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Flint-Garcia S, Feldmann MJ, Dempewolf H, Morrell PL, Ross-Ibarra J. Diamonds in the not-so-rough: Wild relative diversity hidden in crop genomes. PLoS Biol 2023; 21:e3002235. [PMID: 37440605 PMCID: PMC10368281 DOI: 10.1371/journal.pbio.3002235] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 07/25/2023] [Indexed: 07/15/2023] Open
Abstract
Crop production is becoming an increasing challenge as the global population grows and the climate changes. Modern cultivated crop species are selected for productivity under optimal growth environments and have often lost genetic variants that could allow them to adapt to diverse, and now rapidly changing, environments. These genetic variants are often present in their closest wild relatives, but so are less desirable traits. How to preserve and effectively utilize the rich genetic resources that crop wild relatives offer while avoiding detrimental variants and maladaptive genetic contributions is a central challenge for ongoing crop improvement. This Essay explores this challenge and potential paths that could lead to a solution.
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Affiliation(s)
- Sherry Flint-Garcia
- Plant Genetics Research Unit, United States Department of Agriculture, Agricultural Research Service, Columbia, Missouri, United States of America
| | - Mitchell J. Feldmann
- Department of Plant Sciences, University of California, Davis, California, United States of America
| | | | - Peter L. Morrell
- Department of Agronomy and Plant Genetics, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Jeffrey Ross-Ibarra
- Department of Evolution and Ecology, Center for Population Biology, and Genome Center, University of California, Davis, California, United States of America
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2
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Dempewolf H, Krishnan S, Guarino L. Our shared global responsibility: Safeguarding crop diversity for future generations. Proc Natl Acad Sci U S A 2023; 120:e2205768119. [PMID: 36972434 PMCID: PMC10083580 DOI: 10.1073/pnas.2205768119] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023] Open
Abstract
The resilience and sustainability of food systems depend on crop diversity. It is used by breeders to produce new and better varieties, and by farmers to respond to new challenges or demands and to spread risk. However, crop diversity can only be used if it has been conserved, can be identified as the solution for a given problem, and is available. As the ways in which crop diversity is used in research and breeding change and expand, the global conservation system for crop diversity must keep pace; it must provide not only the biological materials themselves, but also the relevant information presented in a comprehensive and coherent way—all while ensuring equitable access and benefit sharing. Here we explore the evolving priorities for global efforts to safeguard and make available the diversity of the world's crops through ex situ genetic resource collections. We suggest that collections held by academic institutions and other holders that are not standard gene banks should be better integrated in global efforts and decision-making to conserve genetic resources. We conclude with key actions that we suggest should be taken to ensure that crop diversity collections of all types are able to fulfill their role to foster more diverse, equitable, resilient, and sustainable food systems globally.
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3
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Eastwood RJ, Tambam BB, Aboagye LM, Akparov ZI, Aladele SE, Allen R, Amri A, Anglin NL, Araya R, Arrieta-Espinoza G, Asgerov A, Awang K, Awas T, Barata AM, Boateng SK, Magos Brehm J, Breidy J, Breman E, Brenes Angulo A, Burle ML, Castañeda-Álvarez NP, Casimiro P, Chaves NF, Clemente AS, Cockel CP, Davey A, De la Rosa L, Debouck DG, Dempewolf H, Dokmak H, Ellis D, Faruk A, Freitas C, Galstyan S, García RM, Ghimire KH, Guarino L, Harker R, Hope R, Humphries AW, Jamora N, Jatoi SA, Khutsishvili M, Kikodze D, Kyratzis AC, León-Lobos P, Liu U, Mainali RP, Mammadov AT, Manrique-Carpintero NC, Manzella D, Mat Ali MS, Medeiros MB, Guzmán MAM, Mikatadze-Pantsulaia T, Mohamed ETI, Monteros-Altamirano Á, Morales A, Müller JV, Mulumba JW, Nersesyan A, Nóbrega H, Nyamongo DO, Obreza M, Okere AU, Orsenigo S, Ortega-Klose F, Papikyan A, Pearce TR, Pinheiro de Carvalho MAA, Prohens J, Rossi G, Salas A, Singh Shrestha D, Siddiqui SU, Smith PP, Sotomayor DA, Tacán M, Tapia C, Toledo Á, Toll J, Vu DT, Vu TD, Way MJ, Yazbek M, Zorrilla C, Kilian B. Adapting Agriculture to Climate Change: A Synopsis of Coordinated National Crop Wild Relative Seed Collecting Programs across Five Continents. Plants 2022; 11:plants11141840. [PMID: 35890473 PMCID: PMC9319254 DOI: 10.3390/plants11141840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 06/29/2022] [Accepted: 06/29/2022] [Indexed: 11/16/2022]
Abstract
The Adapting Agriculture to Climate Change Project set out to improve the diversity, quantity, and accessibility of germplasm collections of crop wild relatives (CWR). Between 2013 and 2018, partners in 25 countries, heirs to the globetrotting legacy of Nikolai Vavilov, undertook seed collecting expeditions targeting CWR of 28 crops of global significance for agriculture. Here, we describe the implementation of the 25 national collecting programs and present the key results. A total of 4587 unique seed samples from at least 355 CWR taxa were collected, conserved ex situ, safety duplicated in national and international genebanks, and made available through the Multilateral System (MLS) of the International Treaty on Plant Genetic Resources for Food and Agriculture (Plant Treaty). Collections of CWR were made for all 28 targeted crops. Potato and eggplant were the most collected genepools, although the greatest number of primary genepool collections were made for rice. Overall, alfalfa, Bambara groundnut, grass pea and wheat were the genepools for which targets were best achieved. Several of the newly collected samples have already been used in pre-breeding programs to adapt crops to future challenges.
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Affiliation(s)
- Ruth J. Eastwood
- Royal Botanic Gardens, Kew, Wakehurst, Ardingly, Haywards Heath RH17 6TN, UK; (R.A.); (E.B.); (C.P.C.); (A.F.); (U.L.); (J.V.M.); (T.R.P.); (M.J.W.)
- Correspondence:
| | - Beri B. Tambam
- Global Crop Diversity Trust, Platz der Vereinten Nationen 7, 53113 Bonn, Germany; (B.B.T.); (N.P.C.-Á.); (H.D.); (L.G.); (N.J.); (M.O.); (J.T.); (B.K.)
| | - Lawrence M. Aboagye
- CSIR—Plant Genetic Resources Research Institute, Bunso P.O. Box 7, Ghana; (L.M.A.); (S.K.B.)
| | - Zeynal I. Akparov
- Genetic Resources Institute of Azerbaijan NAS, 155 Azadlig Avenue, Baku AZ1106, Azerbaijan; (Z.I.A.); (A.A.); (A.T.M.)
| | - Sunday E. Aladele
- National Centre for Genetic Resources and Biotechnology, Moor Plantation, Ibadan PMB 5382, Nigeria; (S.E.A.); (A.U.O.)
| | - Richard Allen
- Royal Botanic Gardens, Kew, Wakehurst, Ardingly, Haywards Heath RH17 6TN, UK; (R.A.); (E.B.); (C.P.C.); (A.F.); (U.L.); (J.V.M.); (T.R.P.); (M.J.W.)
| | - Ahmed Amri
- The International Center for Agricultural Research in the Dry Areas, Dalia Bldg, 2nd Floor Bashir El Kassar Street Verdun, Beirut 1108-2010, Lebanon; (A.A.); (M.Y.)
| | - Noelle L. Anglin
- USDA ARS Small Grains and Potato Germplasm Research, 1691 S 2700 W, Aberdeen, ID 83210, USA;
| | - Rodolfo Araya
- Estación Experimental Agrícola Fabio Baudrit Moreno, Universidad de Costa Rica, 3 km W of Catholic Church of Barrio San José, La Garita, Alajuela 183-4050, Costa Rica; (R.A.); (N.F.C.)
