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Gepts P. Biocultural diversity and crop improvement. Emerg Top Life Sci 2023; 7:ETLS20230067. [PMID: 38084755 PMCID: PMC10754339 DOI: 10.1042/etls20230067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 11/26/2023] [Accepted: 11/27/2023] [Indexed: 12/30/2023]
Abstract
Biocultural diversity is the ever-evolving and irreplaceable sum total of all living organisms inhabiting the Earth. It plays a significant role in sustainable productivity and ecosystem services that benefit humanity and is closely allied with human cultural diversity. Despite its essentiality, biodiversity is seriously threatened by the insatiable and inequitable human exploitation of the Earth's resources. One of the benefits of biodiversity is its utilization in crop improvement, including cropping improvement (agronomic cultivation practices) and genetic improvement (plant breeding). Crop improvement has tended to decrease agricultural biodiversity since the origins of agriculture, but awareness of this situation can reverse this negative trend. Cropping improvement can strive to use more diverse cultivars and a broader complement of crops on farms and in landscapes. It can also focus on underutilized crops, including legumes. Genetic improvement can access a broader range of biodiversity sources and, with the assistance of modern breeding tools like genomics, can facilitate the introduction of additional characteristics that improve yield, mitigate environmental stresses, and restore, at least partially, lost crop biodiversity. The current legal framework covering biodiversity includes national intellectual property and international treaty instruments, which have tended to limit access and innovation to biodiversity. A global system of access and benefit sharing, encompassing digital sequence information, would benefit humanity but remains an elusive goal. The Kunming-Montréal Global Biodiversity Framework sets forth an ambitious set of targets and goals to be accomplished by 2030 and 2050, respectively, to protect and restore biocultural diversity, including agrobiodiversity.
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Affiliation(s)
- Paul Gepts
- Department of Plant Sciences, Section of Crop and Ecosystem Sciences, University of California, Davis, CA 95616-8780, U.S.A
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2
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Young LA, Maughan PJ, Jarvis DE, Hunt SP, Warner HC, Durrant KK, Kohlert T, Curti RN, Bertero D, Filippi GA, Pospíšilíková T, Krak K, Mandák B, Jellen EN. A chromosome-scale reference of Chenopodium watsonii helps elucidate relationships within the North American A-genome Chenopodium species and with quinoa. THE PLANT GENOME 2023; 16:e20349. [PMID: 37195017 DOI: 10.1002/tpg2.20349] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 04/07/2023] [Accepted: 04/13/2023] [Indexed: 05/18/2023]
Abstract
Quinoa (Chenopodium quinoa), an Andean pseudocereal, attained global popularity beginning in the early 2000s due to its protein quality, glycemic index, and high fiber, vitamin, and mineral contents. Pitseed goosefoot (Chenopodium berlandieri), quinoa's North American free-living sister species, grows on disturbed and sandy substrates across the North America, including saline coastal sands, southwestern deserts, subtropical highlands, the Great Plains, and boreal forests. Together with South American avian goosefoot (Chenopodium hircinum) they comprise the American tetraploid goosefoot complex (ATGC). Superimposed on pitseed goosefoot's North American range are approximately 35 AA diploids, most of which are adapted to a diversity of niche environments. We chose to assemble a reference genome for Sonoran A-genome Chenopodium watsonii due to fruit morphological and high (>99.3%) preliminary sequence-match similarities with quinoa, along with its well-established taxonomic status. The genome was assembled into 1377 scaffolds spanning 547.76 Mb (N50 = 55.14 Mb, L50 = 5), with 94% comprised in nine chromosome-scale scaffolds and 93.9% Benchmarking Universal Single-Copy Orthologs genes identified as single copy and 3.4% as duplicated. A high degree of synteny, with minor and mostly telomeric rearrangements, was found when comparing this taxon with the previously reported genome of South American C. pallidicaule and the A-subgenome chromosomes of C. quinoa. Phylogenetic analysis was performed using 10,588 single-nucleotide polymorphisms generated by resequencing a panel of 41 New World AA diploid accessions and the Eurasian H-genome diploid Chenopodium vulvaria, along with three AABB tetraploids previously sequenced. Phylogenetic analysis of these 32 taxa positioned the psammophyte Chenopodium subglabrum on the branch containing A-genome sequences from the ATGC. We also present evidence for long-range dispersal of Chenopodium diploids between North and South America.
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Affiliation(s)
- Lauren A Young
- Plant and Wildlife Sciences Department, Brigham Young University, Provo, Utah, USA
| | | | - David E Jarvis
- Plant and Wildlife Sciences Department, Brigham Young University, Provo, Utah, USA
| | - Spencer P Hunt
- Plant and Wildlife Sciences Department, Brigham Young University, Provo, Utah, USA
| | - Heather C Warner
- Plant and Wildlife Sciences Department, Brigham Young University, Provo, Utah, USA
| | - Kristin K Durrant
- Plant and Wildlife Sciences Department, Brigham Young University, Provo, Utah, USA
| | - Tyler Kohlert
- Plant and Wildlife Sciences Department, Brigham Young University, Provo, Utah, USA
| | - Ramiro N Curti
- Facultad de Ciencias Naturales, Universidad Nacional de Salta, CCT-CONICET, Salta, Argentina
| | - Daniel Bertero
- Cátedra de Producción Vegetal, Facultad de Agronomía, Universidad de Buenos Aires and IFEVA-CONICET, Buenos Aires, Argentina
| | - Gabrielle A Filippi
- Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Tereza Pospíšilíková
- Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Karol Krak
- Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Prague, Czech Republic
- Institute of Botany, Czech Academy of Sciences, Průhonice, Czech Republic
| | - Bohumil Mandák
- Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Prague, Czech Republic
- Institute of Botany, Czech Academy of Sciences, Průhonice, Czech Republic
| | - Eric N Jellen
- Plant and Wildlife Sciences Department, Brigham Young University, Provo, Utah, USA
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3
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Flourish with the wild. NATURE PLANTS 2023; 9:373-374. [PMID: 36944841 DOI: 10.1038/s41477-023-01386-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
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4
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Hoban S, Bruford MW, da Silva JM, Funk WC, Frankham R, Gill MJ, Grueber CE, Heuertz M, Hunter ME, Kershaw F, Lacy RC, Lees C, Lopes-Fernandes M, MacDonald AJ, Mastretta-Yanes A, McGowan PJK, Meek MH, Mergeay J, Millette KL, Mittan-Moreau CS, Navarro LM, O'Brien D, Ogden R, Segelbacher G, Paz-Vinas I, Vernesi C, Laikre L. Genetic diversity goals and targets have improved, but remain insufficient for clear implementation of the post-2020 global biodiversity framework. CONSERV GENET 2023; 24:181-191. [PMID: 36683963 PMCID: PMC9841145 DOI: 10.1007/s10592-022-01492-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 11/30/2022] [Indexed: 01/18/2023]
Abstract
Genetic diversity among and within populations of all species is necessary for people and nature to survive and thrive in a changing world. Over the past three years, commitments for conserving genetic diversity have become more ambitious and specific under the Convention on Biological Diversity's (CBD) draft post-2020 global biodiversity framework (GBF). This Perspective article comments on how goals and targets of the GBF have evolved, the improvements that are still needed, lessons learned from this process, and connections between goals and targets and the actions and reporting that will be needed to maintain, protect, manage and monitor genetic diversity. It is possible and necessary that the GBF strives to maintain genetic diversity within and among populations of all species, to restore genetic connectivity, and to develop national genetic conservation strategies, and to report on these using proposed, feasible indicators.
