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Krieg CP, Smith DD, Adams MA, Berger J, Layegh Nikravesh N, von Wettberg EJ. Greater ecophysiological stress tolerance in the core environment than in extreme environments of wild chickpea (Cicer reticulatum). Sci Rep 2024; 14:5744. [PMID: 38459248 PMCID: PMC10923935 DOI: 10.1038/s41598-024-56457-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 03/05/2024] [Indexed: 03/10/2024] Open
Abstract
Global climate change and land use change underlie a need to develop new crop breeding strategies, and crop wild relatives (CWR) have become an important potential source of new genetic material to improve breeding efforts. Many recent approaches assume adaptive trait variation increases towards the relative environmental extremes of a species range, potentially missing valuable trait variation in more moderate or typical climates. Here, we leveraged distinct genotypes of wild chickpea (Cicer reticulatum) that differ in their relative climates from moderate to more extreme and perform targeted assessments of drought and heat tolerance. We found significance variation in ecophysiological function and stress tolerance between genotypes but contrary to expectations and current paradigms, it was individuals from more moderate climates that exhibited greater capacity for stress tolerance than individuals from warmer and drier climates. These results indicate that wild germplasm collection efforts to identify adaptive variation should include the full range of environmental conditions and habitats instead of only environmental extremes, and that doing so may significantly enhance the success of breeding programs broadly.
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Affiliation(s)
| | | | - Mark A Adams
- Swinburne University of Technology, Hawthorn, VIC, Australia
| | - Jens Berger
- CSIRO, Agriculture and Food, Perth, WA, Australia
| | | | - Eric J von Wettberg
- Department of Plant and Soil Science, University of Vermont, Burlington, VT, USA
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2
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Lazaridi E, Kapazoglou A, Gerakari M, Kleftogianni K, Passa K, Sarri E, Papasotiropoulos V, Tani E, Bebeli PJ. Crop Landraces and Indigenous Varieties: A Valuable Source of Genes for Plant Breeding. PLANTS (BASEL, SWITZERLAND) 2024; 13:758. [PMID: 38592762 PMCID: PMC10975389 DOI: 10.3390/plants13060758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 02/23/2024] [Accepted: 03/02/2024] [Indexed: 04/10/2024]
Abstract
Landraces and indigenous varieties comprise valuable sources of crop species diversity. Their utilization in plant breeding may lead to increased yield and enhanced quality traits, as well as resilience to various abiotic and biotic stresses. Recently, new approaches based on the rapid advancement of genomic technologies such as deciphering of pangenomes, multi-omics tools, marker-assisted selection (MAS), genome-wide association studies (GWAS), and CRISPR/Cas9 gene editing greatly facilitated the exploitation of landraces in modern plant breeding. In this paper, we present a comprehensive overview of the implementation of new genomic technologies and highlight their importance in pinpointing the genetic basis of desirable traits in landraces and indigenous varieties of annual, perennial herbaceous, and woody crop species cultivated in the Mediterranean region. The need for further employment of advanced -omic technologies to unravel the full potential of landraces and indigenous varieties underutilized genetic diversity is also indicated. Ultimately, the large amount of genomic data emerging from the investigation of landraces and indigenous varieties reveals their potential as a source of valuable genes and traits for breeding. The role of landraces and indigenous varieties in mitigating the ongoing risks posed by climate change in agriculture and food security is also highlighted.
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Affiliation(s)
- Efstathia Lazaridi
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.L.); (M.G.); (K.K.); (E.S.); (V.P.); (E.T.)
| | - 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; (E.L.); (M.G.); (K.K.); (E.S.); (V.P.); (E.T.)
| | - Konstantina Kleftogianni
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.L.); (M.G.); (K.K.); (E.S.); (V.P.); (E.T.)
| | - Kondylia Passa
- Department of Agriculture, University of Patras, Nea Ktiria, 30200 Messolonghi, Greece;
| | - Efi Sarri
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.L.); (M.G.); (K.K.); (E.S.); (V.P.); (E.T.)
| | - Vasileios Papasotiropoulos
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.L.); (M.G.); (K.K.); (E.S.); (V.P.); (E.T.)
| | - Eleni Tani
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.L.); (M.G.); (K.K.); (E.S.); (V.P.); (E.T.)
| | - Penelope J. Bebeli
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.L.); (M.G.); (K.K.); (E.S.); (V.P.); (E.T.)
