1
|
Zhang F, Long R, Ma Z, Xiao H, Xu X, Liu Z, Wei C, Wang Y, Peng Y, Yang X, Shi X, Cao S, Li M, Xu M, He F, Jiang X, Zhang T, Wang Z, Li X, Yu LX, Kang J, Zhang Z, Zhou Y, Yang Q. Evolutionary genomics of climatic adaptation and resilience to climate change in alfalfa. MOLECULAR PLANT 2024; 17:867-883. [PMID: 38678365 DOI: 10.1016/j.molp.2024.04.013] [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: 12/11/2023] [Revised: 04/09/2024] [Accepted: 04/24/2024] [Indexed: 04/29/2024]
Abstract
Given the escalating impact of climate change on agriculture and food security, gaining insights into the evolutionary dynamics of climatic adaptation and uncovering climate-adapted variation can empower the breeding of climate-resilient crops to face future climate change. Alfalfa (Medicago sativa subsp. sativa), the queen of forages, shows remarkable adaptability across diverse global environments, making it an excellent model for investigating species responses to climate change. In this study, we performed population genomic analyses using genome resequencing data from 702 accessions of 24 Medicago species to unravel alfalfa's climatic adaptation and genetic susceptibility to future climate change. We found that interspecific genetic exchange has contributed to the gene pool of alfalfa, particularly enriching defense and stress-response genes. Intersubspecific introgression between M. sativa subsp. falcata (subsp. falcata) and alfalfa not only aids alfalfa's climatic adaptation but also introduces genetic burden. A total of 1671 genes were associated with climatic adaptation, and 5.7% of them were introgressions from subsp. falcata. By integrating climate-associated variants and climate data, we identified populations that are vulnerable to future climate change, particularly in higher latitudes of the Northern Hemisphere. These findings serve as a clarion call for targeted conservation initiatives and breeding efforts. We also identified pre-adaptive populations that demonstrate heightened resilience to climate fluctuations, illuminating a pathway for future breeding strategies. Collectively, this study enhances our understanding about the local adaptation mechanisms of alfalfa and facilitates the breeding of climate-resilient alfalfa cultivars, contributing to effective agricultural strategies for facing future climate change.
Collapse
Affiliation(s)
- Fan Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Ruicai Long
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Zhiyao Ma
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Hua Xiao
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Xiaodong Xu
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Zhongjie Liu
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Chunxue Wei
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Yiwen Wang
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Yanling Peng
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Xuanwen Yang
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Xiaoya Shi
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Shuo Cao
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Mingna Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Ming Xu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Fei He
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xueqian Jiang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Tiejun Zhang
- School of Grassland Science, Beijing Forestry University, Beijing 100083, China
| | - Zhen Wang
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Xianran Li
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99163, USA
| | - Long-Xi Yu
- U.S. Department of Agriculture-Agricultural Research Service, Plant Germplasm Introduction and Testing Research, Prosser, WA 99350, USA
| | - Junmei Kang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Zhiwu Zhang
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99163, USA
| | - Yongfeng Zhou
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China; National Key Laboratory of Tropical Crop Breeding, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
| | - Qingchuan Yang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| |
Collapse
|
2
|
Khan AW, Garg V, Sun S, Gupta S, Dudchenko O, Roorkiwal M, Chitikineni A, Bayer PE, Shi C, Upadhyaya HD, Bohra A, Bharadwaj C, Mir RR, Baruch K, Yang B, Coyne CJ, Bansal KC, Nguyen HT, Ronen G, Aiden EL, Veneklaas E, Siddique KHM, Liu X, Edwards D, Varshney RK. Cicer super-pangenome provides insights into species evolution and agronomic trait loci for crop improvement in chickpea. Nat Genet 2024; 56:1225-1234. [PMID: 38783120 DOI: 10.1038/s41588-024-01760-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 04/18/2024] [Indexed: 05/25/2024]
Abstract
Chickpea (Cicer arietinum L.)-an important legume crop cultivated in arid and semiarid regions-has limited genetic diversity. Efforts are being undertaken to broaden its diversity by utilizing its wild relatives, which remain largely unexplored. Here, we present the Cicer super-pangenome based on the de novo genome assemblies of eight annual Cicer wild species. We identified 24,827 gene families, including 14,748 core, 2,958 softcore, 6,212 dispensable and 909 species-specific gene families. The dispensable genome was enriched for genes related to key agronomic traits. Structural variations between cultivated and wild genomes were used to construct a graph-based genome, revealing variations in genes affecting traits such as flowering time, vernalization and disease resistance. These variations will facilitate the transfer of valuable traits from wild Cicer species into elite chickpea varieties through marker-assisted selection or gene-editing. This study offers valuable insights into the genetic diversity and potential avenues for crop improvement in chickpea.
Collapse
Affiliation(s)
- Aamir W Khan
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
- School of Biological Sciences, University of Western Australia, Perth, Western Australia, Australia
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, USA
| | - Vanika Garg
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
- Centre for Crop and Food Innovation, WA State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
| | | | - Saurabh Gupta
- Curtin Health Innovation Research Institute (CHIRI), Curtin Medical School, Curtin University, Perth, Western Australia, Australia
| | - Olga Dudchenko
- Department of Molecular and Human Genetics, Center for Genome Architecture, Baylor College of Medicine, Houston, TX, USA
| | - Manish Roorkiwal
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Annapurna Chitikineni
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
- Centre for Crop and Food Innovation, WA State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
| | - Philipp E Bayer
- School of Biological Sciences, University of Western Australia, Perth, Western Australia, Australia
| | | | - Hari D Upadhyaya
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
- Plant Genome Mapping Laboratory, The University of Georgia, Athens, GA, USA
| | - Abhishek Bohra
- Centre for Crop and Food Innovation, WA State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
| | | | - Reyazul Rouf Mir
- Division of Genetics and Plant Breeding, Faculty of Agriculture (FoA), SKUAST-Kashmir,Wadura Campus, Kashmir, India
| | | | | | - Clarice J Coyne
- USDA-ARS Plant Germplasm Introduction and Testing, Washington State University, Pullman, WA, USA
| | - Kailash C Bansal
- National Academy of Agricultural Sciences (NAAS), NASC Complex, New Delhi, India
| | - Henry T Nguyen
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, USA
| | - Gil Ronen
- NRGene Ltd, Park HaMada, Ness Ziona, Israel
| | - Erez Lieberman Aiden
- Department of Molecular and Human Genetics, Center for Genome Architecture, Baylor College of Medicine, Houston, TX, USA
| | - Erik Veneklaas
- School of Biological Sciences, University of Western Australia, Perth, Western Australia, Australia
| | - Kadambot H M Siddique
- UWA Institute of Agriculture, and School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia
| | - Xin Liu
- BGI Research, Qingdao, China.
- BGI Research, Shenzhen, China.
| | - David Edwards
- School of Biological Sciences, University of Western Australia, Perth, Western Australia, Australia.
| | - Rajeev K Varshney
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India.
- Centre for Crop and Food Innovation, WA State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia.
| |
Collapse
|
3
|
De Meester L, Vázquez-Domínguez E, Kassen R, Forest F, Bellon MR, Koskella B, Scherson RA, Colli L, Hendry AP, Crandall KA, Faith DP, Starger CJ, Geeta R, Araki H, Dulloo EM, Souffreau C, Schroer S, Johnson MTJ. A link between evolution and society fostering the UN sustainable development goals. Evol Appl 2024; 17:e13728. [PMID: 38884021 PMCID: PMC11178947 DOI: 10.1111/eva.13728] [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: 03/28/2023] [Revised: 05/16/2024] [Accepted: 05/17/2024] [Indexed: 06/18/2024] Open
Abstract
Given the multitude of challenges Earth is facing, sustainability science is of key importance to our continued existence. Evolution is the fundamental biological process underlying the origin of all biodiversity. This phylogenetic diversity fosters the resilience of ecosystems to environmental change, and provides numerous resources to society, and options for the future. Genetic diversity within species is also key to the ability of populations to evolve and adapt to environmental change. Yet, the value of evolutionary processes and the consequences of their impairment have not generally been considered in sustainability research. We argue that biological evolution is important for sustainability and that the concepts, theory, data, and methodological approaches used in evolutionary biology can, in crucial ways, contribute to achieving the UN Sustainable Development Goals (SDGs). We discuss how evolutionary principles are relevant to understanding, maintaining, and improving Nature Contributions to People (NCP) and how they contribute to the SDGs. We highlight specific applications of evolution, evolutionary theory, and evolutionary biology's diverse toolbox, grouped into four major routes through which evolution and evolutionary insights can impact sustainability. We argue that information on both within-species evolutionary potential and among-species phylogenetic diversity is necessary to predict population, community, and ecosystem responses to global change and to make informed decisions on sustainable production, health, and well-being. We provide examples of how evolutionary insights and the tools developed by evolutionary biology can not only inspire and enhance progress on the trajectory to sustainability, but also highlight some obstacles that hitherto seem to have impeded an efficient uptake of evolutionary insights in sustainability research and actions to sustain SDGs. We call for enhanced collaboration between sustainability science and evolutionary biology to understand how integrating these disciplines can help achieve the sustainable future envisioned by the UN SDGs.
Collapse
Affiliation(s)
- Luc De Meester
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB) Berlin Germany
- Laboratory of Aquatic Ecology, Evolution and Conservation KU Leuven Leuven Belgium
- Institute of Biology Freie University Berlin Berlin Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
| | - Ella Vázquez-Domínguez
- Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México Ciudad Universitaria Ciudad de México Mexico
- Conservation and Evolutionary Genetics Group Estación Biológica de Doñana (EBD-CSIC) Sevilla Spain
| | - Rees Kassen
- Department of Biology McGill University Montreal Quebec Canada
| | | | - Mauricio R Bellon
- Comisión Nacional Para el Conocimiento y Uso de la Biodiversidad (CONABIO) México City Mexico
- Swette Center for Sustainable Food Systems Arizona State University Tempe Arizona USA
| | - Britt Koskella
- Department of Integrative Biology University of California Berkeley California USA
| | - Rosa A Scherson
- Laboratorio Evolución y Sistemática, Departamento de Silvicultura y Conservación de la Naturaleza Universidad de Chile Santiago Chile
| | - Licia Colli
- Dipartimento di Scienze Animali, Della Nutrizione e Degli Alimenti, BioDNA Centro di Ricerca Sulla Biodiversità e Sul DNA Antico, Facoltà di Scienze Agrarie, Alimentari e Ambientali Università Cattolica del Sacro Cuore Piacenza Italy
| | - Andrew P Hendry
- Redpath Museum & Department of Biology McGill University Montreal Quebec Canada
| | - Keith A Crandall
- Department of Biostatistics and Bioinformatics George Washington University Washington DC USA
- Department of Invertebrate Zoology, US National Museum of Natural History Smithsonian Institution Washington DC USA
| | | | - Craig J Starger
- School of Global Environmental Sustainability Colorado State University Fort Collins Colorado USA
| | - R Geeta
- Department of Botany University of Delhi New Delhi India
| | - Hitoshi Araki
- Research Faculty of Agriculture Hokkaido University Sapporo Japan
| | - Ehsan M Dulloo
- Effective Genetic Resources Conservation and Use Alliance of Bioversity International and CIAT Rome Italy
| | - Caroline Souffreau
- Laboratory of Aquatic Ecology, Evolution and Conservation KU Leuven Leuven Belgium
| | - Sibylle Schroer
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB) Berlin Germany
| | - Marc T J Johnson
- Department of Biology & Centre for Urban Environments University of Toronto Mississauga Mississauga Ontario Canada
| |
Collapse
|
4
|
Khan Q, Wang Y, Xia G, Yang H, Luo Z, Zhang Y. Deleterious Effects of Heat Stress on the Tomato, Its Innate Responses, and Potential Preventive Strategies in the Realm of Emerging Technologies. Metabolites 2024; 14:283. [PMID: 38786760 PMCID: PMC11122942 DOI: 10.3390/metabo14050283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 04/28/2024] [Accepted: 05/08/2024] [Indexed: 05/25/2024] Open
Abstract
The tomato is a fruit vegetable rich in nutritional and medicinal value grown in greenhouses and fields worldwide. It is severely sensitive to heat stress, which frequently occurs with rising global warming. Predictions indicate a 0.2 °C increase in average surface temperatures per decade for the next three decades, which underlines the threat of austere heat stress in the future. Previous studies have reported that heat stress adversely affects tomato growth, limits nutrient availability, hammers photosynthesis, disrupts reproduction, denatures proteins, upsets signaling pathways, and damages cell membranes. The overproduction of reactive oxygen species in response to heat stress is toxic to tomato plants. The negative consequences of heat stress on the tomato have been the focus of much investigation, resulting in the emergence of several therapeutic interventions. However, a considerable distance remains to be covered to develop tomato varieties that are tolerant to current heat stress and durable in the perspective of increasing global warming. This current review provides a critical analysis of the heat stress consequences on the tomato in the context of global warming, its innate response to heat stress, and the elucidation of domains characterized by a scarcity of knowledge, along with potential avenues for enhancing sustainable tolerance against heat stress through the involvement of diverse advanced technologies. The particular mechanism underlying thermotolerance remains indeterminate and requires further elucidatory investigation. The precise roles and interplay of signaling pathways in response to heat stress remain unresolved. The etiology of tomato plants' physiological and molecular responses against heat stress remains unexplained. Utilizing modern functional genomics techniques, including transcriptomics, proteomics, and metabolomics, can assist in identifying potential candidate proteins, metabolites, genes, gene networks, and signaling pathways contributing to tomato stress tolerance. Improving tomato tolerance against heat stress urges a comprehensive and combined strategy including modern techniques, the latest apparatuses, speedy breeding, physiology, and molecular markers to regulate their physiological, molecular, and biochemical reactions.
Collapse
Affiliation(s)
| | | | | | | | | | - Yan Zhang
- Department of Landscape and Horticulture‚ Ecology College‚ Lishui University‚ Lishui 323000‚ China; (Q.K.); (Y.W.); (G.X.); (H.Y.); (Z.L.)
| |
Collapse
|
5
|
Kapoor C, Anamika, Mukesh Sankar S, Singh SP, Singh N, Kumar S. Omics-driven utilization of wild relatives for empowering pre-breeding in pearl millet. PLANTA 2024; 259:155. [PMID: 38750378 DOI: 10.1007/s00425-024-04423-0] [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: 12/17/2023] [Accepted: 04/25/2024] [Indexed: 05/23/2024]
Abstract
MAIN CONCLUSION Pearl millet wild relatives harbour novel alleles which could be utilized to broaden genetic base of cultivated species. Genomics-informed pre-breeding is needed to speed up introgression from wild to cultivated gene pool in pearl millet. Rising episodes of intense biotic and abiotic stresses challenge pearl millet production globally. Wild relatives provide a wide spectrum of novel alleles which could address challenges posed by climate change. Pre-breeding holds potential to introgress novel diversity in genetically narrow cultivated Pennisetum glaucum from diverse gene pool. Practical utilization of gene pool diversity remained elusive due to genetic intricacies. Harnessing promising traits from wild pennisetum is limited by lack of information on underlying candidate genes/QTLs. Next-Generation Omics provide vast scope to speed up pre-breeding in pearl millet. Genomic resources generated out of draft genome sequence and improved genome assemblies can be employed to utilize gene bank accessions effectively. The article highlights genetic richness in pearl millet and its utilization with a focus on harnessing next-generation Omics to empower pre-breeding.
Collapse
Affiliation(s)
- Chandan Kapoor
- ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
| | - Anamika
- ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - S Mukesh Sankar
- ICAR-Indian Institute of Spices Research, Kozhikode, Kerala, 673012, India
| | - S P Singh
- ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Nirupma Singh
- ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Sudhir Kumar
- ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| |
Collapse
|
6
|
Verleysen L, Depecker J, Bollen R, Asimonyio J, Hatangi Y, Kambale JL, Mwanga Mwanga I, Ebele T, Dhed'a B, Stoffelen P, Ruttink T, Vandelook F, Honnay O. Crop-to-wild gene flow in wild coffee species: the case of Coffea canephora in the Democratic Republic of the Congo. ANNALS OF BOTANY 2024; 133:917-930. [PMID: 38441303 PMCID: PMC11089259 DOI: 10.1093/aob/mcae034] [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: 01/22/2024] [Accepted: 03/01/2024] [Indexed: 05/14/2024]
Abstract
BACKGROUND AND AIMS Plant breeders are increasingly turning to crop wild relatives (CWRs) to ensure food security in a rapidly changing environment. However, CWR populations are confronted with various human-induced threats, including hybridization with their nearby cultivated crops. This might be a particular problem for wild coffee species, which often occur near coffee cultivation areas. Here, we briefly review the evidence for wild Coffea arabica (cultivated as Arabica coffee) and Coffea canephora (cultivated as Robusta coffee) and then focused on C. canephora in the Yangambi region in the Democratic Republic of the Congo. There, we examined the geographical distribution of cultivated C. canephora and the incidence of hybridization between cultivated and wild individuals within the rainforest. METHODS We collected 71 C. canephora individuals from home gardens and 12 C. canephora individuals from the tropical rainforest in the Yangambi region and genotyped them using genotyping-by-sequencing (GBS). We compared the fingerprints with existing GBS data from 388 C. canephora individuals from natural tropical rainforests and the INERA Coffee Collection, a Robusta coffee field gene bank and the most probable source of cultivated genotypes in the area. We then established robust diagnostic fingerprints that genetically differentiate cultivated from wild coffee, identified cultivated-wild hybrids and mapped their geographical position in the rainforest. KEY RESULTS We identified cultivated genotypes and cultivated-wild hybrids in zones with clear anthropogenic activity, and where cultivated C. canephora in home gardens may serve as a source for crop-to-wild gene flow. We found relatively few hybrids and backcrosses in the rainforests. CONCLUSIONS The cultivation of C. canephora in close proximity to its wild gene pool has led to cultivated genotypes and cultivated-wild hybrids appearing within the natural habitats of C. canephora. Yet, given the high genetic similarity between the cultivated and wild gene pool, together with the relatively low incidence of hybridization, our results indicate that the overall impact in terms of risk of introgression remains limited so far.
