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Giustina LD, Baldoni AB, Tonini H, Azevedo VCR, Neves LG, Tardin FD, Sebbenn AM. Research Article Hierarchical outcrossing among and within fruits in Bertholletia excelsa Bonpl. (Lecythidaceae) open-pollinated seeds. Genet Mol Res 2018. [DOI: 10.4238/gmr16039872] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Pupin S, Rosse LN, Souza ICG, Cambuim J, Marino CL, Moraes MLT, Sebbenn AM. Analysis of Mendelian inheritance and genetic linkage in microsatellite loci of Eucalyptus urophylla S.T. Blake. Genet Mol Res 2017; 16:gmr-16-03-gmr.16039713. [PMID: 28829896 DOI: 10.4238/gmr16039713] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Eucalyptus urophylla is an important species in the Brazilian forest sector due to its rapid growth rates and resistance to disease. The aim of this study was to verify Mendelian inheritance, genetic linkage, and genotypic disequilibrium for 15 microsatellite loci, with the goal of producing a robust set of genetic markers. Mendelian inheritance and genetic linkage analyses were carried out using genotypes from maternal trees, and their open-pollinated seeds and genotypic disequilibrium were assessed using adult trees. By comparing heterozygous maternal genotypes and their seeds, we found no significant deviations from the expected 1:1 Mendelian segregation and the expected 1:1:1:1 segregation hypothesis for pairwise loci. For adult trees, we did not find strong evidence of genotypic imbalance for pairwise loci. Our results indicated that the analyzed set of microsatellite loci could be used to carry out analyses of genetic diversity, mating system, and parentage in E. urophylla.
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Affiliation(s)
- S Pupin
- Departamento de Fitotecnia, Tecnologia de Alimentos e Sócio Economia, Faculdade de Engenharia, Universidade Estadual Paulista, Ilha Solteira, SP, Brasil
| | - L N Rosse
- Eldorado Brasil, Três Lagoas, MS, Brasil
| | - I C G Souza
- Suzano Papel e Celulose, Itapetininga, SP, Brasil
| | - J Cambuim
- Departamento de Fitotecnia, Tecnologia de Alimentos e Sócio Economia, Faculdade de Engenharia, Universidade Estadual Paulista, Ilha Solteira, SP, Brasil
| | - C L Marino
- Departamento de Genética, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, SP, Brasil
| | - M L T Moraes
- Departamento de Fitotecnia, Tecnologia de Alimentos e Sócio Economia, Faculdade de Engenharia, Universidade Estadual Paulista, Ilha Solteira, SP, Brasil
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Kubota TYK, Silva AM, Cambuim J, Silva AA, Pupin S, Silva MS, Moraes MA, Moraes MLT, Sebbenn AM. Mendelian inheritance, genetic linkage, and genotypic disequilibrium for nine microsatellite loci in Cariniana estrellensis (Raddi) Kuntze (Lecythidaceae). Genet Mol Res 2017; 16:gmr-16-02-gmr.16029653. [PMID: 28481404 DOI: 10.4238/gmr16029653] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Cariniana estrellensis is one of the largest trees found in Brazilian tropical forests. The species is typical of advanced stages of succession, characteristic of climax forests, and essential in genetic conservation and environmental restoration plans. In this study, we assessed Mendelian inheritance, genetic linkage, and genotypic disequilibrium in nine microsatellite loci for a C. estrellensis population. We sampled and genotyped 285 adult trees and collected seeds from 20 trees in a fragmented forest landscape in Brazil. Based on maternal genotypes and their seeds, we found no deviation from the expected 1:1 Mendelian segregation and no genetic linkage between pairwise loci. However, for adults, genotypic disequilibrium was detected for four pairs of loci, suggesting that this result was not caused by genetic linkage. Based on these results, we analyzed microsatellite loci that are suitable for use in population genetic studies assessing genetic diversity, mating system, and gene flow in C. estrellensis populations.