| | - Griselda Arrieta-Espinoza
- Centro de Investigación en Biología Celular y Molecular, Universidad de Costa Rica, Ciudad de la Investigación—C.P., San José 11501-2050, Costa Rica;
| | - Aydin Asgerov
- Genetic Resources Institute of Azerbaijan NAS, 155 Azadlig Avenue, Baku AZ1106, Azerbaijan; (Z.I.A.); (A.A.); (A.T.M.)
| | - Khadijah Awang
- Malaysian Agricultural Research and Development Institute (MARDI), Persiaran MARDI-UPM, Serdang 43400, Malaysia; (K.A.); (M.S.M.A.)
| | - Tesfaye Awas
- Ethiopian Biodiversity Institute, Comoros Street, Yeka Subcity, Addis Ababa P.O. Box 30726, Ethiopia;
| | - Ana Maria Barata
- Banco Português de Germoplasma Vegetal, INIAV, Quinta de S. José, São Pedro de Merelim, 4700-859 Braga, Portugal;
| | - Samuel Kwasi Boateng
- CSIR—Plant Genetic Resources Research Institute, Bunso P.O. Box 7, Ghana; (L.M.A.); (S.K.B.)
| | - Joana Magos Brehm
- Jardim Botânico, Museu Nacional de Historia Natural e da Ciência, Universidade de Lisboa, R. da Escola Politécnica 56, 1250-102 Lisboa, Portugal; (J.M.B.); (A.S.C.)
| | - Joelle Breidy
- Lebanese Agricultural Research Institute, Tal Amara, Rayak P.O. Box 287, Lebanon; (J.B.); (H.D.)
| | - Elinor Breman
- Royal Botanic Gardens, Kew, Wakehurst, Ardingly, Haywards Heath RH17 6TN, UK; (R.A.); (E.B.); (C.P.C.); (A.F.); (U.L.); (J.V.M.); (T.R.P.); (M.J.W.)
| | - Arturo Brenes Angulo
- Centro de Investigaciones Agronómicas, Universidad de Costa Rica, San José 11501-2060, Costa Rica;
| | - Marília L. Burle
- Embrapa Genetic Resources and Biotechnology, Parque Estação Biológica, Av. W5 Norte (Final), Brasília 70770-917, DF, Brazil; (M.L.B.); (M.B.M.)
| | - Nora P. Castañeda-Álvarez
- Global Crop Diversity Trust, Platz der Vereinten Nationen 7, 53113 Bonn, Germany; (B.B.T.); (N.P.C.-Á.); (H.D.); (L.G.); (N.J.); (M.O.); (J.T.); (B.K.)
| | - Pedro Casimiro
- Direção Regional do Ambiente e Alterações Climáticas, Rua Cônsul Dabney, Colónia Alemã, Apartado 140, 9900-014 Horta, Portugal;
| | - Néstor F. Chaves
- Estación Experimental Agrícola Fabio Baudrit Moreno, Universidad de Costa Rica, 3 km W of Catholic Church of Barrio San José, La Garita, Alajuela 183-4050, Costa Rica; (R.A.); (N.F.C.)
| | - Adelaide S. Clemente
- Jardim Botânico, Museu Nacional de Historia Natural e da Ciência, Universidade de Lisboa, R. da Escola Politécnica 56, 1250-102 Lisboa, Portugal; (J.M.B.); (A.S.C.)
| | - Christopher P. Cockel
- Royal Botanic Gardens, Kew, Wakehurst, Ardingly, Haywards Heath RH17 6TN, UK; (R.A.); (E.B.); (C.P.C.); (A.F.); (U.L.); (J.V.M.); (T.R.P.); (M.J.W.)
| | - Alexandra Davey
- Fauna & Flora International, The David Attenborough Building, Pembroke Street, Cambridge CB2 3QZ, UK; (A.D.); (R.H.)
| | - Lucía De la Rosa
- Plant Genetic Resources Centre, National Institute for Agricultural and Food Research and Technology (CRF-INIA), CSIC, Finca La Canaleja, A2 km 36, 28800 Alcalá de Henares, Spain; (L.D.l.R.); (R.M.G.)
| | - Daniel G. Debouck
- Alliance Bioversity International Center of Tropical Agriculture, km 17, Recta Cali-Palmira, Apartado Aéreo 6713, Cali 763537, Colombia;
| | - Hannes Dempewolf
- Global Crop Diversity Trust, Platz der Vereinten Nationen 7, 53113 Bonn, Germany; (B.B.T.); (N.P.C.-Á.); (H.D.); (L.G.); (N.J.); (M.O.); (J.T.); (B.K.)
| | - Hiba Dokmak
- Lebanese Agricultural Research Institute, Tal Amara, Rayak P.O. Box 287, Lebanon; (J.B.); (H.D.)
| | - David Ellis
- International Potato Center, Avenida La Molina 1895, La Molina, Lima 15023, Peru; (D.E.); (N.C.M.-C.); (A.S.)
| | - Aisyah Faruk
- Royal Botanic Gardens, Kew, Wakehurst, Ardingly, Haywards Heath RH17 6TN, UK; (R.A.); (E.B.); (C.P.C.); (A.F.); (U.L.); (J.V.M.); (T.R.P.); (M.J.W.)
| | - Cátia Freitas
- Banco de Sementes dos Açores, Rua de São Lourenço, nº 23 Flamengos, 9900-401 Horta, Portugal;
| | - Sona Galstyan
- Institute of Botany after A. Takhtajyan of the National Academy of Sciences of the Republic of Armenia, Acharyan Street 1, Yerevan 0040, Armenia; (S.G.); (A.N.); (A.P.)
| | - Rosa M. García
- Plant Genetic Resources Centre, National Institute for Agricultural and Food Research and Technology (CRF-INIA), CSIC, Finca La Canaleja, A2 km 36, 28800 Alcalá de Henares, Spain; (L.D.l.R.); (R.M.G.)
| | - Krishna H. Ghimire
- National Agriculture Genetic Resources Centre, Nepal Agricultural Research Council (NARC), Khumaltar, Lalitpur P.O. Box. 3605, Nepal; (K.H.G.); (R.P.M.); (D.S.S.)
| | - Luigi Guarino
- Global Crop Diversity Trust, Platz der Vereinten Nationen 7, 53113 Bonn, Germany; (B.B.T.); (N.P.C.-Á.); (H.D.); (L.G.); (N.J.); (M.O.); (J.T.); (B.K.)
| | - Ruth Harker
- Natural England, Foss House, Kings Pool, 1-2 Peasholme Green, York YO1 7PX, UK;
| | - Roberta Hope
- Fauna & Flora International, The David Attenborough Building, Pembroke Street, Cambridge CB2 3QZ, UK; (A.D.); (R.H.)
| | - Alan W. Humphries
- South Australian Research and Development Institute, Plant Research Centre, Waite Precinct, Gate 2b Hartley Grove, Urrbrae, SA 5064, Australia;
| | - Nelissa Jamora
- Global Crop Diversity Trust, Platz der Vereinten Nationen 7, 53113 Bonn, Germany; (B.B.T.); (N.P.C.-Á.); (H.D.); (L.G.); (N.J.); (M.O.); (J.T.); (B.K.)
| | - Shakeel Ahmad Jatoi
- Bio-Resources Conservation Institute, National Agricultural Research Centre, Park Road, Islamabad 45500, Pakistan; (S.A.J.); (S.U.S.)
| | - Manana Khutsishvili
- Institute of Botany, Ilia State University, 1 Botanikuri str., 0105 Tbilisi, Georgia; (M.K.); (D.K.)
| | - David Kikodze
- Institute of Botany, Ilia State University, 1 Botanikuri str., 0105 Tbilisi, Georgia; (M.K.); (D.K.)
| | - Angelos C. Kyratzis
- Agricultural Research Institute, Athalassa, P.O. Box 22016, Nicosia 1516, Cyprus;
| | - Pedro León-Lobos
- Instituto de Investigaciones Agropecuarias, Fidel Oteíza 1956, Pisos 12, Providencia, Santiago 8320000, Chile; (P.L.-L.); (F.O.-K.)