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Affiliation(s)
- Sean Hoban
- The Morton Arboretum, Center for Tree Science, Lisle, USA.,The University of Chicago, Chicago, USA
| | | | - Jessica M da Silva
- South African National Biodiversity Institute, Pretoria, South Africa.,Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Johannesburg, South Africa
| | - W Chris Funk
- Department of Biology, Colorado State University, Fort Collins, USA
| | - Richard Frankham
- School of Natural Sciences, Macquarie University, Sydney, NSW Australia
| | - Michael J Gill
- NatureServe, Biodiversity Indicators Program, Arlington, USA
| | - Catherine E Grueber
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, Australia
| | | | - Margaret E Hunter
- U.S. Geological Survey, Wetland and Aquatic Research Center, Gainesville, USA
| | - Francine Kershaw
- Oceans Division, Natural Resources Defense Council, NewYork, USA
| | - Robert C Lacy
- Chicago Zoological Society, Species Conservation Toolkit Initiative, Brookfield, USA
| | - Caroline Lees
- Conservation Planning Specialist Group, IUCN SSC, Auckland, New Zealand
| | | | - Anna J MacDonald
- Australian Antarctic Division, Department of Climate Change, Energy, the Environment and Water, Kingston, Australia
| | - Alicia Mastretta-Yanes
- Comisión Nacional para el Conocimiento y Uso de la Biodiversidad (CONABIO), Mexico City, Mexico.,Consejo Nacional de Ciencia Y Tecnología (CONACYT), Mexico City, Mexico
| | - Philip J K McGowan
- School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne, UK
| | - Mariah H Meek
- Department of Integrative Biology; Ecology, Evolution, and Behavior Program, Michigan State University, AgBio Research, Lansing, USA
| | - Joachim Mergeay
- Research Institute for Nature and Forest, Geraardsbergen, Belgium
| | - Katie L Millette
- Group on Earth Observations Biodiversity Observation Network (GEO BON), McGill University, Montreal, Canada
| | - Cinnamon S Mittan-Moreau
- Kellogg Biological Station; Ecology and Evolutionary Biology, Michigan State University, Lansing, USA
| | | | | | - Rob Ogden
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, EH25 9RG, Midlothian, United Kingdom
| | | | - Ivan Paz-Vinas
- Department of Biology, Colorado State University, Fort Collins, USA
| | | | - Linda Laikre
- Department of Zoology, Stockholm University, Stockholm, Sweden
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5
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Aguirre-Liguori JA, Morales-Cruz A, Gaut BS. Evaluating the persistence and utility of five wild Vitis species in the context of climate change. Mol Ecol 2022; 31:6457-6472. [PMID: 36197804 PMCID: PMC10092629 DOI: 10.1111/mec.16715] [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: 02/02/2022] [Revised: 09/23/2022] [Accepted: 09/29/2022] [Indexed: 01/13/2023]
Abstract
Crop wild relatives (CWRs) have the capacity to contribute novel traits to agriculture. Given climate change, these contributions may be especially vital for the persistence of perennial crops, because perennials are often clonally propagated and consequently do not evolve rapidly. By studying the landscape genomics of samples from five Vitis CWRs (V. arizonica, V. mustangensis, V. riparia, V. berlandieri and V. girdiana) in the context of projected climate change, we addressed two goals. The first was to assess the relative potential of different CWR accessions to persist in the face of climate change. By integrating species distribution models with adaptive genetic variation, additional genetic features such as genomic load and a phenotype (resistance to Pierce's Disease), we predicted that accessions from one species (V. mustangensis) are particularly well-suited to persist in future climates. The second goal was to identify which CWR accessions may contribute to bioclimatic adaptation for grapevine (V. vinifera) cultivation. To do so, we evaluated whether CWR accessions have the allelic capacity to persist if moved to locations where grapevines are cultivated in the United States. We identified six candidates from V. mustangensis and hypothesized that they may prove useful for contributing alleles that can mitigate climate impacts on viticulture. By identifying candidate germplasm, this study takes a conceptual step toward assessing the genomic and bioclimatic characteristics of CWRs.