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Affiliation(s)
- T Y K Kubota
- Departamento de Fitotecnia, Tecnologia de Alimentos e Sócio Economia, Faculdade de Engenharia de Ilha Solteira, Universidade Estadual Paulista, Ilha Solteira, SP, Brasil
| | - A M Silva
- Departamento de Fitotecnia, Tecnologia de Alimentos e Sócio Economia, Faculdade de Engenharia de Ilha Solteira, Universidade Estadual Paulista, Ilha Solteira, SP, Brasil
| | - J Cambuim
- Departamento de Fitotecnia, Tecnologia de Alimentos e Sócio Economia, Faculdade de Engenharia de Ilha Solteira, Universidade Estadual Paulista, Ilha Solteira, SP, Brasil
| | - A A Silva
- Departamento de Fitotecnia, Tecnologia de Alimentos e Sócio Economia, Faculdade de Engenharia de Ilha Solteira, Universidade Estadual Paulista, Ilha Solteira, SP, Brasil
| | - S Pupin
- Departamento de Fitotecnia, Tecnologia de Alimentos e Sócio Economia, Faculdade de Engenharia de Ilha Solteira, Universidade Estadual Paulista, Ilha Solteira, SP, Brasil
| | - M S Silva
- Departamento de Fitotecnia, Tecnologia de Alimentos e Sócio Economia, Faculdade de Engenharia de Ilha Solteira, Universidade Estadual Paulista, Ilha Solteira, SP, Brasil
| | - M A Moraes
- Departamento de Fitotecnia, Tecnologia de Alimentos e Sócio Economia, Faculdade de Engenharia de Ilha Solteira, Universidade Estadual Paulista, Ilha Solteira, SP, Brasil
| | - M L T Moraes
- Departamento de Fitotecnia, Tecnologia de Alimentos e Sócio Economia, Faculdade de Engenharia de Ilha Solteira, Universidade Estadual Paulista, Ilha Solteira, SP, Brasil
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Moraes MA, Kubota TYK, Silva ECB, Silva AM, Cambuim J, Moraes MLT, Furlani Junior E, Sebbenn AM. Short Communication Mendelian inheritance, linkage, and genotypic disequilibrium in microsatellite loci of Hymenaea stigonocarpa Mart. ex Hayne (Fabaceae-Caesalpinioideae). Genet Mol Res 2016; 15:gmr8629. [PMID: 27525897 DOI: 10.4238/gmr.15038629] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Hymenaea stigonocarpa is a deciduous and monoecious Neotropical tree species pollinated by bats. Due to overexploitation and habitat destruction, the population size has drastically diminished in nature. No previous study has investigated Mendelian inheritance, linkage, and genotypic disequilibrium in the available microsatellite markers in this species. So, our aim was to estimate these parameters using six microsatellite loci in a sample of 470 adults and 219 juveniles from two populations of H. stigonocarpa. In addition, 30 seeds per tree from 35 seed-trees were collected. Each seed was kept record of the seed-trees and fruit origin. Based on the six microsatellite loci, we found that only 10.6% of the cases showed significant deviations from Mendelian segregation and 15.3% showed linkage. We detected no evidence of genotypic disequilibrium between the loci in the adult trees or juveniles. Thus, our results suggest that these loci can be used with great accuracy in future genetic analyses of H. stigonocarpa populations.
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Affiliation(s)
- M A Moraes
- Departamento de Fitotecnia, Tecnologia de alimentos e Sócio Economia, Faculdade de Engenharia de Ilha Solteira, Universidade Estadual Paulista, Ilha Solteira, SP, Brasil
| | - T Y K Kubota
- Departamento de Fitotecnia, Tecnologia de alimentos e Sócio Economia, Faculdade de Engenharia de Ilha Solteira, Universidade Estadual Paulista, Ilha Solteira, SP, Brasil
| | - E C B Silva
- Departamento de Fitotecnia, Tecnologia de alimentos e Sócio Economia, Faculdade de Engenharia de Ilha Solteira, Universidade Estadual Paulista, Ilha Solteira, SP, Brasil
| | - A M Silva
- Departamento de Fitotecnia, Tecnologia de alimentos e Sócio Economia, Faculdade de Engenharia de Ilha Solteira, Universidade Estadual Paulista, Ilha Solteira, SP, Brasil
| | - J Cambuim
- Departamento de Fitotecnia, Tecnologia de alimentos e Sócio Economia, Faculdade de Engenharia de Ilha Solteira, Universidade Estadual Paulista, Ilha Solteira, SP, Brasil
| | - M L T Moraes
- Departamento de Fitotecnia, Tecnologia de alimentos e Sócio Economia, Faculdade de Engenharia de Ilha Solteira, Universidade Estadual Paulista, Ilha Solteira, SP, Brasil
| | - E Furlani Junior