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3
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Rivas M, Vidal R, Neitzke RS, Priori D, Almeida N, Antunes IF, Galván GA, Barbieri RL. Diversity of vegetable landraces in the Pampa biome of Brazil and Uruguay: utilization and conservation strategies. FRONTIERS IN PLANT SCIENCE 2023; 14:1232589. [PMID: 38023920 PMCID: PMC10668028 DOI: 10.3389/fpls.2023.1232589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 10/24/2023] [Indexed: 12/01/2023]
Abstract
The historical meeting between originally American people, European colonizers, and slaved peoples from Africa in the biome Pampa in South Brazil and Uruguay involved a cultural syncretism and a great genetic diversity of landraces of cultivated species. Genetic richness evolved by selection and cultural processes in response to different environments, cultural backgrounds, and needs. This review summarized the knowledge on vegetable and maize landraces in South Brazilian and Uruguayan Pampa biome, to design a strategy towards the rediscovery, conservation, and sustainable use. Landraces diversity maintained in situ and ex situ is described, specific case studies are presented, and the main problems and tools towards landraces re-valorization are discussed. We show that traditional family farming systems maintain diverse vegetable species, mainly squashes (Cucurbita spp.), sweet potato (Ipomoea batatas), beans (Phaseolus spp.), onion (Allium cepa), peppers (Capsicum spp.), tomato (Solanum lycopersicum), next to leafy vegetables and maize, among others. We propose the priority of systematic surveys as a basis for monitoring genetic erosion, increasing complementariness between in situ and ex situ conservation, and implementing sustainable conservation and utilization. The case studies highlight genetic diversity within each cultivated species, with different crop physiological responses; disease resistances, different quality traits and associated uses, from animal feeding in maize to a range of culinary uses linked to traditional culture in maize and vegetable species, and ornamental uses of specific Capsicum and Cucurbita. Some landraces were the basis for breeding, where improved cultivars allowed the competitiveness of landrace germplasm in the markets. Renewed industrialized products allowed the competitive and sustainable use of Capsicum landraces in Brazilian farmers communities. Strategies towards in situ conservation improvements and valorization are discussed; emphasizing the role played by agroecology, community seed banks and custodian farmers, participatory plant breeding, promotion of landraces specialties among consumers, and the need of research and capacity building, among others. Farmers' participation in the decisions is a key factor, along with the academia and the public sector. Landraces and associated knowledge are treasures to be used to benefit from farmers to consumers, directing the course of agriculture towards sustainable directions.
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Affiliation(s)
- Mercedes Rivas
- Departamento de Biología Vegetal, Facultad de Agronomía, Universidad de la República., Montevideo, Uruguay
- Centro Universitario Regional del Este (CURE), Universidad de la República., Rocha, Uruguay
| | - Rafael Vidal
- Departamento de Biología Vegetal, Facultad de Agronomía, Universidad de la República., Montevideo, Uruguay
| | - Raquel Silviana Neitzke
- Instituto Federal de Educação, Ciência e Tecnologia Sul-rio-grandense (IFSul), Bagé, RS, Brazil
| | - Daniela Priori
- Centro de Ensino Superior Riograndense (CESURG), Beira Campo, Sarandi, RS, Brazil
| | - Natália Almeida
- Departamento de Sostenibilidad Ambiental, Instituto Tecnológico Centro Sur, Universidad Tecnológica del Uruguay (UTEC), Durazno, Uruguay
| | | | - Guillermo A. Galván
- Departamento de Producción Vegetal, Centro Regional Sur (CRS), Facultad de Agronomía, Universidad de la República, Progreso, Canelones, Uruguay
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4
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Martínez‐Ainsworth NE, Scheppler H, Moreno‐Letelier A, Bernau V, Kantar MB, Mercer KL, Jardón‐Barbolla L. Fluctuation of ecological niches and geographic range shifts along chile pepper's domestication gradient. Ecol Evol 2023; 13:e10731. [PMID: 38034338 PMCID: PMC10682905 DOI: 10.1002/ece3.10731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 09/30/2023] [Accepted: 10/31/2023] [Indexed: 12/02/2023] Open
Abstract
