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Development, characterization, validation, and mapping of SSRs derived from Theobroma cacao L.–Moniliophthora perniciosa interaction ESTs

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Abstract

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 EST-SSR 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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Abbreviations

AFLP:

Amplified fragment length polymorphism

EST:

Expressed sequence tag

HWE:

Hardy–Weinberg equilibrium

LD:

Linkage disequilibrium

LG:

Linkage group

MAS:

Marker-assisted selection

ORF:

Open reading frame

PCA:

Principal component analysis

PIC:

Polymorphic information content

QTL:

Quantitative trait locus

RAPD:

Random amplified polymorphic DNA

RFLP:

Restriction fragment length polymorphism

Sca 6:

Scavina 6

SD:

Standard deviation

SNP:

Single nucleotide polymorphism

SSR:

Simple sequence repeats

TSH:

Trinidad selected hybrid

UTR:

Untranslated region, WBD, witches’ broom disease

WBD:

Witches’ broom disease

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Acknowledgments

The present study was carried out in the Molecular Plant Pathology Laboratory (FITOMOL) of the Cocoa Research Center, Bahia, Brazil. This paper is part of an effort for searching novel genes to WBD resistance, coordinated by José Luis Pires and Karina Peres Gramacho at CEPEC/CEPLAC, and is funded by the Brazilian agency of Bahia–FAPESB (FAPESB; research grant no. APR160/2007) and for providing a research fellowship to N. Carels. This research was also supported by the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq; research grant no. 471274/2006-2 and the Ministère des Affaires Etrangères Français (MAE). LSL (Doctor Student) was granted by the Brazilian agency of Bahia–FAPESB.

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Authors and Affiliations

  1. CEPLAC/CEPEC/SEFIT, Molecular Plant Pathology Laboratory, Rodovia Ilhéus-Itabuna, km 22, 45600-970, Ilhéus, Bahia, Brazil

    Lívia Santos Lima, Karina Peres Gramacho, José Luis Pires, Didier Clement & Uilson Vanderlei Lopes

  2. Plant Breeding Section, Rodovia Ilhéus-Itabuna, km 22, 45600-970, Ilhéus, Bahia, Brazil

    José Luis Pires & Uilson Vanderlei Lopes

  3. UESC, DCB, Rodovia Ilhéus-Itabuna, km 16, 45650-000, Ilhéus, Bahia, Brazil

    Nicolas Carels, Abelmon da Silva Gesteira, Fernanda Amato Gaiotto, Júlio Cézar de Mattos Cascardo & Fabienne Micheli

  4. Laboratório de Genômica e Expressão Gênica, Rodovia Ilhéus-Itabuna, km 16, 45650-000, Ilhéus, Bahia, Brazil

    Abelmon da Silva Gesteira, Fernanda Amato Gaiotto, Júlio Cézar de Mattos Cascardo & Fabienne Micheli

  5. Núcleo de Biologia Computacional e Gestão de Informações Biotecnológicas, Rodovia Ilhéus-Itabuna, km 16, 45650-000, Ilhéus, Bahia, Brazil

    Nicolas Carels

  6. Embrapa Mandioca e Fruticultura Tropical, Rua Embrapa, s/nº, 44380-000, Cruz das Almas, Bahia, Brazil

    Abelmon da Silva Gesteira

  7. CIRAD, UMR DAP, Avenue Agropolis TA96/03, 34398, Montpellier cedex 5, France

    Didier Clement & Fabienne Micheli

Authors
  1. Lívia Santos Lima
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  2. Karina Peres Gramacho
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  3. José Luis Pires
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  4. Didier Clement
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  5. Uilson Vanderlei Lopes
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  6. Nicolas Carels
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  7. Abelmon da Silva Gesteira
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  8. Fernanda Amato Gaiotto
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  9. Júlio Cézar de Mattos Cascardo
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  10. Fabienne Micheli
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Correspondence to Karina Peres Gramacho.

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Communicated by J. Davis

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Lima, L.S., Gramacho, K.P., Pires, J.L. et al. Development, characterization, validation, and mapping of SSRs derived from Theobroma cacao L.–Moniliophthora perniciosa interaction ESTs. Tree Genetics & Genomes 6, 663–676 (2010). https://doi.org/10.1007/s11295-010-0282-1

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