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Berenguer P, Clavero C, Saldarriaga-Córdoba M, Rivera-Hutinel A, Seelenfreund D, Martinsson-Wallin H, Castañeda P, Seelenfreund A. Identification of breadfruit (Artocarpus altilis) and South American crops introduced during early settlement of Rapa Nui (Easter Island), as revealed through starch analysis. PLoS One 2024; 19:e0298896. [PMID: 38507346 PMCID: PMC10954183 DOI: 10.1371/journal.pone.0298896] [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: 09/01/2023] [Accepted: 01/31/2024] [Indexed: 03/22/2024] Open
Abstract
Starch residue analysis was carried out on stone tools recovered from the bottom layer of the Anakena site on Rapa Nui (Easter Island). These deposits have been dated to AD 1000-1300 AD and so far, represent the earliest evidence of human settlement on this island. Twenty obsidian tools were analyzed. Analysis of 46 starch grains recovered from 20 obsidian tools from the earliest dated level of the Anakena site on Rapa Nui provides direct evidence for translocation of traditional crop plants at initial stages of the colonization of this island. The analysis of starch grains was based mainly on statistical methods for species identification but was complemented by visual inspection in some cases. Our results identify taxons previously unknown to have been cultivated on the island, such as breadfruit (Artocarpus altilis), Zingiber officinale (ginger), and starch grains of the Spondias dulcis and Inocarpus fagifer tropical trees. Additionally, starch grains of Colocasia esculenta (taro) and Dioscorea sp. (yam), both common species in Pacific agriculture, were identified. Furthermore, the presence of four American taxa Ipomoea batatas (sweet potato), Canna sp. (achira), Manihot esculenta (manioc), and Xanthosoma sp., was detected. The occurrence of Canna sp., M. esculenta, and Xanthosoma sp. starch grains suggests the translocation of previously not described South American cultivars into the Pacific. The detection of I. batatas from this site in Rapa Nui constitutes the earliest record of this cultigen in the Pacific. Our study provides direct evidence for translocation of a set of traditional Polynesian and South American crop plants at the initial stages of colonization in Rapa Nui.
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Affiliation(s)
- Paloma Berenguer
- Escuela de Antropología, Geografía e Historia, Facultad de Ciencias Sociales Universidad Academia de Humanismo Cristiano, Santiago, Chile
| | - Claudia Clavero
- Facultad de Ciencias Básicas, Universidad Metropolitana de Ciencias de la Educación, Ñuñoa, Chile
| | - Mónica Saldarriaga-Córdoba
- Centro de Investigación en Recursos Naturales y Sustentabilidad (CYRENIS), Universidad Bernardo O’Higgins, Santiago, Chile
| | - Antonio Rivera-Hutinel
- Facultad de Ciencias Básicas, Universidad Metropolitana de Ciencias de la Educación, Ñuñoa, Chile
| | - Daniela Seelenfreund
- Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | | | - Patricia Castañeda
- Facultad de Ciencias Básicas, Universidad Metropolitana de Ciencias de la Educación, Ñuñoa, Chile
| | - Andrea Seelenfreund
- Escuela de Antropología, Geografía e Historia, Facultad de Ciencias Sociales Universidad Academia de Humanismo Cristiano, Santiago, Chile
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Lebot V, Lawac F, Muñoz-Cuervo I, Mercier PE, Legendre L. Metabolite fingerprinting of cassava (Manihot esculenta Crantz) landraces assessed for post-harvest physiological deterioration (PPD). Food Chem 2023; 421:136217. [PMID: 37121018 DOI: 10.1016/j.foodchem.2023.136217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 04/14/2023] [Accepted: 04/17/2023] [Indexed: 05/02/2023]
Abstract
Cassava landraces are impacted by post-harvest physiological deterioration (PPD). 34 primary/secondary metabolites (carotenes, flavonols, indols, phenolic, hydroxycinnamic, and organic acids) were analysed using HPLC/GC-MS in 72 landraces harvested 8 months after planting (MAP) to clarify whether these compounds may play a role in PPD tolerance. Cluster analysis differentiated a first group with high organic acids contents, citric acid being dominant, a second group with landraces high in tryptophan, a third group including landraces with high phenolic and hydroxycinnamic acids content, and a fourth group characterised by 8 carotenoids. PPD tolerant and susceptible landraces were present in each group. To determine if PPD is related to age of harvest, 174 landraces were harvested at 6, 8, 10 and 12 MAP. Scopoletin, sucrose and glucose were analysed. PPD was positively correlated with DMC and negatively correlated with scopoletin at all ages of harvest. Scopoletin is a useful biomarker to characterize landraces.