Domestication is an ongoing well-described process. However, while many have studied the changes domestication causes in plant genetics, few have explored its impact on the portion of the geographic landscape in which the plants exist. Therefore, the goal of this study was to understand how the process of domestication changed the geographic space suitable for chile pepper (Capsicum annuum) in its center of origin (domestication). C. annuum is a major crop species globally whose center of domestication, Mexico, has been well-studied. It provides a unique opportunity to explore the degree to which ranges of different domestication classes diverged and how these ranges might be altered by climate change. To this end, we created ecological niche models for four domestication classes (wild, semiwild, landrace, modern cultivar) based on present climate and future climate scenarios for 2050, 2070, and 2090. Considering present environment, we found substantial overlap in the geographic niches of all the domestication classes. Yet, environmental and geographic aspects of the current ranges did vary among classes. Wild and commercial varieties could grow in desert conditions, while landraces could not. With projections into the future, habitat was lost asymmetrically, with wild, semiwild, and landraces at greater risk of territorial declines than modern cultivars. Further, we identified areas where future suitability overlap between landraces and wilds is expected to be lost. While range expansion is widely associated with domestication, we found little support of a constant niche expansion (either in environmental or geographical space) throughout the domestication gradient in chile peppers in Mexico. Instead, particular domestication transitions resulted in loss, followed by capturing or recapturing environmental or geographic space. The differences in environmental characterization among domestication gradient classes and their future potential range shifts increase the need for conservation efforts to preserve landraces and semiwild genotypes.
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Affiliation(s)
- Natalia E. Martínez‐Ainsworth
- Centro de Investigaciones Interdisciplinarias en Ciencias y HumanidadesUniversidad Nacional Autónoma de MéxicoCiudad de MéxicoMexico
| | - Hannah Scheppler
- Department of Horticulture and Crop ScienceOhio State UniversityColumbusOhioUSA
| | - Alejandra Moreno‐Letelier
- Jardín Botánico del Instituto de BiologíaUniversidad Nacional Autónoma de México, Ciudad UniversitariaCiudad de MéxicoMexico
| | - Vivian Bernau
- Plant Introduction Research Unit, United States Department of Agriculture‐Agricultural Research Service (USDA‐ARS), and Department of AgronomyIowa State UniversityAmesIowaUSA
| | - Michael B. Kantar
- Department of Tropical Plant and Soil SciencesUniversity of Hawai'iHonoluluHawaiiUSA
| | - Kristin L. Mercer
- Department of Horticulture and Crop ScienceOhio State UniversityColumbusOhioUSA
| | - Lev Jardón‐Barbolla
- Centro de Investigaciones Interdisciplinarias en Ciencias y HumanidadesUniversidad Nacional Autónoma de MéxicoCiudad de MéxicoMexico
- Department of Horticulture and Crop ScienceOhio State UniversityColumbusOhioUSA
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5
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Cortés AJ, Barnaby JY. Editorial: Harnessing genebanks: High-throughput phenotyping and genotyping of crop wild relatives and landraces. FRONTIERS IN PLANT SCIENCE 2023; 14:1149469. [PMID: 36968416 PMCID: PMC10036837 DOI: 10.3389/fpls.2023.1149469] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 01/26/2023] [Indexed: 06/18/2023]
Affiliation(s)
- Andrés J. Cortés
- Corporación Colombiana de Investigación Agropecuaria – AGROSAVIA, C.I. La Selva, Rionegro, Colombia
| | - Jinyoung Y. Barnaby
- U.S. Department of Agriculture, U.S. National Arboretum, Floral and Nursery Plants Research Unit, Beltsville, MD, United States
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6
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Diversity and conservation of higher plants in Northwest Yunnan-Southeast Tibet. Glob Ecol Conserv 2023. [DOI: 10.1016/j.gecco.2023.e02396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
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7
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Mahaut L, Pironon S, Barnagaud JY, Bretagnolle F, Khoury CK, Mehrabi Z, Milla R, Phillips C, Rieseberg LH, Violle C, Renard D. Matches and mismatches between the global distribution of major food crops and climate suitability. Proc Biol Sci 2022; 289:20221542. [PMID: 36168758 PMCID: PMC9515644 DOI: 10.1098/rspb.2022.1542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 09/06/2022] [Indexed: 09/30/2023] Open
Abstract