Collapse
Affiliation(s)
- Lauren Verleysen
- Division of Ecology, Evolution and Biodiversity Conservation, KU Leuven, Leuven, Belgium
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
| | - Jonas Depecker
- Division of Ecology, Evolution and Biodiversity Conservation, KU Leuven, Leuven, Belgium
- Meise Botanic Garden, Meise, Belgium
- KU Leuven Plant Institute, Leuven, Belgium
| | - Robrecht Bollen
- Division of Ecology, Evolution and Biodiversity Conservation, KU Leuven, Leuven, Belgium
- Meise Botanic Garden, Meise, Belgium
| | - Justin Asimonyio
- Centre de Surveillance de la Biodiversité et Université de Kisangani, Kisangani, DR Congo
| | - Yves Hatangi
- Meise Botanic Garden, Meise, Belgium
- Université de Kisangani, Kisangani, DR Congo
- Liège University, Gembloux Agro-Bio Tech, Gembloux, Belgium
| | - Jean-Léon Kambale
- Centre de Surveillance de la Biodiversité et Université de Kisangani, Kisangani, DR Congo
| | | | - Thsimi Ebele
- Institut National des Etudes et Recherches Agronomique, Yangambi, DR Congo
| | | | | | - Tom Ruttink
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Filip Vandelook
- Division of Ecology, Evolution and Biodiversity Conservation, KU Leuven, Leuven, Belgium
- Meise Botanic Garden, Meise, Belgium
| | - Olivier Honnay
- Division of Ecology, Evolution and Biodiversity Conservation, KU Leuven, Leuven, Belgium
- KU Leuven Plant Institute, Leuven, Belgium
| |
Collapse
|
7
|
Ferrero-Serrano Á, Chakravorty D, Kirven KJ, Assmann SM. Oryza CLIMtools: A genome-environment association resource reveals adaptive roles for heterotrimeric G proteins in the regulation of rice agronomic traits. PLANT COMMUNICATIONS 2024; 5:100813. [PMID: 38213027 PMCID: PMC11009157 DOI: 10.1016/j.xplc.2024.100813] [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: 07/15/2023] [Revised: 10/12/2023] [Accepted: 01/05/2024] [Indexed: 01/13/2024]
Abstract
Modern crop varieties display a degree of mismatch between their current distributions and the suitability of the local climate for their productivity. To address this issue, we present Oryza CLIMtools (https://gramene.org/CLIMtools/oryza_v1.0/), the first resource for pan-genome prediction of climate-associated genetic variants in a crop species. Oryza CLIMtools consists of interactive web-based databases that enable the user to (1) explore the local environments of traditional rice varieties (landraces) in South-East Asia and (2) investigate the environment by genome associations for 658 Indica and 283 Japonica rice landrace accessions collected from georeferenced local environments and included in the 3K Rice Genomes Project. We demonstrate the value of these resources by identifying an interplay between flowering time and temperature in the local environment that is facilitated by adaptive natural variation in OsHD2 and disrupted by a natural variant in OsSOC1. Prior quantitative trait locus analysis has suggested the importance of heterotrimeric G proteins in the control of agronomic traits. Accordingly, we analyzed the climate associations of natural variants in the different heterotrimeric G protein subunits. We identified a coordinated role of G proteins in adaptation to the prevailing potential evapotranspiration gradient and revealed their regulation of key agronomic traits, including plant height and seed and panicle length. We conclude by highlighting the prospect of targeting heterotrimeric G proteins to produce climate-resilient crops.
Collapse
Affiliation(s)
- Ángel Ferrero-Serrano
- Biology Department, Pennsylvania State University, 208 Mueller Laboratory, University Park, PA 16802, USA.
| | - David Chakravorty
- Biology Department, Pennsylvania State University, 208 Mueller Laboratory, University Park, PA 16802, USA
| | - Kobie J Kirven
- Intercollege Graduate Degree Program in Bioinformatics and Genomics, Pennsylvania State University, 208 Mueller Laboratory, University Park, PA 16802, USA
| | - Sarah M Assmann
- Biology Department, Pennsylvania State University, 208 Mueller Laboratory, University Park, PA 16802, USA.
| |
Collapse
|
8
|
Lin S, Zhang W, Wang G, Hu Y, Zhong X, Tang G. Physiological Regulation of Photosynthetic-Related Indices, Antioxidant Defense, and Proline Anabolism on Drought Tolerance of Wild Soybean ( Glycine soja L.). PLANTS (BASEL, SWITZERLAND) 2024; 13:880. [PMID: 38592877 PMCID: PMC10975085 DOI: 10.3390/plants13060880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 03/13/2024] [Accepted: 03/13/2024] [Indexed: 04/11/2024]
Abstract
Wild soybean (Glycine soja L.), drought-tolerant cultivar Tiefeng 31 (Glycine max L.), and drought-sensitive cultivar Fendou 93 (Glycine max L.) were used as materials to investigate the drought tolerance mechanism after 72 h 2.5 M PEG 8000 (osmotic potential -0.54 MPa)-simulated drought stress at the seedling stage. The results indicated that the leaves of the G. soja did not wilt under drought stress. However, both the drought-tolerant and drought-sensitive cultivated soybean cultivars experienced varying degrees of leaf wilt. Notably, the drought-sensitive cultivated soybean cultivars exhibited severe leaf wilt after the drought stress. Drought stress was determined to have a significant impact on the dry matter of the above-ground part of the drought-sensitive cultivar Fendou 93, followed by the drought-tolerant cultivar Tiefeng 31, with the lowest reduction observed in G. soja. Furthermore, the presence of drought stress resulted in the closure of leaf stomata. G. soja exhibited the highest proportion of stomatal opening per unit area, followed by the drought-tolerant cultivar Tiefeng 31, while the drought-sensitive cultivar Fendou 93 displayed the lowest percentage. Photosynthesis-related indexes, including photosynthetic rate, intercellular CO2, transpiration rate, and stomatal conductance, decreased in Fendou 93 and Tiefeng 31 after drought stress, but increased in G. soja. In terms of the antioxidant scavenging system, lower accumulation of malondialdehyde (MDA) was observed in G. soja and Tiefeng 31, along with higher activities of superoxide dismutase (SOD, EC 1.15.1.1) and catalase (CAT, EC 1.11.1.6) to counteract excess reactive oxygen species and maintain cell membrane integrity. In contrast, the drought-sensitive cultivar Fendou 93 had higher MDA content and higher activities of ascorbate peroxidase (APX, EC 1.11.1.11) and peroxidase (POD, 1.11.1.7). G. soja and Tiefeng 31 also exhibited less accumulation of osmolytes, including soluble sugar, soluble protein, and free proline content. The activities of δ-OAT, ProDH, and P5CS, key enzymes in proline anabolism, showed an initial increase under drought stress, followed by a decrease, and then an increase again at the end of drought stress in G. soja. Before drought stress, Tiefeng 31 had higher activities of ProDH and P5CS, which decreased with prolonged drought stress. Fendou 93 experienced an increase in the activities of δ-OAT, ProDH, and P5CS under drought stress. The δ-OAT gene expression levels were up-regulated in all three germplasms. The expression levels of the P5CS gene in Fendou 93 and Tiefeng 31 were down-regulated, while G. soja showed no significant change. The expression of the P5CR gene and ProDH gene was down-regulated in Fendou 93 and Tiefeng 31, but up-regulated in G. soja. This indicates that proline content is regulated at both the transcription and translation levels.
Collapse
Affiliation(s)
- Song Lin
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Zhejiang University, Hangzhou 310058, China; (S.L.); (Y.H.); (X.Z.)
| | - Weimei Zhang
- Lishui Institute of Agriculture and Forest Science, Lishui 323000, China;
| | - Guifeng Wang
- Bureau of Agriculture and Rural Affairs of Lianyungang City, Lianyungang 222001, China;
| | - Yunxiang Hu
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Zhejiang University, Hangzhou 310058, China; (S.L.); (Y.H.); (X.Z.)
| | - Xuanbo Zhong
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Zhejiang University, Hangzhou 310058, China; (S.L.); (Y.H.); (X.Z.)
| | - Guixiang Tang
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Zhejiang University, Hangzhou 310058, China; (S.L.); (Y.H.); (X.Z.)
| |
Collapse
|
9
|
Wang L, Niu F, Wang J, Zhang H, Zhang D, Hu Z. Genome-Wide Association Studies Prioritize Genes Controlling Seed Size and Reproductive Period Length in Soybean. PLANTS (BASEL, SWITZERLAND) 2024; 13:615. [PMID: 38475461 DOI: 10.3390/plants13050615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 02/12/2024] [Accepted: 02/14/2024] [Indexed: 03/14/2024]
Abstract
Hundred-seed weight (HSW) and reproductive period length (RPL) are two major agronomic traits critical for soybean production and adaptation. However, both traits are quantitatively controlled by multiple genes that have yet to be comprehensively elucidated due to the lack of major genes; thereby, the genetic basis is largely unknown. In the present study, we conducted comprehensive genome-wide association analyses (GWAS) of HSW and RPL with multiple sets of accessions that were phenotyped across different environments. The large-scale analysis led to the identification of sixty-one and seventy-four significant QTLs for HSW and RPL, respectively. An ortholog-based search analysis prioritized the most promising candidate genes for the QTLs, including nine genes (TTG2, BZR1, BRI1, ANT, KLU, EOD1/BB, GPA1, ABA2, and ABI5) for HSW QTLs and nine genes (such as AGL8, AGL9, TOC1, and COL4) and six known soybean flowering time genes (E2, E3, E4, Tof11, Tof12, and FT2b) for RPL QTLs. We also demonstrated that some QTLs were targeted during domestication to drive the artificial selection of both traits towards human-favored traits. Local adaptation likely contributes to the increased genomic diversity of the QTLs underlying RPL. The results provide additional insight into the genetic basis of HSW and RPL and prioritize a valuable resource of candidate genes that merits further investigation to reveal the complex molecular mechanism and facilitate soybean improvement.
Collapse
Affiliation(s)
- Le Wang
- State Key Laboratory of Black Soils Conservation and Utilization, Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Fu'an Niu
- Institute of Crop Breeding and Cultivation, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Jinshe Wang
- National Innovation Centre for Bio-Breeding Industry, Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Hengyou Zhang
- State Key Laboratory of Black Soils Conservation and Utilization, Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Dan Zhang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Zhenbin Hu
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD 20705, USA
| |
Collapse
|
10
|
Anwar K, Joshi R, Bahuguna RN, Govindjee G, Sasidharan R, Singla-Pareek SL, Pareek A. Impact of individual, combined and sequential stress on photosynthesis machinery in rice (Oryza sativa L). PHYSIOLOGIA PLANTARUM 2024; 176:e14209. [PMID: 38348703 DOI: 10.1111/ppl.14209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 01/15/2024] [Accepted: 01/30/2024] [Indexed: 02/15/2024]
Abstract
Abiotic stresses such as heat, drought and submergence are major threats to global food security. Despite simultaneous or sequential occurrence of these stresses being recurrent under field conditions, crop response to such stress combinations is poorly understood. Rice is a staple food crop for the majority of human beings. Exploitation of existing genetic diversity in rice for combined and/or sequential stress is a useful approach for developing climate-resilient cultivars. We phenotyped ~400 rice accessions under high temperature, drought, or submergence and their combinations. A cumulative performance index revealed Lomello as the best performer across stress and stress combinations at the seedling stage. Lomello showed a remarkable ability to maintain a higher quantum yield of photosystem (PS) II photochemistry. Moreover, the structural integrity of the photosystems, electron flow through both PSI and PSII and the ability to protect photosystems against photoinhibition were identified as the key traits of Lomello across the stress environments. A higher membrane stability and an increased amount of leaf chlorophyll under stress may be due to an efficient management of reactive oxygen species (ROS) at the cellular level. Further, an efficient electron flow through the photosystems and, thus, a higher photosynthetic rate in Lomello is expected to act as a sink for ROS by reducing the rate of electron transport to the high amount of molecular oxygen present in the chloroplast. However, further studies are needed to identify the molecular mechanism(s) involved in the stability of photosynthetic machinery and stress management in Lomello during stress conditions.
Collapse
Affiliation(s)
- Khalid Anwar
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Rohit Joshi
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Rajeev N Bahuguna
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
- National Agri-Food Biotechnology Institute, Mohali, Punjab, India
| | - Govindjee Govindjee
- Department of Biochemistry, Center of Biophysics & Quantitative Biology, and Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Rashmi Sasidharan
- Plant Stress Resilience, Institute of Environmental Biology, Utrecht University, The Netherlands
| | - Sneh L Singla-Pareek
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Road, New Delhi, India
| | - Ashwani Pareek
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
- National Agri-Food Biotechnology Institute, Mohali, Punjab, India
| |
Collapse
|
11
|
Ferrero-Serrano Á, Chakravorty D, Kirven KJ, Assmann SM. Oryza CLIMtools: A Genome-Environment Association Resource Reveals Adaptive Roles for Heterotrimeric G Proteins in the Regulation of Rice Agronomic Traits. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.10.540241. [PMID: 37214799 PMCID: PMC10197702 DOI: 10.1101/2023.05.10.540241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Modern crop varieties display a degree of mismatch between their current distributions and the suitability of the local climate for their productivity. To this end, we present Oryza CLIMtools (https://gramene.org/CLIMtools/oryza_v1.0/), the first resource for pan-genome prediction of climate-associated genetic variants in a crop species. Oryza CLIMtools consists of interactive web-based databases that allow the user to: i) explore the local environments of traditional rice varieties (landraces) in South-Eastern Asia, and; ii) investigate the environment by genome associations for 658 Indica and 283 Japonica rice landrace accessions collected from georeferenced local environments and included in the 3K Rice Genomes Project. We exemplify the value of these resources, identifying an interplay between flowering time and temperature in the local environment that is facilitated by adaptive natural variation in OsHD2 and disrupted by a natural variant in OsSOC1. Prior QTL analysis has suggested the importance of heterotrimeric G proteins in the control of agronomic traits. Accordingly, we analyzed the climate associations of natural variants in the different heterotrimeric G protein subunits. We identified a coordinated role of G proteins in adaptation to the prevailing Potential Evapotranspiration gradient and their regulation of key agronomic traits including plant height and seed and panicle length. We conclude by highlighting the prospect of targeting heterotrimeric G proteins to produce crops that are climate resilient.
Collapse
Affiliation(s)
- Ángel Ferrero-Serrano
- Biology Department, Pennsylvania State University, 208 Mueller Laboratory, University Park, PA, 16802, USA
| | - David Chakravorty
- Biology Department, Pennsylvania State University, 208 Mueller Laboratory, University Park, PA, 16802, USA
| | - Kobie J. Kirven
- Intercollege Graduate Degree Program in Bioinformatics and Genomics, Pennsylvania State University
| | - Sarah M. Assmann
- Biology Department, Pennsylvania State University, 208 Mueller Laboratory, University Park, PA, 16802, USA
| |
Collapse
|
12
|
Moreels P, Bigot S, Defalque C, Correa F, Martinez JP, Lutts S, Quinet M. Intra- and inter-specific reproductive barriers in the tomato clade. FRONTIERS IN PLANT SCIENCE 2023; 14:1326689. [PMID: 38143584 PMCID: PMC10739309 DOI: 10.3389/fpls.2023.1326689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 11/27/2023] [Indexed: 12/26/2023]
Abstract
Tomato (Solanum lycopersicum L.) domestication and later introduction into Europe resulted in a genetic bottleneck that reduced genetic variation. Crosses with other wild tomato species from the Lycopersicon clade can be used to increase genetic diversity and improve important agronomic traits such as stress tolerance. However, many species in the Lycopersicon clade have intraspecific and interspecific incompatibility, such as gametophytic self-incompatibility and unilateral incompatibility. In this review, we provide an overview of the known incompatibility barriers in Lycopersicon. We begin by addressing the general mechanisms self-incompatibility, as well as more specific mechanisms in the Rosaceae, Papaveraceae, and Solanaceae. Incompatibility in the Lycopersicon clade is discussed, including loss of self-incompatibility, species exhibiting only self-incompatibility and species presenting both self-compatibility and self-incompatibility. We summarize unilateral incompatibility in general and specifically in Lycopersicon, with details on the 'self-compatible x self-incompatible' rule, implications of self-incompatibility in unilateral incompatibility and self-incompatibility-independent pathways of unilateral incompatibility. Finally, we discuss advances in the understanding of compatibility barriers and their implications for tomato breeding.
Collapse
Affiliation(s)
- Pauline Moreels
- Groupe de Recherche en Physiologie végétale, Earth and Life Institute-Agronomy, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Servane Bigot
- Groupe de Recherche en Physiologie végétale, Earth and Life Institute-Agronomy, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Corentin Defalque
- Groupe de Recherche en Physiologie végétale, Earth and Life Institute-Agronomy, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Francisco Correa
- Instituto de Investigaciones Agropecuarias (INIA-Rayentué), Rengo, Chile
| | | | - Stanley Lutts
- Groupe de Recherche en Physiologie végétale, Earth and Life Institute-Agronomy, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Muriel Quinet
- Groupe de Recherche en Physiologie végétale, Earth and Life Institute-Agronomy, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| |
Collapse
|
13
|
Wolff K, Friedhoff R, Schwarzer F, Pucker B. Data literacy in genome research. J Integr Bioinform 2023; 20:jib-2023-0033. [PMID: 38047760 PMCID: PMC10777367 DOI: 10.1515/jib-2023-0033] [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: 09/02/2023] [Accepted: 11/15/2023] [Indexed: 12/05/2023] Open
Abstract
With an ever increasing amount of research data available, it becomes constantly more important to possess data literacy skills to benefit from this valuable resource. An integrative course was developed to teach students the fundamentals of data literacy through an engaging genome sequencing project. Each cohort of students performed planning of the experiment, DNA extraction, nanopore sequencing, genome sequence assembly, prediction of genes in the assembled sequence, and assignment of functional annotation terms to predicted genes. Students learned how to communicate science through writing a protocol in the form of a scientific paper, providing comments during a peer-review process, and presenting their findings as part of an international symposium. Many students enjoyed the opportunity to own a project and to work towards a meaningful objective.
Collapse
Affiliation(s)
- Katharina Wolff
- Plant Biotechnology and Bioinformatics, Institute of Plant Biology & BRICS, TU Braunschweig, Braunschweig, Germany
| | - Ronja Friedhoff
- Plant Biotechnology and Bioinformatics, Institute of Plant Biology & BRICS, TU Braunschweig, Braunschweig, Germany
| | - Friderieke Schwarzer
- Plant Biotechnology and Bioinformatics, Institute of Plant Biology & BRICS, TU Braunschweig, Braunschweig, Germany
| | - Boas Pucker
- Plant Biotechnology and Bioinformatics, Institute of Plant Biology & BRICS, TU Braunschweig, Braunschweig, Germany
| |
Collapse
|
14
|
Jabbour Y, Hakim MS, Al-Yossef A, Saleh MM, Shaaban ASAD, Kabbaj H, Zaïm M, Kleinerman C, Bassi FM. Genomic regions involved in the control of 1,000-kernel weight in wild relative-derived populations of durum wheat. FRONTIERS IN PLANT SCIENCE 2023; 14:1297131. [PMID: 38098797 PMCID: PMC10720367 DOI: 10.3389/fpls.2023.1297131] [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: 09/19/2023] [Accepted: 11/13/2023] [Indexed: 12/17/2023]
Abstract
Terminal drought is one of the most common and devastating climatic stress factors affecting durum wheat (Triticum durum Desf.) production worldwide. The wild relatives of this crop are deemed a vast potential source of useful alleles to adapt to this stress. A nested association mapping (NAM) panel was generated using as a recurrent parent the Moroccan variety 'Nachit' derived from Triticum dicoccoides and known for its large grain size. This was recombined to three top-performing lines derived from T. dicoccoides, T. araraticum, and Aegilops speltoides, for a total of 426 inbred progenies. This NAM was evaluated across eight environments (Syria, Lebanon, and Morocco) experiencing different degrees of terminal moisture stress over two crop seasons. Our results showed that drought stress caused on average 41% loss in yield and that 1,000-kernel weight (TKW) was the most important trait for adaptation to it. Genotyping with the 25K TraitGenetics array resulted in a consensus map of 1,678 polymorphic SNPs, spanning 1,723 cM aligned to the reference 'Svevo' genome assembly. Kinship distinguished the progenies in three clades matching the parent of origin. A total of 18 stable quantitative trait loci (QTLs) were identified as controlling various traits but independent from flowering time. The most significant genomic regions were named Q.ICD.NAM-04, Q.ICD.NAM-14, and Q.ICD.NAM-16. Allelic investigation in a second germplasm panel confirmed that carrying the positive allele at all three loci produced an average TKW advantage of 25.6% when field-tested under drought conditions. The underlying SNPs were converted to Kompetitive Allele-Specific PCR (KASP) markers and successfully validated in a third germplasm set, where they explained up to 19% of phenotypic variation for TKW under moisture stress. These findings confirm the identification of critical loci for drought adaptation derived from wild relatives that can now be readily exploited via molecular breeding.