| | - Udayangani Liu
- Royal Botanic Gardens, Kew, Wakehurst, Ardingly, Haywards Heath RH17 6TN, UK; (R.A.); (E.B.); (C.P.C.); (A.F.); (U.L.); (J.V.M.); (T.R.P.); (M.J.W.)
| | - Ram P. Mainali
- National Agriculture Genetic Resources Centre, Nepal Agricultural Research Council (NARC), Khumaltar, Lalitpur P.O. Box. 3605, Nepal; (K.H.G.); (R.P.M.); (D.S.S.)
| | - Afig T. Mammadov
- Genetic Resources Institute of Azerbaijan NAS, 155 Azadlig Avenue, Baku AZ1106, Azerbaijan; (Z.I.A.); (A.A.); (A.T.M.)
| | | | | | - Mohd Shukri Mat Ali
- Malaysian Agricultural Research and Development Institute (MARDI), Persiaran MARDI-UPM, Serdang 43400, Malaysia; (K.A.); (M.S.M.A.)
| | - Marcelo B. Medeiros
- Embrapa Genetic Resources and Biotechnology, Parque Estação Biológica, Av. W5 Norte (Final), Brasília 70770-917, DF, Brazil; (M.L.B.); (M.B.M.)
| | - María A. Mérida Guzmán
- Institute of Agricultural Science and Technology, km 21.5 Highway to the Pacific, Bárcena, Villa Nueva, Guatemala;
| | | | - El Tahir Ibrahim Mohamed
- Agricultural Plant Genetic Resources Conservation and Research Centre, Agricultural Research Corporation, Wad Medani P.O. Box 126, Sudan;
| | - Álvaro Monteros-Altamirano
- Instituto Nacional de Investigaciones Agropecuarias, Avenida Amazonas y Eloy Alfaro, Edificio MAG, Cuarto Piso, Quito 170518, Ecuador; (Á.M.-A.); (M.T.); (C.T.)
| | - Aura Morales
- Centro Nacional de Tecnología “Enrique Álvarez Córdova”, km 33.5 Carretera a Santa Ana, San Andrés, Ciudad Arce, La Libertad, El Salvador;
| | - Jonas V. Müller
- Royal Botanic Gardens, Kew, Wakehurst, Ardingly, Haywards Heath RH17 6TN, UK; (R.A.); (E.B.); (C.P.C.); (A.F.); (U.L.); (J.V.M.); (T.R.P.); (M.J.W.)
| | - John W. Mulumba
- Plant Genetic Resources Centre, National Agricultural Research Organization, Plot 2-4 Berkeley Road, Entebbe P.O. Box 40, Uganda;
| | - Anush Nersesyan
- Institute of Botany after A. Takhtajyan of the National Academy of Sciences of the Republic of Armenia, Acharyan Street 1, Yerevan 0040, Armenia; (S.G.); (A.N.); (A.P.)
| | - Humberto Nóbrega
- ISOPlexis—Centro de Agricultura Sustentável e Tecnologia Alimentar, Universidade da Madeira, Campus da Penteada, 9020-105 Funchal, Portugal; (M.A.A.P.d.C.); (H.N.)
| | - Desterio O. Nyamongo
- Kenya Agricultural and Livestock Research Organisation, Genetic Resources Research Institute, Nairobi P.O. Box 30148-00100, Kenya;
| | - Matija Obreza
- Global Crop Diversity Trust, Platz der Vereinten Nationen 7, 53113 Bonn, Germany; (B.B.T.); (N.P.C.-Á.); (H.D.); (L.G.); (N.J.); (M.O.); (J.T.); (B.K.)
| | - Anthony U. Okere
- National Centre for Genetic Resources and Biotechnology, Moor Plantation, Ibadan PMB 5382, Nigeria; (S.E.A.); (A.U.O.)
| | - Simone Orsenigo
- Department of Earth and Environmental Sciences, Pavia University, Via Sant’Epifanio 14, 27100 Pavia, Italy; (S.O.); (G.R.)
| | - Fernando Ortega-Klose
- Instituto de Investigaciones Agropecuarias, Fidel Oteíza 1956, Pisos 12, Providencia, Santiago 8320000, Chile; (P.L.-L.); (F.O.-K.)
| | - Astghik Papikyan
- Institute of Botany after A. Takhtajyan of the National Academy of Sciences of the Republic of Armenia, Acharyan Street 1, Yerevan 0040, Armenia; (S.G.); (A.N.); (A.P.)
| | - Timothy R. Pearce
- Royal Botanic Gardens, Kew, Wakehurst, Ardingly, Haywards Heath RH17 6TN, UK; (R.A.); (E.B.); (C.P.C.); (A.F.); (U.L.); (J.V.M.); (T.R.P.); (M.J.W.)
| | - Miguel A. A. Pinheiro de Carvalho
- ISOPlexis—Centro de Agricultura Sustentável e Tecnologia Alimentar, Universidade da Madeira, Campus da Penteada, 9020-105 Funchal, Portugal; (M.A.A.P.d.C.); (H.N.)
- CITAB—Centro de Investigação e Tecnologias Agroambientais e Biológicas, 5001-801 Vila Real, Portugal
| | - Jaime Prohens
- Institute for the Conservation and Improvement of Valencian Agrodiversity (COMAV), Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain;
| | - Graziano Rossi
- Department of Earth and Environmental Sciences, Pavia University, Via Sant’Epifanio 14, 27100 Pavia, Italy; (S.O.); (G.R.)
| | - Alberto Salas
- International Potato Center, Avenida La Molina 1895, La Molina, Lima 15023, Peru; (D.E.); (N.C.M.-C.); (A.S.)
| | - Deepa Singh Shrestha
- National Agriculture Genetic Resources Centre, Nepal Agricultural Research Council (NARC), Khumaltar, Lalitpur P.O. Box. 3605, Nepal; (K.H.G.); (R.P.M.); (D.S.S.)
| | - Sadar Uddin Siddiqui
- Bio-Resources Conservation Institute, National Agricultural Research Centre, Park Road, Islamabad 45500, Pakistan; (S.A.J.); (S.U.S.)
| | - Paul P. Smith
- Botanic Gardens Conservation International, Descanso House, 199 Kew Road, Richmond TW9 3BW, UK;
| | - Diego A. Sotomayor
- Subdirección de Recursos Genéticos, Instituto Nacional de Innovación Agraria, Av. La Molina 1981, La Molina, Lima 15024, Peru;
- Facultad de Ciencias, Universidad Nacional Agraria La Molina, Av. La Molina s/n, La Molina, Lima 15024, Peru
| | - Marcelo Tacán
- Instituto Nacional de Investigaciones Agropecuarias, Avenida Amazonas y Eloy Alfaro, Edificio MAG, Cuarto Piso, Quito 170518, Ecuador; (Á.M.-A.); (M.T.); (C.T.)
| | - César Tapia
- Instituto Nacional de Investigaciones Agropecuarias, Avenida Amazonas y Eloy Alfaro, Edificio MAG, Cuarto Piso, Quito 170518, Ecuador; (Á.M.-A.); (M.T.); (C.T.)
| | - Álvaro Toledo
- Food and Agriculture Organization of the United Nations, Viale delle Terme di Caracalla s/n, 00153 Roma, Italy;
| | - Jane Toll
- Global Crop Diversity Trust, Platz der Vereinten Nationen 7, 53113 Bonn, Germany; (B.B.T.); (N.P.C.-Á.); (H.D.); (L.G.); (N.J.); (M.O.); (J.T.); (B.K.)
| | - Dang Toan Vu
- Plant Resources Center, Vietnam Academy of Agricultural Sciences, An Khanh, Hoai Duc, Ha Noi 131000, Vietnam; (D.T.V.); (T.D.V.)
| | - Tuong Dang Vu
- Plant Resources Center, Vietnam Academy of Agricultural Sciences, An Khanh, Hoai Duc, Ha Noi 131000, Vietnam; (D.T.V.); (T.D.V.)
| | - Michael J. Way
- Royal Botanic Gardens, Kew, Wakehurst, Ardingly, Haywards Heath RH17 6TN, UK; (R.A.); (E.B.); (C.P.C.); (A.F.); (U.L.); (J.V.M.); (T.R.P.); (M.J.W.)
| | - Mariana Yazbek
- The International Center for Agricultural Research in the Dry Areas, Dalia Bldg, 2nd Floor Bashir El Kassar Street Verdun, Beirut 1108-2010, Lebanon; (A.A.); (M.Y.)
| | - Cinthya Zorrilla
- Joint FAO/IAEA Centre of Nuclear Techniques in Food and Agriculture, Plant Breeding and Genetics Section, 1400 Vienna, Austria;
| | - Benjamin Kilian
- Global Crop Diversity Trust, Platz der Vereinten Nationen 7, 53113 Bonn, Germany; (B.B.T.); (N.P.C.-Á.); (H.D.); (L.G.); (N.J.); (M.O.); (J.T.); (B.K.)