Over the course of history, humans have moved crops from their regions of origin to new locations across the world. The social, cultural and economic drivers of these movements have generated differences not only between current distributions of crops and their climatic origins, but also between crop distributions and climate suitability for their production. Although these mismatches are particularly important to inform agricultural strategies on climate change adaptation, they have, to date, not been quantified consistently at the global level. Here, we show that the relationships between the distributions of 12 major food crops and climate suitability for their yields display strong variation globally. After investigating the role of biophysical, socio-economic and historical factors, we report that high-income world regions display a better match between crop distribution and climate suitability. In addition, although crops are farmed predominantly in the same climatic range as their wild progenitors, climate suitability is not necessarily higher there, a pattern that reflects the legacy of domestication history on current crop distribution. Our results reveal how far the global distribution of major crops diverges from their climatic optima and call for greater consideration of the multiple dimensions of the crop socio-ecological niche in climate change adaptive strategies.
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Affiliation(s)
- Lucie Mahaut
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Samuel Pironon
- Royal Botanic Gardens, Kew, Richmond, UK
- UN Environment Programme World Conservation Monitoring Center (UNEP-WCMC), Cambridge, UK
| | | | | | - Colin K. Khoury
- International Center for Tropical Agriculture (CIAT), Km 17, Recta Cali-Palmira, Apartado Aéreo 6713, Cali 763537, Colombia
- San Diego Botanic Garden, 230 Quail Gardens Drive, Encinitas, CA 92024, USA
| | - Zia Mehrabi
- Institute for Resources Environment and Sustainability, School of Public Policy and Global Affairs, University of British Columbia, Vancouver, BC, Canada, V6R 2A5
| | - Ruben Milla
- Universidad Rey Juan Carlos, Escuela Superior de Ciencias Experimentales y Tecnología, Mostoles, Spain
| | | | - Loren H. Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada, V6R 2A5
| | - Cyrille Violle
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Delphine Renard
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
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8
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Cortés AJ, López-Hernández F, Blair MW. Genome-Environment Associations, an Innovative Tool for Studying Heritable Evolutionary Adaptation in Orphan Crops and Wild Relatives. Front Genet 2022; 13:910386. [PMID: 35991553 PMCID: PMC9389289 DOI: 10.3389/fgene.2022.910386] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 05/30/2022] [Indexed: 11/23/2022] Open
Abstract
Leveraging innovative tools to speed up prebreeding and discovery of genotypic sources of adaptation from landraces, crop wild relatives, and orphan crops is a key prerequisite to accelerate genetic gain of abiotic stress tolerance in annual crops such as legumes and cereals, many of which are still orphan species despite advances in major row crops. Here, we review a novel, interdisciplinary approach to combine ecological climate data with evolutionary genomics under the paradigm of a new field of study: genome-environment associations (GEAs). We first exemplify how GEA utilizes in situ georeferencing from genotypically characterized, gene bank accessions to pinpoint genomic signatures of natural selection. We later discuss the necessity to update the current GEA models to predict both regional- and local- or micro-habitat-based adaptation with mechanistic ecophysiological climate indices and cutting-edge GWAS-type genetic association models. Furthermore, to account for polygenic evolutionary adaptation, we encourage the community to start gathering genomic estimated adaptive values (GEAVs) for genomic prediction (GP) and multi-dimensional machine learning (ML) models. The latter two should ideally be weighted by de novo GWAS-based GEA estimates and optimized for a scalable marker subset. We end the review by envisioning avenues to make adaptation inferences more robust through the merging of high-resolution data sources, such as environmental remote sensing and summary statistics of the genomic site frequency spectrum, with the epigenetic molecular functionality responsible for plastic inheritance in the wild. Ultimately, we believe that coupling evolutionary adaptive predictions with innovations in ecological genomics such as GEA will help capture hidden genetic adaptations to abiotic stresses based on crop germplasm resources to assist responses to climate change. "I shall endeavor to find out how nature's forces act upon one another, and in what manner the geographic environment exerts its influence on animals and plants. In short, I must find out about the harmony in nature" Alexander von Humboldt-Letter to Karl Freiesleben, June 1799.