Collapse
Affiliation(s)
- Yaman Jabbour
- Field Crop Department, Faculty of Agriculture Engineering, Aleppo University, Aleppo, Syria
- General Commission for Scientific Agriculture Research (GCSAR), Field Crop Department, Aleppo, Syria
| | - Mohammad Shafik Hakim
- Field Crop Department, Faculty of Agriculture Engineering, Aleppo University, Aleppo, Syria
| | - Abdallah Al-Yossef
- General Commission for Scientific Agriculture Research (GCSAR), Field Crop Department, Aleppo, Syria
| | - Maysoun M. Saleh
- General Commission for Scientific Agriculture Research (GCSAR), Genetic Resources Department, Damascus, Syria
| | - Ahmad Shams Al-Dien Shaaban
- Biotechnology Engineering Department, Faculty of Technological Engineering, Aleppo University, Aleppo, Syria
| | - Hafssa Kabbaj
- International Center for Agricultural Research in the Dry Areas, Biodiversity and Crop Improvement, Rabat, Morocco
| | - Meryem Zaïm
- International Center for Agricultural Research in the Dry Areas, Biodiversity and Crop Improvement, Rabat, Morocco
| | - Charles Kleinerman
- International Center for Agricultural Research in the Dry Areas, Biodiversity and Crop Improvement, Rabat, Morocco
| | - Filippo M. Bassi
- International Center for Agricultural Research in the Dry Areas, Biodiversity and Crop Improvement, Rabat, Morocco
| |
Collapse
|
15
|
Sharma PK, Ahmed HI, Heuberger M, Koo DH, Quiroz-Chavez J, Adhikari L, Raupp J, Cauet S, Rodde N, Cravero C, Callot C, Yadav IS, Kathiresan N, Athiyannan N, Ramirez-Gonzalez RH, Uauy C, Wicker T, Abrouk M, Gu YQ, Poland J, Krattinger SG, Lazo GR, Tiwari VK. An online database for einkorn wheat to aid in gene discovery and functional genomics studies. Database (Oxford) 2023; 2023:baad079. [PMID: 37971714 PMCID: PMC10653128 DOI: 10.1093/database/baad079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 10/02/2023] [Accepted: 10/26/2023] [Indexed: 11/19/2023]
Abstract
Diploid A-genome wheat (einkorn wheat) presents a nutrition-rich option as an ancient grain crop and a resource for the improvement of bread wheat against abiotic and biotic stresses. Realizing the importance of this wheat species, reference-level assemblies of two einkorn wheat accessions were generated (wild and domesticated). This work reports an einkorn genome database that provides an interface to the cereals research community to perform comparative genomics, applied genetics and breeding research. It features queries for annotated genes, the use of a recent genome browser release, and the ability to search for sequence alignments using a modern BLAST interface. Other features include a comparison of reference einkorn assemblies with other wheat cultivars through genomic synteny visualization and an alignment visualization tool for BLAST results. Altogether, this resource will help wheat research and breeding. Database URL https://wheat.pw.usda.gov/GG3/pangenome.
Collapse
Affiliation(s)
- Parva Kumar Sharma
- Department of Plant Science and Landscape Architecture, University of Maryland, Fieldhouse Dr. College Park, MD 20742, USA
| | - Hanin Ibrahim Ahmed
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), 4700 KAUST, Thuwal 23955-6900, Saudi Arabia
- Center for Desert Agriculture, KAUST, 4700 KAUST, Thuwal, Kingdom of Saudi Arabia 23955-6900, Saudi Arabia
| | - Matthias Heuberger
- Department of Plant and Microbial Biology, University of Zurich, 107, Zurich, Zollikerstrasse CH-8008, Switzerland
| | - Dal-Hoe Koo
- Wheat Genetics Resource Center and Department of Plant Pathology, Kansas State University, 4024 Throckmorton, 1712 Claflin Road, Manhattan, KS 66506, USA
| | - Jesus Quiroz-Chavez
- John Innes Centre John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Laxman Adhikari
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), 4700 KAUST, Thuwal 23955-6900, Saudi Arabia
- Center for Desert Agriculture, KAUST, 4700 KAUST, Thuwal, Kingdom of Saudi Arabia 23955-6900, Saudi Arabia
| | - John Raupp
- Wheat Genetics Resource Center and Department of Plant Pathology, Kansas State University, 4024 Throckmorton, 1712 Claflin Road, Manhattan, KS 66506, USA
| | - Stéphane Cauet
- INRAE, CNRGV French Plant Genomic Resource Center, 24 Chemin de Borde Rouge, Castanet Tolosan F-31320, France
| | - Nathalie Rodde
- INRAE, CNRGV French Plant Genomic Resource Center, 24 Chemin de Borde Rouge, Castanet Tolosan F-31320, France
| | - Charlotte Cravero
- INRAE, CNRGV French Plant Genomic Resource Center, 24 Chemin de Borde Rouge, Castanet Tolosan F-31320, France
| | - Caroline Callot
- INRAE, CNRGV French Plant Genomic Resource Center, 24 Chemin de Borde Rouge, Castanet Tolosan F-31320, France
| | - Inderjit Singh Yadav
- Department of Plant Science and Landscape Architecture, University of Maryland, Fieldhouse Dr. College Park, MD 20742, USA
| | - Nagarajan Kathiresan
- Supercomputing Core Lab, King Abdullah University of Science and Technology (KAUST), 4700 KAUST, Thuwal 23955-6900, Saudi Arabia
| | - Naveenkumar Athiyannan
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), 4700 KAUST, Thuwal 23955-6900, Saudi Arabia
- Center for Desert Agriculture, KAUST, 4700 KAUST, Thuwal, Kingdom of Saudi Arabia 23955-6900, Saudi Arabia
| | | | - Cristobal Uauy
- John Innes Centre John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zurich, 107, Zurich, Zollikerstrasse CH-8008, Switzerland
| | - Michael Abrouk
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), 4700 KAUST, Thuwal 23955-6900, Saudi Arabia
- Center for Desert Agriculture, KAUST, 4700 KAUST, Thuwal, Kingdom of Saudi Arabia 23955-6900, Saudi Arabia
| | - Yong Q Gu
- United States Department of Agriculture—Agricultural Research Service, Western Regional Research Center, Crop Improvement and Genetics Research Unit, 800 Buchanan St., Albany, CA 94710, USA
| | - Jesse Poland
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), 4700 KAUST, Thuwal 23955-6900, Saudi Arabia
- Center for Desert Agriculture, KAUST, 4700 KAUST, Thuwal, Kingdom of Saudi Arabia 23955-6900, Saudi Arabia
| | - Simon G Krattinger
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), 4700 KAUST, Thuwal 23955-6900, Saudi Arabia
- Center for Desert Agriculture, KAUST, 4700 KAUST, Thuwal, Kingdom of Saudi Arabia 23955-6900, Saudi Arabia
| | - Gerard R Lazo
- United States Department of Agriculture—Agricultural Research Service, Western Regional Research Center, Crop Improvement and Genetics Research Unit, 800 Buchanan St., Albany, CA 94710, USA
| | - Vijay K Tiwari
- Department of Plant Science and Landscape Architecture, University of Maryland, Fieldhouse Dr. College Park, MD 20742, USA
| |
Collapse
|
16
|
Bedford JA, Carine M, Chapman MA. Detection of locally adapted genomic regions in wild rice (Oryza rufipogon) using environmental association analysis. G3 (BETHESDA, MD.) 2023; 13:jkad194. [PMID: 37619981 PMCID: PMC10542315 DOI: 10.1093/g3journal/jkad194] [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: 07/19/2023] [Revised: 08/14/2023] [Accepted: 08/17/2023] [Indexed: 08/26/2023]
Abstract
Oryza rufipogon is the wild progenitor of cultivated rice Oryza sativa and exhibits high levels of genetic diversity across its distribution, making it a useful resource for the identification of abiotic stress-tolerant varieties and genes that could limit future climate-changed-induced yield losses. To investigate local adaptation in O. rufipogon, we analyzed single nucleotide polymorphism (SNP) data from a panel of 286 samples located across a diverse range of climates. Environmental association analysis (EAA), a genome-wide association study (GWAS)-based method, was used and revealed 15 regions of the genome significantly associated with various climate factors. Genes within these environmentally associated regions have putative functions in abiotic stress response, phytohormone signaling, and the control of flowering time. This provides an insight into potential local adaptation in O. rufipogon and reveals possible locally adaptive genes that may provide opportunities for breeding novel rice varieties with climate change-resilient phenotypes.
Collapse
Affiliation(s)
- James A Bedford
- Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
- Life Sciences, The Natural History Museum, London SW7 5BD, UK
| | - Mark Carine
- Life Sciences, The Natural History Museum, London SW7 5BD, UK
| | - Mark A Chapman
- Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| |
Collapse
|
17
|
Rouichi S, Idrissi O, Sohail Q, Marrou H, Sinclair TR, Hejjaoui K, Amri M, Ghanem ME. Limited-transpiration trait in response to high vapor pressure deficit from wild to cultivated species: study of the Lens genus. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:4875-4887. [PMID: 37422910 DOI: 10.1093/jxb/erad264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 07/06/2023] [Indexed: 07/11/2023]
Abstract
Lentil (Lens culinaris Medik.) is commonly grown in drought-prone areas where terminal heat and drought are frequent. The limited-transpiration (TRlim) trait under high vapor pressure deficit (VPD) could be a way to conserve water and increase yield under water deficit conditions. The TRlim trait was examined in cultivated and wild lentil species together with its evolution throughout the breeding pipeline. Sixty-one accessions representing the six wild lentil species (L. orientalis, L. tomentosus, L. odemensis, L. lamottei, L. ervoides, and L. nigricans) and 13 interspecific advanced lines were evaluated in their transpiration response to high VPD. A large variation in transpiration rate (TR) response to increased VPD was recorded among wild lentil accessions, with 43 accessions exhibiting a breakpoint (BP) in their TR response to increasing VPD, with values ranging from 0.92 kPa to 3.38 kPa under greenhouse conditions. Ten genotypes for the interspecific advanced lines displayed a BP with an average of 1.95 kPa, much lower than previously reported for cultivated lentil. Results from field experiments suggest that the TRlim trait (BP=0.97 kPa) positively affected yield and yield-related parameters during the years with late-season water stress. The selection of TRlim genotypes for high VPD environments could improve lentil productivity in drought-prone areas.
Collapse
Affiliation(s)
- Salma Rouichi
- College of Sustainable Agriculture and Environmental Science, AgroBioSciences Program, Mohammed VI Polytechnic University (UM6P), Ben Guerir, Morocco
| | - Omar Idrissi
- Laboratory of Food Legumes Breeding, Regional Center of Agricultural Research of Settat, National Institute of Agricultural Research, Avenue Ennasr, BP 415 Rabat Principale, Rabat 10090, Morocco
| | - Quahir Sohail
- College of Sustainable Agriculture and Environmental Science, AgroBioSciences Program, Mohammed VI Polytechnic University (UM6P), Ben Guerir, Morocco
| | - Hélène Marrou
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
| | - Thomas R Sinclair
- Crop and Soil Sciences Department, North Carolina State University, Raleigh, NC, USA
| | - Kamal Hejjaoui
- College of Sustainable Agriculture and Environmental Science, AgroBioSciences Program, Mohammed VI Polytechnic University (UM6P), Ben Guerir, Morocco
| | - Moez Amri
- College of Sustainable Agriculture and Environmental Science, AgroBioSciences Program, Mohammed VI Polytechnic University (UM6P), Ben Guerir, Morocco
| | - Michel Edmond Ghanem
- College of Sustainable Agriculture and Environmental Science, AgroBioSciences Program, Mohammed VI Polytechnic University (UM6P), Ben Guerir, Morocco
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
- CIRAD, UMR AGAP Institut, F-34398 Montpellier, France
| |
Collapse
|
18
|
Chen X, Cornille A, An N, Xing L, Ma J, Zhao C, Wang Y, Han M, Zhang D. The East Asian wild apples, Malus baccata (L.) Borkh and Malus hupehensis (Pamp.) Rehder., are additional contributors to the genomes of cultivated European and Chinese varieties. Mol Ecol 2023; 32:5125-5139. [PMID: 35510734 DOI: 10.1111/mec.16485] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 04/09/2022] [Accepted: 04/17/2022] [Indexed: 11/29/2022]
Abstract
The domestication process in long-lived plant perennials differs dramatically from that of annuals, with a huge amount of genetic exchange between crop and wild populations. Though apple is a major fruit crop grown worldwide, the contribution of wild apple species to the genetic makeup of the cultivated apple genome remains a topic of intense study. We used population genomics approaches to investigate the contributions of several wild apple species to European and Chinese rootstock and dessert genomes, with a focus on the extent of wild-crop gene flow. Population genetic structure inferences revealed that the East Asian wild apples, Malus baccata (L.) Borkh and M. hupehensis (Pamp.), form a single panmictic group, and that the European dessert and rootstock apples form a specific gene pool whereas the Chinese dessert and rootstock apples were a mixture of three wild gene pools, suggesting different evolutionary histories of European and Chinese apple varieties. Coalescent-based inferences and gene flow estimates indicated that M. baccata - M. hupehensis contributed to the genome of both European and Chinese cultivated apples through wild-to-crop introgressions, and not as an initial contributor as previously supposed. We also confirmed the contribution through wild-to-crop introgressions of Malus sylvestris Mill. to the cultivated apple genome. Apple tree domestication is therefore one example in woody perennials that involved gene flow from several wild species from multiple geographical areas. This study provides an example of a complex protracted process of domestication in long-lived plant perennials, and is a starting point for apple breeding programmes.
Collapse
Affiliation(s)
- Xilong Chen
- College of Horticulture, Yangling Sub-Center of National Center for Apple Improvement, Northwest A&F University, Yangling, Shaanxi, China
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, Gif-sur-Yvette, France
| | - Amandine Cornille
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, Gif-sur-Yvette, France
| | - Na An
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Libo Xing
- College of Horticulture, Yangling Sub-Center of National Center for Apple Improvement, Northwest A&F University, Yangling, Shaanxi, China
| | - Juanjuan Ma
- College of Horticulture, Yangling Sub-Center of National Center for Apple Improvement, Northwest A&F University, Yangling, Shaanxi, China
| | - Caiping Zhao
- College of Horticulture, Yangling Sub-Center of National Center for Apple Improvement, Northwest A&F University, Yangling, Shaanxi, China
| | - Yibin Wang
- College of Horticulture, Yangling Sub-Center of National Center for Apple Improvement, Northwest A&F University, Yangling, Shaanxi, China
| | - Mingyu Han
- College of Horticulture, Yangling Sub-Center of National Center for Apple Improvement, Northwest A&F University, Yangling, Shaanxi, China
| | - Dong Zhang
- College of Horticulture, Yangling Sub-Center of National Center for Apple Improvement, Northwest A&F University, Yangling, Shaanxi, China
| |
Collapse
|
19
|
Lupitu A, Moisa C, Bortes F, Peteleu D, Dochia M, Chambre D, Ciutină V, Copolovici DM, Copolovici L. The Impact of Increased CO 2 and Drought Stress on the Secondary Metabolites of Cauliflower ( Brassica oleracea var. botrytis) and Cabbage ( Brassica oleracea var. capitata). PLANTS (BASEL, SWITZERLAND) 2023; 12:3098. [PMID: 37687345 PMCID: PMC10490549 DOI: 10.3390/plants12173098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 08/26/2023] [Accepted: 08/27/2023] [Indexed: 09/10/2023]
Abstract
Elevated carbon dioxide and drought are significant stressors in light of climate change. This study explores the interplay between elevated atmospheric CO2, drought stress, and plant physiological responses. Two Brassica oleracea varieties (cauliflowers and cabbage) were utilized as model plants. Our findings indicate that elevated CO2 accelerates assimilation rate decline during drought. The integrity of photosynthetic components influenced electron transport, potentially due to drought-induced nitrate reductase activation changes. While CO2 positively influenced photosynthesis and water-use efficiency during drought, recovery saw decreased stomatal conductance in high-CO2-grown plants. Drought-induced monoterpene emissions varied, influenced by CO2 concentration and species-specific responses. Drought generally increased polyphenols, with an opposing effect under elevated CO2. Flavonoid concentrations fluctuated with drought and CO2 levels, while chlorophyll responses were complex, with high CO2 amplifying drought's effects on chlorophyll content. These findings contribute to a nuanced understanding of CO2-drought interactions and their intricate effects on plant physiology.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Lucian Copolovici
- Institute for Research, Development and Innovation in Technical and Natural Sciences, Faculty of Food Engineering, Tourism and Environmental Protection, Aurel Vlaicu University of Arad, Elena Drăgoi Street., No. 2, 310330 Arad, Romania; (A.L.); (C.M.); (F.B.); (D.P.); (M.D.); (D.C.); (V.C.); (D.M.C.)
| |
Collapse
|
20
|
Klimova A, Ruiz Mondragón KY, Aguirre-Planter E, Valiente A, Lira R, Eguiarte LE. Genomic analysis unveils reduced genetic variability but increased proportion of heterozygotic genotypes of the intensively managed mezcal agave, Agave angustifolia. AMERICAN JOURNAL OF BOTANY 2023; 110:e16216. [PMID: 37478873 DOI: 10.1002/ajb2.16216] [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: 05/04/2023] [Revised: 06/20/2023] [Accepted: 06/20/2023] [Indexed: 07/23/2023]
Abstract
PREMISE The central Oaxaca Basin has a century-long history of agave cultivation and is hypothesized to be the region of origin of other cultivated crops. Widely cultivated for mezcal production, the perennial crop known as "espadín" is putatively derived from wild Agave angustifolia. Nevertheless, little is known about its genetic relationship to the wild A. angustifolia or how the decades-long clonal propagation has affected its genetics. METHODS Using restriction-site-associated DNA sequencing and over 8000 single-nucleotide polymorphisms, we studied aspects of the population genomics of wild and cultivated A. angustifolia in Puebla and Oaxaca, Mexico. We assessed patterns of genetic diversity, inbreeding, distribution of genetic variation, and differentiation among and within wild populations and plantations. RESULTS Genetic differentiation between wild and cultivated plants was strong, and both gene pools harbored multiple unique alleles. Nevertheless, we found several cultivated individuals with high genetic affinity with wild samples. Higher heterozygosity was observed in the cultivated individuals, while in total, they harbored considerably fewer alleles and presented higher linkage disequilibrium compared to the wild plants. Independently of geographic distance among sampled plantations, the genetic relatedness of the cultivated plants was high, suggesting a common origin and prevalent role of clonal propagation. CONCLUSIONS The considerable heterozygosity found in espadín is contained within a network of highly related individuals, displaying high linkage disequilibrium generated by decades of clonal propagation and possibly by the accumulation of somatic mutations. Wild A. angustifolia, on the other hand, represents a significant genetic diversity reservoir that should be carefully studied and conserved.