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Argumedo A, Song Y, Khoury CK, Hunter D, Dempewolf H, Guarino L, de Haan S. Biocultural Diversity for Food System Transformation Under Global Environmental Change. Front Sustain Food Syst 2021. [DOI: 10.3389/fsufs.2021.685299] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Biocultural diversity is central to the nutrition, resilience, and adaptive capacity of Indigenous and traditional peoples, who collectively maintain the longest ongoing human experiences with the provision of food under environmental change. In the form of crops and livestock and associated knowledge on their cultivation and use, food-related biocultural diversity likewise underpins global food security. As food system transformation is increasingly recognized as an urgent priority, we argue that food security, sustainability, resilience, and adaptive capacity can be furthered through greater emphasis on conservation, use, and celebration of food-related biocultural diversity. We provide examples from the Parque de la Papa, Peru, a “food biocultural diversity neighborhood” which through advocacy and partnerships based around its diversity, has both enhanced local communities and contributed to food security at a much larger scale. We outline collaborative actions which we believe are important to up- and out-scale food biocultural diversity neighborhood successes. Further research and knowledge sharing are critical to better document, understand, track, and communicate the value, functions, and state of biocultural diversity in food systems. Expanded training and capacity development opportunities are important to enable the interchange of experiences and visions on food, health, sustainability and resilience, climate adaptation, equity and justice, and livelihood generation with others facing similar challenges. Finally, strengthened networking across food biocultural diversity neighborhoods is essential to their persistence and growth as they increasingly engage with local, national, and international organizations, based on shared interests and on their own terms, across five continents.
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Argumedo A, Song Y, Khoury CK, Hunter D, Dempewolf H. Support Indigenous food system biocultural diversity. Lancet Planet Health 2020; 4:e554. [PMID: 33278371 DOI: 10.1016/s2542-5196(20)30243-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Accepted: 09/24/2020] [Indexed: 05/22/2023]
Affiliation(s)
- Alejandro Argumedo
- Swift Foundation and International Network of Mountain Indigenous Peoples, Wanchaq, Cusco, Peru
| | - Yiching Song
- Center for Chinese Agricultural Policy, Chinese Academy of Sciences, Institute of Geographical Sciences and Natural Resources Research, Beijing, China
| | - Colin K Khoury
- International Center for Tropical Agriculture, 763537 Cali, Colombia.
| | - Danny Hunter
- Bioversity International, Maccarese (Fiumicino), Italy
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Vincent H, Amri A, Castañeda-Álvarez NP, Dempewolf H, Dulloo E, Guarino L, Hole D, Mba C, Toledo A, Maxted N. Modeling of crop wild relative species identifies areas globally for in situ conservation. Commun Biol 2019; 2:136. [PMID: 31044161 PMCID: PMC6478866 DOI: 10.1038/s42003-019-0372-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 03/01/2019] [Indexed: 11/17/2022] Open
Abstract
The impact of climate change is causing challenges for the agricultural production and food systems. More nutritious and climate resilient crop varieties are required, but lack of available and accessible trait diversity is limiting crop improvement. Crop wild relatives (CWR) are the wild cousins of cultivated crops and a vast resource of genetic diversity for breeding new, higher yielding, climate change tolerant crop varieties, but they are under-conserved (particularly in situ), largely unavailable and therefore underutilized. Here we apply species distribution modelling, climate change projections and geographic analyses to 1261 CWR species from 167 major crop genepools to explore key geographical areas for CWR in situ conservation worldwide. We identify 150 sites where 65.7% of the CWR species identified can be conserved for future use.
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Affiliation(s)
- Holly Vincent
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT UK
| | - Ahmed Amri
- International Centre for Agricultural Research in the Dry Areas, Rabat, Morocco
| | - Nora P. Castañeda-Álvarez
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT UK
- International Center for Tropical Agriculture (CIAT), Km 17, Recta Cali-Palmira, Cali, Colombia
- Global Crop Diversity Trust, Platz der Vereinten Nationen 7, 53113 Bonn, Germany
| | - Hannes Dempewolf
- Global Crop Diversity Trust, Platz der Vereinten Nationen 7, 53113 Bonn, Germany
| | - Ehsan Dulloo
- Bioversity International, Via dei Tre Denari 472/a, 00057 Maccarese (Fiumicino), Roma, Italy
| | - Luigi Guarino
- Global Crop Diversity Trust, Platz der Vereinten Nationen 7, 53113 Bonn, Germany
| | - David Hole
- Moore Center for Science, Conservation International, Arlington, VA 22202 USA
- Center for Biodiversity Outcomes, Arizona State University, Tempe, AZ 85281 USA
| | - Chikelu Mba
- Plant Production and Protection Division, Food and Agricultural Organization (FAO), Viale delle Terme di Caracalla, 00153 Rome, Italy
| | - Alvaro Toledo
- Secretariat of the International Treaty on Plant Genetic Resources for Food and Agriculture, FAO, Viale delle Terme di Caracalla, 00153 Rome, Italy
| | - Nigel Maxted
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT UK
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7
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Prohens J, Gramazio P, Plazas M, Dempewolf H, Kilian B, Díez MJ, Fita A, Herraiz FJ, Rodríguez-Burruezo A, Soler S, Knapp S, Vilanova S. Introgressiomics: a new approach for using crop wild relatives in breeding for adaptation to climate change. Euphytica 2017; 213:158. [PMID: 0 DOI: 10.1007/s10681-017-1938-9] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 06/23/2017] [Indexed: 05/29/2023]
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8
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Affiliation(s)
- Hannes Dempewolf
- Global Crop Diversity Trust; Platz der Vereinten Nationen 7 53113 Bonn Germany
- Univ. of British Columbia; Dep. of Botany; 6270 University Blvd. Vancouver BC Canada
| | - Gregory Baute
- Univ. of British Columbia; Dep. of Botany; 6270 University Blvd. Vancouver BC Canada
| | - Justin Anderson
- Univ. of Hawaii at Manoa; Dep. of Tropical Plant & Soil Sciences; 3190 Maile Way Honolulu Hawaii 96822
| | - Benjamin Kilian
- Global Crop Diversity Trust; Platz der Vereinten Nationen 7 53113 Bonn Germany
| | - Chelsea Smith
- Univ. of Waterloo; Dep. of Environment and Resource Studies; 200 University Ave. W. Waterloo ON N2L 3G1 Canada
| | - Luigi Guarino
- Global Crop Diversity Trust; Platz der Vereinten Nationen 7 53113 Bonn Germany
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9
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Khoury CK, Achicanoy HA, Bjorkman AD, Navarro-Racines C, Guarino L, Flores-Palacios X, Engels JMM, Wiersema JH, Dempewolf H, Sotelo S, Ramírez-Villegas J, Castañeda-Álvarez NP, Fowler C, Jarvis A, Rieseberg LH, Struik PC. Origins of food crops connect countries worldwide. Proc Biol Sci 2016. [PMCID: PMC4920324 DOI: 10.1098/rspb.2016.0792] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Research into the origins of food plants has led to the recognition that specific geographical regions around the world have been of particular importance to the development of agricultural crops. Yet the relative contributions of these different regions in the context of current food systems have not been quantified. Here we determine the origins (‘primary regions of diversity’) of the crops comprising the food supplies and agricultural production of countries worldwide. We estimate the degree to which countries use crops from regions of diversity other than their own (‘foreign crops’), and quantify changes in this usage over the past 50 years. Countries are highly interconnected with regard to primary regions of diversity of the crops they cultivate and/or consume. Foreign crops are extensively used in food supplies (68.7% of national food supplies as a global mean are derived from foreign crops) and production systems (69.3% of crops grown are foreign). Foreign crop usage has increased significantly over the past 50 years, including in countries with high indigenous crop diversity. The results provide a novel perspective on the ongoing globalization of food systems worldwide, and bolster evidence for the importance of international collaboration on genetic resource conservation and exchange.
