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Millet CP, Allinne C, Vi T, Marraccini P, Verleysen L, Couderc M, Ruttink T, Zhang D, Sanchéz WS, Tranchant-Dubreuil C, Jeune W, Poncet V. Haitian coffee agroforestry systems harbor complex arabica variety mixtures and under-recognized genetic diversity. PLoS One 2024; 19:e0299493. [PMID: 38625928 PMCID: PMC11020479 DOI: 10.1371/journal.pone.0299493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 02/11/2024] [Indexed: 04/18/2024] Open
Abstract
Though facing significant challenges, coffee (Coffea arabica) grown in Haitian agroforestry systems are important contributors to rural livelihoods and provide several ecosystem services. However, little is known about their genetic diversity and the variety mixtures used. In light of this, there is a need to characterize Haitian coffee diversity to help inform revitalization of this sector. We sampled 28 diverse farms in historically important coffee growing regions of northern and southern Haiti. We performed KASP-genotyping of SNP markers and HiPlex multiplex amplicon sequencing for haplotype calling on our samples, as well as several Ethiopian and commercial accessions from international collections. This allowed us to assign Haitian samples to varietal groups. Our analyses revealed considerable genetic diversity in Haitian farms, higher in fact than many farmers realized. Notably, genetic structure analyses revealed the presence of clusters related to Typica, Bourbon, and Catimor groups, another group that was not represented in our reference accession panel, and several admixed individuals. Across the study areas, we found both mixed-variety farms and monovarietal farms with the historical and traditional Typica variety. This study is, to our knowledge, the first to genetically characterize Haitian C. arabica variety mixtures, and report the limited cultivation of C. canephora (Robusta coffee) in the study area. Our results show that some coffee farms are repositories of historical, widely-abandoned varieties while others are generators of new diversity through genetic mixing.
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Affiliation(s)
- Claude Patrick Millet
- IRD, UMR DIADE, CIRAD, Université Montpellier, Montpellier, France
- Faculté des Sciences de l’Agriculture et de l’Environnement, Université de Quisqueya, Port-au-Prince, Haiti
- Institut Agro, ABSys, Université Montpellier, CIHEAM-IAMM, CIRAD, INRAE, Montpellier, France
- CIRAD, UMR ABSys, F-34398, Montpellier, France
| | - Clémentine Allinne
- Institut Agro, ABSys, Université Montpellier, CIHEAM-IAMM, CIRAD, INRAE, Montpellier, France
- CIRAD, UMR ABSys, F-34398, Montpellier, France
- GECO, Université Montpellier, CIRAD, Montpellier, France
- CIRAD, UPR GECO, F-34398, Montpellier, France
| | - Tram Vi
- IRD, UMR DIADE, CIRAD, Université Montpellier, Montpellier, France
- Agricultural Genetics Institute (AGI), Hanoi, Vietnam
| | - Pierre Marraccini
- IRD, UMR DIADE, CIRAD, Université Montpellier, Montpellier, France
- CIRAD, UMR DIADE, Montpellier, France
| | - Lauren Verleysen
- Faculty of Sciences, Division of Ecology, Evolution and Biodiversity Conservation, KU Leuven, Leuven, Belgium
- ILVO, Melle, Belgium
| | - Marie Couderc
- IRD, UMR DIADE, CIRAD, Université Montpellier, Montpellier, France
| | - Tom Ruttink
- ILVO, Melle, Belgium
- Ghent University, Ghent, Belgium
| | - Dapeng Zhang
- USDA-ARS, SPCL, Beltsville, Maryland, United States of America
| | | | | | - Wesly Jeune
- Faculté des Sciences de l’Agriculture et de l’Environnement, Université de Quisqueya, Port-au-Prince, Haiti
- AVSF, Pétion-Ville, Haïti
| | - Valérie Poncet
- IRD, UMR DIADE, CIRAD, Université Montpellier, Montpellier, France
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Alves-Pereira A, Zucchi MI, Clement CR, Viana JPG, Pinheiro JB, Veasey EA, de Souza AP. Selective signatures and high genome-wide diversity in traditional Brazilian manioc (Manihot esculenta Crantz) varieties. Sci Rep 2022; 12:1268. [PMID: 35075210 PMCID: PMC8786832 DOI: 10.1038/s41598-022-05160-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 01/05/2022] [Indexed: 11/09/2022] Open
Abstract