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Affiliation(s)
- Jonas A Aguirre-Liguori
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA
| | - Abraham Morales-Cruz
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA
| | - Brandon S Gaut
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA
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6
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Tirnaz S, Zandberg J, Thomas WJW, Marsh J, Edwards D, Batley J. Application of crop wild relatives in modern breeding: An overview of resources, experimental and computational methodologies. FRONTIERS IN PLANT SCIENCE 2022; 13:1008904. [PMID: 36466237 PMCID: PMC9712971 DOI: 10.3389/fpls.2022.1008904] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 10/25/2022] [Indexed: 06/01/2023]
Abstract
Global agricultural industries are under pressure to meet the future food demand; however, the existing crop genetic diversity might not be sufficient to meet this expectation. Advances in genome sequencing technologies and availability of reference genomes for over 300 plant species reveals the hidden genetic diversity in crop wild relatives (CWRs), which could have significant impacts in crop improvement. There are many ex-situ and in-situ resources around the world holding rare and valuable wild species, of which many carry agronomically important traits and it is crucial for users to be aware of their availability. Here we aim to explore the available ex-/in- situ resources such as genebanks, botanical gardens, national parks, conservation hotspots and inventories holding CWR accessions. In addition we highlight the advances in availability and use of CWR genomic resources, such as their contribution in pangenome construction and introducing novel genes into crops. We also discuss the potential and challenges of modern breeding experimental approaches (e.g. de novo domestication, genome editing and speed breeding) used in CWRs and the use of computational (e.g. machine learning) approaches that could speed up utilization of CWR species in breeding programs towards crop adaptability and yield improvement.
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7
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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.
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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
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Christov NK, Tsonev S, Dragov R, Taneva K, Bozhanova V, Todorovska EG. Genetic diversity and population structure of modern Bulgarian and foreign durum wheat based on microsatellite and agronomic data. BIOTECHNOL BIOTEC EQ 2022. [DOI: 10.1080/13102818.2022.2116999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
Affiliation(s)
- Nikolai Kirilov Christov
- Department of Functional Genetics, Abiotic and Biotic Stress, AgroBioInstitute, Agricultural Academy, Sofia, Bulgaria
| | - Stefan Tsonev
- Department of Functional Genetics, Abiotic and Biotic Stress, AgroBioInstitute, Agricultural Academy, Sofia, Bulgaria
| | - Rangel Dragov
- Department of Durum Wheat Breeding, Field Crops Institute, Agricultural Academy, Chirpan, Bulgaria
| | - Krasimira Taneva
- Department of Durum Wheat Breeding, Field Crops Institute, Agricultural Academy, Chirpan, Bulgaria
| | - Violeta Bozhanova
- Department of Durum Wheat Breeding, Field Crops Institute, Agricultural Academy, Chirpan, Bulgaria
| | - Elena Georgieva Todorovska
- Department of Functional Genetics, Abiotic and Biotic Stress, AgroBioInstitute, Agricultural Academy, Sofia, Bulgaria
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9
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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.
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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
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10
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Zumwalde BA, Fredlock B, Beckman E, Duckett D, McCauley RA, Spence ES, Hoban S. Assessing ex situ genetic and ecogeographic conservation in a threatened but widespread oak after range‐wide collecting effort. Evol Appl 2022; 15:1002-1017. [PMID: 35782011 PMCID: PMC9234636 DOI: 10.1111/eva.13391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 04/11/2022] [Accepted: 04/12/2022] [Indexed: 11/04/2022] Open
Affiliation(s)
- Bethany A. Zumwalde
- The Morton Arboretum Center for Tree Science 4100 Illinois 53 Lisle IL 60532 USA
- Department of Biology University of Florida Gainesville FL 32611 USA
| | - Bailie Fredlock
- The Morton Arboretum Center for Tree Science 4100 Illinois 53 Lisle IL 60532 USA
| | - Emily Beckman
- The Morton Arboretum Center for Tree Science 4100 Illinois 53 Lisle IL 60532 USA
| | - Drew Duckett
- The Morton Arboretum Center for Tree Science 4100 Illinois 53 Lisle IL 60532 USA
- Department of Evolution, Ecology and Organismal Biology The Ohio State University 1315 Kinnear Rd Columbus OH 43212 USA
| | - Ross A. McCauley
- Department of Biology Fort Lewis College 1000 Rim Drive Durango CO 81301 USA
| | - Emma Suzuki Spence
- The Morton Arboretum Center for Tree Science 4100 Illinois 53 Lisle IL 60532 USA
| | - Sean Hoban
- The Morton Arboretum Center for Tree Science 4100 Illinois 53 Lisle IL 60532 USA
- The Field Museum Chicago IL USA
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11
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Mertens A, Bawin Y, Vanden Abeele S, Kallow S, Swennen R, Vu DT, Vu TD, Minh HT, Panis B, Vandelook F, Janssens SB. Phylogeography and conservation gaps of Musa balbisiana Colla genetic diversity revealed by microsatellite markers. GENETIC RESOURCES AND CROP EVOLUTION 2022; 69:2515-2534. [PMID: 36017134 PMCID: PMC9393128 DOI: 10.1007/s10722-022-01389-4] [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: 11/05/2021] [Accepted: 04/11/2022] [Indexed: 06/15/2023]
Abstract
UNLABELLED Collection and storage of crop wild relative (CWR) germplasm is crucial for preserving species genetic diversity and crop improvement. Nevertheless, much of the genetic variation of CWRs is absent in ex situ collections and detailed passport data are often lacking. Here, we focussed on Musa balbisiana, one of the two main progenitor species of many banana cultivars. We investigated the genetic structure of M. balbisiana across its distribution range using microsatellite markers. Accessions stored at the International Musa Germplasm Transit Centre (ITC) ex situ collection were compared with plant material collected from multiple countries and home gardens from Vietnam. Genetic structure analyses revealed that accessions could be divided into three main clusters. Vietnamese and Chinese populations were assigned to a first and second cluster respectively. A third cluster consisted of ITC and home garden accessions. Samples from Papua New Guinea were allocated to the cluster with Chinese populations but were assigned to a separate fourth cluster if the number of allowed clusters was set higher. Only one ITC accession grouped with native M. balbisiana populations and one group of ITC accessions was nearly genetically identical to home garden samples. This questioned their wild status, including accessions used as reference for wild M. balbisiana. Moreover, most ITC accessions and home garden samples were genetically distinct from wild populations. Our results highlight that additional germplasm should be collected from the native distribution range, especially from Northeast India, Myanmar, China, and the Philippines and stored for ex situ conservation at the ITC. The lack of passport data for many M. balbisiana accessions also complicates the interpretation of genetic information in relation to cultivation and historical dispersal routes. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s10722-022-01389-4.
