Development, characterization, validation, and mapping of SSRs derived from Theobroma cacao L.?Moniliophthora perniciosa interaction ESTs.
In this study, we report results of the detection and analysis of SSR markers derived of cacao?Moniliophthora perniciosa expressed sequence tags (ESTs) in relation to cacao resistance to witches? broom disease (WBD), and we compare the polymorphism of those ESTs (EST-simple sequence repeat (SSR)) with classical neutral SSR markers. A total of 3,487 ESTs was used in this investigation. SSRs were identified in 430 sequences: 277 from the resistant genotype TSH 1188 and 153 from the susceptible one Catongo, totalizing 505 EST-SSRs with three types of motifs: dinucleotides (72.1%), trinucleotides (27.3%), and tetranucleotides (0.6%). EST-SSRs were classified into 16 main categories; most of the EST-SSRs belonged to ?Unknown function? and ?No homology? categories (45.82%). A high frequency of SSRs was found in the 5?UTR and in the ORF (about 27%) and a low frequency was observed in the 3?UTR (about 8%). Forty-nine ESTSSR primers were designed and evaluated in 21 cacao accessions, 12 revealed polymorphism, having 47 alleles in total, with an average of 3.92 alleles per locus. On the other hand, the 11 genomic SSR markers revealed a total of 47 alleles, with an average of 5.22 alleles per locus. The association of EST-SSR with the genomic SSR enhanced the analysis of genetic distance among the genotypes. Among the 12 polymorphic EST-SSR markers, two were mapped on the F2 Sca 6×ICS 1 population reference for WBD resistance.
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Format: | Artigo de periódico biblioteca |
Language: | Ingles English |
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2010-07-21
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Subjects: | Witches' broom disease, Microsatellite, Resistance, Genetic diversity, Theobroma cacao L, Cacau, Doença de Planta, Marcador Molecular, Vassoura de Bruxa, |
Online Access: | http://www.alice.cnptia.embrapa.br/alice/handle/doc/858299 |
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dig-alice-doc-8582992022-08-16T13:28:25Z Development, characterization, validation, and mapping of SSRs derived from Theobroma cacao L.?Moniliophthora perniciosa interaction ESTs. LIMA, L. S. GRAMACHO, K. P. PIRES, J. L. CLEMENT, D. LOPES, U. V. CARELS, N. GESTEIRA, A. da S. GAIOTTO, F. A. CASCARDO, J. C. de MATTOS MICHELI, F. Lívia Santos Lima, CEPLAC/CEPEC/SEFIT; Karina Peres Gramacho, CEPLAC/CEPEC/SEFIT; José Luis Pires, CEPLAC/CEPEC/SEFIT; Didier Clement, CIRAD//UMR DAP; Uilson Vanderlei Lopes, CEPLC/CEPEC/SEFIT; Nicolas Carels, UESC; ABELMON DA SILVA GESTEIRA, CNPMF; Fernanda Amato Gaiotto, UESC; Júlio Cézar de Mattos Cascardo, UESC; Fabienne Micheli, CIRAD, UMR DAP. Witches' broom disease Microsatellite Resistance Genetic diversity Theobroma cacao L Cacau Doença de Planta Marcador Molecular Vassoura de Bruxa In this study, we report results of the detection and analysis of SSR markers derived of cacao?Moniliophthora perniciosa expressed sequence tags (ESTs) in relation to cacao resistance to witches? broom disease (WBD), and we compare the polymorphism of those ESTs (EST-simple sequence repeat (SSR)) with classical neutral SSR markers. A total of 3,487 ESTs was used in this investigation. SSRs were identified in 430 sequences: 277 from the resistant genotype TSH 1188 and 153 from the susceptible one Catongo, totalizing 505 EST-SSRs with three types of motifs: dinucleotides (72.1%), trinucleotides (27.3%), and tetranucleotides (0.6%). EST-SSRs were classified into 16 main categories; most of the EST-SSRs belonged to ?Unknown function? and ?No homology? categories (45.82%). A high frequency of SSRs was found in the 5?UTR and in the ORF (about 27%) and a low frequency was observed in the 3?UTR (about 8%). Forty-nine ESTSSR primers were designed and evaluated in 21 cacao accessions, 12 revealed polymorphism, having 47 alleles in total, with an average of 3.92 alleles per locus. On the other hand, the 11 genomic SSR markers revealed a total of 47 alleles, with an average of 5.22 alleles per locus. The association of EST-SSR with the genomic SSR enhanced the analysis of genetic distance among the genotypes. Among the 12 polymorphic EST-SSR markers, two were mapped on the F2 Sca 6×ICS 1 population reference for WBD resistance. On line first: 10 march 2010. 2022-08-16T13:28:17Z 2022-08-16T13:28:17Z 2010-07-21 2010 Artigo de periódico Tree Genetics & Genomes, Heidelberg, mar. 2010. 1614-2950 (Online) http://www.alice.cnptia.embrapa.br/alice/handle/doc/858299 10.1007/s11295-010-0282-1 Ingles en openAccess |