Knowledge about genetic diversity is essential to promote effective use and conservation of crops, because it enables farmers to adapt their crops to specific needs and is the raw material for breeding. Manioc (Manihot esculenta ssp. esculenta) is one of the world's major food crops and has the potential to help achieve food security in the context of on-going climate changes. We evaluated single nucleotide polymorphisms in traditional Brazilian manioc varieties conserved in the gene bank of the Luiz de Queiroz College of Agriculture, University of São Paulo. We assessed genome-wide diversity and identified selective signatures contrasting varieties from different biomes with samples of manioc's wild ancestor M. esculenta ssp. flabellifolia. We identified signatures of selection putatively associated with resistance genes, plant development and response to abiotic stresses that might have been important for the crop's domestication and diversification resulting from cultivation in different environments. Additionally, high neutral genetic diversity within groups of varieties from different biomes and low genetic divergence among biomes reflect the complexity of manioc's evolutionary dynamics under traditional cultivation. Our results exemplify how smallholder practices contribute to conserve manioc's genetic resources, maintaining variation of potential adaptive significance and high levels of neutral genetic diversity.
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Affiliation(s)
- Alessandro Alves-Pereira
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Av. Cândido Rondon, 400, Cidade Universitária, CP: 6010, Campinas, SP, 13083-875, Brazil.,Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (UNICAMP), Av. Cândido Rondon, 400, Cidade Universitária, CP: 6010, Campinas, SP, 13083-875, Brazil
| | - Maria Imaculada Zucchi
- Agência Paulista de Tecnologia Dos Agronegócios (APTA), Pólo Centro-Sul. Rodovia SP 127, km 30, Piracicaba, SP, 13400-970, Brazil
| | - Charles R Clement
- Instituto Nacional de Pesquisas da Amazônia (INPA), Av. André Araújo, 2936, Petrópolis, Manaus, AM, 69067-375, Brazil
| | - João Paulo Gomes Viana
- Department of Crop Sciences, University of Illinois at Urbana-Champaign (UIUC), AW-101 Turner Hall, 1102 South Goodwin Avenue, Urbana, IL, 61801-4798, USA
| | - José Baldin Pinheiro
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiróz", Universidade de São Paulo (ESALQ/USP), Av. Pádua Dias, 11, Piracicaba, SP, 13400-970, Brazil
| | - Elizabeth Ann Veasey
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiróz", Universidade de São Paulo (ESALQ/USP), Av. Pádua Dias, 11, Piracicaba, SP, 13400-970, Brazil
| | - Anete Pereira de Souza
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Av. Cândido Rondon, 400, Cidade Universitária, CP: 6010, Campinas, SP, 13083-875, Brazil. .,Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (UNICAMP), Av. Cândido Rondon, 400, Cidade Universitária, CP: 6010, Campinas, SP, 13083-875, Brazil.
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Pérez D, Mora R, López Carrascal C. Conservación de la diversidad de yuca en los sistemas tradicionales de cultivo de la Amazonía. ACTA BIOLÓGICA COLOMBIANA 2019. [DOI: 10.15446/abc.v24n2.75428] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
La yuca es determinante para la seguridad alimentaria de cientos de millones de personas alrededor del mundo. A pesar de que el principal medio de propagación del cultivo es a través de semilla asexual por estacas (tallos maduros) se ha revelado una relativamente alta diversidad intraespecífica, principalmente en los sistemas de cultivo de manejo tradicional. En esta revisión se documentan algunos estudios realizados sobre la diversidad de la yuca, tanto por marcadores moleculares como morfológicos, centrándose en aquellos realizados en el Amazonas. También se exponen los principales factores que han determinado el aprovechamiento y conservación de esta diversidad, tales como la aparición espontánea de semillas de origen sexual, el sistema de chagras indígenas, la memoria biocultural y la facilidad de intercambio de semilla entre comunidades. Finalmente, se pone de manifiesto que en los sistemas de manejo tradicional la conservación y uso de la diversidad intraespecífica se constituye en un elemento prioritario que se ha perdido en los sistemas de cultivo a gran escala. En los sistemas de manejo tradicional existe un vínculo etnobotánico que pervive e invita a buscar prácticas alternativas que aseguran un mantenimiento de la diversidad, permitiendo una productividad eficiente e incluso se hace un mejor manejo para disminuir los riesgos de incidencia de algunas plagas y enfermedades.