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Affiliation(s)
- Vincent Lebot
- CIRAD-VARTC, P.O. Box 946, Port-Vila, Vanuatu; UMR AGAP Institut, Université de Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France.
| | | | - Ismaël Muñoz-Cuervo
- Université Claude Bernard Lyon 1, Laboratoire d'Écologie Microbienne, Équipe 3 - Rhizosphère, CESN (Centre d'Étude des Substances Naturelles), France; UMR UCBL CNRS 5557 - INRA 1418. 16 rue Raphaël Dubois. F-69100 Villeurbanne Cedex, France
| | - Pierre-Edouard Mercier
- Université Claude Bernard Lyon 1, Laboratoire d'Écologie Microbienne, Équipe 3 - Rhizosphère, CESN (Centre d'Étude des Substances Naturelles), France; UMR UCBL CNRS 5557 - INRA 1418. 16 rue Raphaël Dubois. F-69100 Villeurbanne Cedex, France.
| | - Laurent Legendre
- Université Claude Bernard Lyon 1, Laboratoire d'Écologie Microbienne, Équipe 3 - Rhizosphère, CESN (Centre d'Étude des Substances Naturelles), France; UMR UCBL CNRS 5557 - INRA 1418. 16 rue Raphaël Dubois. F-69100 Villeurbanne Cedex, France.
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Sardos J, Breton C, Perrier X, Van den Houwe I, Carpentier S, Paofa J, Rouard M, Roux N. Hybridization, missing wild ancestors and the domestication of cultivated diploid bananas. FRONTIERS IN PLANT SCIENCE 2022; 13:969220. [PMID: 36275535 PMCID: PMC9586208 DOI: 10.3389/fpls.2022.969220] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 09/05/2022] [Indexed: 06/08/2023]
Abstract
Hybridization and introgressions are important evolutionary forces in plants. They contribute to the domestication of many species, including understudied clonal crops. Here, we examine their role in the domestication of a clonal crop of outmost importance, banana (Musa ssp.). We used genome-wide SNPs generated for 154 diploid banana cultivars and 68 samples of the wild M. acuminata to estimate and geo-localize the contribution of the different subspecies of M. acuminata to cultivated banana. We further investigated the wild to domesticate transition in New Guinea, an important domestication center. We found high levels of admixture in many cultivars and confirmed the existence of unknown wild ancestors with unequal contributions to cultivated diploid. In New Guinea, cultivated accessions exhibited higher diversity than their direct wild ancestor, the latter recovering from a bottleneck. Introgressions, balancing selection and positive selection were identified as important mechanisms for banana domestication. Our results shed new lights on the radiation of M. acuminata subspecies and on how they shaped banana domestication. They point candidate regions of origin for two unknown ancestors and suggest another contributor in New Guinea. This work feed research on the evolution of clonal crops and has direct implications for conservation, collection, and breeding.
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Affiliation(s)
- Julie Sardos
- Bioversity International, Parc Scientifique Agropolis II, Montpellier, France
| | - Catherine Breton
- Bioversity International, Parc Scientifique Agropolis II, Montpellier, France
| | - Xavier Perrier
- CIRAD, UMR AGAP Institut, Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | | | | | - Janet Paofa
- Papua New Guinea (PNG) National Agricultural Research Institute, Southern Regional Centre, Laloki, Port Moresby, Papua New Guinea
| | - Mathieu Rouard
- Bioversity International, Parc Scientifique Agropolis II, Montpellier, France
| | - Nicolas Roux
- Bioversity International, Parc Scientifique Agropolis II, 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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Palanivel H, Shah S. Unlocking the inherent potential of plant genetic resources: food security and climate adaptation strategy in Fiji and the Pacific. ENVIRONMENT, DEVELOPMENT AND SUSTAINABILITY 2021; 23:14264-14323. [PMID: 33619427 PMCID: PMC7888530 DOI: 10.1007/s10668-021-01273-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 01/28/2021] [Indexed: 06/12/2023]
Abstract
Pacific Island Countries (PICs) are the center of origin and diversity for several root, fruit and nut crops, which are indispensable for food security, rural livelihoods, and cultural identity of local communities. However, declining genetic diversity of traditional food crops and high vulnerability to climate change are major impediments for maintaining agricultural productivity. Limited initiatives to achieve food self-sufficiency and utilization of Plant Genetic Resources (PGR) for enhancing resilience of agro-ecosystems are other serious constraints. This review focuses on the visible and anticipated impacts of climate ge, on major food and tree crops in agriculture and agroforestry systems in the PICs. We argue that crop improvement through plant breeding is a viable strategy to enhance food security and climatic resilience in the region. The exploitation of adaptive traits: abiotic and biotic stress tolerance, yield and nutritional efficiency, is imperative in a world threatened by climatic extremes. However, the insular constraints of Fiji and other small PICs are major limitations for the utilization of PGR through high throughput techniques which are also cost prohibitive. Crop Improvement programs should instead focus on the identification, conservation, documentation and dissemination of information on unique landraces, community seed banks, introduction of new resistant genotypes, and sustaining and enhancing allelic diversity.
