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Identification, characterization and mapping of EST-derived SSRs from the cacao–Ceratocystis cacaofunesta interaction

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Abstract

Ceratocystis cacaofunesta is an ascomycete responsible for the lethal wilt disease of cacao (Theobroma cacao L.). Marker-assisted selection combined with conventional breeding is one powerful approach to improve cacao resistance to Ceratocystis wilt. In this study we screened a set of ESTs obtained from cacao elicited with C. cacaofunesta to identify EST-SSRs and test their efficacy for mapping. Among the 3,432 ESTs analysed, 384 contained SSRs and 428 EST-SSRs were identified, mainly dinucleotides (78.5 %), with four repeats (75.23 %), and preferentially AG/CT motif (25.47 %). Gene ontology function was assigned to the ESTs containing SSRs: 4.04 % belonged to “defense response” category, with 20.69 % of them to the sub-category “defense response to fungi”. In relation to the ORF, the same quantity of EST-SSRs was observed in the 5′ UTR, ORF and the 3′ UTR (about 30 %). From the 428 EST-SSRs identified, 12 were polymorphic, revealing a total of 41 alleles. The number of alleles per locus ranged from 2 to 6, with an average of 3.41. Four EST-SSRs were mapped on the F2 Sca 6 × ICS 1 population segregating for Ceratocystis wilt, and were distributed on the 2, 3, 4 and 8 linkage groups. These markers will have potential applications in linkage mapping and will be valuable for the research community to improve the cacao breeding program.

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Abbreviations

AFLP:

Amplified fragment length polymorphism

EST:

Expressed sequence tag

GO:

Gene ontology

HWE:

Hardy–Weinberg equilibrium

ICS 1:

Imperial College Selections 1

LG:

Linkage group

MAS:

Marker-assisted selection

ORF:

Open reading frame

PIC:

Polymorphic information content

RAPD:

Random amplified polymorphic DNA

RFLP:

Restriction fragment length polymorphism

Sca 6:

Scavina 6

SSH:

Suppressive and subtractive hybridization

SNP:

Single-nucleotide polymorphism

SSR:

Simple sequence repeats

UTR:

Untranslated region

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Acknowledgments

This research was carried out in the facilities of the Cocoa Research Center—CEPEC/CEPLAC-Molecular Plant Pathology Laboratory. This research was supported by the Fundação de Amparo à Pesquisa da Bahia (FAPESB, Brazil). The work of RMF Santos was supported by the FAPESB, the Centre de Cooperation International en Recherche Agronomique pour le Développement (Cirad, France) and the Cocoa Research Center CEPEC/CEPLAC. We thank Claudia Fortes Ferreira (Embrapa) for the critical reading of the manuscript.

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Authors and Affiliations

  1. Cocoa Research Center, CEPLAC/CEPEC, 45600-970, Itabuna, Bahia, Brazil

    Rogério Mercês Ferreira Santos, Didier Clement, Lívia Santos Lima Lemos, Jose Luis Pires, Uilson Vanderlei Lopes & Karina Peres Gramacho

  2. CIRAD, UMR AGAP, Avenue Agropolis TA96/03, 34398, Montpellier cedex 5, France

    Didier Clement, Thierry Legravre, Claire Lanaud & Fabienne Micheli

  3. USDA-ARS, 13601 Old Cutler Rd, Miami, FL, 33158-0000, USA

    Raymond J. Schnell

  4. UESC, DCB, Centro de Biotecnologia e Genética, Rodovia Ilhéus-Itabuna Km 16, 45662-900, Ilhéus, Bahia, Brazil

    Fabienne Micheli

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  1. Rogério Mercês Ferreira Santos
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  2. Didier Clement
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  3. Lívia Santos Lima Lemos
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  4. Thierry Legravre
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  5. Claire Lanaud
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  6. Raymond J. Schnell
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  7. Jose Luis Pires
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  8. Uilson Vanderlei Lopes
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  9. Fabienne Micheli
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  10. Karina Peres Gramacho
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Correspondence to Fabienne Micheli.

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Communicated by J. Wegrzyn

Fabienne Micheli and Karina Peres Gramacho contributed equally to the work.

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Santos, R.M.F., Clement, D., Lemos, L.S.L. et al. Identification, characterization and mapping of EST-derived SSRs from the cacao–Ceratocystis cacaofunesta interaction. Tree Genetics & Genomes 9, 117–127 (2013). https://doi.org/10.1007/s11295-012-0539-y

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