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Alves-Pereira A, Clement CR, Picanço-Rodrigues D, Veasey EA, Dequigiovanni G, Ramos SLF, Pinheiro JB, Zucchi MI. Patterns of nuclear and chloroplast genetic diversity and structure of manioc along major Brazilian Amazonian rivers. ANNALS OF BOTANY 2018; 121:625-639. [PMID: 29309531 PMCID: PMC5853005 DOI: 10.1093/aob/mcx190] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 11/23/2017] [Indexed: 05/20/2023]
Abstract
Background and Aims Amazonia is a major world centre of plant domestication, but little is known about how the crops were dispersed across the region. Manioc (Manihot esculenta) was domesticated in the south-western Amazon basin, and is the most important staple food crop that originated in Amazonia. Current contrasting distributions may reflect distinct histories of dispersal of bitter and sweet manioc landraces. To produce new insights into the evolutionary history of the crop, we investigated the contemporary genetic diversity and structure of bitter and sweet manioc along major Amazonian rivers. Methods The patterns of genetic structure and diversity of wild and cultivated sweet and bitter manioc with four chloroplast and 14 nuclear microsatellite markers were evaluated. Results were interpreted in terms of the crop's dispersal. Key results No phylogeographic patterns among rivers were detected, and genetic structure among rivers was confounded by the bitter-sweet divergence. However, differences in the distribution of nuclear diversity and somewhat distinctive patterns of genetic structure across rivers were observed within bitter and sweet manioc. Conclusions Various pre-Columbian and post-European conquest events in the history of Amazonian occupation may explain the absence of clearer patterns of genetic structure. However, the wide distribution of the most common chloroplast haplotype agrees with an early dispersal of manioc across Brazilian Amazonia. Furthermore, differences in genetic structure and in the spatial distribution of genetic diversity suggest that bitter and sweet manioc had distinct dispersal histories. Knowledge about how prehistoric and contemporary Amazonian peoples manage their crops is valuable for the maintenance and conservation of the impressive diversity of their native crops.
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Affiliation(s)
- Alessandro Alves-Pereira
- Departamento de Genética, Escola Superior de Agricultura ‘Luiz de Queiróz’, Universidade de São Paulo (ESALQ-USP), Piracicaba, SP, Brazil
| | - Charles R Clement
- Instituto Nacional de Pesquisas da Amazônia (INPA), Manaus, AM, Brazil
| | | | - Elizabeth A Veasey
- Departamento de Genética, Escola Superior de Agricultura ‘Luiz de Queiróz’, Universidade de São Paulo (ESALQ-USP), Piracicaba, SP, Brazil
| | - Gabriel Dequigiovanni
- Departamento de Genética, Escola Superior de Agricultura ‘Luiz de Queiróz’, Universidade de São Paulo (ESALQ-USP), Piracicaba, SP, Brazil
| | - Santiago L F Ramos
- Departamento de Genética, Escola Superior de Agricultura ‘Luiz de Queiróz’, Universidade de São Paulo (ESALQ-USP), Piracicaba, SP, Brazil
| | - José B Pinheiro
- Departamento de Genética, Escola Superior de Agricultura ‘Luiz de Queiróz’, Universidade de São Paulo (ESALQ-USP), Piracicaba, SP, Brazil
| | - Maria I Zucchi
- Agência Paulista de Tecnologia dos Agronegócios, Pólo Centro-Sul (APTA), Piracicaba, SP, Brazil
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Renard D, Schatz B, McKey DB. Ant nest architecture and seed burial depth: Implications for seed fate and germination success in a myrmecochorous savanna shrub. ECOSCIENCE 2015. [DOI: 10.2980/17-2-3335] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Milla R, Morente-López J. Limited evolutionary divergence of seedlings after the domestication of plant species. PLANT BIOLOGY (STUTTGART, GERMANY) 2015; 17:169-176. [PMID: 24943713 DOI: 10.1111/plb.12220] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 05/08/2014] [Indexed: 06/03/2023]
Abstract
