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Garin V, Diallo C, Tékété ML, Théra K, Guitton B, Dagno K, Diallo AG, Kouressy M, Leiser W, Rattunde F, Sissoko I, Touré A, Nébié B, Samaké M, Kholovà J, Berger A, Frouin J, Pot D, Vaksmann M, Weltzien E, Témé N, Rami JF. Characterization of adaptation mechanisms in sorghum using a multireference back-cross nested association mapping design and envirotyping. Genetics 2024; 226:iyae003. [PMID: 38381593 PMCID: PMC10990433 DOI: 10.1093/genetics/iyae003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 12/20/2023] [Indexed: 02/23/2024] Open
Abstract
Identifying the genetic factors impacting the adaptation of crops to environmental conditions is of key interest for conservation and selection purposes. It can be achieved using population genomics, and evolutionary or quantitative genetics. Here we present a sorghum multireference back-cross nested association mapping population composed of 3,901 lines produced by crossing 24 diverse parents to 3 elite parents from West and Central Africa-back-cross nested association mapping. The population was phenotyped in environments characterized by differences in photoperiod, rainfall pattern, temperature levels, and soil fertility. To integrate the multiparental and multi-environmental dimension of our data we proposed a new approach for quantitative trait loci (QTL) detection and parental effect estimation. We extended our model to estimate QTL effect sensitivity to environmental covariates, which facilitated the integration of envirotyping data. Our models allowed spatial projections of the QTL effects in agro-ecologies of interest. We utilized this strategy to analyze the genetic architecture of flowering time and plant height, which represents key adaptation mechanisms in environments like West Africa. Our results allowed a better characterization of well-known genomic regions influencing flowering time concerning their response to photoperiod with Ma6 and Ma1 being photoperiod-sensitive and the region of possible candidate gene Elf3 being photoperiod-insensitive. We also accessed a better understanding of plant height genetic determinism with the combined effects of phenology-dependent (Ma6) and independent (qHT7.1 and Dw3) genomic regions. Therefore, we argue that the West and Central Africa-back-cross nested association mapping and the presented analytical approach constitute unique resources to better understand adaptation in sorghum with direct application to develop climate-smart varieties.
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Affiliation(s)
- Vincent Garin
- Crop Physiology Laboratory, International Crops Research Institute for the Semi-Arid Tropics, Patancheru, 502 324, India
- CIRAD, UMR AGAP Institut, Montpellier, F-34398, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, F-34398, France
| | - Chiaka Diallo
- Sorghum Program, International Crops Research Institute for the Semi-Arid Tropics, Bamako, BP 320, Mali
- Département d’Enseignement et de Recherche des Sciences et Techniques Agricoles, Institut polytechnique rural de formation et de recherche appliquée de Katibougou, Koulikoro, BP 06, Mali
| | - Mohamed Lamine Tékété
- Institut d’Economie Rurale, Bamako, BP 262, Mali
- Faculté des Sciences et Techniques, Université des Sciences des Techniques et des Technologies de Bamako, Bamako, BP E 3206, Mali
| | | | - Baptiste Guitton
- CIRAD, UMR AGAP Institut, Montpellier, F-34398, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, F-34398, France
| | - Karim Dagno
- Institut d’Economie Rurale, Bamako, BP 262, Mali
| | | | | | - Willmar Leiser
- Sorghum Program, International Crops Research Institute for the Semi-Arid Tropics, Bamako, BP 320, Mali
| | - Fred Rattunde
- Agronomy Department, University of Wisconsin, Madison, WI 53705, WI, USA
| | - Ibrahima Sissoko
- Sorghum Program, International Crops Research Institute for the Semi-Arid Tropics, Bamako, BP 320, Mali
| | - Aboubacar Touré
- Sorghum Program, International Crops Research Institute for the Semi-Arid Tropics, Bamako, BP 320, Mali
| | - Baloua Nébié
- Dryland Crops Program, International Maize and Wheat Improvement Center (CIMMYT-Senegal) U/C CERAAS, Thiès, Po Box 3320, Senegal
| | - Moussa Samaké
- Faculté des Sciences et Techniques, Université des Sciences des Techniques et des Technologies de Bamako, Bamako, BP E 3206, Mali
| | - Jana Kholovà
- Crop Physiology Laboratory, International Crops Research Institute for the Semi-Arid Tropics, Patancheru, 502 324, India
- Department of Information Technologies, Faculty of Economics and Management, Czech University of Life Sciences, Prague, 165 00, Czech Republic
| | - Angélique Berger
- CIRAD, UMR AGAP Institut, Montpellier, F-34398, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, F-34398, France
| | - Julien Frouin
- CIRAD, UMR AGAP Institut, Montpellier, F-34398, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, F-34398, France
| | - David Pot
- CIRAD, UMR AGAP Institut, Montpellier, F-34398, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, F-34398, France
| | - Michel Vaksmann
- CIRAD, UMR AGAP Institut, Montpellier, F-34398, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, F-34398, France
| | - Eva Weltzien