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Affiliation(s)
- Hemalatha Palanivel
- Department of Biotechnology, College of Biological and Chemical Engineering, Addis Ababa Science and Technology University, PO Box 16417, Addis Ababa, Ethiopia
| | - Shipra Shah
- Department of Forestry, College of Agriculture, Fisheries and Forestry, Koronivia Campus, Fiji National University, PO Box 1544, Nausori, Republic of Fiji
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Tang X, Zhong R, Jiang J, He L, Huang Z, Shi G, Wu H, Liu J, Xiong F, Han Z, Tang R, He L. Cassava/peanut intercropping improves soil quality via rhizospheric microbes increased available nitrogen contents. BMC Biotechnol 2020; 20:13. [PMID: 32111197 PMCID: PMC7049180 DOI: 10.1186/s12896-020-00606-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 02/21/2020] [Indexed: 01/06/2023] Open
Abstract
Background Intercropping, an essential cultivation pattern in modern agricultural systems, increases crop yields and soil quality. Cassava and peanut intercropping systems exhibit advantages in solar utilization and cadmium absorption, etc. However, the inner mechanisms need to be elucidated. In this study, Illumina MiSeq platform was used to reveal the rhizospheric microbes and soil quality in cassava/peanut intercropping systems, and the results provided a reference for the application of this method in studying other intercropping systems. Results Both intercropping cassava/peanut (IP) and intercropping peanut/cassava (IC) systems significantly increased available N, available K, pH value, and urease activity, comparing with that in monocropping cassava (MC) and monocropping peanut (MP) system. However, there were few effects on the total N, total P, total K, available P, organic matter, protease activity, catalase activity, sucrase activity, and acid phosphatase activity. Both IP and MP soils contained more bacteria and fungi than those in the IC and MC soils, which were mainly made of Proteobacteria and Actinobacteria. Intercropping remarkably increased the number of Nitrospirae in IP and IC soils comparing those in MC and MP soils. Redundancy analysis (RDA) revealed that the abundances of DA101, Pilimelia, and Ramlibacter were positively correlated to the soil quality. These results suggest that intercropping enhances the available nitrogen content of soil through increasing the quantity of rhizospheric microbes, especially that of DA101 and Pilimelia. Conclusions The cassava/peanut intercropping system improves soil quality through increasing the available nitrogen content and abundance of DA101, Pilimelia, and Ramlibacter in the soil.
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Affiliation(s)
- Xiumei Tang
- Agricultural College of Guangxi University, Nanning, 530005, Guangxi, China. .,Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China.
| | - Ruichun Zhong
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China
| | - Jing Jiang
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China
| | - Liangqiong He
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China
| | - Zhipeng Huang
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China
| | - Guoying Shi
- Microbiology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China
| | - Haining Wu
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China
| | - Jing Liu
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China
| | - Faqian Xiong
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China
| | - Zhuqiang Han
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China
| | - Ronghua Tang
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China.
| | - Longfei He
- Agricultural College of Guangxi University, Nanning, 530005, Guangxi, China.