- Departamento de Fitotecnia, Tecnologia de alimentos e Sócio Economia, Faculdade de Engenharia de Ilha Solteira, Universidade Estadual Paulista, Ilha Solteira, SP, Brasil
| | - A M Sebbenn
- Instituto Florestal de São Paulo, São Paulo, SP, Brasil
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Manoel RO, Freitas MLM, Tambarussi EV, Cambuim J, Moraes MLT, Sebbenn AM. Mendelian inheritance, genetic linkage, and genotypic disequilibrium at microsatellite loci in Genipa americana L. (Rubiaceae). Genet Mol Res 2015; 14:8161-9. [PMID: 26345742 DOI: 10.4238/2015.july.27.4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Genipa americana is a tropical tree species that is widely distributed in the humid tropical and subtropical regions of Central and South America. This study investigated Mendelian inheritance, genetic linkage, and genotypic disequilibrium at six microsatellite loci developed for G. americana. Adult trees (188) and regenerants (163) were sampled and genotyped in a fragmented population of the species. We also genotyped open-pollinated seeds from 12 seed-trees during reproductive events in 2010 and 2011. Significant deviations from the expected 1:1 Mendelian segregation were detected in 29.5% of the tests. Significant genetic linkage between pairwise loci was detected in 54.4% of the tests, but no genotypic disequilibrium was detected between pairwise loci for adult trees and regenerants. Overall, the results indicate that the six loci analyzed may be used in studies of G. americana's genetic diversity and structure, its mating system, and in parentage analyses.
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Affiliation(s)
- R O Manoel
- Faculdade de Engenharia de Ilha Solteira, Universidade Estadual Paulista "Júlio de Mesquita Filho", Ilha Solteira
| | - M L M Freitas
- Instituto Florestal de São Paulo, São Paulo, SP, Brasil
| | | | - J Cambuim
- Faculdade de Engenharia de Ilha Solteira, Universidade Estadual Paulista "Júlio de Mesquita Filho", Ilha Solteira
| | - M L T Moraes
- Faculdade de Engenharia de Ilha Solteira, Universidade Estadual Paulista "Júlio de Mesquita Filho", Ilha Solteira
| | - A M Sebbenn
- Instituto Florestal de São Paulo, São Paulo, SP, Brasil
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Vinson CC, Kanashiro M, Sebbenn AM, Williams TCR, Harris SA, Boshier DH. Long-term impacts of selective logging on two Amazonian tree species with contrasting ecological and reproductive characteristics: inferences from Eco-gene model simulations. Heredity (Edinb) 2014; 115:130-9. [PMID: 24424164 DOI: 10.1038/hdy.2013.146] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Revised: 07/11/2013] [Accepted: 11/22/2013] [Indexed: 11/09/2022] Open
Abstract
The impact of logging and subsequent recovery after logging is predicted to vary depending on specific life history traits of the logged species. The Eco-gene simulation model was used to evaluate the long-term impacts of selective logging over 300 years on two contrasting Brazilian Amazon tree species, Dipteryx odorata and Jacaranda copaia. D. odorata (Leguminosae), a slow growing climax tree, occurs at very low densities, whereas J. copaia (Bignoniaceae) is a fast growing pioneer tree that occurs at high densities. Microsatellite multilocus genotypes of the pre-logging populations were used as data inputs for the Eco-gene model and post-logging genetic data was used to verify the output from the simulations. Overall, under current Brazilian forest management regulations, there were neither short nor long-term impacts on J. copaia. By contrast, D. odorata cannot be sustainably logged under current regulations, a sustainable scenario was achieved by increasing the minimum cutting diameter at breast height from 50 to 100 cm over 30-year logging cycles. Genetic parameters were only slightly affected by selective logging, with reductions in the numbers of alleles and single genotypes. In the short term, the loss of alleles seen in J. copaia simulations was the same as in real data, whereas fewer alleles were lost in D. odorata simulations than in the field. The different impacts and periods of recovery for each species support the idea that ecological and genetic information are essential at species, ecological guild or reproductive group levels to help derive sustainable management scenarios for tropical forests.