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Affiliation(s)
- Arne Mertens
- Department of Biosystems, Laboratory of Tropical Crop Improvement, KU Leuven, Leuven, Belgium
- Meise Botanic Garden, Meise, Belgium
| | - Yves Bawin
- Meise Botanic Garden, Meise, Belgium
- Department of Biology, KU Leuven, Leuven, Belgium
| | | | - Simon Kallow
- Department of Biosystems, Laboratory of Tropical Crop Improvement, KU Leuven, Leuven, Belgium
- Royal Botanic Gardens Kew, Millennium Seed Bank, Ardingly, UK
| | - Rony Swennen
- Department of Biosystems, Laboratory of Tropical Crop Improvement, KU Leuven, Leuven, Belgium
- International Institute of Tropical Agriculture, Kampala, Uganda
| | - Dang Toan Vu
- Research Planning and International Cooperation Department, Plant Resources Center, Hanoi, Vietnam
- Faculty of Agronomy, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Tuong Dang Vu
- Research Planning and International Cooperation Department, Plant Resources Center, Hanoi, Vietnam
| | - Ho Thi Minh
- Research Planning and International Cooperation Department, Plant Resources Center, Hanoi, Vietnam
| | - Bart Panis
- Bioversity International, Leuven, Belgium
| | | | - Steven B. Janssens
- Meise Botanic Garden, Meise, Belgium
- Department of Biology, KU Leuven, Leuven, Belgium
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12
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Ramirez-Villegas J, Khoury CK, Achicanoy HA, Diaz MV, Mendez AC, Sosa CC, Kehel Z, Guarino L, Abberton M, Aunario J, Awar BA, Alarcon JC, Amri A, Anglin NL, Azevedo V, Aziz K, Capilit GL, Chavez O, Chebotarov D, Costich DE, Debouck DG, Ellis D, Falalou H, Fiu A, Ghanem ME, Giovannini P, Goungoulou AJ, Gueye B, Hobyb AIE, Jamnadass R, Jones CS, Kpeki B, Lee JS, McNally KL, Muchugi A, Ndjiondjop MN, Oyatomi O, Payne TS, Ramachandran S, Rossel G, Roux N, Ruas M, Sansaloni C, Sardos J, Setiyono TD, Tchamba M, van den Houwe I, Velazquez JA, Venuprasad R, Wenzl P, Yazbek M, Zavala C. State of ex situ conservation of landrace groups of 25 major crops. NATURE PLANTS 2022; 8:491-499. [PMID: 35534721 PMCID: PMC9122826 DOI: 10.1038/s41477-022-01144-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 03/28/2022] [Indexed: 06/14/2023]
Abstract
Crop landraces have unique local agroecological and societal functions and offer important genetic resources for plant breeding. Recognition of the value of landrace diversity and concern about its erosion on farms have led to sustained efforts to establish ex situ collections worldwide. The degree to which these efforts have succeeded in conserving landraces has not been comprehensively assessed. Here we modelled the potential distributions of eco-geographically distinguishable groups of landraces of 25 cereal, pulse and starchy root/tuber/fruit crops within their geographic regions of diversity. We then analysed the extent to which these landrace groups are represented in genebank collections, using geographic and ecological coverage metrics as a proxy for genetic diversity. We find that ex situ conservation of landrace groups is currently moderately comprehensive on average, with substantial variation among crops; a mean of 63% ± 12.6% of distributions is currently represented in genebanks. Breadfruit, bananas and plantains, lentils, common beans, chickpeas, barley and bread wheat landrace groups are among the most fully represented, whereas the largest conservation gaps persist for pearl millet, yams, finger millet, groundnut, potatoes and peas. Geographic regions prioritized for further collection of landrace groups for ex situ conservation include South Asia, the Mediterranean and West Asia, Mesoamerica, sub-Saharan Africa, the Andean mountains of South America and Central to East Asia. With further progress to fill these gaps, a high degree of representation of landrace group diversity in genebanks is feasible globally, thus fulfilling international targets for their ex situ conservation.
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Affiliation(s)
- Julian Ramirez-Villegas
- International Center for Tropical Agriculture (CIAT), Cali, Colombia.
- CGIAR Research Program on Climate Change, Agriculture and Food Security (CCAFS), Cali, Colombia.
- Wageningen University & Research (WUR), Plant Production Systems Group, Wageningen, The Netherlands.
| | - Colin K Khoury
- International Center for Tropical Agriculture (CIAT), Cali, Colombia.
- San Diego Botanic Garden, Encinitas, CA, USA.