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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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Delaquis E, Andersen KF, Minato N, Cu TTL, Karssenberg ME, Sok S, Wyckhuys KAG, Newby JC, Burra DD, Srean P, Phirun I, Le ND, Pham NT, Garrett KA, Almekinders CJM, Struik PC, de Haan S. Raising the Stakes: Cassava Seed Networks at Multiple Scales in Cambodia and Vietnam. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2018. [DOI: 10.3389/fsufs.2018.00073] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Curk F, Ollitrault F, Garcia-Lor A, Luro F, Navarro L, Ollitrault P. Phylogenetic origin of limes and lemons revealed by cytoplasmic and nuclear markers. ANNALS OF BOTANY 2016; 117:565-83. [PMID: 26944784 PMCID: PMC4817432 DOI: 10.1093/aob/mcw005] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 10/21/2015] [Accepted: 12/08/2015] [Indexed: 05/20/2023]
Abstract
BACKGROUND AND AIMS The origin of limes and lemons has been a source of conflicting taxonomic opinions. Biochemical studies, numerical taxonomy and recent molecular studies suggested that cultivated Citrus species result from interspecific hybridization between four basic taxa (C. reticulata,C. maxima,C. medica and C. micrantha). However, the origin of most lemons and limes remains controversial or unknown. The aim of this study was to perform extended analyses of the diversity, genetic structure and origin of limes and lemons. METHODS The study was based on 133 Citrus accessions. It combined maternal phylogeny studies based on mitochondrial and chloroplastic markers, and nuclear structure analysis based on the evaluation of ploidy level and the use of 123 markers, including 73 basic taxa diagnostic single nucleotide polymorphism (SNP) and indel markers. KEY RESULTS The lime and lemon horticultural group appears to be highly polymorphic, with diploid, triploid and tetraploid varieties, and to result from many independent reticulation events which defined the sub-groups. Maternal phylogeny involves four cytoplasmic types out of the six encountered in the Citrus genus. All lime and lemon accessions were highly heterozygous, with interspecific admixture of two, three and even the four ancestral taxa genomes. Molecular polymorphism between varieties of the same sub-group was very low. CONCLUSIONS Citrus medica contributed to all limes and lemons and was the direct male parent for the main sub-groups in combination with C. micrantha or close papeda species (for C. aurata, C. excelsa, C. macrophylla and C. aurantifolia--'Mexican' lime types of Tanaka's taxa), C. reticulata(for C. limonia, C. karna and C. jambhiri varieties of Tanaka's taxa, including popular citrus rootstocks such as 'Rangpur' lime, 'Volkamer' and 'Rough' lemons), C. aurantium (for C. limetta and C. limon--yellow lemon types--varieties of Tanaka's taxa) or the C. maxima × C. reticulate hybrid (for C. limettioides--'Palestine sweet' lime types--and C. meyeri). Among triploid limes, C. latifolia accessions ('Tahiti' and 'Persian' lime types) result from the fertilization of a haploid ovule of C. limon by a diploid gamete of C. aurantifolia, while C. aurantifolia triploid accessions ('Tanepao' lime types and 'Madagascar' lemon) probably result from an interspecific backcross (a diploid ovule of C. aurantifolia fertilized by C. medica). As limes and lemons were vegetatively propagated (apomixis, horticultural practices) the intra-sub-group phenotypic diversity results from asexual variations.
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Affiliation(s)
- Franck Curk
- Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes (UMR Agap), Institut National de la Recherche Agronomique (INRA), F-20230 San Giuliano, France, Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Moncada (Valencia), Spain and
| | - Frédérique Ollitrault
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Moncada (Valencia), Spain and
| | - Andres Garcia-Lor
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Moncada (Valencia), Spain and
| | - François Luro
- Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes (UMR Agap), Institut National de la Recherche Agronomique (INRA), F-20230 San Giuliano, France
| | - Luis Navarro
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Moncada (Valencia), Spain and
| | - Patrick Ollitrault
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Moncada (Valencia), Spain and Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes (UMR Agap), Centre de coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Station de Roujol, F-97170, Petit-Bourg, Guadeloupe, France
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Thai elite cassava genetic diversity was fortuitously conserved through farming with different sets of varieties. CONSERV GENET 2014. [DOI: 10.1007/s10592-014-0631-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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de Oliveira EJ, Ferreira CF, da Silva Santos V, de Jesus ON, Oliveira GAF, da Silva MS. Potential of SNP markers for the characterization of Brazilian cassava germplasm. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:1423-40. [PMID: 24737135 DOI: 10.1007/s00122-014-2309-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Accepted: 03/31/2014] [Indexed: 05/20/2023]
Abstract
High-throughput markers, such as SNPs, along with different methodologies were used to evaluate the applicability of the Bayesian approach and the multivariate analysis in structuring the genetic diversity in cassavas. The objective of the present work was to evaluate the diversity and genetic structure of the largest cassava germplasm bank in Brazil. Complementary methodological approaches such as discriminant analysis of principal components (DAPC), Bayesian analysis and molecular analysis of variance (AMOVA) were used to understand the structure and diversity of 1,280 accessions genotyped using 402 single nucleotide polymorphism markers. The genetic diversity (0.327) and the average observed heterozygosity (0.322) were high considering the bi-allelic markers. In terms of population, the presence of a complex genetic structure was observed indicating the formation of 30 clusters by DAPC and 34 clusters by Bayesian analysis. Both methodologies presented difficulties and controversies in terms of the allocation of some accessions to specific clusters. However, the clusters suggested by the DAPC analysis seemed to be more consistent for presenting higher probability of allocation of the accessions within the clusters. Prior information related to breeding patterns and geographic origins of the accessions were not sufficient for providing clear differentiation between the clusters according to the AMOVA analysis. In contrast, the F ST was maximized when considering the clusters suggested by the Bayesian and DAPC analyses. The high frequency of germplasm exchange between producers and the subsequent alteration of the name of the same material may be one of the causes of the low association between genetic diversity and geographic origin. The results of this study may benefit cassava germplasm conservation programs, and contribute to the maximization of genetic gains in breeding programs.