Collapse
Affiliation(s)
- Anastasia Klimova
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Karen Y Ruiz Mondragón
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Erika Aguirre-Planter
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Alfonso Valiente
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Rafael Lira
- Laboratorio de Recursos Naturales, Unidad de Biotecnología y Prototipos (UBIPRO), Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Luis E Eguiarte
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| |
Collapse
|
21
|
Mbhele Z, Zharare GE, Zimudzi C, Ntuli NR. Assessing Genetic Variation among Strychnos spinosa Lam. Morphotypes Using Simple Sequence Repeat Markers. PLANTS (BASEL, SWITZERLAND) 2023; 12:2810. [PMID: 37570964 PMCID: PMC10421500 DOI: 10.3390/plants12152810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 07/26/2023] [Accepted: 07/27/2023] [Indexed: 08/13/2023]
Abstract
Strychnos spinosa Lam., commonly known as green monkey orange, is a highly valued indigenous fruit tree in South Africa with potential for domestication and commercialization. However, no study has reported on the molecular diversity of Strychnos spinosa morphotypes. Therefore, this study aimed to determine genetic variation among 32 Strychnos spinosa morphotypes using simple sequence repeat (SSR) markers. Fourteen amplified SSR markers produced 159 alleles, with a mean of 5.68 per locus. The polymorphic information content (PIC) values ranged from 0.22 (Ssp_1) to 0.84 (Ssp_6). Morphotypes were clustered in a biplot based on their genetic distances. The dendrogram chiefly discriminated morphotypes according to variation of pericarp texture. The population structure had the highest delta value K = 3, thus the 32 morphotypes were divided into three subpopulations based on the Bayesian approach. The affinities produced by the population structure agreed with the genetic distance of closely related morphotypes. This study is the first to report on SSR marker development and their successful use for genetic diversity and population structure studies of Strychnos spinosa. It provides insights into the molecular characterisation of Strychnos spinosa. This can lead to breeding programs and crop improvement programs, particularly in varietal developmental programs, which can contribute to alleviating food security challenges.
Collapse
Affiliation(s)
- Zoliswa Mbhele
- Department of Botany, Faculty of Science, Agriculture and Engineering, University of Zululand, KwaDlangezwa 3886, South Africa;
| | | | - Clemence Zimudzi
- Department of Biological Sciences and Ecology, Faculty of Science, University of Zimbabwe, Harare P.O. Box MP167, Zimbabwe;
| | - Nontuthuko Rosemary Ntuli
- Department of Botany, Faculty of Science, Agriculture and Engineering, University of Zululand, KwaDlangezwa 3886, South Africa;
| |
Collapse
|
22
|
Chen X, Avia K, Forler A, Remoué C, Venon A, Rousselet A, Lucas G, Kwarteng AO, Rover R, Le Guilloux M, Belcram H, Combes V, Corti H, Olverà-Vazquez S, Falque M, Alins G, Kirisits T, Ursu TM, Roman A, Volk GM, Bazot S, Cornille A. Ecological and evolutionary drivers of phenotypic and genetic variation in the European crabapple [Malus sylvestris (L.) Mill.], a wild relative of the cultivated apple. ANNALS OF BOTANY 2023; 131:1025-1037. [PMID: 37148364 PMCID: PMC10332392 DOI: 10.1093/aob/mcad061] [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: 12/30/2022] [Accepted: 05/03/2023] [Indexed: 05/08/2023]
Abstract
BACKGROUND AND AIMS Studying the relationship between phenotypic and genetic variation in populations distributed across environmental gradients can help us to understand the ecological and evolutionary processes involved in population divergence. We investigated the patterns of genetic and phenotypic diversity in the European crabapple, Malus sylvestris, a wild relative of the cultivated apple (Malus domestica) that occurs naturally across Europe in areas subjected to different climatic conditions, to test for divergence among populations. METHODS Growth rates and traits related to carbon uptake in seedlings collected across Europe were measured in controlled conditions and associated with the genetic status of the seedlings, which was assessed using 13 microsatellite loci and the Bayesian clustering method. Isolation-by-distance, isolation-by-climate and isolation-by-adaptation patterns, which can explain genetic and phenotypic differentiation among M. sylvestris populations, were also tested. KEY RESULTS A total of 11.6 % of seedlings were introgressed by M. domestica, indicating that crop-wild gene flow is ongoing in Europe. The remaining seedlings (88.4 %) belonged to seven M. sylvestris populations. Significant phenotypic trait variation among M. sylvestris populations was observed. We did not observe significant isolation by adaptation; however, the significant association between genetic variation and the climate during the Last Glacial Maximum suggests that there has been local adaptation of M. sylvestris to past climates. CONCLUSIONS This study provides insight into the phenotypic and genetic differentiation among populations of a wild relative of the cultivated apple. This might help us to make better use of its diversity and provide options for mitigating the impact of climate change on the cultivated apple through breeding.
Collapse
Affiliation(s)
- X Chen
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, 91190 Gif-sur-Yvette, France
| | - K Avia
- Université de Strasbourg, INRAE, SVQV UMR-A 1131, F-68000 Colmar, France
| | - A Forler
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, 91190 Gif-sur-Yvette, France
| | - C Remoué
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, 91190 Gif-sur-Yvette, France
| | - A Venon
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, 91190 Gif-sur-Yvette, France
| | - A Rousselet
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, 91190 Gif-sur-Yvette, France
| | - G Lucas
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette 91198, France
| | - A O Kwarteng
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, 91190 Gif-sur-Yvette, France
| | - R Rover
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, 91190 Gif-sur-Yvette, France
| | - M Le Guilloux
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, 91190 Gif-sur-Yvette, France
| | - H Belcram
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, 91190 Gif-sur-Yvette, France
| | - V Combes
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, 91190 Gif-sur-Yvette, France
| | - H Corti
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, 91190 Gif-sur-Yvette, France
| | - S Olverà-Vazquez
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, 91190 Gif-sur-Yvette, France
| | - M Falque
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, 91190 Gif-sur-Yvette, France
| | - G Alins
- Institut de Recerca i Tecnologia Agroalimentàries, IRTA-Fruit Production, PCiTAL, Parc 21 de Gardeny, edifici Fruitcentre, 25003 Lleida, Spain
| | - T Kirisits
- Institute of Forest Entomology, Forest Pathology and Forest Protection (IFFF), Department of Forest and Soil Sciences, University of Natural Resources and Life Sciences, Vienna (BOKU), Peter-Jordan-Straße 82 (Franz Schwackhöfer-Haus), A-1190 Vienna, Austria
| | - T M Ursu
- NIRDBS, Institute of Biological Research Cluj-Napoca, 48 Republicii St., Cluj-Napoca, Romania
| | - A Roman
- NIRDBS, Institute of Biological Research Cluj-Napoca, 48 Republicii St., Cluj-Napoca, Romania
| | - G M Volk
- USDA-ARS National Laboratory for Genetic Resources Preservation, 1111 South Mason Street, Fort Collins, CO 80521, USA
| | - S Bazot
- Ecologie Systématique et Evolution, CNRS, AgroParisTech, Ecologie Systématique Evolution, Université Paris‐Saclay, Orsay, France
| | - A Cornille
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, 91190 Gif-sur-Yvette, France
| |
Collapse
|
23
|
Liu Y, Gao S, Hu Y, Zhang T, Guo J, Shi L, Li M. Comparative study of leaf nutrient reabsorption by two different ecotypes of wild soybean under low-nitrogen stress. PeerJ 2023; 11:e15486. [PMID: 37397019 PMCID: PMC10312162 DOI: 10.7717/peerj.15486] [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: 12/07/2022] [Accepted: 05/10/2023] [Indexed: 07/04/2023] Open
Abstract
Wild soybean (Glycine soja), the ancestor of cultivated soybean, has evolved into many ecotypes with different adaptations to adversity under the action of divergent evolution. Barren-tolerant wild soybean has developed adaptation to most nutrient-stress environments, especially with respect to low nitrogen (LN) conditions. This study describes the differences in physiological and metabolomic changes between common wild soybean (GS1) and barren-tolerant wild soybean(GS2) under LN stress. Compared with plants grown under the unstressed control (CK) conditions, the young leaves of barren-tolerant wild soybean under LN conditions maintained relatively stable chlorophyll, concentration and rates of photosynthesis and transpiration, as well as increased carotenoid content, whereas the net photosynthetic rate (PN) of GS1 decreased significantly 0.64-fold (p < 0.05) in the young leaves of GS1. The ratio of internal to atmospheric CO2 concentrations increased significantly 0.07-fold (p < 0.05), 0.09-fold (p < 0.05) in the young leaves of GS1 and GS2, respectively, and increased significantly 0.05-fold (p < 0.05) and 0.07-fold (p < 0.05) in the old leaves of GS1 and GS2, respectively, relative to the CK. The concentration of chlorophylls a and b decreased significantly 0.45-fold (p < 0.05), 0.13-fold (p > 0.05) in the young leaves of GS1 and GS2, respectively, and decreased significantly 0.74-fold (p < 0.01) and 0.60-fold (p < 0.01) in the old leaves of GS1 and GS2, respectively. Under LN stress, nitrate concentration in the young leaves of GS1 and GS2 decreased significantly 0.69- and 0.50-fold (p < 0.01), respectively, relative to CK, and decreased significantly 2.10-fold and 1.77-fold (p < 0.01) in the old leaves of GS1 and GS2, respectively. Barren-tolerant wild soybean increased the concentration of beneficial ion pairs. Under LN stress, Zn2+ significantly increased by 1.06- and 1.35-fold (p < 0.01) in the young and old leaves of GS2 (p < 0.01), but there was no significant change in GS1. The metabolism of amino acids and organic acids was high in GS2 young and old leaves, and the metabolites related to the TCA cycle were significantly increased. The 4-aminobutyric acid (GABA) concertation decreased significantly 0.70-fold (p < 0.05) in the young leaves of GS1 but increased 0.21-fold (p < 0.05) significantly in GS2. The relative concentration of proline increased significantly 1.21-fold (p < 0.01) and 2.85-fold (p < 0.01) in the young and old leaves of GS2. Under LN stress, GS2 could maintain photosynthesis rate and enhance the reabsorption of nitrate and magnesium in young leaves, compared to GS1. More importantly, GS2 exhibited increased amino acid and TCA cycle metabolism in young and old leaves. Adequate reabsorption of mineral and organic nutrients is an important strategy for barren-tolerant wild soybeans to survive under LN stress. Our research provides a new perspective on the exploitation and utilization of wild soybean resources.
Collapse
Affiliation(s)
- Yuan Liu
- Northeast Normal University, Changchun, China
- ChiFeng University, ChiFeng, China
| | - Shujuan Gao
- Northeast Normal University, Changchun, China
| | - Yunan Hu
- Northeast Normal University, Changchun, China
| | - Tao Zhang
- Northeast Normal University, Changchun, China
| | - Jixun Guo
- Northeast Normal University, Changchun, China
| | | | - Mingxia Li
- ChangChun Normal University, Changchun, China
| |
Collapse
|
24
|
Hawliczek A, Borzęcka E, Tofil K, Alachiotis N, Bolibok L, Gawroński P, Siekmann D, Hackauf B, Dušinský R, Švec M, Bolibok-Brągoszewska H. Selective sweeps identification in distinct groups of cultivated rye (Secale cereale L.) germplasm provides potential candidate genes for crop improvement. BMC PLANT BIOLOGY 2023; 23:323. [PMID: 37328739 PMCID: PMC10273710 DOI: 10.1186/s12870-023-04337-1] [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: 01/22/2023] [Accepted: 06/07/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND During domestication and subsequent improvement plants were subjected to intensive positive selection for desirable traits. Identification of selection targets is important with respect to the future targeted broadening of diversity in breeding programmes. Rye (Secale cereale L.) is a cereal that is closely related to wheat, and it is an important crop in Central, Eastern and Northern Europe. The aim of the study was (i) to identify diverse groups of rye accessions based on high-density, genome-wide analysis of genetic diversity within a set of 478 rye accessions, covering a full spectrum of diversity within the genus, from wild accessions to inbred lines used in hybrid breeding, and (ii) to identify selective sweeps in the established groups of cultivated rye germplasm and putative candidate genes targeted by selection. RESULTS Population structure and genetic diversity analyses based on high-quality SNP (DArTseq) markers revealed the presence of three complexes in the Secale genus: S. sylvestre, S. strictum and S. cereale/vavilovii, a relatively narrow diversity of S. sylvestre, very high diversity of S. strictum, and signatures of strong positive selection in S. vavilovii. Within cultivated ryes we detected the presence of genetic clusters and the influence of improvement status on the clustering. Rye landraces represent a reservoir of variation for breeding, and especially a distinct group of landraces from Turkey should be of special interest as a source of untapped variation. Selective sweep detection in cultivated accessions identified 133 outlier positions within 13 sweep regions and 170 putative candidate genes related, among others, to response to various environmental stimuli (such as pathogens, drought, cold), plant fertility and reproduction (pollen sperm cell differentiation, pollen maturation, pollen tube growth), and plant growth and biomass production. CONCLUSIONS Our study provides valuable information for efficient management of rye germplasm collections, which can help to ensure proper safeguarding of their genetic potential and provides numerous novel candidate genes targeted by selection in cultivated rye for further functional characterisation and allelic diversity studies.
Collapse
Affiliation(s)
- Anna Hawliczek
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw, University of Life Sciences-SGGW, Warsaw, Poland
| | - Ewa Borzęcka
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw, University of Life Sciences-SGGW, Warsaw, Poland
| | - Katarzyna Tofil
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw, University of Life Sciences-SGGW, Warsaw, Poland
| | - Nikolaos Alachiotis
- Faculty of Electrical Engineering, Mathematics and Computer Science, University of Twente, Enschede, The Netherlands
| | - Leszek Bolibok
- Department of Silviculture, Institute of Forest Sciences, Warsaw University of Life Sciences-SGGW, Warsaw, Poland
| | - Piotr Gawroński
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw, University of Life Sciences-SGGW, Warsaw, Poland
| | | | | | - Roman Dušinský
- Department of Botany, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Miroslav Švec
- Department of Botany, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Hanna Bolibok-Brągoszewska
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw, University of Life Sciences-SGGW, Warsaw, Poland.
| |
Collapse
|
25
|
An B, Cai H, Li B, Zhang S, He Y, Wang R, Jiao C, Guo Y, Xu L, Xu Y. Molecular Evolution of Histone Methylation Modification Families in the Plant Kingdom and Their Genome-Wide Analysis in Barley. Int J Mol Sci 2023; 24:ijms24098043. [PMID: 37175750 PMCID: PMC10178440 DOI: 10.3390/ijms24098043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/15/2023] [Accepted: 04/19/2023] [Indexed: 05/15/2023] Open
Abstract
In this study, based on the OneKP database and through comparative genetic analysis, we found that HMT and HDM may originate from Chromista and are highly conserved in green plants, and that during the evolution from algae to land plants, histone methylation modifications gradually became complex and diverse, which is more conducive to the adaptation of plants to complex and variable environments. We also characterized the number of members, genetic similarity, and phylogeny of HMT and HDM families in barley using the barley pangenome and the Tibetan Lasa Goumang genome. The results showed that HMT and HDM were highly conserved in the domestication of barley, but there were some differences in the Lasa Goumang SDG subfamily. Expression analysis showed that HvHMTs and HvHDMs were highly expressed in specific tissues and had complex expression patterns under multiple stress treatments. In summary, the amplification and variation of HMT and HDM facilitate plant adaptation to complex terrestrial environments, while they are highly conserved in barley and play an important role in barley growth and development with abiotic stresses. In brief, our findings provide a novel perspective on the origin and evolutionary history of plant HvHMTs and HvHDMs, and lay a foundation for further investigation of their functions in barley.
Collapse
Affiliation(s)
- Bingzhuang An
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Key Laboratory of Ministry of Agriculture and Rural Affairs for Crop Molecular Breeding, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
- College of Agriculture, Yangtze University, Jingzhou 434025, China
| | - Haiya Cai
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Key Laboratory of Ministry of Agriculture and Rural Affairs for Crop Molecular Breeding, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Bo Li
- College of Agriculture, Yangtze University, Jingzhou 434025, China
| | - Shuo Zhang
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Key Laboratory of Ministry of Agriculture and Rural Affairs for Crop Molecular Breeding, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Yonggang He
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Key Laboratory of Ministry of Agriculture and Rural Affairs for Crop Molecular Breeding, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Rong Wang
- College of Agriculture, Yangtze University, Jingzhou 434025, China
| | - Chunhai Jiao
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Key Laboratory of Ministry of Agriculture and Rural Affairs for Crop Molecular Breeding, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Ying Guo
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Key Laboratory of Ministry of Agriculture and Rural Affairs for Crop Molecular Breeding, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Le Xu
- College of Agriculture, Yangtze University, Jingzhou 434025, China
| | - Yanhao Xu
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Key Laboratory of Ministry of Agriculture and Rural Affairs for Crop Molecular Breeding, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
- Scientific Observation and Experiment Station for Crop Gene Resources and Germplasm Enhancement in Hubei, Ministry of Agriculture and Rural Affairs, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| |
Collapse
|
26
|
Vercellino RB, Hernández F, Pandolfo C, Ureta S, Presotto A. Agricultural weeds: the contribution of domesticated species to the origin and evolution of feral weeds. PEST MANAGEMENT SCIENCE 2023; 79:922-934. [PMID: 36507604 DOI: 10.1002/ps.7321] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 11/04/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
Agricultural weeds descended from domesticated ancestors, directly from crops (endoferality) and/or from crop-wild hybridization (exoferality), may have evolutionary advantages by rapidly acquiring traits pre-adapted to agricultural habitats. Understanding the role of crops on the origin and evolution of agricultural weeds is essential to develop more effective weed management programs, minimize crop losses due to weeds, and accurately assess the risks of cultivated genes escaping. In this review, we first describe relevant traits of weediness: shattering, seed dormancy, branching, early flowering and rapid growth, and their role in the feralization process. Furthermore, we discuss how the design of "super-crops" can affect weed evolution. We then searched for literature documenting cases of agricultural weeds descended from well-domesticated crops, and describe six case studies of feral weeds evolved from major crops: maize, radish, rapeseed, rice, sorghum, and sunflower. Further studies on the origin and evolution of feral weeds can improve our understanding of the physiological and genetic mechanisms underpinning the adaptation to agricultural habitats and may help to develop more effective weed-control practices and breeding better crops. © 2022 Society of Chemical Industry.