| | | | | | - Andres C Mendez
- International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Chrystian C Sosa
- International Center for Tropical Agriculture (CIAT), Cali, Colombia
- Pontificia Universidad Javeriana Cali, Cali, Colombia
- Universidad del Quindío, Armenia, Colombia
| | - Zakaria Kehel
- International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat, Morocco
| | | | - Michael Abberton
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Jorrel Aunario
- International Rice Research Institute (IRRI), Los Baños, Philippines
| | - Bashir Al Awar
- International Center for Agricultural Research in the Dry Areas (ICARDA), Beirut, Lebanon
| | | | - Ahmed Amri
- International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat, Morocco
| | - Noelle L Anglin
- International Potato Center (CIP), Lima, Peru
- United States Department of Agriculture (USDA), Agricultural Research Service, Aberdeen, ID, USA
| | - Vania Azevedo
- International Potato Center (CIP), Lima, Peru
- International Crops Research Institute for the Semi-arid Tropics (ICRISAT), Hyderabad, India
| | - Khadija Aziz
- International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat, Morocco
| | - Grace Lee Capilit
- International Rice Research Institute (IRRI), Los Baños, Philippines
| | | | - Dmytro Chebotarov
- International Rice Research Institute (IRRI), Los Baños, Philippines
| | - Denise E Costich
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, México
| | - Daniel G Debouck
- International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - David Ellis
- International Potato Center (CIP), Lima, Peru
| | - Hamidou Falalou
- International Crops Research Institute for the Semi-arid Tropics (ICRISAT), Niamey, Niger
| | - Albert Fiu
- Centre for Pacific Crops and Trees (CePaCT), Narere, Fiji
| | | | | | | | - Badara Gueye
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Amal Ibn El Hobyb
- International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat, Morocco
| | | | - Chris S Jones
- International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
| | | | - Jae-Sung Lee
- International Rice Research Institute (IRRI), Los Baños, Philippines
| | - Kenneth L McNally
- International Rice Research Institute (IRRI), Los Baños, Philippines
| | - Alice Muchugi
- International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
| | | | - Olaniyi Oyatomi
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Thomas S Payne
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, México
| | - Senthil Ramachandran
- International Crops Research Institute for the Semi-arid Tropics (ICRISAT), Hyderabad, India
| | | | | | - Max Ruas
- Bioversity International, Montpellier, France
| | - Carolina Sansaloni
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, México
| | | | - Tri Deri Setiyono
- International Rice Research Institute (IRRI), Los Baños, Philippines
- Louisiana State University, Baton Rouge, LA, USA
| | - Marimagne Tchamba
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | | | | | | | - Peter Wenzl
- International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Mariana Yazbek
- International Center for Agricultural Research in the Dry Areas (ICARDA), Beirut, Lebanon
| | - Cristian Zavala
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, México
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13
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Innes P, Gossweiler A, Jensen S, Tilley D, St. John L, Jones T, Kitchen S, Hulke BS. Assessment of biogeographic variation in traits of Lewis flax ( Linum lewisii) for use in restoration and agriculture. AOB PLANTS 2022; 14:plac005. [PMID: 35273788 PMCID: PMC8906388 DOI: 10.1093/aobpla/plac005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 01/31/2022] [Indexed: 06/14/2023]
Abstract
Lewis flax (Linum lewisii) is widely distributed across western North America and is currently used in native ecosystem restoration. There is also growing interest in de novo domestication of Lewis flax as a perennial oilseed crop. To better understand this species and facilitate both restoration and domestication, we used common gardens to assess biogeographical variation in a variety of seed and growth traits from 37 flax accessions, consisting of 35 wild populations from the Intermountain West region, the pre-variety germplasm Maple Grove (L. lewisii) and the cultivar 'Appar' (L. perenne) and related this variation to collection site geography and climate. Results from linear mixed models suggest there is extensive phenotypic variation among populations of Lewis flax within the Intermountain West. Using a multivariate approach, we identify a key suite of traits that are related to latitude and climate and may facilitate adaptation, including flowering indeterminacy, seed mass and stem number. These traits should be taken into account when considering the release of new germplasm for restoration efforts. We also find that Lewis flax seed contains desirably high amounts of alpha-linolenic acid and is otherwise mostly indistinguishable in fatty acid composition from oil-type varieties of domesticated flax (L. usitatissimum), making it a strong candidate for domestication. This study provides fundamental knowledge for future research into the ecology and evolution of Lewis flax, which will inform its use in both restoration and agriculture.
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Affiliation(s)
- Peter Innes
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA
| | - André Gossweiler
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58108, USA
| | - Scott Jensen
- Rocky Mountain Research Station, United States Department of Agriculture – Forest Service, Provo, UT 84606, USA
| | - Derek Tilley
- Aberdeen Plant Materials Center, United States Department of Agriculture – Natural Resources Conservation Service, Aberdeen, ID 83210, USA
| | - Loren St. John
- Aberdeen Plant Materials Center, United States Department of Agriculture – Natural Resources Conservation Service, Aberdeen, ID 83210, USA
| | - Thomas Jones
- Forage and Range Research Laboratory, United States Department of Agriculture – Agricultural Research Service, Logan, UT 84322, USA
| | - Stanley Kitchen
- Rocky Mountain Research Station, United States Department of Agriculture – Forest Service, Provo, UT 84606, USA
| | - Brent S Hulke
- Edward T. Schafer Agricultural Research Center, United States Department of Agriculture – Agricultural Research Service, Fargo, ND 58102, USA
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14
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Gibson AK. Genetic diversity and disease: The past, present, and future of an old idea. Evolution 2022; 76:20-36. [PMID: 34796478 PMCID: PMC9064374 DOI: 10.1111/evo.14395] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 10/03/2021] [Accepted: 10/08/2021] [Indexed: 01/21/2023]
Abstract
Why do infectious diseases erupt in some host populations and not others? This question has spawned independent fields of research in evolution, ecology, public health, agriculture, and conservation. In the search for environmental and genetic factors that predict variation in parasitism, one hypothesis stands out for its generality and longevity: genetically homogeneous host populations are more likely to experience severe parasitism than genetically diverse populations. In this perspective piece, I draw on overlapping ideas from evolutionary biology, agriculture, and conservation to capture the far-reaching implications of the link between genetic diversity and disease. I first summarize the development of this hypothesis and the results of experimental tests. Given the convincing support for the protective effect of genetic diversity, I then address the following questions: (1) Where has this idea been put to use, in a basic and applied sense, and how can we better use genetic diversity to limit disease spread? (2) What new hypotheses does the established disease-diversity relationship compel us to test? I conclude that monitoring, preserving, and augmenting genetic diversity is one of our most promising evolutionarily informed strategies for buffering wild, domesticated, and human populations against future outbreaks.