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12
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Scarcelli N, Couderc M, Baco MN, Egah J, Vigouroux Y. Clonal diversity and estimation of relative clone age: application to agrobiodiversity of yam (Dioscorea rotundata). BMC PLANT BIOLOGY 2013; 13:178. [PMID: 24219837 PMCID: PMC3832681 DOI: 10.1186/1471-2229-13-178] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Accepted: 11/06/2013] [Indexed: 05/04/2023]
Abstract
BACKGROUND Clonal propagation is a particular reproductive system found in both the plant and animal kingdoms, from human parasites to clonally propagated crops. Clonal diversity provides information about plant and animal evolutionary history, i.e. how clones spread, or the age of a particular clone. In plants, this could provide valuable information about agrobiodiversity dynamics and more broadly about the evolutionary history of a particular crop. We studied the evolutionary history of yam, Dioscorea rotundata. In Africa, Yam is cultivated by tuber clonal propagation. RESULTS We used 12 microsatellite markers to identify intra-clonal diversity in yam varieties. We then used this diversity to assess the relative ages of clones. Using simulations, we assessed how Approximate Bayesian Computation could use clonal diversity to estimate the age of a clone depending on the size of the sample, the number of independent samples and the number of markers. We then applied this approach to our particular dataset and showed that the relative ages of varieties could be estimated, and that each variety could be ranked by age. CONCLUSIONS We give a first estimation of clone age in an approximate Bayesian framework. However the precise estimation of clone age depends on the precision of the mutation rate. We provide useful information on agrobiodiversity dynamics and suggest recurrent creation of varietal diversity in a clonally propagated crop.
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Affiliation(s)
- Nora Scarcelli
- UMR DIADE, Team DYNADIV, Institut de Recherche pour le Développement (IRD), 911 Avenue Agropolis, BP 64501, 34394 Montpellier Cedex 5, France
| | - Marie Couderc
- UMR DIADE, Team DYNADIV, Institut de Recherche pour le Développement (IRD), 911 Avenue Agropolis, BP 64501, 34394 Montpellier Cedex 5, France
| | - Mohamed N Baco
- Faculté d’Agronomie, Université de Parakou, BP 123 Parakou, Bénin
| | - Janvier Egah
- Faculté d’Agronomie, Université de Parakou, BP 123 Parakou, Bénin
| | - Yves Vigouroux
- UMR DIADE, Team DYNADIV, Institut de Recherche pour le Développement (IRD), 911 Avenue Agropolis, BP 64501, 34394 Montpellier Cedex 5, France
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Roullier C, Kambouo R, Paofa J, McKey D, Lebot V. On the origin of sweet potato (Ipomoea batatas (L.) Lam.) genetic diversity in New Guinea, a secondary centre of diversity. Heredity (Edinb) 2013; 110:594-604. [PMID: 23531982 DOI: 10.1038/hdy.2013.14] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
New Guinea is considered the most important secondary centre of diversity for sweet potato (Ipomoea batatas). We analysed nuclear and chloroplast genetic diversity of 417 New Guinea sweet potato landraces, representing agro-morphological diversity collected throughout the island, and compared this diversity with that in tropical America. The molecular data reveal moderate diversity across all accessions analysed, lower than that found in tropical America. Nuclear data confirm previous results, suggesting that New Guinea landraces are principally derived from the Northern neotropical genepool (Camote and Batata lines, from the Caribbean and Central America). However, chloroplast data suggest that South American clones (early Kumara line clones or, more probably, later reintroductions) were also introduced into New Guinea and then recombined with existing genotypes. The frequency distribution of pairwise distances between New Guinea landraces suggests that sexual reproduction, rather than somaclonal variation, has played a predominant role in the diversification of sweet potato. The frequent incorporation of plants issued from true seed by farmers, and the geographical and cultural barriers constraining crop diffusion in this topographically and linguistically heterogeneous island, has led to the accumulation of an impressive number of variants. As the diversification of sweet potato in New Guinea is primarily the result of farmers' management of the reproductive biology of their crop, we argue that on-farm conservation programmes that implement distribution of core samples (clones representing the useful diversity of the species) and promote on-farm selection of locally adapted variants may allow local communities to fashion relatively autonomous strategies for coping with ongoing global change.