- Sorghum Program, International Crops Research Institute for the Semi-Arid Tropics, Bamako, BP 320, Mali
- Agronomy Department, University of Wisconsin, Madison, WI 53705, WI, USA
| | - Niaba Témé
- Institut d’Economie Rurale, Bamako, BP 262, Mali
| | - Jean-François Rami
- CIRAD, UMR AGAP Institut, Montpellier, F-34398, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, F-34398, France
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van Ittersum MK, van Bussel LGJ, Wolf J, Grassini P, van Wart J, Guilpart N, Claessens L, de Groot H, Wiebe K, Mason-D'Croz D, Yang H, Boogaard H, van Oort PAJ, van Loon MP, Saito K, Adimo O, Adjei-Nsiah S, Agali A, Bala A, Chikowo R, Kaizzi K, Kouressy M, Makoi JHJR, Ouattara K, Tesfaye K, Cassman KG. Can sub-Saharan Africa feed itself? Proc Natl Acad Sci U S A 2016; 113:14964-14969. [PMID: 27956604 PMCID: PMC5206509 DOI: 10.1073/pnas.1610359113] [Citation(s) in RCA: 188] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Although global food demand is expected to increase 60% by 2050 compared with 2005/2007, the rise will be much greater in sub-Saharan Africa (SSA). Indeed, SSA is the region at greatest food security risk because by 2050 its population will increase 2.5-fold and demand for cereals approximately triple, whereas current levels of cereal consumption already depend on substantial imports. At issue is whether SSA can meet this vast increase in cereal demand without greater reliance on cereal imports or major expansion of agricultural area and associated biodiversity loss and greenhouse gas emissions. Recent studies indicate that the global increase in food demand by 2050 can be met through closing the gap between current farm yield and yield potential on existing cropland. Here, however, we estimate it will not be feasible to meet future SSA cereal demand on existing production area by yield gap closure alone. Our agronomically robust yield gap analysis for 10 countries in SSA using location-specific data and a spatial upscaling approach reveals that, in addition to yield gap closure, other more complex and uncertain components of intensification are also needed, i.e., increasing cropping intensity (the number of crops grown per 12 mo on the same field) and sustainable expansion of irrigated production area. If intensification is not successful and massive cropland land expansion is to be avoided, SSA will depend much more on imports of cereals than it does today.
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Affiliation(s)
- Martin K van Ittersum
- Plant Production Systems Group, Wageningen University, 6700 AK Wageningen, The Netherlands;
| | - Lenny G J van Bussel
- Plant Production Systems Group, Wageningen University, 6700 AK Wageningen, The Netherlands
| | - Joost Wolf
- Plant Production Systems Group, Wageningen University, 6700 AK Wageningen, The Netherlands
| | - Patricio Grassini
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68583-0915
| | - Justin van Wart
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68583-0915
| | - Nicolas Guilpart
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68583-0915
| | - Lieven Claessens
- International Crops Research Institute for the Semi-Arid Tropics, 00623 Nairobi, Kenya
| | - Hugo de Groot
- Wageningen Environmental Research, Wageningen University & Research, 6700 AA, Wageningen, The Netherlands
| | - Keith Wiebe
- Environment and Production Technology Division, International Food Policy Research Institute, Washington, DC 20006-1002
| | - Daniel Mason-D'Croz
- Environment and Production Technology Division, International Food Policy Research Institute, Washington, DC 20006-1002
| | - Haishun Yang
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68583-0915
| | - Hendrik Boogaard
- Wageningen Environmental Research, Wageningen University & Research, 6700 AA, Wageningen, The Netherlands
| | - Pepijn A J van Oort
- Africa Rice Center, Sustainable Productivity Enhancement Program, 01 BP 2031, Cotonou, Benin
- Centre for Crop Systems Analysis, Wageningen University, 6700 AK Wageningen, The Netherlands
| | - Marloes P van Loon
- Plant Production Systems Group, Wageningen University, 6700 AK Wageningen, The Netherlands
| | - Kazuki Saito
- Africa Rice Center, Sustainable Productivity Enhancement Program, 01 BP 2031, Cotonou, Benin
| | - Ochieng Adimo
- Jomo Kenyatta University of Agriculture and Technology, 00200 Nairobi, Kenya
| | | | | | - Abdullahi Bala
- Department of Soil Science, Federal University of Technology Minna, P.M.B 65 Gidan-Kwano, Niger State, Nigeria
| | - Regis Chikowo
- Crop Science Department, University of Zimbabwe, MP167 Mount Pleasant, Harare, Zimbabwe
| | - Kayuki Kaizzi
- National Agricultural Research Laboratories, Kampala Nabweru 7065, Uganda
| | | | - Joachim H J R Makoi
- National Irrigation Commission, Ministry of Water and Irrigation, 14473 Dar es Salaam, The United Republic of Tanzania
| | - Korodjouma Ouattara
- Institut de l'Environnement et de Recherches Agricoles, 04 BP: 8645 Ouagadougou 04, Ouagadougou, Burkina Faso
| | - Kindie Tesfaye
- International Maize and Wheat Improvement Centre, Addis Ababa, Ethiopia
| | - Kenneth G Cassman
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68583-0915
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