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Affiliation(s)
- Amanda Kyle Gibson
- Department of Biology University of Virginia Charlottesville Virginia 22903
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15
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Cao B, Bai C, Zhang M, Lu Y, Gao P, Yang J, Xue Y, Li G. Future landscape of renewable fuel resources: Current and future conservation and utilization of main biofuel crops in China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:150946. [PMID: 34655627 DOI: 10.1016/j.scitotenv.2021.150946] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 10/07/2021] [Accepted: 10/09/2021] [Indexed: 06/13/2023]
Abstract
Biofuel crops are one of the most promising regenerative alternatives of energy resources to fossil fuels. Revealing the current and future resource distribution patterns of biofuel crops will promote the development of green energies and the mitigation of greenhouse gas emissions. In this study, we first conducted a comprehensive and systematic analysis on the distribution patterns of main biofuel crops in China, using 22,352 occurrence records of 31 biofuel plant species and thirty-year environmental variables (1970-2000) with maximum entropy modeling, as well as nine-year field investigation of land use (2011-2019). The results showed that there were six different sub-regions for main biofuel crops in China, while Southwest China and South China were determined as the main concentrated potential regions. Specifically, the ranges of these regions were wider than those of current land use of main biofuel crops in China, indicating great potential for industrial cultivation. Moreover, the main biofuel crops had diverse changing patterns including increase, decrease and unstable under future climate change. Among them, biofuel crops with increase pattern (six crops) and decrease pattern (seven crops) should receive high attention for future resource utilization and production. Further field validation results confirmed that the above distribution patterns were mainly determined by increasing global temperature and precipitation. Collectively, these results will provide valuable references for the utilization and development of main biofuel resources under climate change in China, thereby shedding light on studies regarding the production of green biofuels globally.
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Affiliation(s)
- Bo Cao
- Core Research Laboratory, the Second Affiliated Hospital, School of Medicine, Xi'an Jiaotong University, Xi'an 710004, China; College of Life Sciences, Shaanxi Normal University, Xi'an 710062, China.
| | - Chengke Bai
- College of Life Sciences, Shaanxi Normal University, Xi'an 710062, China; National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest of China, College of Life Sciences, Shaanxi Normal University, Xi'an 710062, China
| | - Meng Zhang
- College of Life Sciences, Shaanxi Normal University, Xi'an 710062, China
| | - Yumeng Lu
- College of Life Sciences, Shaanxi Normal University, Xi'an 710062, China
| | - Pufan Gao
- College of Life Sciences, Shaanxi Normal University, Xi'an 710062, China
| | - Jingjing Yang
- College of Life Sciences, Shaanxi Normal University, Xi'an 710062, China
| | - Ying Xue
- College of Life Sciences, Shaanxi Normal University, Xi'an 710062, China
| | - Guishuang Li
- College of Life Sciences, Shaanxi Normal University, Xi'an 710062, China; National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest of China, College of Life Sciences, Shaanxi Normal University, Xi'an 710062, China
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16
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Khoury CK, Brush S, Costich DE, Curry HA, de Haan S, Engels JMM, Guarino L, Hoban S, Mercer KL, Miller AJ, Nabhan GP, Perales HR, Richards C, Riggins C, Thormann I. Crop genetic erosion: understanding and responding to loss of crop diversity. THE NEW PHYTOLOGIST 2022; 233:84-118. [PMID: 34515358 DOI: 10.1111/nph.17733] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 08/13/2021] [Indexed: 06/13/2023]
Abstract
Crop diversity underpins the productivity, resilience and adaptive capacity of agriculture. Loss of this diversity, termed crop genetic erosion, is therefore concerning. While alarms regarding evident declines in crop diversity have been raised for over a century, the magnitude, trajectory, drivers and significance of these losses remain insufficiently understood. We outline the various definitions, measurements, scales and sources of information on crop genetic erosion. We then provide a synthesis of evidence regarding changes in the diversity of traditional crop landraces on farms, modern crop cultivars in agriculture, crop wild relatives in their natural habitats and crop genetic resources held in conservation repositories. This evidence indicates that marked losses, but also maintenance and increases in diversity, have occurred in all these contexts, the extent depending on species, taxonomic and geographic scale, and region, as well as analytical approach. We discuss steps needed to further advance knowledge around the agricultural and societal significance, as well as conservation implications, of crop genetic erosion. Finally, we propose actions to mitigate, stem and reverse further losses of crop diversity.
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Affiliation(s)
- Colin K Khoury
- International Center for Tropical Agriculture (CIAT), Km 17, Recta Cali-Palmira, Apartado Aéreo 6713, 763537, Cali, Colombia
- Department of Biology, Saint Louis University, 1 N. Grand Blvd, St Louis, MO, 63103, USA
- San Diego Botanic Garden, 230 Quail Gardens Dr., Encinitas, CA, 92024, USA
| | - Stephen Brush
- University of California Davis, 1 Shields Ave., Davis, CA, 95616, USA
| | - Denise E Costich
- International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz, Km. 45, El Batán, 56237, Texcoco, México
| | - Helen Anne Curry
- Department of History and Philosophy of Science, University of Cambridge, Free School Lane, Cambridge, CB2 3RH, UK
| | - Stef de Haan
- International Potato Center (CIP), Avenida La Molina 1895, La Molina, Apartado Postal 1558, Lima, Peru
| | | | - Luigi Guarino
- Global Crop Diversity Trust, Platz der Vereinten Nationen 7, 53113, Bonn, Germany
| | - Sean Hoban
- The Morton Arboretum, The Center for Tree Science, 4100 IL-53, Lisle, IL, 60532, USA
| | - Kristin L Mercer
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, OH, 43210, USA
| | - Allison J Miller
- Department of Biology, Saint Louis University, 1 N. Grand Blvd, St Louis, MO, 63103, USA
- Donald Danforth Plant Science Center, 975 N Warson Rd, St Louis, MO, 63132, USA
| | - Gary P Nabhan
- Southwest Center and Institute of the Environment, University of Arizona, 1401 E. First St., PO Box 210185, Tucson, AZ, 85721-0185, USA
| | - Hugo R Perales
- Departamento de Agroecología, El Colegio de la Frontera Sur, San Cristóbal, Chiapas, 29290, México
| | - Chris Richards
- National Laboratory for Genetic Resources Preservation, United States Department of Agriculture, Agricultural Research Service, 1111 South Mason Street, Fort Collins, CO, 80521, USA
| | - Chance Riggins
- Department of Crop Sciences, University of Illinois, 331 Edward R. Madigan Lab, 1201 W. Gregory Dr., Urbana, IL, 61801, USA
| | - Imke Thormann
- Federal Office for Agriculture and Food (BLE), Information and Coordination Centre for Biological Diversity (IBV), Deichmanns Aue 29, 53179, Bonn, Germany
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17
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Cortés AJ, Cornille A, Yockteng R. Evolutionary Genetics of Crop-Wild Complexes. Genes (Basel) 2021; 13:1. [PMID: 35052346 PMCID: PMC8774885 DOI: 10.3390/genes13010001] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 12/07/2021] [Indexed: 12/12/2022] Open
Abstract
Since Darwin's time, the role of crop wild relatives (CWR), landraces, and cultivated genepools in shaping plant diversity and boosting food resources has been a major question [...].