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Affiliation(s)
- Andrés J. Cortés
- Corporacion Colombiana de Investigacion Agropecuaria AGROSAVIA, C.I. La Selva, Rionegro, Colombia
| | - Felipe López-Hernández
- Corporacion Colombiana de Investigacion Agropecuaria AGROSAVIA, C.I. La Selva, Rionegro, Colombia
| | - Matthew W. Blair
- Department of Agricultural & Environmental Sciences, Tennessee State University, Nashville, TN, United States
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9
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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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10
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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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11
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González‐Orozco CE, Sosa CC, Thornhill AH, Laffan SW. Phylogenetic diversity and conservation of crop wild relatives in Colombia. Evol Appl 2021; 14:2603-2617. [PMID: 34815742 PMCID: PMC8591330 DOI: 10.1111/eva.13295] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 08/17/2021] [Accepted: 08/20/2021] [Indexed: 11/29/2022] Open
Abstract
Crop wild relatives (CWR) are an important agricultural resource as they contain genetic traits not found in cultivated species due to localized adaptation to unique environmental and climatic conditions. Phylogenetic diversity (PD) measures the evolutionary relationship of species using the tree of life. Our knowledge of CWR PD in neotropical regions is in its infancy. We analysed the distribution of CWR PD across Colombia and assessed its conservation status. The areas with the largest concentration of PD were identified as being in the northern part of the central and western Andean mountain ranges and the Pacific region. These centres of high PD were comprised of predominantly short and closely related branches, mostly of species of wild tomatoes and black peppers. In contrast, the CWR PD in the lowland ecosystems of the Amazon and Orinoquia regions had deeply diverging clades predominantly represented by long and distantly related branches (i.e. tuberous roots, grains and cacao). We categorized 50 (52.6%) of the CWR species as 'high priority', 36 as 'medium priority' and nine as 'low priority' for further ex-situ and in situ conservation actions. New areas of high PD and richness with large ex-situ gap collections were identified mainly in the northern part of the Andes of Colombia. We found that 56% of the grid cells with the highest PD values were unprotected. These baseline data could be used to create a comprehensive national strategy of CWR conservation in Colombia.
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Affiliation(s)
- Carlos E. González‐Orozco
- Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA)Centro de Investigación La LibertadVillavicencioColombia
| | - Chrystian C. Sosa
- Departamento de Ciencias naturales y MatemáticasPontificia Universidad Javeriana CaliCaliColombia
- Grupo de Investigación en EvoluciónEcología y Conservación EECOPrograma de BiologíaFacultad de Ciencias Básicas y TecnologíasUniversidad del QuindíoArmeniaColombia
| | - Andrew H. Thornhill
- Environment InstituteThe University of AdelaideAdelaideSAAustralia
- Department for Environment and WaterState Herbarium of South AustraliaBotanic Gardens and State HerbariumAdelaideSAAustralia
| | - Shawn W. Laffan
- Earth and Sustainability Science Research CentreSchool of Biological, Earth and Environmental SciencesThe University of New South WalesKensingtonNSWAustralia
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12
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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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13
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Halewood M, Jamora N, Noriega IL, Anglin NL, Wenzl P, Payne T, Ndjiondjop MN, Guarino L, Kumar PL, Yazbek M, Muchugi A, Azevedo V, Tchamba M, Jones CS, Venuprasad R, Roux N, Rojas E, Lusty C. Germplasm Acquisition and Distribution by CGIAR Genebanks. PLANTS 2020; 9:plants9101296. [PMID: 33019539 PMCID: PMC7601315 DOI: 10.3390/plants9101296] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/03/2020] [Accepted: 09/10/2020] [Indexed: 12/22/2022]
Abstract
The international collections of plant genetic resources for food and agriculture (PGRFA) hosted by 11 CGIAR Centers are important components of the United Nations Food and Agriculture Organization's global system of conservation and use of PGRFA. They also play an important supportive role in realizing Target 2.5 of the Sustainable Development Goals. This paper analyzes CGIAR genebanks' trends in acquiring and distributing PGRFA over the last 35 years, with a particular focus on the last decade. The paper highlights a number of factors influencing the Centers' acquisition of new PGRFA to include in the international collections, including increased capacity to analyze gaps in those collections and precisely target new collecting missions, availability of financial resources, and the state of international and national access and benefit-sharing laws and phytosanitary regulations. Factors contributing to Centers' distributions of PGRFA included the extent of accession-level information, users' capacity to identify the materials they want, and policies. The genebanks' rates of both acquisition and distribution increased over the last decade. The paper ends on a cautionary note concerning the potential of unresolved tensions regarding access and benefit sharing and digital genomic sequence information to undermine international cooperation to conserve and use PGRFA.