Collapse
Affiliation(s)
- Román B Vercellino
- Departamento de Agronomía, CERZOS, Universidad Nacional del Sur (UNS)-CONICET, Bahía Blanca, Argentina
| | - Fernando Hernández
- Departamento de Agronomía, CERZOS, Universidad Nacional del Sur (UNS)-CONICET, Bahía Blanca, Argentina
| | - Claudio Pandolfo
- Departamento de Agronomía, CERZOS, Universidad Nacional del Sur (UNS)-CONICET, Bahía Blanca, Argentina
| | - Soledad Ureta
- Departamento de Agronomía, CERZOS, Universidad Nacional del Sur (UNS)-CONICET, Bahía Blanca, Argentina
| | - Alejandro Presotto
- Departamento de Agronomía, CERZOS, Universidad Nacional del Sur (UNS)-CONICET, Bahía Blanca, Argentina
| |
Collapse
|
27
|
Barazani O, Dag A, Dunseth Z. The history of olive cultivation in the southern Levant. FRONTIERS IN PLANT SCIENCE 2023; 14:1131557. [PMID: 36909452 PMCID: PMC9996078 DOI: 10.3389/fpls.2023.1131557] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
The olive tree (Olea europaea L. subsp. europaea var. europaea) is one of the most important crops across the Mediterranean, particularly the southern Levant. Its regional economic importance dates at least to the Early Bronze Age (~3600 BCE) and its cultivation contributed significantly to the culture and heritage of ancient civilizations in the region. In the southern Levant, pollen, pits and wood remains of wild olives (O. europaea subsp. europaea var. sylvestris) has been found in Middle Pleistocene sediments dating to approximately 780 kya, and are present in numerous palynological sequences throughout the Pleistocene and into the Holocene. Archeological evidence indicates the olive oil production from at least the Pottery Neolithic to Chalcolithic transition (~7600-7000 BP), and clear evidence for cultivation by, 7000 BP. It is hypothesized that olive cultivation began through the selection of local genotypes of the wild var. sylvestris. Local populations of naturally growing trees today have thus been considered wild relatives of the olive. However, millennia of cultivation raises questions about whether genuine populations of var. sylvestris remain in the region. Ancient olive landraces might thus represent an ancient genetic stock closer to the ancestor gene pool. This review summarizes the evidence supporting the theory that olives were first cultivated in the southern Levant and reviews our genetic work characterizing local ancient cultivars. The significance and importance of old cultivars and wild populations are discussed, given the immediate need to adapt agricultural practices and crops to environmental degradation and global climate change.
Collapse
Affiliation(s)
- Oz Barazani
- Agricultural Research Organization, Institute of Plant Sciences, Department of Vegetables and Field Crops, Rishon LeZion, Israel
| | - Arnon Dag
- Agricultural Research Organization, Institute of Plant Sciences, Department of Fruit Tree Sciences, Gilat Research Center, Gilat, Israel
| | - Zachary Dunseth
- Joukowsky Institute for Archaeology and the Ancient World, Brown University, Providence, RI, United States
| |
Collapse
|
28
|
Nicolao R, Gaiero P, Castro CM, Heiden G. Solanum malmeanum, a promising wild relative for potato breeding. FRONTIERS IN PLANT SCIENCE 2023; 13:1046702. [PMID: 36891130 PMCID: PMC9986444 DOI: 10.3389/fpls.2022.1046702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 12/28/2022] [Indexed: 06/18/2023]
Abstract
Crop wild relatives are gaining increasing attention. Their use in plant breeding is essential to broaden the genetic basis of crops as well as to meet industrial demands, for global food security and sustainable production. Solanum malmeanum (Solanum sect. Petota, Solanaceae) is a wild relative of potatoes (S. tuberosum) from Southern South America, occurring in Argentina, Brazil, Paraguay and Uruguay. This wild potato has been largely mistaken for or historically considered as conspecific with S. commersonii. Recently, it was reinstated at the species level. Retrieving information on its traits and applied uses is challenging, because the species name has not always been applied correctly and also because species circumscriptions and morphological criteria applied to recognize it have not been consistent. To overcome these difficulties, we performed a thorough literature reference survey, herbaria specimens' identification revision and genebank database queries to review and update the information available on this potato wild relative, contributing to an increase in research on it to fully understand and explore its potential for potato breeding. Scarce studies have been carried out concerning its reproductive biology, resistance against pests and diseases as well as tolerance to abiotic stresses and evaluation of quality traits. The scattered information available makes it less represented in genebanks and genetic studies are missing. We compile, update and present available information for S. malmeanum on taxonomy, geographical distribution, ecology, reproductive biology, relationship with its closest relatives, biotic and abiotic stresses resistance and quality traits and discuss ways to overcome sexual barriers of hybridization and future perspectives for its use in potato breeding. As a final remark, we highlight that this species' potential uses have been neglected and must be unlocked. Thus, further studies on morphological and genetic variability with molecular tools are fundamental for an efficient conservation and applied use of this promising genetic resource.
Collapse
Affiliation(s)
- Rodrigo Nicolao
- Programa de Pós-Graduação em Agronomia/Fitomelhoramento - Universidade Federal de Pelotas (UFPel), Pelotas, RS, Brazil
| | - Paola Gaiero
- Departamento de Biología Vegetal, Facultad de Agronomía, Universidad de la República, Montevideo, Uruguay
| | - Caroline M. Castro
- Laboratório de Recursos Genéticos, Embrapa Clima Temperado, Pelotas, RS, Brazil
| | - Gustavo Heiden
- Laboratório de Recursos Genéticos, Embrapa Clima Temperado, Pelotas, RS, Brazil
| |
Collapse
|
29
|
Giovenali G, Kuzmanović L, Capoccioni A, Ceoloni C. The Response of Chromosomally Engineered Durum Wheat- Thinopyrum ponticum Recombinant Lines to the Application of Heat and Water-Deficit Stresses: Effects on Physiological, Biochemical and Yield-Related Traits. PLANTS (BASEL, SWITZERLAND) 2023; 12:704. [PMID: 36840052 PMCID: PMC9965029 DOI: 10.3390/plants12040704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/27/2023] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
Abiotic stress occurrence and magnitude are alarmingly intensifying worldwide. In the Mediterranean basin, heat waves and precipitation scarcity heavily affect major crops such as durum wheat (DW). In the search for tolerant genotypes, the identification of genes/QTL in wild wheat relatives, naturally adapted to harsh environments, represents a useful strategy. We tested three DW-Thinopyrum ponticum recombinant lines (R5+, R112+, R23+), their control sibs lacking any alien introgression, and the heat-tolerant cv. Margherita for their physiological, biochemical and yield response to heat stress (HS) application at anthesis, also in combination with water-deficit stress applied from booting until maturity. Under HS, R5+ and R112+ (23%- and 28%-long 7el1L Th. ponticum chromosome segment distally inserted on DW 7AL, respectively) showed remarkable stability of the yield-related traits; in turn, R23+ (40%-long 7el1L segment), despite a decreased grain yield, exhibited a greater spike fertility index and proline content in spike than its control sib. Under water-deficit + HS, R5+ showed the highest increment in water use efficiency and in flag leaf proline content, accompanied by the lowest yield penalty even vs. Margherita. This research confirms the value of harnessing wild gene pools to enhance DW stress tolerance and represents a starting point for elucidating the mechanisms of Thinopyrum spp. contribution to this relevant breeding target.
Collapse
|
30
|
Su Y, Liu Y, Xiao S, Wang Y, Deng Y, Zhao L, Wang Y, Zhao D, Dai X, Zhou Z, Cao Q. Isolation, characterization, and functional verification of salt stress response genes of NAC transcription factors in Ipomoea pes-caprae. FRONTIERS IN PLANT SCIENCE 2023; 14:1119282. [PMID: 36818867 PMCID: PMC9929455 DOI: 10.3389/fpls.2023.1119282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 01/19/2023] [Indexed: 06/18/2023]
Abstract
Adverse environmental stress is a major environmental factor threatening food security, which is why improving plant stress resistance is essential for agricultural productivity and environmental sustainability. The NAC (NAM, ATAF, and CUC) transcription factors (TFs) play a dominant role in plant responses to abiotic and biotic stresses, but they have been poorly studied in Ipomoea pes-caprae. In this research, 12 NAC TFs, named IpNAC1-IpNAC12, were selected from transcriptome data. The homologous evolution tree divided IpNACs into four major categories, and six IpNACs were linearly associated with Arabidopsis ANAC genes. From the gene structures, protein domains, and promoter upstream regulatory elements, IpNACs were shown to contain complete NAC-specific subdomains (A-E) and cis-acting elements corresponding to different stress stimuli. We measured the expression levels of the 12 IpNACs under abiotic stress (salt, heat, and drought) and hormone treatment (abscisic acid, methyl jasmonate, and salicylic acid), and their transcription levels differed. IpNAC5/8/10/12 were located in the nucleus through subcellular localization, and the overexpressing transgenic Arabidopsis plants showed high tolerance to salt stress. The cellular Na+ homeostasis content in the mature and elongation zones of the four IpNAC transgenic sweetpotato roots showed an obvious efflux phenomenon. These conclusions demonstrate that IpNAC5/8/10/12 actively respond to abiotic stress, have significant roles in improving plant salt tolerance, and are important salt tolerance candidate genes in I. pes-caprae and sweetpotato. This study laid the foundation for further studies on the function of IpNACs in response to abiotic stress. It provides options for improving the stress resistance of sweetpotato using gene introgression from I. pes-caprae.
Collapse
|
31
|
Thingnam SS, Lourembam DS, Tongbram PS, Lokya V, Tiwari S, Khan MK, Pandey A, Hamurcu M, Thangjam R. A Perspective Review on Understanding Drought Stress Tolerance in Wild Banana Genetic Resources of Northeast India. Genes (Basel) 2023; 14:genes14020370. [PMID: 36833297 PMCID: PMC9957078 DOI: 10.3390/genes14020370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 01/22/2023] [Accepted: 01/25/2023] [Indexed: 02/04/2023] Open
Abstract
The enormous perennial monocotyledonous herb banana (Musa spp.), which includes dessert and cooking varieties, is found in more than 120 countries and is a member of the order Zingiberales and family Musaceae. The production of bananas requires a certain amount of precipitation throughout the year, and its scarcity reduces productivity in rain-fed banana-growing areas due to drought stress. To increase the tolerance of banana crops to drought stress, it is necessary to explore crop wild relatives (CWRs) of banana. Although molecular genetic pathways involved in drought stress tolerance of cultivated banana have been uncovered and understood with the introduction of high-throughput DNA sequencing technology, next-generation sequencing (NGS) techniques, and numerous "omics" tools, unfortunately, such approaches have not been thoroughly implemented to utilize the huge potential of wild genetic resources of banana. In India, the northeastern region has been reported to have the highest diversity and distribution of Musaceae, with more than 30 taxa, 19 of which are unique to the area, accounting for around 81% of all wild species. As a result, the area is regarded as one of the main locations of origin for the Musaceae family. The understanding of the response of the banana genotypes of northeastern India belonging to different genome groups to water deficit stress at the molecular level will be useful for developing and improving drought tolerance in commercial banana cultivars not only in India but also worldwide. Hence, in the present review, we discuss the studies conducted to observe the effect of drought stress on different banana species. Moreover, the article highlights the tools and techniques that have been used or that can be used for exploring and understanding the molecular basis of differentially regulated genes and their networks in different drought stress-tolerant banana genotypes of northeast India, especially wild types, for unraveling their potential novel traits and genes.
Collapse
Affiliation(s)
| | | | - Punshi Singh Tongbram
- Department of Biotechnology, School of Life Sciences, Mizoram University, Aizawl 796004, India
| | - Vadthya Lokya
- Plant Tissue Culture and Genetic Engineering Lab, National Agri-Food Biotechnology Institute (NABI), Department of Biotechnology, Ministry of Science and Technology (Government of India), Sector 81, Knowledge City, S.A.S. Nagar, Mohali 140306, India
| | - Siddharth Tiwari
- Plant Tissue Culture and Genetic Engineering Lab, National Agri-Food Biotechnology Institute (NABI), Department of Biotechnology, Ministry of Science and Technology (Government of India), Sector 81, Knowledge City, S.A.S. Nagar, Mohali 140306, India
| | - Mohd. Kamran Khan
- Department of Soil Science and Plant Nutrition, Faculty of Agriculture, Selcuk University, Konya 42079, Turkey
| | - Anamika Pandey
- Department of Soil Science and Plant Nutrition, Faculty of Agriculture, Selcuk University, Konya 42079, Turkey
| | - Mehmet Hamurcu
- Department of Soil Science and Plant Nutrition, Faculty of Agriculture, Selcuk University, Konya 42079, Turkey
| | - Robert Thangjam
- Department of Biotechnology, School of Life Sciences, Mizoram University, Aizawl 796004, India
- Department of Life Sciences, School of Life Sciences, Manipur University, Imphal 795003, India
- Correspondence:
| |
Collapse
|
32
|
Hasanuzzaman M, Zhou M, Shabala S. How Does Stomatal Density and Residual Transpiration Contribute to Osmotic Stress Tolerance? PLANTS (BASEL, SWITZERLAND) 2023; 12:494. [PMID: 36771579 PMCID: PMC9919688 DOI: 10.3390/plants12030494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/12/2023] [Accepted: 01/18/2023] [Indexed: 06/18/2023]
Abstract
Osmotic stress that is induced by salinity and drought affects plant growth and development, resulting in significant losses to global crop production. Consequently, there is a strong need to develop stress-tolerant crops with a higher water use efficiency through breeding programs. Water use efficiency could be improved by decreasing stomatal transpiration without causing a reduction in CO2 uptake under osmotic stress conditions. The genetic manipulation of stomatal density could be one of the most promising strategies for breeders to achieve this goal. On the other hand, a substantial amount of water loss occurs across the cuticle without any contribution to carbon gain when the stomata are closed and under osmotic stress. The minimization of cuticular (otherwise known as residual) transpiration also determines the fitness and survival capacity of the plant under the conditions of a water deficit. The deposition of cuticular wax on the leaf epidermis acts as a limiting barrier for residual transpiration. However, the causal relationship between the frequency of stomatal density and plant osmotic stress tolerance and the link between residual transpiration and cuticular wax is not always straightforward, with controversial reports available in the literature. In this review, we focus on these controversies and explore the potential physiological and molecular aspects of controlling stomatal and residual transpiration water loss for improving water use efficiency under osmotic stress conditions via a comparative analysis of the performance of domesticated crops and their wild relatives.
Collapse
Affiliation(s)
- Md. Hasanuzzaman
- Department of Agronomy, Faculty of Agriculture, Sher-e-Bangla Agricultural University, Sher-e-Bangla Nagar, Dhaka 1207, Bangladesh
| | - Meixue Zhou
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS 7001, Australia
| | - Sergey Shabala
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS 7001, Australia
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan 528000, China
- School of Biological Science, University of Western Australia, Perth, WA 6009, Australia
| |
Collapse
|
33
|
Kapazoglou A, Gerakari M, Lazaridi E, Kleftogianni K, Sarri E, Tani E, Bebeli PJ. Crop Wild Relatives: A Valuable Source of Tolerance to Various Abiotic Stresses. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12020328. [PMID: 36679041 PMCID: PMC9861506 DOI: 10.3390/plants12020328] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 05/27/2023]
Abstract
Global climate change is one of the major constraints limiting plant growth, production, and sustainability worldwide. Moreover, breeding efforts in the past years have focused on improving certain favorable crop traits, leading to genetic bottlenecks. The use of crop wild relatives (CWRs) to expand genetic diversity and improve crop adaptability seems to be a promising and sustainable approach for crop improvement in the context of the ongoing climate challenges. In this review, we present the progress that has been achieved towards CWRs exploitation for enhanced resilience against major abiotic stressors (e.g., water deficiency, increased salinity, and extreme temperatures) in crops of high nutritional and economic value, such as tomato, legumes, and several woody perennial crops. The advances in -omics technologies have facilitated the elucidation of the molecular mechanisms that may underlie abiotic stress tolerance. Comparative analyses of whole genome sequencing (WGS) and transcriptomic profiling (RNA-seq) data between crops and their wild relative counterparts have unraveled important information with respect to the molecular basis of tolerance to abiotic stressors. These studies have uncovered genomic regions, specific stress-responsive genes, gene networks, and biochemical pathways associated with resilience to adverse conditions, such as heat, cold, drought, and salinity, and provide useful tools for the development of molecular markers to be used in breeding programs. CWRs constitute a highly valuable resource of genetic diversity, and by exploiting the full potential of this extended allele pool, new traits conferring abiotic-stress tolerance may be introgressed into cultivated varieties leading to superior and resilient genotypes. Future breeding programs may greatly benefit from CWRs utilization for overcoming crop production challenges arising from extreme environmental conditions.
Collapse
Affiliation(s)
- Aliki Kapazoglou
- Institute of Olive Tree, Subtropical Crops and Viticulture (IOSV), Department of Vitis, Hellenic Agricultural Organization-Dimitra (ELGO-Dimitra), Sofokli Venizelou 1, Lykovrysi, 14123 Athens, Greece
| | - Maria Gerakari
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
| | - Efstathia Lazaridi
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
| | - Konstantina Kleftogianni
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
| | - Efi Sarri
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
| | - Eleni Tani
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
| | - Penelope J. Bebeli
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
| |
Collapse
|
34
|
Behn A, Lizana C, Zapata F, Gonzalez A, Reyes-Díaz M, Fuentes D. Phenolic and anthocyanin content characterization related to genetic diversity analysis of Solanum tuberosum subsp. tuberosum Chilotanum Group in southern Chile. FRONTIERS IN PLANT SCIENCE 2023; 13:1045894. [PMID: 36704150 PMCID: PMC9872146 DOI: 10.3389/fpls.2022.1045894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 12/16/2022] [Indexed: 06/18/2023]
Abstract
The potato (Solanum tuberosum L) is one of the four most important crops worldwide in production and consumption. It originated from South America along the Andes, where six hotspots of diversity known as subcenters of origin are described from Venezuela to Chiloe Island in Chile, and where the greatest diversity of potatoes in the world is found. Today, the use of ancestral genetic resources has gained significant relevance, recovering and producing foods with a greater nutrient content and beneficial to human health. Therefore, native potatoes possess a set of characteristics with great potential for use in potato breeding guided primarily to produce better feed, especially potatoes of the Chilotanum Group that are easily crossed with conventional varieties. The primary objective of this study was to evaluate 290 accessions of S. tuberosum subsp tuberosum belonging to the Chilotanum Group using a set of molecular markers and correlate them to its phenotypic traits for future use in breeding programs. For this purpose, 290 accessions were analysed through 22 specific microsatellites described previously, correlating them with flesh and skin colour, total phenolic content, and anthocyanin content. A division into groups considering all the 290 accessions resulted in two clusters using STRUCTURE analysis and seven different genetic clusters using UPGMA. The latter exhibited common phenotypic characteristics as well as anthocyanin content, strongly supporting a correlation between phenotypic traits and the genetic fingerprint. These results will enable breeders to focus on the development of potatoes with high polyphenol and anthocyanin content.
Collapse
Affiliation(s)
- Anita Behn
- Instituto de Producción y Sanidad Vegetal, Facultad de Ciencias Agrarias y Alimentarias, Universidad Austral de Chile, Valdivia, Chile
| | - Carolina Lizana
- Instituto de Producción y Sanidad Vegetal, Facultad de Ciencias Agrarias y Alimentarias, Universidad Austral de Chile, Valdivia, Chile
| | - Felipe Zapata
- Biocomputing and Applied Genetics, Center for Systems Biotechnology, Fraunhofer Chile Research Foundation, Santiago, Chile
| | - Alvaro Gonzalez
- Biocomputing and Applied Genetics, Center for Systems Biotechnology, Fraunhofer Chile Research Foundation, Santiago, Chile
| | - Marjorie Reyes-Díaz
- Departamento de Ciencias Químicas y Recursos Naturales, Facultad de Ingeniería y Ciencias, Universidad de La Frontera, Temuco, Chile
| | - Derie Fuentes
- Biocomputing and Applied Genetics, Center for Systems Biotechnology, Fraunhofer Chile Research Foundation, Santiago, Chile
- Centro de Biotecnología de Sistemas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| |
Collapse
|
35
|
Eckardt NA, Ainsworth EA, Bahuguna RN, Broadley MR, Busch W, Carpita NC, Castrillo G, Chory J, DeHaan LR, Duarte CM, Henry A, Jagadish SVK, Langdale JA, Leakey ADB, Liao JC, Lu KJ, McCann MC, McKay JK, Odeny DA, Jorge de Oliveira E, Platten JD, Rabbi I, Rim EY, Ronald PC, Salt DE, Shigenaga AM, Wang E, Wolfe M, Zhang X. Climate change challenges, plant science solutions. THE PLANT CELL 2023; 35:24-66. [PMID: 36222573 PMCID: PMC9806663 DOI: 10.1093/plcell/koac303] [Citation(s) in RCA: 36] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Climate change is a defining challenge of the 21st century, and this decade is a critical time for action to mitigate the worst effects on human populations and ecosystems. Plant science can play an important role in developing crops with enhanced resilience to harsh conditions (e.g. heat, drought, salt stress, flooding, disease outbreaks) and engineering efficient carbon-capturing and carbon-sequestering plants. Here, we present examples of research being conducted in these areas and discuss challenges and open questions as a call to action for the plant science community.