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Affiliation(s)
- C C Vinson
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, UK
| | - M Kanashiro
- Embrapa Amazônia Oriental, Trav. Dr.Enéas Pinheiro Marco, CP 48, Belém, Brazil
| | - A M Sebbenn
- Instituto Florestal de São Paulo, CP 1322, São Paulo, Brazil
| | - T C R Williams
- Universidade de Brasília, Departamento de Botânica, Campus Universitário Darcy Ribeiro, Brasília, Brazil
| | - S A Harris
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, UK
| | - D H Boshier
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, UK
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Tambarussi EV, Vencovsky R, Freitas MLM, Sebbenn AM. Mendelian inheritance, genetic linkage, and genotypic disequilibrium at nine microsatellite loci of Cariniana legalis (Mart.) O. Kuntze. Genet Mol Res 2013; 12:5442-57. [PMID: 24301917 DOI: 10.4238/2013.november.11.6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Cariniana legalis is one of the largest tropical trees with a wide distribution in the Brazilian Atlantic rainforest. We investigated the Mendelian inheritance, genetic linkage, and genotypic disequilibrium at seven microsatellite loci specifically isolated for C. legalis, and at two previously developed heterologous microsatellite loci. Forty to 100 open-pollinated seeds were collected from 22 seed-trees in two populations. Using the Bonferroni correction, no remarkable deviations from the expected Mendelian segregation, linkage, or genotypic disequilibrium were detected in the nine loci studied. Only 3.7% of the tests were significant for investigations of the Mendelian proportions. On the other hand, only 2.8% of tests for linkage detection showed significance. In addition, among all pairwise tests used for investigating linkage disequilibrium, significance was found in 9.7% of the locus pairs. Our results show clear evidence that the nine simple sequence repeat loci can be used without restriction in genetic diversity, mating system, and parentage analyses.
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Affiliation(s)
- E V Tambarussi
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, SP, Brasil
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Tarazi R, Sebbenn AM, Kageyama PY, Vencovsky R. Edge effects enhance selfing and seed harvesting efforts in the insect-pollinated Neotropical tree Copaifera langsdorffii (Fabaceae). Heredity (Edinb) 2013; 110:578-85. [PMID: 23486081 DOI: 10.1038/hdy.2013.8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Edge effects may affect the mating system of tropical tree species and reduce the genetic diversity and variance effective size of collected seeds at the boundaries of forest fragments because of a reduction in the density of reproductive trees, neighbour size and changes in the behaviour of pollinators. Here, edge effects on the genetic diversity, mating system and pollen pool of the insect-pollinated Neotropical tree Copaifera langsdorffii were investigated using eight microsatellite loci. Open-pollinated seeds were collected from 17 seed trees within continuous savannah woodland (SW) and were compared with seeds from 11 seed trees at the edge of the savannah remnant. Seeds collected from the SW had significantly higher heterozygosity levels (Ho=0.780; He=0.831) than seeds from the edge (Ho=0.702; He=0.800). The multilocus outcrossing rate was significantly higher in the SW (tm=0.859) than in the edge (tm=0.759). Pollen pool differentiation was significant, however, it did not differ between the SW (=0.105) and the edge (=0.135). The variance effective size within the progenies was significantly higher in the SW (Ne=2.65) than at the edge (Ne=2.30). The number of seed trees to retain the reference variance effective size of 500 was 189 at the SW and 217 at the edge. Therefore, it is preferable that seed harvesting for conservation and environmental restoration strategies be conducted in the SW, where genetic diversity and variance effective size within progenies are higher.
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Affiliation(s)
- R Tarazi
- Departamento de Genética, Universidade de São Paulo, CP 9, Piracicaba, SP, Brazil.
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Moura TM, Martins K, Sujii PS, Sebbenn AM, Chaves LJ. Genetic structure in fragmented populations of Solanum lycocarpum A. St.-Hil. with distinct anthropogenic histories in a Cerrado region of Brazil. Genet Mol Res 2012; 11:2674-82. [PMID: 22869081 DOI: 10.4238/2012.july.10.16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Solanum lycocarpum is a woody tree widely distributed in the Cerrado that reaches high population densities in disturbed environments. We examined the genetic diversity and population differentiation of six S. lycocarpum populations with different degrees of human disturbance in order to determine if they are negatively affected by anthropogenic activity. Three populations located in southern and three located in southeastern regions of Goiás State, Central Brazil, were genotyped with five microsatellite markers. The population located in a protected area had higher number of alleles (26) than the remaining populations (19 to 21 alleles). It indicates that extensive and continuous areas of preserved native vegetation contribute positively to the conservation of genetic diversity, even with S. lycocarpum that easily adapts to disturbed environments. The three southeastern populations, although fragmented, had preserved native vegetation and were not significantly different from each other (θp = 0.002). All other population pairs compared were significantly divergent (θp varied from 0.03 to 0.11 between pairs, P < 0.05). We found three distinct sets of allele frequencies. The three southeastern populations shared similar gene pools, as well as the two disturbed southern populations, which are secondary vegetation. The southern population located in protected area had the most dissimilar gene pool. In conclusion, populations showing a higher degree of human disturbance tends to show a larger population differentiation than expected from the isolation by distance model, which in the current scenario of the Cerrado destruction points out to a threat to the long-term conservation of the species.