The most vulnerable stage in the life of plants is the seedling. The transition from wild to agricultural land that plants experienced during and after domestication implied a noticeable change in the seedlings' environment. Building on current knowledge of seedling ecology, and on previous studies of cassava, we hypothesise that cultivation should have promoted epigeal germination of seedlings, and more exposed and photosynthetic cotyledons. To test this hypothesis, we phenotyped seedling morpho-functional traits in a set of domesticated and wild progenitor accessions of 20 Eudicot herbaceous crop species. Qualitative traits like epi- versus hypogeal germination, leafy versus storage type of cotyledons, or crypto- versus phanerocotyledonar germination, remained conserved during the domestication of all 20 species. Lengths of hypocotyls and epicotyls, of cotyledon petioles, and indices of cotyledon exposure to the aboveground environment changed during evolution under cultivation. However, those changes occurred in diverse directions, depending on the crop species. No common seedling phenotypic convergence in response to domestication was thus detected among the group of species studied here. Also, none of the 20 crops evolved in accordance with our initial hypothesis. Our results reject the idea that strong selective filters exerted unconsciously by artificial selection should have resulted in generalised channelling of seedling morphology towards more productive and more herbivore risky phenotypes. This result opens up unexplored opportunities for directional breeding of seedling traits.
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Affiliation(s)
- R Milla
- Departamento de Biología y Geología, Área de Biodiversidad y Conservación, Escuela Superior de Ciencias Experimentales y Tecnología, Universidad Rey Juan Carlos, Móstoles, Spain
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Ménard L, McKey D, Mühlen GS, Clair B, Rowe NP. The evolutionary fate of phenotypic plasticity and functional traits under domestication in manioc: changes in stem biomechanics and the appearance of stem brittleness. PLoS One 2013; 8:e74727. [PMID: 24023960 PMCID: PMC3762774 DOI: 10.1371/journal.pone.0074727] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Accepted: 08/05/2013] [Indexed: 11/19/2022] Open
Abstract
Domestication can influence many functional traits in plants, from overall life-history and growth form to wood density and cell wall ultrastructure. Such changes can increase fitness of the domesticate in agricultural environments but may negatively affect survival in the wild. We studied effects of domestication on stem biomechanics in manioc by comparing domesticated and ancestral wild taxa from two different regions of greater Amazonia. We compared mechanical properties, tissue organisation and wood characteristics including microfibril angles in both wild and domesticated plants, each growing in two different habitats (forest or savannah) and varying in growth form (shrub or liana). Wild taxa grew as shrubs in open savannah but as lianas in overgrown and forested habitats. Growth form plasticity was retained in domesticated manioc. However, stems of the domesticate showed brittle failure. Wild plants differed in mechanical architecture between shrub and liana phenotypes, a difference that diminished between shrubs and lianas of the domesticate. Stems of wild plants were generally stiffer, failed at higher bending stresses and were less prone to brittle fracture compared with shrub and liana phenotypes of the domesticate. Biomechanical differences between stems of wild and domesticated plants were mainly due to changes in wood density and cellulose microfibril angle rather than changes in secondary growth or tissue geometry. Domestication did not significantly modify "large-scale" trait development or growth form plasticity, since both wild and domesticated manioc can develop as shrubs or lianas. However, "finer-scale" developmental traits crucial to mechanical stability and thus ecological success of the plant were significantly modified. This profoundly influenced the likelihood of brittle failure, particularly in long climbing stems, thereby also influencing the survival of the domesticate in natural situations vulnerable to mechanical perturbation. We discuss the different selective pressures that could explain evolutionary modifications of stem biomechanical properties under domestication in manioc.
