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Honorio Coronado EN, Blanc-Jolivet C, Mader M, García-Dávila CR, Aldana Gomero D, Del Castillo Torres D, Flores Llampazo G, Hidalgo Pizango G, Sebbenn AM, Meyer-Sand BRV, Paredes-Villanueva K, Tysklind N, Troispoux V, Massot M, Carvalho C, de Lima HC, Cardoso D, Degen B. SNP Markers as a Successful Molecular Tool for Assessing Species Identity and Geographic Origin of Trees in the Economically Important South American Legume Genus Dipteryx. J Hered 2020; 111:346-356. [PMID: 32402074 DOI: 10.1093/jhered/esaa011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 04/28/2020] [Indexed: 11/13/2022] Open
Abstract
Dipteryx timber has been heavily exploited in South America since 2000s due to the increasing international demand for hardwood. Developing tools for the genetic identification of Dipteryx species and their geographical origin can help to promote legal trading of timber. A collection of 800 individual trees, belonging to 6 different Dipteryx species, was genotyped based on 171 molecular markers. After the exclusion of markers out of Hardy-Weinberg equilibrium or with no polymorphism or low amplification, 83 nuclear, 29 chloroplast, 13 mitochondrial single nucleotide polymorphisms (SNPs), and 2 chloroplast and 5 mitochondrial INDELS remained. Six genetic groups were identified using Bayesian Structure analyses of the nuclear SNPs, which corresponded to the different Dipteryx species collected in the field. Seventeen highly informative markers were identified as suitable for species identification and obtained self-assignment success rates to species level of 78-96%. An additional set of 15 molecular markers was selected to determine the different genetic clusters found in Dipteryx odorata and Dipteryx ferrea, obtaining self-assignment success rates of 91-100%. The success to assign samples to the correct country of origin using all or only the informative markers improved when using the nearest neighbor approach (69-92%) compared to the Bayesian approach (33-80%). While nuclear and chloroplast SNPs were more suitable for differentiating the different Dipteryx species, mitochondrial SNPs were ideal for determining the genetic clusters of D. odorata and D. ferrea. These 32 selected SNPs will be invaluable genetic tools for the accurate identification of species and country of origin of Dipteryx timber.
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Affiliation(s)
| | | | - Malte Mader
- Thünen Institute of Forest Genetics, Grosshansdorf, Germany
| | | | | | | | | | | | | | - Barbara R V Meyer-Sand
- Departamento de Fitotecnia, Faculdade de Engenharia de Ilha Solteira, Universidade Estadual Paulista, Ilha Solteira, SP, Brazil
| | - Kathelyn Paredes-Villanueva
- Carrera de Ingeniería Forestal, Laboratorio de Dendrocronología, Facultad de Ciencias Agrícolas, Universidad Autónoma Gabriel René Moreno, El Vallecito, Santa Cruz, Bolivia
| | - Niklas Tysklind
- INRA, UMR0745 EcoFoG, AgroParisTech, Cirad, CNRS, Université des Antilles, Université de Guyane, Campus Agronomique, Kourou Cedex, France
| | - Valerie Troispoux
- INRA, UMR0745 EcoFoG, AgroParisTech, Cirad, CNRS, Université des Antilles, Université de Guyane, Campus Agronomique, Kourou Cedex, France
| | - Marie Massot
- BIOGECO, INRAE, University of Bordeaux, Cestas, France
| | - Catarina Carvalho
- Escola Nacional de Botânica Tropical, Horto, Rio de Janeiro, RJ, Brazil.,Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Haroldo C de Lima
- Escola Nacional de Botânica Tropical, Horto, Rio de Janeiro, RJ, Brazil.,Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Domingos Cardoso
- Instituto de Biologia, Universidade Federal da Bahia, Ondina, Salvador, BA, Brazil
| | - Bernd Degen
- Thünen Institute of Forest Genetics, Grosshansdorf, Germany
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Sebbenn AM, Blanc-Jolivet C, Mader M, Meyer-Sand BRV, Paredes-Villanueva K, Honorio Coronado EN, García-Dávila C, Tysklind N, Troispoux V, Delcamp A, Degen B. Nuclear and plastidial SNP and INDEL markers for genetic tracking studies of Jacaranda copaia. CONSERV GENET RESOUR 2019. [DOI: 10.1007/s12686-019-01097-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Tysklind N, Blanc-Jolivet C, Mader M, Meyer-Sand BRV, Paredes-Villanueva K, Honorio Coronado EN, García-Dávila CR, Sebbenn AM, Caron H, Troispoux V, Guichoux E, Degen B. Development of nuclear and plastid SNP and INDEL markers for population genetic studies and timber traceability of Carapa species. CONSERV GENET RESOUR 2019. [DOI: 10.1007/s12686-019-01090-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Honorio Coronado EN, Blanc-Jolivet C, Mader M, García-Dávila CR, Sebbenn AM, Meyer-Sand BRV, Paredes-Villanueva K, Tysklind N, Troispoux V, Massot M, Degen B. Development of nuclear and plastid SNP markers for genetic studies of Dipteryx tree species in Amazonia. CONSERV GENET RESOUR 2019. [DOI: 10.1007/s12686-019-01081-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Chaves CL, Blanc-Jolivet C, Sebbenn AM, Mader M, Meyer-Sand BRV, Paredes-Villanueva K, Honorio Coronado EN, Garcia-Davila C, Tysklind N, Troispoux V, Massot M, Degen B. Nuclear and chloroplastic SNP markers for genetic studies of timber origin for Hymenaea trees. CONSERV GENET RESOUR 2018. [DOI: 10.1007/s12686-018-1077-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Meyer-Sand BRV, Blanc-Jolivet C, Mader M, Paredes-Villanueva K, Tysklind N, Sebbenn AM, Guichoux E, Degen B. Development of a set of SNP markers for population genetics studies of Ipe (Handroanthus sp.), a valuable tree genus from Latin America. CONSERV GENET RESOUR 2017. [DOI: 10.1007/s12686-017-0928-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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