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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
- Centre for Crop Systems Analysis, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- United States Department of Agriculture, Agricultural Research Service, National Laboratory for Genetic Resources Preservation, 1111 South Mason Street, Fort Collins, CO 80521, USA
| | - Harold A. Achicanoy
- International Center for Tropical Agriculture (CIAT), Km 17, Recta Cali-Palmira, Apartado Aéreo 6713, 763537 Cali, Colombia
| | - Anne D. Bjorkman
- German Centre for Integrative Biodiversity Research, Leipzig, Germany
- School of Geosciences, University of Edinburgh, James Hutton Road, Edinburgh EH9 3FE, UK
| | - Carlos Navarro-Racines
- International Center for Tropical Agriculture (CIAT), Km 17, Recta Cali-Palmira, Apartado Aéreo 6713, 763537 Cali, Colombia
- CGIAR Research Program on Climate Change, Agriculture and Food Security (CCAFS), Km 17, Recta Cali-Palmira, Apartado Aéreo 6713, 763537 Cali, Colombia
| | - Luigi Guarino
- Global Crop Diversity Trust, Platz der Vereinten Nationen 7, 53113 Bonn, Germany
| | | | | | - John H. Wiersema
- United States Department of Agriculture, Agricultural Research Service, National Germplasm Research Laboratory, Building 003, BARC-West, Beltsville, MD 20705-2350, USA
| | - Hannes Dempewolf
- Global Crop Diversity Trust, Platz der Vereinten Nationen 7, 53113 Bonn, Germany
| | - Steven Sotelo
- International Center for Tropical Agriculture (CIAT), Km 17, Recta Cali-Palmira, Apartado Aéreo 6713, 763537 Cali, Colombia
| | - Julian Ramírez-Villegas
- International Center for Tropical Agriculture (CIAT), Km 17, Recta Cali-Palmira, Apartado Aéreo 6713, 763537 Cali, Colombia
- CGIAR Research Program on Climate Change, Agriculture and Food Security (CCAFS), Km 17, Recta Cali-Palmira, Apartado Aéreo 6713, 763537 Cali, Colombia
- School of Earth and Environment, University of Leeds, Leeds, UK
| | - Nora P. Castañeda-Álvarez
- International Center for Tropical Agriculture (CIAT), Km 17, Recta Cali-Palmira, Apartado Aéreo 6713, 763537 Cali, Colombia
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Cary Fowler
- Global Crop Diversity Trust, Platz der Vereinten Nationen 7, 53113 Bonn, Germany
| | - Andy Jarvis
- International Center for Tropical Agriculture (CIAT), Km 17, Recta Cali-Palmira, Apartado Aéreo 6713, 763537 Cali, Colombia
- CGIAR Research Program on Climate Change, Agriculture and Food Security (CCAFS), Km 17, Recta Cali-Palmira, Apartado Aéreo 6713, 763537 Cali, Colombia
| | - Loren H. Rieseberg
- The Biodiversity Research Centre, Vancouver, British Columbia, Canada V6T 1Z4
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Paul C. Struik
- Centre for Crop Systems Analysis, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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10
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Abberton M, Batley J, Bentley A, Bryant J, Cai H, Cockram J, de Oliveira AC, Cseke LJ, Dempewolf H, De Pace C, Edwards D, Gepts P, Greenland A, Hall AE, Henry R, Hori K, Howe GT, Hughes S, Humphreys M, Lightfoot D, Marshall A, Mayes S, Nguyen HT, Ogbonnaya FC, Ortiz R, Paterson AH, Tuberosa R, Valliyodan B, Varshney RK, Yano M. Global agricultural intensification during climate change: a role for genomics. Plant Biotechnol J 2016; 14:1095-8. [PMID: 26360509 PMCID: PMC5049667 DOI: 10.1111/pbi.12467] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Revised: 07/23/2015] [Accepted: 08/06/2015] [Indexed: 05/03/2023]
Abstract
Agriculture is now facing the 'perfect storm' of climate change, increasing costs of fertilizer and rising food demands from a larger and wealthier human population. These factors point to a global food deficit unless the efficiency and resilience of crop production is increased. The intensification of agriculture has focused on improving production under optimized conditions, with significant agronomic inputs. Furthermore, the intensive cultivation of a limited number of crops has drastically narrowed the number of plant species humans rely on. A new agricultural paradigm is required, reducing dependence on high inputs and increasing crop diversity, yield stability and environmental resilience. Genomics offers unprecedented opportunities to increase crop yield, quality and stability of production through advanced breeding strategies, enhancing the resilience of major crops to climate variability, and increasing the productivity and range of minor crops to diversify the food supply. Here we review the state of the art of genomic-assisted breeding for the most important staples that feed the world, and how to use and adapt such genomic tools to accelerate development of both major and minor crops with desired traits that enhance adaptation to, or mitigate the effects of climate change.
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Affiliation(s)
- Michael Abberton
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Jacqueline Batley
- School of Plant Biology and Institute of Agriculture, University of Western Australia, Perth, WA, Australia
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Qld, Australia
| | | | - John Bryant
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | - Hongwei Cai
- Forage Crop Research Institute, Japan Grassland Agriculture and Forage Seed Association, Nasushiobara, Japan
- Department of Plant Genetics and Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | | | - Antonio Costa de Oliveira
- Plant Genomics and Breeding Center, Eliseu Maciel School of Agriculture, Federal University of Pelotas, Pelotas, RS, Brazil
| | - Leland J Cseke
- Department of Biological Sciences Huntsville, The University of Alabama in Huntsville, Huntsville, AL, USA
| | | | - Ciro De Pace
- Department of Agriculture, Forests, Nature and Energy (DAFNE), University of Tuscia, Viterbo, Italy
| | - David Edwards
- School of Plant Biology and Institute of Agriculture, University of Western Australia, Perth, WA, Australia
| | - Paul Gepts
- Department of Plant Sciences, University of California, Davis, CA, USA
| | | | | | - Robert Henry
- The Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Qld, Australia
| | - Kiyosumi Hori
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
| | - Glenn Thomas Howe
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, USA
| | | | - Mike Humphreys
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Ceredigion, UK
| | - David Lightfoot
- College of Agricultural Sciences, Southern Illinois University, Carbondale, IL, USA
| | - Athole Marshall
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Ceredigion, UK
| | - Sean Mayes
- Biotechnology and Crop Genetics, Crops for the Future, Kuala Lumpur, Malaysia
| | - Henry T Nguyen
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, USA
| | | | - Rodomiro Ortiz
- Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, USA
| | - Roberto Tuberosa
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Babu Valliyodan
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, USA
| | - Rajeev K Varshney
- School of Plant Biology and Institute of Agriculture, University of Western Australia, Perth, WA, Australia
- Centre of Excellence in Genomics, International Crops Research Institute for the Semi- Arid Tropics (ICRISAT), Hyderabad, India
| | - Masahiro Yano
- National Agriculture and Food Research Organization (NARO), Institute of Crop Science, Tsukuba, Japan
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11
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Castañeda-Álvarez NP, Khoury CK, Achicanoy HA, Bernau V, Dempewolf H, Eastwood RJ, Guarino L, Harker RH, Jarvis A, Maxted N, Müller JV, Ramirez-Villegas J, Sosa CC, Struik PC, Vincent H, Toll J. Global conservation priorities for crop wild relatives. Nat Plants 2016; 2:16022. [PMID: 27249561 DOI: 10.1038/nplants.2016.22] [Citation(s) in RCA: 174] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 02/05/2016] [Indexed: 05/04/2023]
Abstract
The wild relatives of domesticated crops possess genetic diversity useful for developing more productive, nutritious and resilient crop varieties. However, their conservation status and availability for utilization are a concern, and have not been quantified globally. Here, we model the global distribution of 1,076 taxa related to 81 crops, using occurrence information collected from biodiversity, herbarium and gene bank databases. We compare the potential geographic and ecological diversity encompassed in these distributions with that currently accessible in gene banks, as a means to estimate the comprehensiveness of the conservation of genetic diversity. Our results indicate that the diversity of crop wild relatives is poorly represented in gene banks. For 313 (29.1% of total) taxa associated with 63 crops, no germplasm accessions exist, and a further 257 (23.9%) are represented by fewer than ten accessions. Over 70% of taxa are identified as high priority for further collecting in order to improve their representation in gene banks, and over 95% are insufficiently represented in regard to the full range of geographic and ecological variation in their native distributions. The most critical collecting gaps occur in the Mediterranean and the Near East, western and southern Europe, Southeast and East Asia, and South America. We conclude that a systematic effort is needed to improve the conservation and availability of crop wild relatives for use in plant breeding.