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Affiliation(s)
- Léa Ménard
- Université Montpellier 2, UMR AMAP, Montpellier, France; CNRS, UMR AMAP, Montpellier, France
| | - Doyle McKey
- Université Montpellier 2, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), UMR 5175 CNRS, Montpellier, France
- Institut Universitaire de France, Paris, France
| | - Gilda S. Mühlen
- Department of Agronomy, Federal University of Rondônia, Rolim de Moura, Rondônia, Brazil
| | - Bruno Clair
- CNRS, Laboratoire de Mécanique et Génie Civil (LMGC), Université Montpellier 2, Montpellier, France
- CNRS, UMR Ecologie des Forêts de Guyane (EcoFoG), Campus Agronomique, Kourou, French Guiana
| | - Nick P. Rowe
- Université Montpellier 2, UMR AMAP, Montpellier, France; CNRS, UMR AMAP, Montpellier, France
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Alves-Pereira A, Peroni N, Abreu AG, Gribel R, Clement CR. Genetic structure of traditional varieties of bitter manioc in three soils in Central Amazonia. Genetica 2012; 139:1259-71. [PMID: 22228136 DOI: 10.1007/s10709-011-9627-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Accepted: 12/23/2011] [Indexed: 11/24/2022]
Abstract
Manioc is the most important food crop that originated in Amazonia. Many studies have increased our understanding of its evolutionary dynamics under cultivation. However, most of them focused on manioc cultivation in environments with low soil fertility, generally Oxisols. Recent ethnobotanical observations showed that bitter manioc also performs well in high fertility soils, such as Amazonian dark earths (ADE) and the floodplain. We used 10 microsatellite loci to investigate the genetic diversity and structure of bitter manioc varieties grown in different soil types in communities of smallholder farmers along the middle Madeira River in Central Amazonia. The genetic diversity of some sweet varieties and seedlings was also evaluated. Adult individuals showed higher levels of genetic diversity and smaller inbreeding coefficients (A ( R ) = 5.52, H ( O ) = 0.576, f = 0.086) than seedlings (A ( R ) = 4.39, H ( O ) = 0.421, f = 0.242). Bitter manioc varieties from the floodplain showed higher levels of genetic diversity (A ( R ) = 5.19, H ( O ) = 0.606) than those from ADE (A ( R ) = 4.45, H ( O ) = 0.538) and from Oxisols (A ( R ) = 4.15, H ( O ) = 0.559). The varieties grown in the floodplain were strongly differentiated from the varieties grown in Oxisols (F ( ST ) = 0.093) and ADE (F ( ST ) = 0.108), suggesting important genetic structuring among varieties grown in the floodplain and upland soils (ADE and Oxisols). This is the first time that genetic divergence of bitter manioc varieties in cultivation in different Amazonian soils in a small geographic area is reported.
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Affiliation(s)
- Alessandro Alves-Pereira
- Instituto Nacional de Pesquisas da Amazônia, INPA, Av. André Araújo, 2936, Aleixo, Manaus, AM 69060-001, Brazil.
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Bousalem M, Viader V, Mariac C, Gomez RM, Hochu I, Santoni S, David J. Evidence of diploidy in the wild Amerindian yam, a putative progenitor of the endangered species Dioscorea trifida (Dioscoreaceae). Genome 2010; 53:371-83. [DOI: 10.1139/g10-016] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The fundamental question about Dioscorea trifida (Dioscoreaceae), the most important Amerindian yam, that remains unresolved concerns its evolutionary origin, since no wild relative has been reported. In this paper we report the existence of D. trifida’s wild relative for the first time. The diploidy of wild D. trifida (2n = 40) is clearly demonstrated by flow cytometry, chromosome counts, and microsatellite pattern analysis, whereas the cultivated form was previously shown to be autotetraploid (2n = 80). In the coastal region where the wild and cultivated forms are sympatric, tetraploid and triploid cytotypes coexist within the same populations. In the sites where the wild and cultivated forms are allopatric, the wild diploid cytotype predominates. AFLP (amplified fragment length polymorphism) analyses gave an initial idea of the position of the wild forms in relation to the cultivated forms. All the wild and cultivated types form a monophyletic group structured into two major subgroups corresponding to the tetraploid cytotype of the cultivated form and the diploid cytotype of the wild form. The triploid cytotypes of the wild form are in an intermediary position. Wild accessions are grouped on the basis of their geographic origin. The data presented in this paper are significant for the effective breeding and conservation of D. trifida and to assess its genetic diversity and population structure for the general understanding of the evolution and domestication of the species.