Collapse
Affiliation(s)
| | - Elizabeth A Ainsworth
- USDA ARS Global Change and Photosynthesis Research Unit, Urbana, Illinois 61801, USA
| | - Rajeev N Bahuguna
- Centre for Advanced Studies on Climate Change, Dr Rajendra Prasad Central Agricultural University, Samastipur 848125, Bihar, India
| | - Martin R Broadley
- School of Biosciences, University of Nottingham, Nottingham, NG7 2RD, UK
- Rothamsted Research, West Common, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Wolfgang Busch
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Nicholas C Carpita
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, USA
| | - Gabriel Castrillo
- School of Biosciences, University of Nottingham, Nottingham, NG7 2RD, UK
- Future Food Beacon of Excellence, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Joanne Chory
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | | | - Carlos M Duarte
- Red Sea Research Center (RSRC) and Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Amelia Henry
- International Rice Research Institute, Rice Breeding Innovations Platform, Los Baños, Laguna 4031, Philippines
| | - S V Krishna Jagadish
- Department of Plant and Soil Science, Texas Tech University, Lubbock, Texas 79410, USA
| | - Jane A Langdale
- Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Andrew D B Leakey
- Department of Plant Biology, Department of Crop Sciences, and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Illinois 61801, USA
| | - James C Liao
- Institute of Biological Chemistry, Academia Sinica, Taipei 11528, Taiwan
| | - Kuan-Jen Lu
- Institute of Biological Chemistry, Academia Sinica, Taipei 11528, Taiwan
| | - Maureen C McCann
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, USA
| | - John K McKay
- Department of Agricultural Biology, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Damaris A Odeny
- The International Crops Research Institute for the Semi-Arid Tropics–Eastern and Southern Africa, Gigiri 39063-00623, Nairobi, Kenya
| | | | - J Damien Platten
- International Rice Research Institute, Rice Breeding Innovations Platform, Los Baños, Laguna 4031, Philippines
| | - Ismail Rabbi
- International Institute of Tropical Agriculture (IITA), PMB 5320 Ibadan, Oyo, Nigeria
| | - Ellen Youngsoo Rim
- Department of Plant Pathology and the Genome Center, University of California, Davis, California 95616, USA
| | - Pamela C Ronald
- Department of Plant Pathology and the Genome Center, University of California, Davis, California 95616, USA
- Innovative Genomics Institute, Berkeley, California 94704, USA
| | - David E Salt
- School of Biosciences, University of Nottingham, Nottingham, NG7 2RD, UK
- Future Food Beacon of Excellence, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Alexandra M Shigenaga
- Department of Plant Pathology and the Genome Center, University of California, Davis, California 95616, USA
| | - Ertao Wang
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Marnin Wolfe
- Auburn University, Dept. of Crop Soil and Environmental Sciences, College of Agriculture, Auburn, Alabama 36849, USA
| | - Xiaowei Zhang
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| |
Collapse
|
36
|
Civantos-Gómez I, Rubio Teso ML, Galeano J, Rubiales D, Iriondo JM, García-Algarra J. Climate change conditions the selection of rust-resistant candidate wild lentil populations for in situ conservation. FRONTIERS IN PLANT SCIENCE 2022; 13:1010799. [PMID: 36407589 PMCID: PMC9669080 DOI: 10.3389/fpls.2022.1010799] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 10/14/2022] [Indexed: 06/02/2023]
Abstract
Crop Wild Relatives (CWR) are a valuable source of genetic diversity that can be transferred to commercial crops, so their conservation will become a priority in the face of climate change. Bizarrely, in situ conserved CWR populations and the traits one might wish to preserve in them are themselves vulnerable to climate change. In this study, we used a quantitative machine learning predictive approach to project the resistance of CWR populations of lentils to a common disease, lentil rust, caused by fungus Uromyces viciae-fabae. Resistance is measured through a proxy quantitative value, DSr (Disease Severity relative), quite complex and expensive to get. Therefore, machine learning is a convenient tool to predict this magnitude using a well-curated georeferenced calibration set. Previous works have provided a binary outcome (resistant vs. non-resistant), but that approach is not fine enough to answer three practical questions: which variables are key to predict rust resistance, which CWR populations are resistant to rust under current environmental conditions, and which of them are likely to keep this trait under different climate change scenarios. We first predict rust resistance in present time for crop wild relatives that grow up inside protected areas. Then, we use the same models under future climate IPCC (Intergovernmental Panel on Climate Change) scenarios to predict future DSr values. Populations that are rust-resistant by now and under future conditions are optimal candidates for further evaluation and in situ conservation of this valuable trait. We have found that rust-resistance variation as a result of climate change is not uniform across the geographic scope of the study (the Mediterranean basin), and that candidate populations share some interesting common environmental conditions.
Collapse
Affiliation(s)
- Iciar Civantos-Gómez
- Complex System Group, Universidad Politécnica de Madrid, Madrid, Spain
- Faculty of Economics and Business Administration, Universidad Pontificia Comillas, Madrid, Spain
| | - María Luisa Rubio Teso
- ECOEVO Research Group, Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos, Madrid, Spain
| | - Javier Galeano
- Complex System Group, Universidad Politécnica de Madrid, Madrid, Spain
| | - Diego Rubiales
- Instituto de Agricultura Sostenible (CSIC) Avenida Menéndez Pidal s/n Campus Alameda del Obispo, Córdoba, Spain
| | - José María Iriondo
- ECOEVO Research Group, Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos, Madrid, Spain
| | - Javier García-Algarra
- DRACO Research Group, Centro Universitario de Tecnología y Arte Digital, Las Rozas, Spain
| |
Collapse
|
37
|
Bina H, Yousefzadeh H, Venon A, Remoué C, Rousselet A, Falque M, Faramarzi S, Chen X, Samanchina J, Gill D, Kabaeva A, Giraud T, Hosseinpour B, Abdollahi H, Gabrielyan I, Nersesyan A, Cornille A. Evidence of an additional centre of apple domestication in Iran, with contributions from the Caucasian crab apple Malus orientalis Uglitzk. to the cultivated apple gene pool. Mol Ecol 2022; 31:5581-5601. [PMID: 35984725 DOI: 10.1111/mec.16667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 07/08/2022] [Accepted: 08/09/2022] [Indexed: 12/29/2022]
Abstract
Divergence processes in crop-wild fruit tree complexes in pivotal regions for plant domestication such as the Caucasus and Iran remain little studied. We investigated anthropogenic and natural divergence processes in apples in these regions using 26 microsatellite markers amplified in 550 wild and cultivated samples. We found two genetically distinct cultivated populations in Iran that are differentiated from Malus domestica, the standard cultivated apple worldwide. Coalescent-based inferences showed that these two cultivated populations originated from specific domestication events of Malus orientalis in Iran. We found evidence of substantial wild-crop and crop-crop gene flow in the Caucasus and Iran, as has been described in apple in Europe. In addition, we identified seven genetically differentiated populations of wild apple (M. orientalis), not introgressed by the cultivated apple. Niche modelling combined with genetic diversity estimates indicated that these wild populations likely resulted from range changes during past glaciations. This study identifies Iran as a key region in the domestication of apple and M. orientalis as an additional contributor to the cultivated apple gene pool. Domestication of the apple tree therefore involved multiple origins of domestication in different geographic locations and substantial crop-wild hybridization, as found in other fruit trees. This study also highlights the impact of climate change on the natural divergence of a wild fruit tree and provides a starting point for apple conservation and breeding programmes in the Caucasus and Iran.
Collapse
Affiliation(s)
- Hamid Bina
- Department of Forestry, Tarbiat Modares University, Noor, Iran
| | - Hamed Yousefzadeh
- Department of Environmental Science, Biodiversity Branch, Natural Resources Faculty, Tarbiat Modares University, Noor, Iran
| | - Anthony Venon
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, Gif-sur-Yvette, France
| | - Carine Remoué
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, Gif-sur-Yvette, France
| | - Agnès Rousselet
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, Gif-sur-Yvette, France
| | - Matthieu Falque
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, Gif-sur-Yvette, France
| | - Shadab Faramarzi
- Department of Plant Production and Genetics, Faculty of Agriculture, Razi University, Kermanshah, Iran
| | - Xilong Chen
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, Gif-sur-Yvette, France
| | | | - David Gill
- Fauna & Flora International, Cambridge, UK
| | | | - Tatiana Giraud
- Ecologie Systematique Evolution, Universite Paris-Saclay, CNRS, AgroParisTech, Gif-sur-Yvette, France
| | - Batool Hosseinpour
- Department of Agriculture, Iranian Research Organization for Science and Technology (IROST), Institute of Agriculture, Tehran, Iran
| | - Hamid Abdollahi
- Temperate Fruits Research Centre, Horticultural Sciences Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Ivan Gabrielyan
- Department of Palaeobotany, A. Takhtajyan Institute of Botany, Armenian National Academy of Sciences, Yerevan, Armenia
| | - Anush Nersesyan
- Department of Conservation of Genetic Resources of Armenian Flora, A. Takhtajyan Institute of Botany, Armenian National Academy of Sciences, Yerevan, Armenia
| | - Amandine Cornille
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, Gif-sur-Yvette, France
| |
Collapse
|
38
|
Haq I, Binjawhar DN, Ullah Z, Ali A, Sher H, Ali I. Wild Vicia Species Possess a Drought Tolerance System for Faba Bean Improvement. Genes (Basel) 2022; 13:genes13101877. [PMID: 36292762 PMCID: PMC9601676 DOI: 10.3390/genes13101877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 10/05/2022] [Accepted: 10/11/2022] [Indexed: 11/23/2022] Open
Abstract
Faba bean (Vicia faba L.), a drought-sensitive crop, is drastically affected by drought stresses compromising its growth and yield. However, wild relatives of faba bean are considered a reservoir of potential genetic resources for tolerance against abiotic stresses. This study was conducted to characterize wild relatives of faba bean for identification of a specific tolerance system required for its improvement against drought stress. The study focused on physiological, biochemical, and anatomical responses of wild Vicia species under drought stress conditions. The experiment was carried out under various levels of drought stress imposed through different field capacities (FC) which included 80% FC ie (well-watered condition), 55% FC (moderate stress), and 30% FC (severe stress). When compared to plants grown in a control environment, drought stress significantly reduced the studied physiological attributes including soluble sugars (21.3% and 15.8%), protein contents (14.7 and 14.6%), and chlorophyll (8.4 and 28.6%) under moderate (55% FC) and severe drought stress (30% FC), respectively. However, proline content increased by 20.5% and 27.6%, peroxidase activity by 48.5% and 57.1%, and superoxide dismutase activity by 72.6% and 64.8% under moderate and severe stress, respectively. The studied anatomical attributes were also affected under drought stress treatments, including diameter of stem xylem vessels (9.1% and 13.7%), leaf lower epidermal thickness (8.05% and 13.34%), and leaf phloem width (5.3% and 10.1%) under moderate and severe stress, respectively. Wild Vicia spp. showed better tolerance to water-deficit conditions as compared to cultivated Vicia L. The observed potential diversity for drought tolerance in wild Vicia spp. may assist in improvement of faba bean and may also help in understanding the mechanisms of adaptations in drought-prone environments.
Collapse
Affiliation(s)
- Irfanul Haq
- Center for Plant Sciences and Biodiversity, University of Swat, Charbagh Swat 19120, Pakistan
| | - Dalal Nasser Binjawhar
- Department of Chemistry, College of Science, Princess Nourah bint Abdulrahman University, Riyadh 11671, Saudi Arabia
| | - Zahid Ullah
- Center for Plant Sciences and Biodiversity, University of Swat, Charbagh Swat 19120, Pakistan
- Correspondence: (Z.U.); (I.A.)
| | - Ahmad Ali
- Center for Plant Sciences and Biodiversity, University of Swat, Charbagh Swat 19120, Pakistan
| | - Hassan Sher
- Center for Plant Sciences and Biodiversity, University of Swat, Charbagh Swat 19120, Pakistan
| | - Iftikhar Ali
- Center for Plant Sciences and Biodiversity, University of Swat, Charbagh Swat 19120, Pakistan
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- Correspondence: (Z.U.); (I.A.)
| |
Collapse
|
39
|
Khan A, Ali A, Ullah Z, Ali I, Kaushik P, Alyemeni MN, Rasheed A, Sher H. Exploiting the drought tolerance of wild Elymus species for bread wheat improvement. FRONTIERS IN PLANT SCIENCE 2022; 13:982844. [PMID: 36275557 PMCID: PMC9583530 DOI: 10.3389/fpls.2022.982844] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/29/2022] [Indexed: 05/27/2023]
Abstract
Crop wild resources are excellent sources of new genetic variation for resilience against climate extremes. However, detailed characterization of the desirable phenotypes is essential before using these crop wild resources in breeding programs. This current study was, therefore, conducted to investigate the water stress responses of eight wild Elymus species and two wheat cultivars. The experiment was carried out under varying levels of osmotic stress induced by polyethylene glycol and progressive water stress through different field capacities. Water stress significantly reduced both physiological and biochemical traits compared to control, ranging from 7.1% (protein content) to 34.5% (chlorophyll) under moderate stress and 9.1-45.8% under severe stress. The anatomical features were also affected under progressive water stress, including a reduction in xylem vessel diameter (7.92 and 16.50%), phloem length (4.36 and 7.18%), vascular bundle length (3.09 and 6.04%), and ground tissue thickness (2.36 and 5.52%), respectively. Conclusively, Elymus borianus (endemic to Swat, Pakistan), E. russelli, E. caninus, E. longioristatus, and E. dauhuricus outperformed the check wheat cultivar, Pirsabak 2005, which is a rainfed variety. The results revealed that Elymus species belonging to the tertiary gene pool of bread wheat could be an excellent drought tolerance source for use in a breeding program.
Collapse
Affiliation(s)
- Ajab Khan
- Center for Plant Sciences and Biodiversity, University of Swat, Swat, Pakistan
| | - Ahmad Ali
- Center for Plant Sciences and Biodiversity, University of Swat, Swat, Pakistan
| | - Zahid Ullah
- Center for Plant Sciences and Biodiversity, University of Swat, Swat, Pakistan
| | - Iftikhar Ali
- Center for Plant Sciences and Biodiversity, University of Swat, Swat, Pakistan
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Prashant Kaushik
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politécnica de Valéncia, Valencia, Spain
| | | | - Awais Rasheed
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Hassan Sher
- Center for Plant Sciences and Biodiversity, University of Swat, Swat, Pakistan
| |
Collapse
|
40
|
Zhang J, Pan D, Fan Z, Yu H, Jiang L, Lv S, Sun B, Chen W, Mao X, Liu Q, Li C. Genetic diversity of wild rice accessions ( Oryza rufipogon Griff.) in Guangdong and Hainan Provinces, China, and construction of a wild rice core collection. FRONTIERS IN PLANT SCIENCE 2022; 13:999454. [PMID: 36262660 PMCID: PMC9576158 DOI: 10.3389/fpls.2022.999454] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 09/02/2022] [Indexed: 05/28/2023]
Abstract
Oryza rufipogon Griff. is a valuable germplasm resource for rice genetic improvement. However, natural habitat loss has led to the erosion of the genetic diversity of wild rice populations. Genetic diversity analysis of O. rufipogon accessions and development of the core collection are crucial for conserving natural genetic diversity and providing novel traits for rice breeding. In the present study, we developed 1,592 SNPs by multiplex PCR and next-generation sequencing (NGS) technology and used them to genotype 998 O. rufipogon accessions from 14 agroclimatic zones in Guangdong and Hainan Provinces, China. These SNPs were mapped onto 12 chromosomes, and the average MAF value was 0.128 with a minimum of 0.01 and a maximum of 0.499. The O. rufipogon accessions were classified into ten groups. The mean Nei's diversity index and Shannon-Wiener index (I) were 0.187 and 0.308, respectively, in all populations, indicating that O. rufipogon accessions had rich genetic diversity. There were also differences in the genetic diversity of O. rufipogon resources in the 14 regions. Hainan populations possessed higher levels of genetic diversity, whereas the Guangzhou population had lower levels of genetic diversity than did the other populations. Phylogenetic analysis revealed that the genetic relationship among the distribution sites of O. rufipogon was closely related to geographical location. Based on genetic distance, a core collection of 299 accessions captured more than 99% of the genetic variation in the germplasm. This study provides insights into O. rufipogon conservation, and the constructed core collection provides valuable resources for future research and genomics-assisted breeding of rice.
Collapse
Affiliation(s)
- Jing Zhang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Dajian Pan
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Zhilan Fan
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Hang Yu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Liqun Jiang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Shuwei Lv
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Bingrui Sun
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Wenfeng Chen
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Xingxue Mao
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Qing Liu
- *Correspondence: Qing Liu, ; Chen Li,
| | - Chen Li
- *Correspondence: Qing Liu, ; Chen Li,
| |
Collapse
|
41
|
Molecular Pathways of WRKY Genes in Regulating Plant Salinity Tolerance. Int J Mol Sci 2022; 23:ijms231810947. [PMID: 36142857 PMCID: PMC9502527 DOI: 10.3390/ijms231810947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 09/05/2022] [Accepted: 09/14/2022] [Indexed: 11/17/2022] Open
Abstract
Salinity is a natural and anthropogenic process that plants overcome using various responses. Salinity imposes a two-phase effect, simplified into the initial osmotic challenges and subsequent salinity-specific ion toxicities from continual exposure to sodium and chloride ions. Plant responses to salinity encompass a complex gene network involving osmotic balance, ion transport, antioxidant response, and hormone signaling pathways typically mediated by transcription factors. One particular transcription factor mega family, WRKY, is a principal regulator of salinity responses. Here, we categorize a collection of known salinity-responding WRKYs and summarize their molecular pathways. WRKYs collectively play a part in regulating osmotic balance, ion transport response, antioxidant response, and hormone signaling pathways in plants. Particular attention is given to the hormone signaling pathway to illuminate the relationship between WRKYs and abscisic acid signaling. Observed trends among WRKYs are highlighted, including group II WRKYs as major regulators of the salinity response. We recommend renaming existing WRKYs and adopting a naming system to a standardized format based on protein structure.