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Affiliation(s)
- T M Moura
- Programa de Pós-Graduação em Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brasil.
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Carneiro FS, Lacerda AEB, Lemes MR, Gribel R, Kanashiro M, Sebbenn AM. Mendelian inheritance, linkage and genotypic disequilibrium in microsatellite loci isolated from Hymenaea courbaril (Leguminosae). Genet Mol Res 2012; 11:1942-8. [PMID: 22869549 DOI: 10.4238/2012.july.19.13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The Neotropical tree Hymenaea courbaril, locally known as Jatobá, is a valuable source of lumber and also produces comestible and medicinal fruit. We characterized Mendelian inheritance, linkage and genotypic disequilibrium at nine microsatellite loci isolated from H. courbaril, in order to determine if they would provide accurate estimates of population genetic parameters of this important Amazon species. The study was made on 250 open-pollinated offspring originated from 14 seed trees. Only one of nine loci presented significant deviation from the expected Mendelian segregation (1:1). Genotypic disequilibrium between pairwise loci was investigated based on samples from 55 adult and 56 juvenile trees. No genetic linkage between any paired loci was observed. After Bonferroni's corrections for multiple tests, we found no evidence of genotypic disequilibrium between pairs of loci. We conclude that this set of loci can be used for genetic diversity/ structure, mating system, gene flow, and parentage analyses in H. courbaril populations.
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Affiliation(s)
- F S Carneiro
- Universidade Estadual de São Paulo Júlio de Mesquita Filho, Ilha Solteira, SP, Brasil
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Degen B, Ward SE, Lemes MR, Navarro C, Cavers S, Sebbenn AM. Verifying the geographic origin of mahogany (Swietenia macrophylla King) with DNA-fingerprints. Forensic Sci Int Genet 2012; 7:55-62. [PMID: 22770645 DOI: 10.1016/j.fsigen.2012.06.003] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Revised: 05/18/2012] [Accepted: 06/03/2012] [Indexed: 11/26/2022]
Abstract
Illegal logging is one of the main causes of ongoing worldwide deforestation and needs to be eradicated. The trade in illegal timber and wood products creates market disadvantages for products from sustainable forestry. Although various measures have been established to counter illegal logging and the subsequent trade, there is a lack of practical mechanisms for identifying the origin of timber and wood products. In this study, six nuclear microsatellites were used to generate DNA fingerprints for a genetic reference database characterising the populations of origin of a large set of mahogany (Swietenia macrophylla King, Meliaceae) samples. For the database, leaves and/or cambium from 1971 mahogany trees sampled in 31 stands from Mexico to Bolivia were genotyped. A total of 145 different alleles were found, showing strong genetic differentiation (δ(Gregorious)=0.52, F(ST)=0.18, G(ST(Hedrick))=0.65) and clear correlation between genetic and spatial distances among stands (r=0.82, P<0.05). We used the genetic reference database and Bayesian assignment testing to determine the geographic origins of two sets of mahogany wood samples, based on their multilocus genotypes. In both cases the wood samples were assigned to the correct country of origin. We discuss the overall applicability of this methodology to tropical timber trading.
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Affiliation(s)
- B Degen
- Johann Heinrich von Thünen-Institut, Institut für Forstgenetik, Sieker Landstrasse 2, D-22927 Grosshansdorf, Germany.
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Bittencourt JVM, Sebbenn AM. Patterns of pollen and seed dispersal in a small, fragmented population of the wind-pollinated tree Araucaria angustifolia in southern Brazil. Heredity (Edinb) 2007; 99:580-91. [DOI: 10.1038/sj.hdy.6801019] [Citation(s) in RCA: 158] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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