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Affiliation(s)
- Mustapha Bousalem
- INRA-URPV, Domaine Duclos, Prise d’Eau, 97170 Petit-Bourg, Guadeloupe, France
- UMR Diversité et Génomes des Plantes Cultivées, Station d’Amélioration des Plantes, INRA, 2, place Viala, 34060 Montpellier, France
| | - Véronique Viader
- INRA-URPV, Domaine Duclos, Prise d’Eau, 97170 Petit-Bourg, Guadeloupe, France
- UMR Diversité et Génomes des Plantes Cultivées, Station d’Amélioration des Plantes, INRA, 2, place Viala, 34060 Montpellier, France
| | - Cedric Mariac
- INRA-URPV, Domaine Duclos, Prise d’Eau, 97170 Petit-Bourg, Guadeloupe, France
- UMR Diversité et Génomes des Plantes Cultivées, Station d’Amélioration des Plantes, INRA, 2, place Viala, 34060 Montpellier, France
| | - Rose-Marie Gomez
- INRA-URPV, Domaine Duclos, Prise d’Eau, 97170 Petit-Bourg, Guadeloupe, France
- UMR Diversité et Génomes des Plantes Cultivées, Station d’Amélioration des Plantes, INRA, 2, place Viala, 34060 Montpellier, France
| | - Isabelle Hochu
- INRA-URPV, Domaine Duclos, Prise d’Eau, 97170 Petit-Bourg, Guadeloupe, France
- UMR Diversité et Génomes des Plantes Cultivées, Station d’Amélioration des Plantes, INRA, 2, place Viala, 34060 Montpellier, France
| | - Sylvain Santoni
- INRA-URPV, Domaine Duclos, Prise d’Eau, 97170 Petit-Bourg, Guadeloupe, France
- UMR Diversité et Génomes des Plantes Cultivées, Station d’Amélioration des Plantes, INRA, 2, place Viala, 34060 Montpellier, France
| | - Jacques David
- INRA-URPV, Domaine Duclos, Prise d’Eau, 97170 Petit-Bourg, Guadeloupe, France
- UMR Diversité et Génomes des Plantes Cultivées, Station d’Amélioration des Plantes, INRA, 2, place Viala, 34060 Montpellier, France
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McKey D, Elias M, Pujol B, Duputié A. The evolutionary ecology of clonally propagated domesticated plants. THE NEW PHYTOLOGIST 2010; 186:318-32. [PMID: 20202131 DOI: 10.1111/j.1469-8137.2010.03210.x] [Citation(s) in RCA: 160] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
While seed-propagated crops have contributed many evolutionary insights, evolutionary biologists have often neglected clonally propagated crops. We argue that widespread notions about their evolution under domestication are oversimplified, and that they offer rich material for evolutionary studies. The diversity of their wild ancestors, the diverse ecologies of the crop populations themselves, and the intricate mix of selection pressures, acting not only on the parts harvested but also on the parts used by humans to make clonal propagules, result in complex and diverse evolutionary trajectories under domestication. We examine why farmers propagate some plants clonally, and discuss the evolutionary dynamics of sexual reproduction in clonal crops. We explore how their mixed clonal/sexual reproductive systems function, based on the sole example studied in detail, cassava (Manihot esculenta). Biotechnology is now expanding the number of clonal crops, continuing the 10 000-yr-old trend to increase crop yields by propagating elite genotypes. In an era of rapid global change, it is more important than ever to understand how the adaptive potential of clonal crops can be maintained. A key component of strategies for preserving this adaptive potential is the maintenance of mixed clonal/sexual systems, which can be achieved by encouraging and valuing farmer knowledge about the sexual reproductive biology of their clonal crops.