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Affiliation(s)
- Nora P Castañeda-Álvarez
- International Center for Tropical Agriculture (CIAT), Km 17, Recta Cali-Palmira, Cali 763537, Colombia
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Colin K Khoury
- International Center for Tropical Agriculture (CIAT), Km 17, Recta Cali-Palmira, Cali 763537, Colombia
- Centre for Crop Systems Analysis, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Harold A Achicanoy
- International Center for Tropical Agriculture (CIAT), Km 17, Recta Cali-Palmira, Cali 763537, Colombia
| | - Vivian Bernau
- International Center for Tropical Agriculture (CIAT), Km 17, Recta Cali-Palmira, Cali 763537, Colombia
| | - Hannes Dempewolf
- Global Crop Diversity Trust, Platz der Vereinten Nationen 7, 53115 Bonn, Germany
| | - Ruth J Eastwood
- Royal Botanic Gardens, Kew, Conservation Science, Millennium Seed Bank, Wakehurst Place, Ardingly RH17 6TN, UK
| | - Luigi Guarino
- Global Crop Diversity Trust, Platz der Vereinten Nationen 7, 53115 Bonn, Germany
| | - Ruth H Harker
- Royal Botanic Gardens, Kew, Conservation Science, Millennium Seed Bank, Wakehurst Place, Ardingly RH17 6TN, UK
| | - Andy Jarvis
- International Center for Tropical Agriculture (CIAT), Km 17, Recta Cali-Palmira, Cali 763537, Colombia
- CGIAR Research Program on Climate Change, Agriculture and Food Security (CCAFS), Km 17, Recta Cali-Palmira, Cali 763537, Colombia
| | - Nigel Maxted
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Jonas V Müller
- Royal Botanic Gardens, Kew, Conservation Science, Millennium Seed Bank, Wakehurst Place, Ardingly RH17 6TN, UK
| | - Julian Ramirez-Villegas
- International Center for Tropical Agriculture (CIAT), Km 17, Recta Cali-Palmira, Cali 763537, Colombia
- CGIAR Research Program on Climate Change, Agriculture and Food Security (CCAFS), Km 17, Recta Cali-Palmira, Cali 763537, Colombia
- Institute for Climate and Atmospheric Science, School of Earth and Environment, University of Leeds, LS2 9JT, UK
| | - Chrystian C Sosa
- International Center for Tropical Agriculture (CIAT), Km 17, Recta Cali-Palmira, Cali 763537, Colombia
| | - Paul C Struik
- Centre for Crop Systems Analysis, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Holly Vincent
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Jane Toll
- Global Crop Diversity Trust, Platz der Vereinten Nationen 7, 53115 Bonn, Germany
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12
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Kole C, Muthamilarasan M, Henry R, Edwards D, Sharma R, Abberton M, Batley J, Bentley A, Blakeney M, Bryant J, Cai H, Cakir M, Cseke LJ, Cockram J, de Oliveira AC, De Pace C, Dempewolf H, Ellison S, Gepts P, Greenland A, Hall A, Hori K, Hughes S, Humphreys MW, Iorizzo M, Ismail AM, Marshall A, Mayes S, Nguyen HT, Ogbonnaya FC, Ortiz R, Paterson AH, Simon PW, Tohme J, Tuberosa R, Valliyodan B, Varshney RK, Wullschleger SD, Yano M, Prasad M. Application of genomics-assisted breeding for generation of climate resilient crops: progress and prospects. Front Plant Sci 2015; 6:563. [PMID: 26322050 PMCID: PMC4531421 DOI: 10.3389/fpls.2015.00563] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 07/08/2015] [Indexed: 05/19/2023]
Abstract
Climate change affects agricultural productivity worldwide. Increased prices of food commodities are the initial indication of drastic edible yield loss, which is expected to increase further due to global warming. This situation has compelled plant scientists to develop climate change-resilient crops, which can withstand broad-spectrum stresses such as drought, heat, cold, salinity, flood, submergence and pests, thus helping to deliver increased productivity. Genomics appears to be a promising tool for deciphering the stress responsiveness of crop species with adaptation traits or in wild relatives toward identifying underlying genes, alleles or quantitative trait loci. Molecular breeding approaches have proven helpful in enhancing the stress adaptation of crop plants, and recent advances in high-throughput sequencing and phenotyping platforms have transformed molecular breeding to genomics-assisted breeding (GAB). In view of this, the present review elaborates the progress and prospects of GAB for improving climate change resilience in crops, which is likely to play an ever increasing role in the effort to ensure global food security.