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Snoussi H, Duval MF, Garcia-Lor A, Belfalah Z, Froelicher Y, Risterucci AM, Perrier X, Jacquemoud-Collet JP, Navarro L, Harrabi M, Ollitrault P. Assessment of the genetic diversity of the Tunisian citrus rootstock germplasm. BMC Genet 2012; 13:16. [PMID: 22429788 PMCID: PMC3323426 DOI: 10.1186/1471-2156-13-16] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Accepted: 03/19/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Citrus represents a substantial income for farmers in the Mediterranean Basin. However, the Mediterranean citrus industry faces increasing biotic and abiotic constraints. Therefore the breeding and selection of new rootstocks are now of the utmost importance. In Tunisia, in addition to sour orange, the most widespread traditional rootstock of the Mediterranean area, other citrus rootstocks and well adapted to local environmental conditions, are traditionally used and should be important genetic resources for breeding. To characterize the diversity of Tunisian citrus rootstocks, two hundred and one local accessions belonging to four facultative apomictic species (C. aurantium, sour orange; C. sinensis, orange; C. limon, lemon; and C. aurantifolia, lime) were collected and genotyped using 20 nuclear SSR markers and four indel mitochondrial markers. Multi-locus genotypes (MLGs) were compared to references from French and Spanish collections. RESULTS The differentiation of the four varietal groups was well-marked. The groups displayed a relatively high allelic diversity, primarily due to very high heterozygosity. Sixteen distinct MLGs were identified. Ten of these were noted in sour oranges. However, the majority of the analysed sour orange accessions corresponded with only two MLGs, differentiated by a single allele, likely due to a mutation. The most frequent MLG is shared with the reference sour oranges. No polymorphism was found within the sweet orange group. Two MLGs, differentiated by a single locus, were noted in lemon. The predominant MLG was shared with the reference lemons. Limes were represented by three genotypes. Two corresponded to the 'Mexican lime' and 'limonette de Marrakech' references. The MLG of 'Chiiri' lime was unique. CONCLUSIONS The Tunisian citrus rootstock genetic diversity is predominantly due to high heterozygosity and differentiation between the four varietal groups. The phenotypic diversity within the varietal groups has resulted from multiple introductions, somatic mutations and rare sexual recombination events. Finally, this diversity study enabled the identification of a core sample of accessions for further physiological and agronomical evaluations. These core accessions will be integrated into citrus rootstock breeding programs for the Mediterranean Basin.
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Affiliation(s)
- Hager Snoussi
- Horticultural Laboratory, Tunisian National Agronomic Research Institute (INRAT), Rue Hedi Karray, 2049 Ariana, Tunisia.
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Genetic structure of farmer-managed varieties in clonally-propagated crops. Genetica 2011; 139:1055-64. [PMID: 21898046 DOI: 10.1007/s10709-011-9607-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2010] [Accepted: 08/26/2011] [Indexed: 10/17/2022]
Abstract
The relative role of sexual reproduction and mutation in shaping the diversity of clonally propagated crops is largely unknown. We analyzed the genetic diversity of yam-a vegetatively-propagated crop-to gain insight into how these two factors shape its diversity in relation with farmers' classifications. Using 15 microsatellite loci, we analyzed 485 samples of 10 different yam varieties. We identified 33 different genotypes organized in lineages supported by high bootstrap values. We computed the probability that these genotypes appeared by sexual reproduction or mutation within and between each lineage. This allowed us to interpret each lineage as a product of sexual reproduction that has evolved by mutation. Moreover, we clearly noted a similarity between the genetic structure and farmers' classifications. Each variety could thus be interpreted as being the product of sexual reproduction having evolved by mutation. This highly structured diversity of farmer-managed varieties has consequences for the preservation of yam diversity.
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