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Affiliation(s)
- Doyle McKey
- Centre d'Ecologie Fonctionnelle et Evolutive, UMR 5175, 1919 route de Mende, 34293 Montpellier cedex 5, France.
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Duputié A, Delêtre M, De Granville JJ, McKey D. Population genetics of Manihot esculenta ssp. flabellifolia gives insight into past distribution of xeric vegetation in a postulated forest refugium area in northern Amazonia. Mol Ecol 2009; 18:2897-907. [PMID: 19500251 DOI: 10.1111/j.1365-294x.2009.04231.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The Guianas have often been proposed as a forest refugium; however, this view has received little testing. Studies of population genetics of forest taxa suggest that the central part of French Guiana remained forested, while the southern part (currently forested) may have harboured more open vegetation. Insights into the population structure of species restricted to non-forested habitats can help test this hypothesis. Using six microsatellite loci, we investigated the population genetics of French Guianan accessions of Manihot esculenta ssp. flabellifolia, a taxon restricted to coastal savannas and to rocky outcrops in the densely forested inland. Coastal populations were highly differentiated from one another, and our data suggest a recent colonization of these savannas by M. esculenta ssp. flabellifolia in a west-to-east process. Coastal populations were strongly differentiated from inselberg populations, consistent with an ancient separation of these two groups, with no or low subsequent gene flow. This supports the hypothesis that the central part of the region may have remained forested since the Last Glacial Maximum, impeding the establishment of Manihot. Contrary to coastal populations, inselberg Manihot populations were strikingly homogeneous at a broad spatial scale. This suggests they were connected until recently, either by a large continuous savanna area or by smaller, temporary disturbed areas shifting in space.
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Affiliation(s)
- Anne Duputié
- CEFE UMR5175, 1919 Route de Mende, 34293 Montpellier Cedex 5, France.
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Sardos J, McKey D, Duval MF, Malapa R, Noyer JL, Lebot V. Evolution of cassava (Manihot esculenta Crantz) after recent introduction into a South Pacific Island system: the contribution of sex to the diversification of a clonally propagated crop. Genome 2009; 51:912-21. [PMID: 18956024 DOI: 10.1139/g08-080] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Cassava (Manihot esculenta Crantz) is a clonally propagated crop that was introduced into the South Pacific archipelago of Vanuatu in the 1850s. Based on a survey conducted in 10 different villages throughout the archipelago, we present here a study of its diversity. Farmers' knowledge about cultivation cycle and sexual reproduction of cassava was recorded during group interviews in each village. Using a set of 11 SSR markers, we genotyped the 104 landraces collected and 60 supplementary accessions from a within-landrace study (12 landraces x 5 plants). Out of the 104 landraces collected, we discovered 77 different multilocus genotypes and the within-landrace study identified several polyclonal landraces. Our data suggest a number of hypotheses about the dynamics of diversity of cassava in Vanuatu.
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Affiliation(s)
- J Sardos
- CIRAD, UMR DAP 1098, Montpellier, F-34398 France.
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Rival L, McKey D. Domestication and Diversity in Manioc (Manihot esculentaCrantz ssp.esculenta, Euphorbiaceae). CURRENT ANTHROPOLOGY 2008. [DOI: 10.1086/593119] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Pujol B, McKey D. Size asymmetry in intraspecific competition and the density-dependence of inbreeding depression in a natural plant population: a case study in cassava (Manihot esculenta Crantz, Euphorbiaceae). J Evol Biol 2006; 19:85-96. [PMID: 16405580 DOI: 10.1111/j.1420-9101.2005.00990.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The effects of competition on the genetic composition of natural populations are not well understood. We combined demography and molecular genetics to study how intraspecific competition affects microevolution in cohorts of volunteer plants of cassava (Manihot esculenta) originating from seeds in slash-and-burn fields of Palikur Amerindians in French Guiana. In this clonally propagated crop, genotypic diversity is enhanced by the incorporation of volunteer plants into farmers' stocks of clonal propagules. Mortality of volunteer plants was density-dependent. Furthermore, the size asymmetry of intraspecific competition increased with local clustering of plants. Size of plants was correlated with their multilocus heterozygosity, and stronger size-dependence of survival in clusters of plants, compared with solitary plants, increased the magnitude of inbreeding depression when competition was severe. The density-dependence of inbreeding depression of volunteer plants helps explain the high heterozygosity of volunteers that survive to harvest time and thus become candidates for clonal propagation. This effect could help favour the maintenance of sex in this 'vegetatively' propagated crop plant.
