies has enabled the identification of unique and agronomically important traits. Application of next-generation sequencing on lablab as a pioneer orphan crop is currently underway. This has enabled description of the whole genome, generation of reference genome and resequencing that provide information on variation within the entire genome. Information from these technological advances helps in identifying potential traits for biotic and abiotic stress for further breeding programs. Storage pests specifically bruchids (Callosobruchus spp.), are considered a major obstacle in lablab production. Screening of available genotypes for bruchid resistance and studies on the physical and biochemical factors that confer resistance in lablab is required. Applying advanced technologies provides precise and reliable identification of the novel markers responsible for bruchid resistance allowing for introgression of important genes to breeding programs. This review provides a detailed analysis on the characterization of lablab and the information on bruchid resistance vital for breeding farmer-preferred varieties that possess agronomically beneficial traits. Concerted efforts and research on this neglected crop will enhance its production, utilization and consumption.
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Affiliation(s)
- Fanuel K. Letting
- Department of Sustainable Agriculture, Biodiversity and Ecosystems Management, School of Life Science and Bio-Engineering, The Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
- Department of Seed, Crop and Horticultural Sciences, School of Agriculture and Biotechnology, University of Eldoret, Eldoret, Kenya
| | - Pavithravani B. Venkataramana
- Department of Sustainable Agriculture, Biodiversity and Ecosystems Management, School of Life Science and Bio-Engineering, The Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
| | - Patrick A. Ndakidemi
- Department of Sustainable Agriculture, Biodiversity and Ecosystems Management, School of Life Science and Bio-Engineering, The Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
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Old Ways, New Ways—Scaling Up from Customary Use of Plant Products to Commercial Harvest Taking a Multifunctional, Landscape Approach. LAND 2020. [DOI: 10.3390/land9050171] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Globally, the agricultural sector is facing many challenges in response to climate change, unsustainable farming practices and human population growth. Despite advances in technology and innovation in agriculture, governments around the world are recognizing a need for transformative agricultural systems that offer solutions to the interrelated issues of food security, climate change, and conservation of environmental and cultural values. Approaches to production are needed that are holistic and multisectoral. In planning for future agricultural models, it is worth exploring indigenous agricultural heritage systems that have demonstrated success in community food security without major environmental impacts. We demonstrate how indigenous practices of customary harvest, operating in multifunctional landscapes, can be scaled up to service new markets while still maintaining natural and cultural values. We do this through a case analysis of the wild harvest of Kakadu plum fruit by Aboriginal people across the tropical savannas of northern Australia. We conclude that this system would ideally operate at a landscape scale to ensure sustainability of harvest, maintenance of important patterns and processes for landscape health, and incorporate cultural and livelihood objectives. Applied to a variety of similar native products, such a production system has potential to make a substantial contribution to niche areas of global food and livelihood security.
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Draft Genomes of Two Artocarpus Plants, Jackfruit (A. heterophyllus) and Breadfruit (A. altilis). Genes (Basel) 2019; 11:genes11010027. [PMID: 31878322 PMCID: PMC7017358 DOI: 10.3390/genes11010027] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 12/18/2019] [Accepted: 12/18/2019] [Indexed: 01/25/2023] Open
Abstract
Two of the most economically important plants in the Artocarpus genus are jackfruit (A. heterophyllus Lam.) and breadfruit (A. altilis (Parkinson) Fosberg). Both species are long-lived trees that have been cultivated for thousands of years in their native regions. Today they are grown throughout tropical to subtropical areas as an important source of starch and other valuable nutrients. There are hundreds of breadfruit varieties that are native to Oceania, of which the most commonly distributed types are seedless triploids. Jackfruit is likely native to the Western Ghats of India and produces one of the largest tree-borne fruit structures (reaching up to 45 kg). To-date, there is limited genomic information for these two economically important species. Here, we generated 273 Gb and 227 Gb of raw data from jackfruit and breadfruit, respectively. The high-quality reads from jackfruit were assembled into 162,440 scaffolds totaling 982 Mb with 35,858 genes. Similarly, the breadfruit reads were assembled into 180,971 scaffolds totaling 833 Mb with 34,010 genes. A total of 2822 and 2034 expanded gene families were found in jackfruit and breadfruit, respectively, enriched in pathways including starch and sucrose metabolism, photosynthesis, and others. The copy number of several starch synthesis-related genes were found to be increased in jackfruit and breadfruit compared to closely-related species, and the tissue-specific expression might imply their sugar-rich and starch-rich characteristics. Overall, the publication of high-quality genomes for jackfruit and breadfruit provides information about their specific composition and the underlying genes involved in sugar and starch metabolism.
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Bekkering CS, Tian L. Thinking Outside of the Cereal Box: Breeding Underutilized (Pseudo)Cereals for Improved Human Nutrition. Front Genet 2019; 10:1289. [PMID: 31921317 PMCID: PMC6933008 DOI: 10.3389/fgene.2019.01289] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 11/22/2019] [Indexed: 11/30/2022] Open
Abstract
Cereal grains have historically played a critical role in sustaining the caloric needs of the human population. The major cereal crops, wheat, rice, and maize, are widely cultivated and have been subjected to biofortification to enhance the vitamin and mineral nutrient content of grains. In contrast, grains of several other cereals as well as non-grass pseudocereals are naturally rich in micronutrients, but have yet to be explored for broad-scale cultivation and consumption. This mini review focuses on the micronutrient and phytochemical profiles of a few emerging (pseudo)cereals and examines the current constraints of their integration into the global food system. Prospects of leveraging whole genome sequence information and modern breeding technologies to promote the breeding and accessibility of these crops are also discussed.
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Affiliation(s)
| | - Li Tian
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
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