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Affiliation(s)
- Andrés J. Cortés
- Corporación Colombiana de Investigación Agropecuaria AGROSAVIA, C.I. La Selva, Km 7 vía Rionegro—Las Palmas, Rionegro 054048, Colombia
- Facultad de Ciencias Agrarias—Departamento de Ciencias Forestales, Universidad Nacional de Colombia—Sede Medellín, Medellín 050034, Colombia
| | - Amandine Cornille
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE—Le Moulon, Gif-sur-Yvette, France; or
| | - Roxana Yockteng
- Corporación Colombiana de Investigación Agropecuaria AGROSAVIA, C.I. Tibaitatá, Km 14 vía Mosquera, Cundinamarca 250047, Colombia;
- Institut de Systématique, Evolution, Biodiversité-UMR-CNRS 7205, National Museum of Natural History, 75005 Paris, France
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18
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Kallow S, Mertens A, Janssens SB, Vandelook F, Dickie J, Swennen R, Panis B. Banana seed genetic resources for food security: Status, constraints, and future priorities. Food Energy Secur 2021; 11:e345. [PMID: 35866053 PMCID: PMC9285888 DOI: 10.1002/fes3.345] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 10/14/2021] [Accepted: 10/25/2021] [Indexed: 11/21/2022] Open
Abstract
Storing seed collections of crop wild relatives, wild plant taxa genetically related to crops, is an essential component in global food security. Seed banking protects genetic resources from degradation and extinction and provides material for use by breeders. Despite being among the most important crops in the world, banana and plantain crop wild relatives are largely under‐represented in genebanks. Nevertheless, banana crop wild relative seed collections are in fact held in different countries, but these have not previously been part of reporting or analysis. To fill this gap, we firstly collated banana seed accession data from 13 institutions in 10 countries. These included 537 accessions containing an estimated 430,000 seeds of 56 species. We reviewed their taxonomic coverage and seed storage conditions including viability estimates. We found that seed accessions have low viability (25% mean) representing problems in seed storage and processing. Secondly, we surveyed 22 institutions involved in banana genetic resource conservation regarding the key constraints and knowledge gaps that institutions face related to banana seed conservation. Major constraints were identified including finding suitable material and populations to collect seeds from, lack of knowledge regarding optimal storage conditions and germination conditions. Thirdly, we carried out a conservation prioritization and gap analysis of Musaceae taxa, using established methods, to index representativeness. Overall, our conservation assessment showed that despite this extended data set banana crop wild relatives are inadequately conserved, with 51% of taxa not represented in seed collections at all; the average conservation assessment showing high priority for conservation according to the index. Finally, we provide recommendations for future collecting, research, and management, to conserve banana and plantain crop wild relatives in seed banks for future generations.
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Affiliation(s)
- Simon Kallow
- Royal Botanic Gardens Kew Millennium Seed Bank Ardingly UK
- Department of Biosystems Katholieke Universiteit Leuven Leuven Belgium
- Meise Botanic Garden Meise Belgium
| | - Arne Mertens
- Department of Biosystems Katholieke Universiteit Leuven Leuven Belgium
- Meise Botanic Garden Meise Belgium
| | - Steven B. Janssens
- Meise Botanic Garden Meise Belgium
- Biology Department Katholieke Universiteit Leuven Leuven Belgium
| | | | - John Dickie
- Royal Botanic Gardens Kew Millennium Seed Bank Ardingly UK
| | - Rony Swennen
- Department of Biosystems Katholieke Universiteit Leuven Leuven Belgium
- International Institute of Tropical Agriculture Kampala Uganda
| | - Bart Panis
- Department of Biosystems Katholieke Universiteit Leuven Leuven Belgium
- Bioversity International Leuven Belgium
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19
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20
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Mabry ME, Turner-Hissong SD, Gallagher EY, McAlvay AC, An H, Edger PP, Moore JD, Pink DAC, Teakle GR, Stevens CJ, Barker G, Labate J, Fuller DQ, Allaby RG, Beissinger T, Decker JE, Gore MA, Pires JC. The Evolutionary History of Wild, Domesticated, and Feral Brassica Oleracea (Brassicaceae). Mol Biol Evol 2021; 38:4419-4434. [PMID: 34157722 PMCID: PMC8476135 DOI: 10.1093/molbev/msab183] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Understanding the evolutionary history of crops, including identifying wild relatives, helps to provide insight for conservation and crop breeding efforts. Cultivated Brassica oleracea has intrigued researchers for centuries due to its wide diversity in forms, which include cabbage, broccoli, cauliflower, kale, kohlrabi, and Brussels sprouts. Yet, the evolutionary history of this species remains understudied. With such different vegetables produced from a single species, B. oleracea is a model organism for understanding the power of artificial selection. Persistent challenges in the study of B. oleracea include conflicting hypotheses regarding domestication and the identity of the closest living wild relative. Using newly generated RNA-seq data for a diversity panel of 224 accessions, which represents 14 different B. oleracea crop types and nine potential wild progenitor species, we integrate phylogenetic and population genetic techniques with ecological niche modeling, archaeological, and literary evidence to examine relationships among cultivars and wild relatives to clarify the origin of this horticulturally important species. Our analyses point to the Aegean endemic B. cretica as the closest living relative of cultivated B. oleracea, supporting an origin of cultivation in the Eastern Mediterranean region. Additionally, we identify several feral lineages, suggesting that cultivated plants of this species can revert to a wild-like state with relative ease. By expanding our understanding of the evolutionary history in B. oleracea, these results contribute to a growing body of knowledge on crop domestication that will facilitate continued breeding efforts including adaptation to changing environmental conditions.