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Affiliation(s)
| | - Mehanathan Muthamilarasan
- Department of Plant Molecular Genetics and Genomics, National Institute of Plant Genome ResearchNew Delhi, India
| | - Robert Henry
- Queensland Alliance for Agriculture and Food Innovation, University of QueenslandSt Lucia, QLD, Australia
| | - David Edwards
- School of Agriculture and Food Sciences, University of QueenslandBrisbane, QLD, Australia
| | - Rishu Sharma
- Department of Plant Pathology, Faculty of Agriculture, Bidhan Chandra Krishi ViswavidyalayaMohanpur, India
| | - Michael Abberton
- Genetic Resources Centre, International Institute of Tropical AgricultureIbadan, Nigeria
| | - Jacqueline Batley
- Centre for Integrated Legume Research, University of QueenslandBrisbane, QLD, Australia
| | - Alison Bentley
- The John Bingham Laboratory, National Institute of Agricultural BotanyCambridge, UK
| | | | - John Bryant
- CLES, Hatherly Laboratories, University of ExeterExeter, UK
| | - Hongwei Cai
- Forage Crop Research Institute, Japan Grassland Agriculture and Forage Seed AssociationNasushiobara, Japan
- Department of Plant Genetics and Breeding, College of Agronomy and Biotechnology, China Agricultural UniversityBeijing, China
| | - Mehmet Cakir
- Faculty of Science and Engineering, School of Biological Sciences and Biotechnology, Murdoch UniversityMurdoch, WA, Australia
| | - Leland J. Cseke
- Department of Biological Sciences, The University of Alabama in HuntsvilleHuntsville, AL, USA
| | - James Cockram
- The John Bingham Laboratory, National Institute of Agricultural BotanyCambridge, UK
| | | | - Ciro De Pace
- Department of Agriculture, Forests, Nature and Energy, University of TusciaViterbo, Italy
| | - Hannes Dempewolf
- Global Crop Diversity Trust, Platz der Vereinten NationenBonn, Germany
| | - Shelby Ellison
- Department of Horticulture, University of WisconsinMadison, WI, USA
| | - Paul Gepts
- Section of Crop and Ecosystem Sciences, Department of Plant Sciences, University of California, DavisDavis, CA, USA
| | - Andy Greenland
- The John Bingham Laboratory, National Institute of Agricultural BotanyCambridge, UK
| | - Anthony Hall
- Department of Botany and Plant Sciences, University of CaliforniaRiverside, Riverside, USA
| | - Kiyosumi Hori
- Agrogenomics Research Center, National Institute of Agrobiological SciencesTsukuba, Japan
| | | | - Mike W. Humphreys
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityWales, UK
| | - Massimo Iorizzo
- Department of Horticulture, University of WisconsinMadison, WI, USA
| | | | - Athole Marshall
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityWales, UK
| | - Sean Mayes
- Biotechnology and Crop Genetics, Crops for the FutureSemenyih, Malaysia
| | - Henry T. Nguyen
- National Center for Soybean Biotechnology and Division of Plant Science, University of MissouriColumbia, MO, USA
| | | | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural SciencesSundvagen, Sweden
| | | | - Philipp W. Simon
- Department of Horticulture, USDA-ARS, University of WisconsinMadison, WI, USA
| | - Joe Tohme
- Agrobiodiversity and Biotechnology Project, Centro International de Agricultura TropicalCali, Columbia
| | | | - Babu Valliyodan
- National Center for Soybean Biotechnology and Division of Plant Science, University of MissouriColumbia, MO, USA
| | - Rajeev K. Varshney
- Center of Excellence in Genomics, International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
| | - Stan D. Wullschleger
- Oak Ridge National Laboratory, Environmental Sciences Division, Climate Change Science InstituteOak Ridge, TN, USA
| | - Masahiro Yano
- National Agriculture and Food Research Organization, Institute of Crop ScienceTsukuba, Japan
| | - Manoj Prasad
- Department of Plant Molecular Genetics and Genomics, National Institute of Plant Genome ResearchNew Delhi, India
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13
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Dempewolf H, Tesfaye M, Teshome A, Bjorkman AD, Andrew RL, Scascitelli M, Black S, Bekele E, Engels JMM, Cronk QCB, Rieseberg LH. Patterns of domestication in the Ethiopian oil-seed crop noug (Guizotia abyssinica). Evol Appl 2015; 8:464-75. [PMID: 26029260 PMCID: PMC4430770 DOI: 10.1111/eva.12256] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 02/13/2015] [Indexed: 11/27/2022] Open
Abstract
Noug (Guizotia abyssinica) is a semidomesticated oil-seed crop, which is primarily cultivated in Ethiopia. Unlike its closest crop relative, sunflower, noug has small seeds, small flowering heads, many branches, many flowering heads, and indeterminate flowering, and it shatters in the field. Here, we conducted common garden studies and microsatellite analyses of genetic variation to test whether high levels of crop-wild gene flow and/or unfavorable phenotypic correlations have hindered noug domestication. With the exception of one population, analyses of microsatellite variation failed to detect substantial recent admixture between noug and its wild progenitor. Likewise, only very weak correlations were found between seed mass and the number or size of flowering heads. Thus, noug's 'atypical' domestication syndrome does not seem to be a consequence of recent introgression or unfavorable phenotypic correlations. Nonetheless, our data do reveal evidence of local adaptation of noug cultivars to different precipitation regimes, as well as high levels of phenotypic plasticity, which may permit reasonable yields under diverse environmental conditions. Why noug has not been fully domesticated remains a mystery, but perhaps early farmers selected for resilience to episodic drought or untended environments rather than larger seeds. Domestication may also have been slowed by noug's outcrossing mating system.
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Affiliation(s)
- Hannes Dempewolf
- Department of Botany and Biodiversity Research Centre, University of British Columbia Vancouver, BC, Canada
| | - Misteru Tesfaye
- Ethiopian Institute of Agricultural Research, Holetta Agricultural Research Centre Addis Ababa, Ethiopia
| | - Abel Teshome
- Department of Plant Breeding, Swedish University of Agricultural Sciences Alnarp, Sweden
| | - Anne D Bjorkman
- Department of Geography and Biodiversity Research Centre, University of British Columbia Vancouver, BC, Canada
| | - Rose L Andrew
- Department of Botany and Biodiversity Research Centre, University of British Columbia Vancouver, BC, Canada
| | - Moira Scascitelli
- Department of Botany and Biodiversity Research Centre, University of British Columbia Vancouver, BC, Canada
| | - Scott Black
- Department of Botany and Biodiversity Research Centre, University of British Columbia Vancouver, BC, Canada
| | - Endashaw Bekele
- College of Natural Sciences, Addis Ababa University Addis Ababa, Ethiopia
| | | | - Quentin C B Cronk
- Department of Botany and Biodiversity Research Centre, University of British Columbia Vancouver, BC, Canada
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia Vancouver, BC, Canada ; Department of Biology, Indiana University Bloomington, IN, USA
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14
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Hodgins KA, Lai Z, Oliveira LO, Still DW, Scascitelli M, Barker MS, Kane NC, Dempewolf H, Kozik A, Kesseli RV, Burke JM, Michelmore RW, Rieseberg LH. Genomics of Compositae crops: reference transcriptome assemblies and evidence of hybridization with wild relatives. Mol Ecol Resour 2013; 14:166-77. [DOI: 10.1111/1755-0998.12163] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Revised: 08/14/2013] [Accepted: 08/15/2013] [Indexed: 11/30/2022]
Affiliation(s)
- Kathryn A. Hodgins
- Department of Botany and Biodiversity Research Centre; University of British Columbia; Vancouver BC V6T 1Z4 Canada
| | - Zhao Lai
- Department of Biology and Center for Genomics and Bioinformatics; Indiana University; Bloomington IN 47405 USA
| | - Luiz O. Oliveira
- Departamento de Bioquímica e Biologia Molecular; Universidade Federal de Viçosa; 36570-000 Viçosa Brazil
| | - David W. Still
- Department of Plant Sciences; Cal Poly Pomona; Pomona CA 91768 USA
| | - Moira Scascitelli
- Department of Botany and Biodiversity Research Centre; University of British Columbia; Vancouver BC V6T 1Z4 Canada
| | - Michael S. Barker
- Department of Ecology and Evolutionary Biology; University of Arizona; Tucson AZ 85721 USA
| | - Nolan C. Kane
- Department of Ecology and Evolutionary Biology; University of Colorado Boulder; Boulder CO 80309 USA
| | - Hannes Dempewolf
- Department of Botany and Biodiversity Research Centre; University of British Columbia; Vancouver BC V6T 1Z4 Canada
| | - Alex Kozik
- The Genome Center; University of California; Davis CA 95616 USA
| | | | - John M. Burke
- Department of Plant Biology; University of Georgia; Athens GA 30602 USA
| | - Richard W. Michelmore
- The Genome Center; University of California; Davis CA 95616 USA
- Departments of Plant Sciences, Molecular & Cellular Biology, and Medical Microbiology & Immunology; University of California; Davis CA 95616 USA
| | - Loren H. Rieseberg
- Department of Botany and Biodiversity Research Centre; University of British Columbia; Vancouver BC V6T 1Z4 Canada
- Department of Biology and Center for Genomics and Bioinformatics; Indiana University; Bloomington IN 47405 USA
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Dempewolf H, Kane NC, Ostevik KL, Geleta M, Barker MS, Lai Z, Stewart ML, Bekele E, Engels JMM, Cronk QCB, Rieseberg LH. Establishing genomic tools and resources for Guizotia abyssinica (L.f.) Cass.-the development of a library of expressed sequence tags, microsatellite loci, and the sequencing of its chloroplast genome. Mol Ecol Resour 2013; 10:1048-58. [PMID: 21565115 DOI: 10.1111/j.1755-0998.2010.02859.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present an EST library, chloroplast genome sequence, and nuclear microsatellite markers that were developed for the semi-domesticated oilseed crop noug (Guizotia abyssinica) from Ethiopia. The EST library consists of 25 711 Sanger reads, assembled into 17 538 contigs and singletons, of which 4781 were functionally annotated using the Arabidopsis Information Resource (TAIR). The age distribution of duplicated genes in the EST library shows evidence of two paleopolyploidizations-a pattern that noug shares with several other species in the Heliantheae tribe (Compositae family). From the EST library, we selected 43 microsatellites and then designed and tested primers for their amplification. The number of microsatellite alleles varied between 2 and 10 (average 4.67), and the average observed and expected heterozygosities were 0.49 and 0.54, respectively. The chloroplast genome was sequenced de novo using Illumina's sequencing technology and completed with traditional Sanger sequencing. No large re-arrangements were found between the noug and sunflower chloroplast genomes, but 1.4% of sites have indels and 1.8% show sequence divergence between the two species. We identified 34 tRNAs, 4 rRNA sequences, and 80 coding sequences, including one region (trnH-psbA) with 15% sequence divergence between noug and sunflower that may be particularly useful for phylogeographic studies in noug and its wild relatives.