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Witches' broom disease Microsatellite Resistance Genetic diversity Theobroma cacao L Cacau Doença de Planta Marcador Molecular Vassoura de Bruxa Witches' broom disease Microsatellite Resistance Genetic diversity Theobroma cacao L Cacau Doença de Planta Marcador Molecular Vassoura de Bruxa |
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Witches' broom disease Microsatellite Resistance Genetic diversity Theobroma cacao L Cacau Doença de Planta Marcador Molecular Vassoura de Bruxa Witches' broom disease Microsatellite Resistance Genetic diversity Theobroma cacao L Cacau Doença de Planta Marcador Molecular Vassoura de Bruxa LIMA, L. S. GRAMACHO, K. P. PIRES, J. L. CLEMENT, D. LOPES, U. V. CARELS, N. GESTEIRA, A. da S. GAIOTTO, F. A. CASCARDO, J. C. de MATTOS MICHELI, F. Development, characterization, validation, and mapping of SSRs derived from Theobroma cacao L.?Moniliophthora perniciosa interaction ESTs. |
description |
In this study, we report results of the detection and analysis of SSR markers derived of cacao?Moniliophthora perniciosa expressed sequence tags (ESTs) in relation to cacao resistance to witches? broom disease (WBD), and we compare the polymorphism of those ESTs (EST-simple sequence repeat (SSR)) with classical neutral SSR markers. A total of 3,487 ESTs was used in this investigation. SSRs were identified in 430 sequences: 277 from the resistant genotype TSH 1188 and 153 from the susceptible one Catongo, totalizing 505 EST-SSRs with three types of motifs: dinucleotides (72.1%), trinucleotides (27.3%), and tetranucleotides (0.6%). EST-SSRs were classified into 16 main categories; most of the EST-SSRs belonged to ?Unknown function? and ?No homology? categories (45.82%). A high frequency of SSRs was found in the 5?UTR and in the ORF (about 27%) and a low frequency was observed in the 3?UTR (about 8%). Forty-nine ESTSSR primers were designed and evaluated in 21 cacao accessions, 12 revealed polymorphism, having 47 alleles in total, with an average of 3.92 alleles per locus. On the other hand, the 11 genomic SSR markers revealed a total of 47 alleles, with an average of 5.22 alleles per locus. The association of EST-SSR with the genomic SSR enhanced the analysis of genetic distance among the genotypes. Among the 12 polymorphic EST-SSR markers, two were mapped on the F2 Sca 6×ICS 1 population reference for WBD resistance. |
author2 |
Lívia Santos Lima, CEPLAC/CEPEC/SEFIT; Karina Peres Gramacho, CEPLAC/CEPEC/SEFIT; José Luis Pires, CEPLAC/CEPEC/SEFIT; Didier Clement, CIRAD//UMR DAP; Uilson Vanderlei Lopes, CEPLC/CEPEC/SEFIT; Nicolas Carels, UESC; ABELMON DA SILVA GESTEIRA, CNPMF; Fernanda Amato Gaiotto, UESC; Júlio Cézar de Mattos Cascardo, UESC; Fabienne Micheli, CIRAD, UMR DAP. |
author_facet |
Lívia Santos Lima, CEPLAC/CEPEC/SEFIT; Karina Peres Gramacho, CEPLAC/CEPEC/SEFIT; José Luis Pires, CEPLAC/CEPEC/SEFIT; Didier Clement, CIRAD//UMR DAP; Uilson Vanderlei Lopes, CEPLC/CEPEC/SEFIT; Nicolas Carels, UESC; ABELMON DA SILVA GESTEIRA, CNPMF; Fernanda Amato Gaiotto, UESC; Júlio Cézar de Mattos Cascardo, UESC; Fabienne Micheli, CIRAD, UMR DAP. LIMA, L. S. GRAMACHO, K. P. PIRES, J. L. CLEMENT, D. LOPES, U. V. CARELS, N. GESTEIRA, A. da S. GAIOTTO, F. A. CASCARDO, J. C. de MATTOS MICHELI, F. |
format |
Artigo de periódico |
topic_facet |
Witches' broom disease Microsatellite Resistance Genetic diversity Theobroma cacao L Cacau Doença de Planta Marcador Molecular Vassoura de Bruxa |
author |
LIMA, L. S. GRAMACHO, K. P. PIRES, J. L. CLEMENT, D. LOPES, U. V. CARELS, N. GESTEIRA, A. da S. GAIOTTO, F. A. CASCARDO, J. C. de MATTOS MICHELI, F. |
author_sort |
LIMA, L. S. |
title |
Development, characterization, validation, and mapping of SSRs derived from Theobroma cacao L.?Moniliophthora perniciosa interaction ESTs. |
title_short |
Development, characterization, validation, and mapping of SSRs derived from Theobroma cacao L.?Moniliophthora perniciosa interaction ESTs. |
title_full |
Development, characterization, validation, and mapping of SSRs derived from Theobroma cacao L.?Moniliophthora perniciosa interaction ESTs. |
title_fullStr |
Development, characterization, validation, and mapping of SSRs derived from Theobroma cacao L.?Moniliophthora perniciosa interaction ESTs. |
title_full_unstemmed |
Development, characterization, validation, and mapping of SSRs derived from Theobroma cacao L.?Moniliophthora perniciosa interaction ESTs. |
title_sort |
development, characterization, validation, and mapping of ssrs derived from theobroma cacao l.?moniliophthora perniciosa interaction ests. |
publishDate |
2010-07-21 |
url |
http://www.alice.cnptia.embrapa.br/alice/handle/doc/858299 |
work_keys_str_mv |
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