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Affiliation(s)
- Makenzie E Mabry
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, MO, U.S.A
| | | | - Evan Y Gallagher
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, MO, U.S.A
| | - Alex C McAlvay
- Institute of Economic Botany, The New York Botanical Garden, Bronx, NY, U.S.A
| | - Hong An
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, MO, U.S.A
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, MI, USA
| | | | - David A C Pink
- Agriculture and Environment Department, Harper Adams University, UK
| | | | - Chris J Stevens
- School of Archaeology and Museology, Peking University, Beijing, China.,Institute of Archaeology, University College London, London, UK
| | - Guy Barker
- School of Life Science, University of Warwick, UK
| | - Joanne Labate
- USDA, ARS Plant Genetic Resources Unit, Cornell AgriTech, Geneva, NY, USA
| | - Dorian Q Fuller
- Institute of Archaeology, University College London, London, UK.,School of Cultural Heritage, Northwest University, Xi'an, Shaanxi, China.,Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
| | | | - Timothy Beissinger
- Division of Plant Breeding Methodology, Department of Crop Sciences, University of Goettingen, Goettingen, Germany
| | - Jared E Decker
- Division of Animal Sciences, University of Missouri, Columbia, USA
| | - Michael A Gore
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, U.S.A
| | - J Chris Pires
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, MO, U.S.A
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21
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Cortés AJ, López-Hernández F. Harnessing Crop Wild Diversity for Climate Change Adaptation. Genes (Basel) 2021; 12:783. [PMID: 34065368 PMCID: PMC8161384 DOI: 10.3390/genes12050783] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/28/2021] [Accepted: 05/19/2021] [Indexed: 12/20/2022] Open
Abstract
Warming and drought are reducing global crop production with a potential to substantially worsen global malnutrition. As with the green revolution in the last century, plant genetics may offer concrete opportunities to increase yield and crop adaptability. However, the rate at which the threat is happening requires powering new strategies in order to meet the global food demand. In this review, we highlight major recent 'big data' developments from both empirical and theoretical genomics that may speed up the identification, conservation, and breeding of exotic and elite crop varieties with the potential to feed humans. We first emphasize the major bottlenecks to capture and utilize novel sources of variation in abiotic stress (i.e., heat and drought) tolerance. We argue that adaptation of crop wild relatives to dry environments could be informative on how plant phenotypes may react to a drier climate because natural selection has already tested more options than humans ever will. Because isolated pockets of cryptic diversity may still persist in remote semi-arid regions, we encourage new habitat-based population-guided collections for genebanks. We continue discussing how to systematically study abiotic stress tolerance in these crop collections of wild and landraces using geo-referencing and extensive environmental data. By uncovering the genes that underlie the tolerance adaptive trait, natural variation has the potential to be introgressed into elite cultivars. However, unlocking adaptive genetic variation hidden in related wild species and early landraces remains a major challenge for complex traits that, as abiotic stress tolerance, are polygenic (i.e., regulated by many low-effect genes). Therefore, we finish prospecting modern analytical approaches that will serve to overcome this issue. Concretely, genomic prediction, machine learning, and multi-trait gene editing, all offer innovative alternatives to speed up more accurate pre- and breeding efforts toward the increase in crop adaptability and yield, while matching future global food demands in the face of increased heat and drought. In order for these 'big data' approaches to succeed, we advocate for a trans-disciplinary approach with open-source data and long-term funding. The recent developments and perspectives discussed throughout this review ultimately aim to contribute to increased crop adaptability and yield in the face of heat waves and drought events.
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Affiliation(s)
- Andrés J. Cortés
- Corporación Colombiana de Investigación Agropecuaria AGROSAVIA, C.I. La Selva, Km 7 Vía Rionegro, Las Palmas, Rionegro 054048, Colombia;
- Departamento de Ciencias Forestales, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia, Sede Medellín, Medellín 050034, Colombia
| | - Felipe López-Hernández
- Corporación Colombiana de Investigación Agropecuaria AGROSAVIA, C.I. La Selva, Km 7 Vía Rionegro, Las Palmas, Rionegro 054048, Colombia;
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22
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Laying the groundwork for crop wild relative conservation in the United States. Proc Natl Acad Sci U S A 2021; 118:2024375118. [PMID: 33414278 DOI: 10.1073/pnas.2024375118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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23
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Hübner S, Kantar MB. Tapping Diversity From the Wild: From Sampling to Implementation. FRONTIERS IN PLANT SCIENCE 2021; 12:626565. [PMID: 33584776 PMCID: PMC7873362 DOI: 10.3389/fpls.2021.626565] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 01/07/2021] [Indexed: 05/05/2023]
Abstract
The diversity observed among crop wild relatives (CWRs) and their ability to flourish in unfavorable and harsh environments have drawn the attention of plant scientists and breeders for many decades. However, it is also recognized that the benefit gained from using CWRs in breeding is a potential rose between thorns of detrimental genetic variation that is linked to the trait of interest. Despite the increased interest in CWRs, little attention was given so far to the statistical, analytical, and technical considerations that should guide the sampling design, the germplasm characterization, and later its implementation in breeding. Here, we review the entire process of sampling and identifying beneficial genetic variation in CWRs and the challenge of using it in breeding. The ability to detect beneficial genetic variation in CWRs is strongly affected by the sampling design which should be adjusted to the spatial and temporal variation of the target species, the trait of interest, and the analytical approach used. Moreover, linkage disequilibrium is a key factor that constrains the resolution of searching for beneficial alleles along the genome, and later, the ability to deplete linked deleterious genetic variation as a consequence of genetic drag. We also discuss how technological advances in genomics, phenomics, biotechnology, and data science can improve the ability to identify beneficial genetic variation in CWRs and to exploit it in strive for higher-yielding and sustainable crops.
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Affiliation(s)
- Sariel Hübner
- Galilee Research Institute (MIGAL), Tel-Hai College, Qiryat Shemona, Israel
- *Correspondence: Sariel Hübner,
| | - Michael B. Kantar
- Department of Tropical Plant and Soil Sciences, University of Hawai’i at Mânoa, Honolulu, HI, United States
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