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Affiliation(s)
- B Pujol
- Department of Population Biology, Centre d'Ecologie Fonctionnelle et Evolutive, CEFE, Montpellier Cedex, France.
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Pujol B, Mühlen G, Garwood N, Horoszowski Y, Douzery EJP, McKey D. Evolution under domestication: contrasting functional morphology of seedlings in domesticated cassava and its closest wild relatives. THE NEW PHYTOLOGIST 2005; 166:305-318. [PMID: 15760372 DOI: 10.1111/j.1469-8137.2004.01295.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Although cassava (Manihot esculenta ssp. esculenta) is asexually propagated, farmers incorporate plants from seedlings into planting stocks. These products of sex are exposed to selection, which in agricultural environments should favour rapid growth. To examine whether seedling morphology has evolved under domestication, we compared domesticated cassava, its wild progenitor (M. esculenta ssp. flabellifolia) and their sister species (M. pruinosa) under controlled conditions. Field observations complemented laboratory study. In both wild taxa, the hypocotyl did not elongate (hypogeal germination) and cotyledons remained enclosed in the testa. In domesticated cassava, the hypocotyl elongated (epigeal germination), and cotyledons emerged and became foliaceous. The difference in hypocotyl elongation was fixed, whereas cotyledon morphology varied with environmental conditions in M. pruinosa. Comparative analysis suggests that epigeal germination is primitive in Manihot, that the lineage including wild ancestors of cassava evolved hypogeal germination--which confers greater tolerance to risks in their savanna environment--and that with domestication, there was a reversion to epigeal germination and photosynthetic cotyledons, traits conferring high initial growth rates in agricultural habitats.
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Affiliation(s)
- Benoît Pujol
- Department of Population Biology, Centre for Functional and Evolutionary Ecology (CEFE, UMR 5175 CNRS), 1919, route de Mende, 34293 Montpellier Cedex 05, France.
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Elias M, Penet L, Vindry P, McKey D, Panaud O, Robert T. Unmanaged sexual reproduction and the dynamics of genetic diversity of a vegetatively propagated crop plant, cassava (Manihot esculenta Crantz), in a traditional farming system. Mol Ecol 2001; 10:1895-907. [PMID: 11555234 DOI: 10.1046/j.0962-1083.2001.01331.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Occurrence of intervarietal or interspecific natural crosses has been reported for many crop plants in traditional farming systems, underlining the potential importance of this source of genetic exchange for the dynamics of genetic diversity of crop plants. In this study, we use microsatellite loci to investigate the role of volunteer seedlings (plants originating from unmanaged sexual reproduction) in the dynamics of genetic diversity of cassava (Manihot esculenta Crantz), a vegetatively propagated crop, in a traditional farming system in Guyana. A previous field study showed that farmers incorporate such plants into the germplasm for vegetative propagation, and that many of them are likely to be assigned by farmers to recognized varieties. Under strict vegetative propagation clonality of varieties is expected. The high proportion of polyclonal varieties observed suggests that incorporation of seedlings into the germplasm for propagation is a frequent event. The molecular variability assessed with microsatellite markers shows that there is high differentiation among heterozygous varieties, whereas populations of seedlings do not depart from the proportions expected under Hardy-Weinberg assumptions. Assignment of seedlings to a recognized variety on the basis of morphological similarity greatly increases genetic diversity within the variety. We argue that recombination and gene flow play a major role in the dynamics of genetic diversity of cassava in traditional farming systems. Documenting unmanaged sexual reproduction and its genetic consequences is a prerequisite for defining strategies of in situ conservation of crop plant genetic resources.
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Affiliation(s)
- M Elias
- CEFE-CNRS, 1919 route de Mende, 34293 Montpellier cedex 5, France
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