Collapse
|
42
|
Reactive oxygen species in plants: an invincible fulcrum for biotic stress mitigation. Appl Microbiol Biotechnol 2022; 106:5945-5955. [PMID: 36063177 DOI: 10.1007/s00253-022-12138-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 08/17/2022] [Accepted: 08/18/2022] [Indexed: 11/02/2022]
Abstract
Climate change-associated environmental vagaries have amplified the incidence of pests and pathogens on plants, thus imparting the increased quest for management strategies. Plants respond to stresses through intricate signaling networks that regulate diverse cellular mechanisms. Reactive oxygen species (ROS) are cardinal towards the maintenance of normal plant activities as well as improving stress management. Plants that exhibit a fine balance between ROS levels and its management apparently mitigate stresses better. There have been very many compendiums on signaling and management of ROS during several abiotic stresses. However, expansion of knowledge related to ROS induction and homeostasis during biotic stresses is pertinent. Hence, considering its importance, we provide insights in this review on how plants signal and manage ROS upon an oxidative burst during their interaction with pathogens and herbivores. Substantial degree of molecular changes and pivotal roles of ROS have been detected during phyto-pathogen/herbivore interactions, opening novel platforms to understand signaling/management of events under varied biotic stresses. It is interesting to know that, though plants react to biotic stresses through oxidative burst, receptors and elicitors involved in the signal transduction differ across stresses. The review provides explicit details about the specific signaling of ROS production in plants under pathogen and herbivore attack. Furthermore, we also provide an update about tackling the accumulated ROS under biotic stresses as another pivotal step. ROS signaling and homeostasis can be exploited as critical players and a fulcrum to tackle biotic stresses, thus paving the way for futuristic combinatorial stress management strategies. KEY POINTS: • The review is a comprehension of redox signaling and management in plants during herbivory and pathogen infection • Reactive oxygen species (ROS) is an important factor during normal plant activities as well as in their response to stresses. Diverse modes of ROS signaling and management have been observed during both biotic stresses independently • Exploration of plant biology in multi-stress resistant plants like the crop wild relatives could pave the way for combinatorial management of stress for a better tomorrow.
Collapse
|
43
|
Eastwood RJ, Tambam BB, Aboagye LM, Akparov ZI, Aladele SE, Allen R, Amri A, Anglin NL, Araya R, Arrieta-Espinoza G, Asgerov A, Awang K, Awas T, Barata AM, Boateng SK, Magos Brehm J, Breidy J, Breman E, Brenes Angulo A, Burle ML, Castañeda-Álvarez NP, Casimiro P, Chaves NF, Clemente AS, Cockel CP, Davey A, De la Rosa L, Debouck DG, Dempewolf H, Dokmak H, Ellis D, Faruk A, Freitas C, Galstyan S, García RM, Ghimire KH, Guarino L, Harker R, Hope R, Humphries AW, Jamora N, Jatoi SA, Khutsishvili M, Kikodze D, Kyratzis AC, León-Lobos P, Liu U, Mainali RP, Mammadov AT, Manrique-Carpintero NC, Manzella D, Mat Ali MS, Medeiros MB, Guzmán MAM, Mikatadze-Pantsulaia T, Mohamed ETI, Monteros-Altamirano Á, Morales A, Müller JV, Mulumba JW, Nersesyan A, Nóbrega H, Nyamongo DO, Obreza M, Okere AU, Orsenigo S, Ortega-Klose F, Papikyan A, Pearce TR, Pinheiro de Carvalho MAA, Prohens J, Rossi G, Salas A, Singh Shrestha D, Siddiqui SU, Smith PP, Sotomayor DA, Tacán M, Tapia C, Toledo Á, Toll J, Vu DT, Vu TD, Way MJ, Yazbek M, Zorrilla C, Kilian B. Adapting Agriculture to Climate Change: A Synopsis of Coordinated National Crop Wild Relative Seed Collecting Programs across Five Continents. PLANTS 2022; 11:plants11141840. [PMID: 35890473 PMCID: PMC9319254 DOI: 10.3390/plants11141840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 06/29/2022] [Accepted: 06/29/2022] [Indexed: 11/16/2022]
Abstract
The Adapting Agriculture to Climate Change Project set out to improve the diversity, quantity, and accessibility of germplasm collections of crop wild relatives (CWR). Between 2013 and 2018, partners in 25 countries, heirs to the globetrotting legacy of Nikolai Vavilov, undertook seed collecting expeditions targeting CWR of 28 crops of global significance for agriculture. Here, we describe the implementation of the 25 national collecting programs and present the key results. A total of 4587 unique seed samples from at least 355 CWR taxa were collected, conserved ex situ, safety duplicated in national and international genebanks, and made available through the Multilateral System (MLS) of the International Treaty on Plant Genetic Resources for Food and Agriculture (Plant Treaty). Collections of CWR were made for all 28 targeted crops. Potato and eggplant were the most collected genepools, although the greatest number of primary genepool collections were made for rice. Overall, alfalfa, Bambara groundnut, grass pea and wheat were the genepools for which targets were best achieved. Several of the newly collected samples have already been used in pre-breeding programs to adapt crops to future challenges.
Collapse
Affiliation(s)
- Ruth J. Eastwood
- Royal Botanic Gardens, Kew, Wakehurst, Ardingly, Haywards Heath RH17 6TN, UK; (R.A.); (E.B.); (C.P.C.); (A.F.); (U.L.); (J.V.M.); (T.R.P.); (M.J.W.)
- Correspondence:
| | - Beri B. Tambam
- Global Crop Diversity Trust, Platz der Vereinten Nationen 7, 53113 Bonn, Germany; (B.B.T.); (N.P.C.-Á.); (H.D.); (L.G.); (N.J.); (M.O.); (J.T.); (B.K.)
| | - Lawrence M. Aboagye
- CSIR—Plant Genetic Resources Research Institute, Bunso P.O. Box 7, Ghana; (L.M.A.); (S.K.B.)
| | - Zeynal I. Akparov
- Genetic Resources Institute of Azerbaijan NAS, 155 Azadlig Avenue, Baku AZ1106, Azerbaijan; (Z.I.A.); (A.A.); (A.T.M.)
| | - Sunday E. Aladele
- National Centre for Genetic Resources and Biotechnology, Moor Plantation, Ibadan PMB 5382, Nigeria; (S.E.A.); (A.U.O.)
| | - Richard Allen
- Royal Botanic Gardens, Kew, Wakehurst, Ardingly, Haywards Heath RH17 6TN, UK; (R.A.); (E.B.); (C.P.C.); (A.F.); (U.L.); (J.V.M.); (T.R.P.); (M.J.W.)
| | - Ahmed Amri
- The International Center for Agricultural Research in the Dry Areas, Dalia Bldg, 2nd Floor Bashir El Kassar Street Verdun, Beirut 1108-2010, Lebanon; (A.A.); (M.Y.)
| | - Noelle L. Anglin
- USDA ARS Small Grains and Potato Germplasm Research, 1691 S 2700 W, Aberdeen, ID 83210, USA;
| | - Rodolfo Araya
- Estación Experimental Agrícola Fabio Baudrit Moreno, Universidad de Costa Rica, 3 km W of Catholic Church of Barrio San José, La Garita, Alajuela 183-4050, Costa Rica; (R.A.); (N.F.C.)
| | - Griselda Arrieta-Espinoza
- Centro de Investigación en Biología Celular y Molecular, Universidad de Costa Rica, Ciudad de la Investigación—C.P., San José 11501-2050, Costa Rica;
| | - Aydin Asgerov
- Genetic Resources Institute of Azerbaijan NAS, 155 Azadlig Avenue, Baku AZ1106, Azerbaijan; (Z.I.A.); (A.A.); (A.T.M.)
| | - Khadijah Awang
- Malaysian Agricultural Research and Development Institute (MARDI), Persiaran MARDI-UPM, Serdang 43400, Malaysia; (K.A.); (M.S.M.A.)
| | - Tesfaye Awas
- Ethiopian Biodiversity Institute, Comoros Street, Yeka Subcity, Addis Ababa P.O. Box 30726, Ethiopia;
| | - Ana Maria Barata
- Banco Português de Germoplasma Vegetal, INIAV, Quinta de S. José, São Pedro de Merelim, 4700-859 Braga, Portugal;
| | - Samuel Kwasi Boateng
- CSIR—Plant Genetic Resources Research Institute, Bunso P.O. Box 7, Ghana; (L.M.A.); (S.K.B.)
| | - Joana Magos Brehm
- Jardim Botânico, Museu Nacional de Historia Natural e da Ciência, Universidade de Lisboa, R. da Escola Politécnica 56, 1250-102 Lisboa, Portugal; (J.M.B.); (A.S.C.)
| | - Joelle Breidy
- Lebanese Agricultural Research Institute, Tal Amara, Rayak P.O. Box 287, Lebanon; (J.B.); (H.D.)
| | - Elinor Breman
- Royal Botanic Gardens, Kew, Wakehurst, Ardingly, Haywards Heath RH17 6TN, UK; (R.A.); (E.B.); (C.P.C.); (A.F.); (U.L.); (J.V.M.); (T.R.P.); (M.J.W.)
| | - Arturo Brenes Angulo
- Centro de Investigaciones Agronómicas, Universidad de Costa Rica, San José 11501-2060, Costa Rica;
| | - Marília L. Burle
- Embrapa Genetic Resources and Biotechnology, Parque Estação Biológica, Av. W5 Norte (Final), Brasília 70770-917, DF, Brazil; (M.L.B.); (M.B.M.)
| | - Nora P. Castañeda-Álvarez
- Global Crop Diversity Trust, Platz der Vereinten Nationen 7, 53113 Bonn, Germany; (B.B.T.); (N.P.C.-Á.); (H.D.); (L.G.); (N.J.); (M.O.); (J.T.); (B.K.)
| | - Pedro Casimiro
- Direção Regional do Ambiente e Alterações Climáticas, Rua Cônsul Dabney, Colónia Alemã, Apartado 140, 9900-014 Horta, Portugal;
| | - Néstor F. Chaves
- Estación Experimental Agrícola Fabio Baudrit Moreno, Universidad de Costa Rica, 3 km W of Catholic Church of Barrio San José, La Garita, Alajuela 183-4050, Costa Rica; (R.A.); (N.F.C.)
| | - Adelaide S. Clemente
- Jardim Botânico, Museu Nacional de Historia Natural e da Ciência, Universidade de Lisboa, R. da Escola Politécnica 56, 1250-102 Lisboa, Portugal; (J.M.B.); (A.S.C.)
| | - Christopher P. Cockel
- Royal Botanic Gardens, Kew, Wakehurst, Ardingly, Haywards Heath RH17 6TN, UK; (R.A.); (E.B.); (C.P.C.); (A.F.); (U.L.); (J.V.M.); (T.R.P.); (M.J.W.)
| | - Alexandra Davey
- Fauna & Flora International, The David Attenborough Building, Pembroke Street, Cambridge CB2 3QZ, UK; (A.D.); (R.H.)
| | - Lucía De la Rosa
- Plant Genetic Resources Centre, National Institute for Agricultural and Food Research and Technology (CRF-INIA), CSIC, Finca La Canaleja, A2 km 36, 28800 Alcalá de Henares, Spain; (L.D.l.R.); (R.M.G.)
| | - Daniel G. Debouck
- Alliance Bioversity International Center of Tropical Agriculture, km 17, Recta Cali-Palmira, Apartado Aéreo 6713, Cali 763537, Colombia;
| | - Hannes Dempewolf
- Global Crop Diversity Trust, Platz der Vereinten Nationen 7, 53113 Bonn, Germany; (B.B.T.); (N.P.C.-Á.); (H.D.); (L.G.); (N.J.); (M.O.); (J.T.); (B.K.)
| | - Hiba Dokmak
- Lebanese Agricultural Research Institute, Tal Amara, Rayak P.O. Box 287, Lebanon; (J.B.); (H.D.)
| | - David Ellis
- International Potato Center, Avenida La Molina 1895, La Molina, Lima 15023, Peru; (D.E.); (N.C.M.-C.); (A.S.)
| | - Aisyah Faruk
- Royal Botanic Gardens, Kew, Wakehurst, Ardingly, Haywards Heath RH17 6TN, UK; (R.A.); (E.B.); (C.P.C.); (A.F.); (U.L.); (J.V.M.); (T.R.P.); (M.J.W.)
| | - Cátia Freitas
- Banco de Sementes dos Açores, Rua de São Lourenço, nº 23 Flamengos, 9900-401 Horta, Portugal;
| | - Sona Galstyan
- Institute of Botany after A. Takhtajyan of the National Academy of Sciences of the Republic of Armenia, Acharyan Street 1, Yerevan 0040, Armenia; (S.G.); (A.N.); (A.P.)
| | - Rosa M. García
- Plant Genetic Resources Centre, National Institute for Agricultural and Food Research and Technology (CRF-INIA), CSIC, Finca La Canaleja, A2 km 36, 28800 Alcalá de Henares, Spain; (L.D.l.R.); (R.M.G.)
| | - Krishna H. Ghimire
- National Agriculture Genetic Resources Centre, Nepal Agricultural Research Council (NARC), Khumaltar, Lalitpur P.O. Box. 3605, Nepal; (K.H.G.); (R.P.M.); (D.S.S.)
| | - Luigi Guarino
- Global Crop Diversity Trust, Platz der Vereinten Nationen 7, 53113 Bonn, Germany; (B.B.T.); (N.P.C.-Á.); (H.D.); (L.G.); (N.J.); (M.O.); (J.T.); (B.K.)
| | - Ruth Harker
- Natural England, Foss House, Kings Pool, 1-2 Peasholme Green, York YO1 7PX, UK;
| | - Roberta Hope
- Fauna & Flora International, The David Attenborough Building, Pembroke Street, Cambridge CB2 3QZ, UK; (A.D.); (R.H.)
| | - Alan W. Humphries
- South Australian Research and Development Institute, Plant Research Centre, Waite Precinct, Gate 2b Hartley Grove, Urrbrae, SA 5064, Australia;
| | - Nelissa Jamora
- Global Crop Diversity Trust, Platz der Vereinten Nationen 7, 53113 Bonn, Germany; (B.B.T.); (N.P.C.-Á.); (H.D.); (L.G.); (N.J.); (M.O.); (J.T.); (B.K.)
| | - Shakeel Ahmad Jatoi
- Bio-Resources Conservation Institute, National Agricultural Research Centre, Park Road, Islamabad 45500, Pakistan; (S.A.J.); (S.U.S.)
| | - Manana Khutsishvili
- Institute of Botany, Ilia State University, 1 Botanikuri str., 0105 Tbilisi, Georgia; (M.K.); (D.K.)
| | - David Kikodze
- Institute of Botany, Ilia State University, 1 Botanikuri str., 0105 Tbilisi, Georgia; (M.K.); (D.K.)
| | - Angelos C. Kyratzis
- Agricultural Research Institute, Athalassa, P.O. Box 22016, Nicosia 1516, Cyprus;
| | - Pedro León-Lobos
- Instituto de Investigaciones Agropecuarias, Fidel Oteíza 1956, Pisos 12, Providencia, Santiago 8320000, Chile; (P.L.-L.); (F.O.-K.)
| | - Udayangani Liu
- Royal Botanic Gardens, Kew, Wakehurst, Ardingly, Haywards Heath RH17 6TN, UK; (R.A.); (E.B.); (C.P.C.); (A.F.); (U.L.); (J.V.M.); (T.R.P.); (M.J.W.)
| | - Ram P. Mainali
- National Agriculture Genetic Resources Centre, Nepal Agricultural Research Council (NARC), Khumaltar, Lalitpur P.O. Box. 3605, Nepal; (K.H.G.); (R.P.M.); (D.S.S.)
| | - Afig T. Mammadov
- Genetic Resources Institute of Azerbaijan NAS, 155 Azadlig Avenue, Baku AZ1106, Azerbaijan; (Z.I.A.); (A.A.); (A.T.M.)
| | | | | | - Mohd Shukri Mat Ali
- Malaysian Agricultural Research and Development Institute (MARDI), Persiaran MARDI-UPM, Serdang 43400, Malaysia; (K.A.); (M.S.M.A.)
| | - Marcelo B. Medeiros
- Embrapa Genetic Resources and Biotechnology, Parque Estação Biológica, Av. W5 Norte (Final), Brasília 70770-917, DF, Brazil; (M.L.B.); (M.B.M.)
| | - María A. Mérida Guzmán
- Institute of Agricultural Science and Technology, km 21.5 Highway to the Pacific, Bárcena, Villa Nueva, Guatemala;
| | | | - El Tahir Ibrahim Mohamed
- Agricultural Plant Genetic Resources Conservation and Research Centre, Agricultural Research Corporation, Wad Medani P.O. Box 126, Sudan;
| | - Álvaro Monteros-Altamirano
- Instituto Nacional de Investigaciones Agropecuarias, Avenida Amazonas y Eloy Alfaro, Edificio MAG, Cuarto Piso, Quito 170518, Ecuador; (Á.M.-A.); (M.T.); (C.T.)
| | - Aura Morales
- Centro Nacional de Tecnología “Enrique Álvarez Córdova”, km 33.5 Carretera a Santa Ana, San Andrés, Ciudad Arce, La Libertad, El Salvador;
| | - Jonas V. Müller
- Royal Botanic Gardens, Kew, Wakehurst, Ardingly, Haywards Heath RH17 6TN, UK; (R.A.); (E.B.); (C.P.C.); (A.F.); (U.L.); (J.V.M.); (T.R.P.); (M.J.W.)
| | - John W. Mulumba
- Plant Genetic Resources Centre, National Agricultural Research Organization, Plot 2-4 Berkeley Road, Entebbe P.O. Box 40, Uganda;
| | - Anush Nersesyan
- Institute of Botany after A. Takhtajyan of the National Academy of Sciences of the Republic of Armenia, Acharyan Street 1, Yerevan 0040, Armenia; (S.G.); (A.N.); (A.P.)
| | - Humberto Nóbrega
- ISOPlexis—Centro de Agricultura Sustentável e Tecnologia Alimentar, Universidade da Madeira, Campus da Penteada, 9020-105 Funchal, Portugal; (M.A.A.P.d.C.); (H.N.)
| | - Desterio O. Nyamongo
- Kenya Agricultural and Livestock Research Organisation, Genetic Resources Research Institute, Nairobi P.O. Box 30148-00100, Kenya;
| | - Matija Obreza
- Global Crop Diversity Trust, Platz der Vereinten Nationen 7, 53113 Bonn, Germany; (B.B.T.); (N.P.C.-Á.); (H.D.); (L.G.); (N.J.); (M.O.); (J.T.); (B.K.)
| | - Anthony U. Okere
- National Centre for Genetic Resources and Biotechnology, Moor Plantation, Ibadan PMB 5382, Nigeria; (S.E.A.); (A.U.O.)
| | - Simone Orsenigo
- Department of Earth and Environmental Sciences, Pavia University, Via Sant’Epifanio 14, 27100 Pavia, Italy; (S.O.); (G.R.)
| | - Fernando Ortega-Klose
- Instituto de Investigaciones Agropecuarias, Fidel Oteíza 1956, Pisos 12, Providencia, Santiago 8320000, Chile; (P.L.-L.); (F.O.-K.)
| | - Astghik Papikyan
- Institute of Botany after A. Takhtajyan of the National Academy of Sciences of the Republic of Armenia, Acharyan Street 1, Yerevan 0040, Armenia; (S.G.); (A.N.); (A.P.)
| | - Timothy R. Pearce
- Royal Botanic Gardens, Kew, Wakehurst, Ardingly, Haywards Heath RH17 6TN, UK; (R.A.); (E.B.); (C.P.C.); (A.F.); (U.L.); (J.V.M.); (T.R.P.); (M.J.W.)
| | - Miguel A. A. Pinheiro de Carvalho
- ISOPlexis—Centro de Agricultura Sustentável e Tecnologia Alimentar, Universidade da Madeira, Campus da Penteada, 9020-105 Funchal, Portugal; (M.A.A.P.d.C.); (H.N.)