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Affiliation(s)
- Hannes Dempewolf
- The Biodiversity Research Centre and Department of Botany, 3529-6270 University Blvd, University of British Columbia, Vancouver, British Columbia, Canada
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McCouch S, Baute GJ, Bradeen J, Bramel P, Bretting PK, Buckler E, Burke JM, Charest D, Cloutier S, Cole G, Dempewolf H, Dingkuhn M, Feuillet C, Gepts P, Grattapaglia D, Guarino L, Jackson S, Knapp S, Langridge P, Lawton-Rauh A, Lijua Q, Lusty C, Michael T, Myles S, Naito K, Nelson RL, Pontarollo R, Richards CM, Rieseberg L, Ross-Ibarra J, Rounsley S, Hamilton RS, Schurr U, Stein N, Tomooka N, van der Knaap E, van Tassel D, Toll J, Valls J, Varshney RK, Ward J, Waugh R, Wenzl P, Zamir D. Agriculture: Feeding the future. Nature 2013; 499:23-4. [PMID: 23823779 DOI: 10.1038/499023a] [Citation(s) in RCA: 240] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Dempewolf H, Hodgins KA, Rummell SE, Ellstrand NC, Rieseberg LH. Reproductive isolation during domestication. Plant Cell 2012; 24:2710-7. [PMID: 22773750 PMCID: PMC3426109 DOI: 10.1105/tpc.112.100115] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Revised: 04/30/2012] [Accepted: 06/18/2012] [Indexed: 05/02/2023]
Abstract
It has been hypothesized that reproductive isolation should facilitate evolution under domestication. However, a systematic comparison of reproductive barrier strength between crops and their progenitors has not been conducted to test this hypothesis. Here, we present a systematic survey of reproductive barriers between 32 economically important crop species and their progenitors to better understand the role of reproductive isolation during the domestication process. We took a conservative approach, avoiding those types of reproductive isolation that are poorly known for these taxa (e.g., differences in flowering time). We show that the majority of crops surveyed are isolated from their progenitors by one or more reproductive barriers, despite the fact that the most important reproductive barrier in natural systems, geographical isolation, was absent, at least in the initial stages of domestication for most species. Thus, barriers to reproduction between crops and wild relatives are closely associated with domestication and may facilitate it, thereby raising the question whether reproductive isolation could be viewed as a long-overlooked "domestication trait." Some of the reproductive barriers observed (e.g., polyploidy and uniparental reproduction), however, may have been favored for reasons other than, or in addition to, their effects on gene flow.
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Affiliation(s)
- Hannes Dempewolf
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Kathryn A. Hodgins
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Sonja E. Rummell
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Norman C. Ellstrand
- Department of Botany and Plant Sciences and Center for Conservation Biology, University of California, Riverside, California 92521
| | - Loren H. Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
- Department of Biology, Indiana University, Bloomington, Indiana 47405
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Kane N, Sveinsson S, Dempewolf H, Yang JY, Zhang D, Engels JMM, Cronk Q. Ultra-barcoding in cacao (Theobroma spp.; Malvaceae) using whole chloroplast genomes and nuclear ribosomal DNA. Am J Bot 2012; 99:320-9. [PMID: 22301895 DOI: 10.3732/ajb.1100570] [Citation(s) in RCA: 149] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
PREMISE OF STUDY To reliably identify lineages below the species level such as subspecies or varieties, we propose an extension to DNA-barcoding using next-generation sequencing to produce whole organellar genomes and substantial nuclear ribosomal sequence. Because this method uses much longer versions of the traditional DNA-barcoding loci in the plastid and ribosomal DNA, we call our approach ultra-barcoding (UBC). METHODS We used high-throughput next-generation sequencing to scan the genome and generate reliable sequence of high copy number regions. Using this method, we examined whole plastid genomes as well as nearly 6000 bases of nuclear ribosomal DNA sequences for nine genotypes of Theobroma cacao and an individual of the related species T. grandiflorum, as well as an additional publicly available whole plastid genome of T. cacao. KEY RESULTS All individuals of T. cacao examined were uniquely distinguished, and evidence of reticulation and gene flow was observed. Sequence variation was observed in some of the canonical barcoding regions between species, but other regions of the chloroplast were more variable both within species and between species, as were ribosomal spacers. Furthermore, no single region provides the level of data available using the complete plastid genome and rDNA. CONCLUSIONS Our data demonstrate that UBC is a viable, increasingly cost-effective approach for reliably distinguishing varieties and even individual genotypes of T. cacao. This approach shows great promise for applications where very closely related or interbreeding taxa must be distinguished.
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Affiliation(s)
- Nolan Kane
- Department of Botany, University of British Columbia, Vancouver BC, Canada V6T 1Z4.
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Yang JY, Motilal LA, Dempewolf H, Maharaj K, Cronk QCB. Chloroplast microsatellite primers for cacao (Theobroma cacao) and other Malvaceae. Am J Bot 2011; 98:e372-e374. [PMID: 22114220 DOI: 10.3732/ajb.1100306] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
PREMISE OF THE STUDY Chloroplast microsatellites were developed in Theobroma cacao to examine the genetic diversity of cacao cultivars in Trinidad and Tobago. METHODS AND RESULTS Nine polymorphic microsatellites were designed from the chloroplast genomes of two T. cacao accessions. These microsatellites were tested in 95 hybrid accessions from Trinidad and Tobago. An average of 2.9 alleles per locus was found. CONCLUSIONS These chloroplast microsatellites, particularly the highly polymorphic pentameric repeat, were useful in assessing genetic variation in T. cacao. In addition, these markers should also prove to be useful for population genetic studies in other species of Malvaceae.
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Affiliation(s)
- Ji Y Yang
- Department of Botany, University of British Columbia, Vancouver, Canada.
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Abstract
Knowledge of the identities and characteristics of genes that govern the dramatic phenotypic differences between cultivated plants and their wild ancestors has greatly enhanced our understanding of the domestication process. In this issue of Molecular Ecology, Sigmon & Vollbrecht report the discovery of a new maize domestication gene, ramosa1, which encodes a putative transcription factor in the ramosa developmental pathway. Ramosa1 appears to be instrumental in determining the straightness of kernel rows on the maize cob. The key domestication alleles at ramosa1 are prevalent in landraces of maize. These results reinforce findings from previous studies of crop evolution by highlighting the importance of standing genetic variation and changes in transcriptional regulators in domestication. The evolutionary genetics of domestication also provides a framework for predicting the evolutionary response of organisms to strong human-induced selection pressures over limited time intervals.
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Affiliation(s)
- Hannes Dempewolf
- The Biodiversity Research Centre and Department of Botany, University of British Columbia, 3529-6270 University Blvd, Vancouver, BC, V6T 1Z4 Canada.
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de Boef WS, Dempewolf H, Byakweli JM, Engels JMM. Integrating Genetic Resource Conservation and Sustainable Development into Strategies to Increase the Robustness of Seed Systems. ACTA ACUST UNITED AC 2010. [DOI: 10.1080/10440046.2010.484689] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Abstract
The wire syndrome shared by plants in New Zealand and Madagascar appears to have evolved convergently as a defence against herbivory from now extinct avian giants.
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Affiliation(s)
- Hannes Dempewolf
- Department of Botany, University of British-Columbia, Vancouver, British Columbia, Canada
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