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Affiliation(s)
- Michael Halewood
- Alliance of Bioversity International and the International Center for Tropical Agriculture (Alliance of Bioversity and CIAT), Via dei Tre Denari 472/a, 00057 Maccarese (Fiumicino) Rome, Italy; (I.L.N.); (P.W.); (N.R.)
- Correspondence:
| | - Nelissa Jamora
- Global Crop Diversity Trust (Crop Trust), Platz der Vereinten Nationen 7, 53113 Bonn, Germany; (N.J.); (L.G.); (C.L.)
| | - Isabel Lopez Noriega
- Alliance of Bioversity International and the International Center for Tropical Agriculture (Alliance of Bioversity and CIAT), Via dei Tre Denari 472/a, 00057 Maccarese (Fiumicino) Rome, Italy; (I.L.N.); (P.W.); (N.R.)
| | - Noelle L. Anglin
- International Potato Center (CIP), Av. La Molina 1895, La Molina Apartado 1558, Lima 12, Peru; (N.L.A.); (E.R.)
| | - Peter Wenzl
- Alliance of Bioversity International and the International Center for Tropical Agriculture (Alliance of Bioversity and CIAT), Via dei Tre Denari 472/a, 00057 Maccarese (Fiumicino) Rome, Italy; (I.L.N.); (P.W.); (N.R.)
| | - Thomas Payne
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600 Mexico, D.F., Mexico;
| | | | - Luigi Guarino
- Global Crop Diversity Trust (Crop Trust), Platz der Vereinten Nationen 7, 53113 Bonn, Germany; (N.J.); (L.G.); (C.L.)
| | - P. Lava Kumar
- International Institute for Tropical Agriculture (IITA), PMB 5320, Ibadan 200001, Oyo State, Nigeria; (P.L.K.); (M.T.)
| | - Mariana Yazbek
- International Center for Agricultural Research in the Dry Areas (ICARDA), P.O. Box 114/5055, Beirut, Lebanon;
| | - Alice Muchugi
- World Agroforestry (ICRAF), Box 30677, Nairobi 00100, Kenya;
| | - Vania Azevedo
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502 324, Telangana State, India;
| | - Marimagne Tchamba
- International Institute for Tropical Agriculture (IITA), PMB 5320, Ibadan 200001, Oyo State, Nigeria; (P.L.K.); (M.T.)
| | - Chris S. Jones
- International Livestock Research Institute (ILRI), Box 30709, Nairobi 00100, Kenya;
| | - Ramaiah Venuprasad
- International Rice Research Institute (IRRI), Los Baños 4030, Laguna, Philippines;
| | - Nicolas Roux
- Alliance of Bioversity International and the International Center for Tropical Agriculture (Alliance of Bioversity and CIAT), Via dei Tre Denari 472/a, 00057 Maccarese (Fiumicino) Rome, Italy; (I.L.N.); (P.W.); (N.R.)
| | - Edwin Rojas
- International Potato Center (CIP), Av. La Molina 1895, La Molina Apartado 1558, Lima 12, Peru; (N.L.A.); (E.R.)
| | - Charlotte Lusty
- Global Crop Diversity Trust (Crop Trust), Platz der Vereinten Nationen 7, 53113 Bonn, Germany; (N.J.); (L.G.); (C.L.)
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