- CITAB—Centro de Investigação e Tecnologias Agroambientais e Biológicas, 5001-801 Vila Real, Portugal
| | - Jaime Prohens
- Institute for the Conservation and Improvement of Valencian Agrodiversity (COMAV), Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain;
| | - Graziano Rossi
- Department of Earth and Environmental Sciences, Pavia University, Via Sant’Epifanio 14, 27100 Pavia, Italy; (S.O.); (G.R.)
| | - Alberto Salas
- International Potato Center, Avenida La Molina 1895, La Molina, Lima 15023, Peru; (D.E.); (N.C.M.-C.); (A.S.)
| | - Deepa Singh Shrestha
- National Agriculture Genetic Resources Centre, Nepal Agricultural Research Council (NARC), Khumaltar, Lalitpur P.O. Box. 3605, Nepal; (K.H.G.); (R.P.M.); (D.S.S.)
| | - Sadar Uddin Siddiqui
- Bio-Resources Conservation Institute, National Agricultural Research Centre, Park Road, Islamabad 45500, Pakistan; (S.A.J.); (S.U.S.)
| | - Paul P. Smith
- Botanic Gardens Conservation International, Descanso House, 199 Kew Road, Richmond TW9 3BW, UK;
| | - Diego A. Sotomayor
- Subdirección de Recursos Genéticos, Instituto Nacional de Innovación Agraria, Av. La Molina 1981, La Molina, Lima 15024, Peru;
- Facultad de Ciencias, Universidad Nacional Agraria La Molina, Av. La Molina s/n, La Molina, Lima 15024, Peru
| | - Marcelo Tacán
- Instituto Nacional de Investigaciones Agropecuarias, Avenida Amazonas y Eloy Alfaro, Edificio MAG, Cuarto Piso, Quito 170518, Ecuador; (Á.M.-A.); (M.T.); (C.T.)
| | - César Tapia
- Instituto Nacional de Investigaciones Agropecuarias, Avenida Amazonas y Eloy Alfaro, Edificio MAG, Cuarto Piso, Quito 170518, Ecuador; (Á.M.-A.); (M.T.); (C.T.)
| | - Álvaro Toledo
- Food and Agriculture Organization of the United Nations, Viale delle Terme di Caracalla s/n, 00153 Roma, Italy;
| | - Jane Toll
- Global Crop Diversity Trust, Platz der Vereinten Nationen 7, 53113 Bonn, Germany; (B.B.T.); (N.P.C.-Á.); (H.D.); (L.G.); (N.J.); (M.O.); (J.T.); (B.K.)
| | - Dang Toan Vu
- Plant Resources Center, Vietnam Academy of Agricultural Sciences, An Khanh, Hoai Duc, Ha Noi 131000, Vietnam; (D.T.V.); (T.D.V.)
| | - Tuong Dang Vu
- Plant Resources Center, Vietnam Academy of Agricultural Sciences, An Khanh, Hoai Duc, Ha Noi 131000, Vietnam; (D.T.V.); (T.D.V.)
| | - Michael J. Way
- Royal Botanic Gardens, Kew, Wakehurst, Ardingly, Haywards Heath RH17 6TN, UK; (R.A.); (E.B.); (C.P.C.); (A.F.); (U.L.); (J.V.M.); (T.R.P.); (M.J.W.)
| | - Mariana Yazbek
- The International Center for Agricultural Research in the Dry Areas, Dalia Bldg, 2nd Floor Bashir El Kassar Street Verdun, Beirut 1108-2010, Lebanon; (A.A.); (M.Y.)
| | - Cinthya Zorrilla
- Joint FAO/IAEA Centre of Nuclear Techniques in Food and Agriculture, Plant Breeding and Genetics Section, 1400 Vienna, Austria;
| | - Benjamin Kilian
- Global Crop Diversity Trust, Platz der Vereinten Nationen 7, 53113 Bonn, Germany; (B.B.T.); (N.P.C.-Á.); (H.D.); (L.G.); (N.J.); (M.O.); (J.T.); (B.K.)
| |
Collapse
|
44
|
Deciphering of Pod Borer [Helicoverpa armigera (Hübner)] Resistance in Cajanus platycarpus (Benth.) Offers Novel Insights on the Reprogramming and Role of Flavonoid Biosynthesis Pathway. Toxins (Basel) 2022; 14:toxins14070455. [PMID: 35878193 PMCID: PMC9325000 DOI: 10.3390/toxins14070455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 06/03/2022] [Accepted: 06/08/2022] [Indexed: 11/23/2022] Open
Abstract
Management of pod borer, Helicoverpa armigera in pigeonpea (Cajanus cajan L.), an important legume crop, has been a pertinent endeavor globally. As with other crops, wild relatives of pigeonpea are bestowed with various resistance traits that include the ability to deter the H. armigera. Understanding the molecular basis of pod borer resistance could provide useful leads for the management of this notorious herbivore. Earlier studies by our group in deciphering the resistance response to herbivory through multiomics approaches in the pigeonpea wild relative, Cajanus platycarpus, divulged the involvement of the flavonoid biosynthesis pathway, speculating an active chemical response of the wild relative to herbivory. The present study is a deeper understanding of the chemical basis of pod borer (H. armigera) resistance in, C. platycarpus, with focus on the flavonoid biosynthesis pathway. To substantiate, quantification of transcripts in H. armigera-challenged C. platycarpus (8 h, 24 h, 48 h, 96 h) showed dynamic upregulation (up to 11-fold) of pivotal pathway genes such as chalcone synthase, dihydroflavonol-4-reductase, flavonoid-3'5'-hydroxylase, flavonol synthase, leucoanthocyanidin reductase, and anthocyanidin synthase. Targeted LC-MS analyses demonstrated a concomitant increase (up to 4-fold) in naringenin, kaempferol, quercetin, delphinidin, cyanidin, epigallocatechin, and epicatechin-3-gallate. Interestingly, H. armigera diet overlaid with the over-produced flavonoids (100 ppm) showed deleterious effects on growth leading to a prolonged larval period demonstrating noteworthy coherence between over-accumulation of pathway transcripts/metabolites. The study depicts novel evidence for the directed metabolic reprogramming of the flavonoid biosynthesis pathway in the wild relative to pod borer; plant metabolic potential is worth exploiting for pest management.
Collapse
|
45
|
Renzi JP, Coyne CJ, Berger J, von Wettberg E, Nelson M, Ureta S, Hernández F, Smýkal P, Brus J. How Could the Use of Crop Wild Relatives in Breeding Increase the Adaptation of Crops to Marginal Environments? FRONTIERS IN PLANT SCIENCE 2022; 13:886162. [PMID: 35783966 PMCID: PMC9243378 DOI: 10.3389/fpls.2022.886162] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/11/2022] [Indexed: 06/01/2023]
Abstract
Alongside the use of fertilizer and chemical control of weeds, pests, and diseases modern breeding has been very successful in generating cultivars that have increased agricultural production several fold in favorable environments. These typically homogeneous cultivars (either homozygous inbreds or hybrids derived from inbred parents) are bred under optimal field conditions and perform well when there is sufficient water and nutrients. However, such optimal conditions are rare globally; indeed, a large proportion of arable land could be considered marginal for agricultural production. Marginal agricultural land typically has poor fertility and/or shallow soil depth, is subject to soil erosion, and often occurs in semi-arid or saline environments. Moreover, these marginal environments are expected to expand with ongoing climate change and progressive degradation of soil and water resources globally. Crop wild relatives (CWRs), most often used in breeding as sources of biotic resistance, often also possess traits adapting them to marginal environments. Wild progenitors have been selected over the course of their evolutionary history to maintain their fitness under a diverse range of stresses. Conversely, modern breeding for broad adaptation has reduced genetic diversity and increased genetic vulnerability to biotic and abiotic challenges. There is potential to exploit genetic heterogeneity, as opposed to genetic uniformity, in breeding for the utilization of marginal lands. This review discusses the adaptive traits that could improve the performance of cultivars in marginal environments and breeding strategies to deploy them.
Collapse
Affiliation(s)
- Juan Pablo Renzi
- Instituto Nacional de Tecnología Agropecuaria, Hilario Ascasubi, Argentina
- CERZOS, Departamento de Agronomía, Universidad Nacional del Sur (CONICET), Bahía Blanca, Argentina
| | | | - Jens Berger
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Wembley, WA, Australia
| | - Eric von Wettberg
- Department of Plant and Soil Science, Gund Institute for Environment, University of Vermont, Burlington, VT, United States
- Department of Applied Mathematics, Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Matthew Nelson
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Wembley, WA, Australia
- The UWA Institute of Agriculture, University of Western Australia, Crawley, WA, Australia
| | - Soledad Ureta
- CERZOS, Departamento de Agronomía, Universidad Nacional del Sur (CONICET), Bahía Blanca, Argentina
| | - Fernando Hernández
- CERZOS, Departamento de Agronomía, Universidad Nacional del Sur (CONICET), Bahía Blanca, Argentina
| | - Petr Smýkal
- Department of Botany, Faculty of Science, Palacký University, Olomouc, Czechia
| | - Jan Brus
- Department of Geoinformatics, Faculty of Sciences, Palacký University, Olomouc, Czechia
| |
Collapse
|
46
|
Manda L, Idohou R, Assogbadjo AE, Agbangla C. Climate Change Reveals Contractions and Expansions in the Distribution of Suitable Habitats for the Neglected Crop Wild Relatives of the Genus Vigna (Savi) in Benin. FRONTIERS IN CONSERVATION SCIENCE 2022. [DOI: 10.3389/fcosc.2022.870041] [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
Sustainable conservation of crop wild relatives is one of the pathways to securing global food security amid climate change threats to biodiversity. However, their conservation is partly limited by spatio-temporal distribution knowledge gaps mostly because they are not morphologically charismatic species to attract conservation attention. Therefore, to contribute to the conservation planning of crop wild relatives, this study assessed the present-day distribution and predicted the potential effect of climate change on the distribution of 15 Vigna crop wild relative taxa in Benin under two future climate change scenarios (RCP 4.5 and RCP 8.5) at the 2055-time horizon. MaxEnt model, species occurrence records, and a combination of climate- and soil-related variables were used. The model performed well (AUC, mean = 0.957; TSS, mean = 0.774). The model showed that (i) precipitation of the driest quarter and isothermality were the dominant environmental variables influencing the distribution of the 15 wild Vigna species in Benin; (ii) about half of the total land area of Benin was potentially a suitable habitat of the studied species under the present climate; (iii) nearly one-third of the species may shift their potentially suitable habitat ranges northwards and about half of the species may lose their suitable habitats by 5 to 40% by 2055 due to climate change; and (iv) the existing protected area network in Benin was ineffective in conserving wild Vigna under the current or future climatic conditions, as it covered only about 10% of the total potentially suitable habitat of the studied species. The study concludes that climate change will have both negative and positive effects on the habitat suitability distribution of Vigna crop wild relatives in Benin such that the use of the existing protected areas alone may not be the only best option to conserve the wild Vigna diversity. Integrating multiple in situ and ex situ conservation approaches taking into account “other effective area-based conservation measures” is recommended. This study provides a crucial step towards the development of sustainable conservation strategies for Vigna crop wild relatives in Benin and West Africa.
Collapse
|
47
|
Eyland D, Luchaire N, Cabrera‐Bosquet L, Parent B, Janssens SB, Swennen R, Welcker C, Tardieu F, Carpentier SC. High-throughput phenotyping reveals differential transpiration behaviour within the banana wild relatives highlighting diversity in drought tolerance. PLANT, CELL & ENVIRONMENT 2022; 45:1647-1663. [PMID: 35297073 PMCID: PMC9310827 DOI: 10.1111/pce.14310] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 01/22/2022] [Indexed: 06/14/2023]
Abstract
Crop wild relatives, the closely related species of crops, may harbour potentially important sources of new allelic diversity for (a)biotic tolerance or resistance. However, to date, wild diversity is only poorly characterized and evaluated. Banana has a large wild diversity but only a narrow proportion is currently used in breeding programmes. The main objective of this study was to evaluate genotype-dependent transpiration responses in relation to the environment. By applying continuous high-throughput phenotyping, we were able to construct genotype-specific transpiration response models in relation to light, VPD and soil water potential. We characterized and evaluated six (sub)species and discerned four phenotypic clusters. Significant differences were observed in leaf area, cumulative transpiration and transpiration efficiency. We confirmed a general stomatal-driven 'isohydric' drought avoidance behaviour, but discovered genotypic differences in the onset and intensity of stomatal closure. We pinpointed crucial genotype-specific soil water potentials when drought avoidance mechanisms were initiated and when stress kicked in. Differences between (sub)species were dependent on environmental conditions, illustrating the need for high-throughput dynamic phenotyping, modelling and validation. We conclude that the banana wild relatives contain useful drought tolerance traits, emphasising the importance of their conservation and potential for use in breeding programmes.
Collapse
Affiliation(s)
- David Eyland
- Laboratory of Tropical Crop Improvement, Division of Crop BiotechnicsKU LeuvenLeuvenBelgium
| | - Nathalie Luchaire
- Département Environnement et AgronomieLEPSE, Univ Montpellier, INRAE, Institut AgroMontpellierFrance
| | - Llorenç Cabrera‐Bosquet
- Département Environnement et AgronomieLEPSE, Univ Montpellier, INRAE, Institut AgroMontpellierFrance
| | - Boris Parent
- Département Environnement et AgronomieLEPSE, Univ Montpellier, INRAE, Institut AgroMontpellierFrance
| | - Steven B. Janssens
- Department ResearchMeise Botanic GardenMeiseBelgium
- Department of BiologyKU LeuvenLeuvenBelgium
| | - Rony Swennen
- Laboratory of Tropical Crop Improvement, Division of Crop BiotechnicsKU LeuvenLeuvenBelgium
- Banana and Plantain Crop ImprovementInternational Institute of Tropical AgricultureKampalaUganda
| | - Claude Welcker
- Département Environnement et AgronomieLEPSE, Univ Montpellier, INRAE, Institut AgroMontpellierFrance
| | - François Tardieu
- Département Environnement et AgronomieLEPSE, Univ Montpellier, INRAE, Institut AgroMontpellierFrance
| | - Sebastien C. Carpentier
- Laboratory of Tropical Crop Improvement, Division of Crop BiotechnicsKU LeuvenLeuvenBelgium
- Biodiversity for Food and AgricultureBioversity InternationalLeuvenBelgium
| |
Collapse
|
48
|
Mohd Saad NS, Neik TX, Thomas WJW, Amas JC, Cantila AY, Craig RJ, Edwards D, Batley J. Advancing designer crops for climate resilience through an integrated genomics approach. CURRENT OPINION IN PLANT BIOLOGY 2022; 67:102220. [PMID: 35489163 DOI: 10.1016/j.pbi.2022.102220] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 03/15/2022] [Accepted: 03/25/2022] [Indexed: 06/14/2023]
Abstract
Climate change and exponential population growth are exposing an immediate need for developing future crops that are highly resilient and adaptable to changing environments to maintain global food security in the next decade. Rigorous selection from long domestication history has rendered cultivated crops genetically disadvantaged, raising concerns in their ability to adapt to these new challenges and limiting their usefulness in breeding programmes. As a result, future crop improvement efforts must rely on integrating various genomic strategies ranging from high-throughput sequencing to machine learning, in order to exploit germplasm diversity and overcome bottlenecks created by domestication, expansive multi-dimensional phenotypes, arduous breeding processes, complex traits and big data.
Collapse
Affiliation(s)
- Nur Shuhadah Mohd Saad
- UWA School of Biological Sciences and the UWA Institute of Agriculture, University of Western Australia, Crawley, WA, Australia
| | - Ting Xiang Neik
- Sunway College Kuala Lumpur, Bandar Sunway, 47500, Selangor, Malaysia
| | - William J W Thomas
- UWA School of Biological Sciences and the UWA Institute of Agriculture, University of Western Australia, Crawley, WA, Australia
| | - Junrey C Amas
- UWA School of Biological Sciences and the UWA Institute of Agriculture, University of Western Australia, Crawley, WA, Australia
| | - Aldrin Y Cantila
- UWA School of Biological Sciences and the UWA Institute of Agriculture, University of Western Australia, Crawley, WA, Australia
| | - Ryan J Craig
- UWA School of Biological Sciences and the UWA Institute of Agriculture, University of Western Australia, Crawley, WA, Australia
| | - David Edwards
- UWA School of Biological Sciences and the UWA Institute of Agriculture, University of Western Australia, Crawley, WA, Australia
| | - Jacqueline Batley
- UWA School of Biological Sciences and the UWA Institute of Agriculture, University of Western Australia, Crawley, WA, Australia.
| |
Collapse
|
49
|
Smith WJ, Quilodrán CS, Jezierski MT, Sendell-Price AT, Clegg SM. The wild ancestors of domestic animals as a neglected and threatened component of biodiversity. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2022; 36:e13867. [PMID: 34811819 DOI: 10.1111/cobi.13867] [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: 07/28/2021] [Revised: 09/27/2021] [Accepted: 11/12/2021] [Indexed: 06/13/2023]
Abstract
Domestic animals have immense economic, cultural, and practical value and have played pivotal roles in the development of human civilization. Many domesticates have, among their wild relatives, undomesticated forms representative of their ancestors. Resurgent interest in these ancestral forms has highlighted the unclear genetic status of many, and some are threatened with extinction by hybridization with domestic conspecifics. We considered the contemporary status of these ancestral forms relative to their scientific, practical, and ecological importance; the varied impacts of wild-domestic hybridization; and the challenges and potential resolutions involved in conservation efforts. Identifying and conserving ancestral forms, particularly with respect to disentangling patterns of gene flow from domesticates, is complex because of the lack of available genomic and phenotypic baselines. Comparative behavioral, ecological, and genetic studies of ancestral-type, feral, and domestic animals should be prioritized to establish the contemporary status of the former. Such baseline information will be fundamental in ensuring successful conservation efforts.
Collapse
Affiliation(s)
- William J Smith
- Edward Grey Institute of Field Ornithology, Department of Zoology, University of Oxford, Oxford, UK
| | - Claudio S Quilodrán
- Edward Grey Institute of Field Ornithology, Department of Zoology, University of Oxford, Oxford, UK
- Department of Biology and Biochemistry, University of Fribourg, Fribourg, Switzerland
| | - Michał T Jezierski
- Edward Grey Institute of Field Ornithology, Department of Zoology, University of Oxford, Oxford, UK
| | - Ashley T Sendell-Price
- Edward Grey Institute of Field Ornithology, Department of Zoology, University of Oxford, Oxford, UK
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Sonya M Clegg
- Edward Grey Institute of Field Ornithology, Department of Zoology, University of Oxford, Oxford, UK
| |
Collapse
|
50
|
Massatti R, Winkler DE. Spatially explicit management of genetic diversity using ancestry probability surfaces. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.13902] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Rob Massatti
- US Geological Survey, Southwest Biological Science Center Flagstaff AZ USA
| | - Daniel E. Winkler
- US Geological Survey, Southwest Biological Science Center Tucson AZ USA
| |
Collapse
|