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Creation of BAC genomic resources for cocoa (Theobroma cacao L.) for physical mapping of RGA containing BAC clones

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Abstract

We have constructed and validated the first cocoa (Theobroma cacao L.) BAC library, with the aim of developing molecular resources to study the structure and evolution of the genome of this perennial crop. This library contains 36,864 clones with an average insert size of 120 kb, representing approximately ten haploid genome equivalents. It was constructed from the genotype Scavina-6 (Sca-6), a Forastero clone highly resistant to cocoa pathogens and a parent of existing mapping populations. Validation of the BAC library was carried out with a set of 13 genetically-anchored single copy and one duplicated markers. An average of nine BAC clones per probe was identified, giving an initial experimental estimation of the genome coverage represented in the library. Screening of the library with a set of resistance gene analogues (RGAs), previously mapped in cocoa and co-localizing with QTL for resistance to Phytophthora traits, confirmed at the physical level the tight clustering of RGAs in the cocoa genome and provided the first insights into the relationships between genetic and physical distances in the cocoa genome. This library represents an available BAC resource for structural genomic studies or map-based cloning of genes corresponding to important QTLs for agronomic traits such as resistance genes to major cocoa pathogens like Phytophthora spp (palmivora and megakarya), Crinipellis perniciosa and Moniliophthora roreri.

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References

  • Adomako D (1972) Cocoa pod husk pectin. Phytochemistry 11:1145–1148

    Article  CAS  Google Scholar 

  • Baker NR, Hardwick K, Jones P (1975) Biochemical and physiological aspects of leaf development in cocoa (Theobroma cacao) II. Development of chloroplast ultrastructure and carotenoids. New Phytol 75:513–518

    CAS  Google Scholar 

  • Ballvora A, Schornack S, Baker BJ, Ganal M, Bonas U, Lahaye T (2001) Chromosome landing at the tomato Bs4 locus. Mol Genet Genomics 266:639–645

    Google Scholar 

  • Ballvora A, Ercolano MR, Weis J, Meksem K, Bornmann CA, Oberhagemann P, Salamini F, Gebhart C (2002) The R1 gene for potato resistance to late blight (Phytophthora infestans) belongs to the leucine zipper/ NBS/ LRR class of plant resistance genes. Plant J 30:361–371

    Article  PubMed  Google Scholar 

  • Blakemore WR, Dewar ET, Hodge RA (1966) Polysaccharides of the cocoa pod husk. J Sci Food Agric 17:558–560

    CAS  Google Scholar 

  • Botella MA, Coleman MJ, Hughes DE, Nishimura MT, Jones JD, Somerville SC (1997) Map positions of 47 Arabidopsis sequences with sequence similarity to disease resistance genes. Plant J 12:1197–1211

    PubMed  Google Scholar 

  • Botella MA, Parker JE, Frost LN, Bittner-Eddy PD, Beynon JL, Daniels MJ, Holub EB, Jones JD (1998) Three genes of the Arabidopsis RPP1 complex resistance locus recognize distinct Peronospora parasitica avirulence determinants. Plant Cell 10:1847–1860

    CAS  PubMed  Google Scholar 

  • Chauhan RS, Farman ML, Zhang HB, Leong SA (2002) Genetic and physical mapping of a rice blast resistance locus, Pi-CO39(t), that corresponds to the avirulence gene AVR1-CO39 of Magnaporthe grisea. Mol Genet Genomics 267:603–612

    Article  CAS  PubMed  Google Scholar 

  • Clément D, Risterucci AM, Motamayor JC, N’Goran JD, Lanaud C (2003a) Mapping quantitative trait loci for bean trait and ovule number in Theobroma cacao L. Genome 46:103–111

    Article  CAS  PubMed  Google Scholar 

  • Clément D, Risterucci AM, Motamayor JC, N’Goran JD, Lanaud C (2003b) Mapping QTL for yield components, vigor and resistance to phytophthora palmivora in Theobroma cacao L. Genome 46:204–212

    Article  PubMed  Google Scholar 

  • Collins NC, Webb CA, Seah S, Ellis JG, Hulbert SH, Pryor A (1998) The isolation and mapping of disease resistance gene analogues in maize. Mol Plant Microbe Interact 11:968–978

    CAS  PubMed  Google Scholar 

  • Crouzillat D, Phillips W, Fritz PJ, Pétiard V (2000) Quantitative trait loci analysis in Theobroma cacao L. using molecular markers. Inheritance of polygenic resistance to Phytophthora palmivora in two related cacao populations. Euphytica 114:25–36

    CAS  Google Scholar 

  • Dangl JL, Jones JD (2001) Plant pathogens and integrated defence responses to infection. Nature 411:826–833

    CAS  PubMed  Google Scholar 

  • Demesure B, Sodzi N, Petit RJ (1995) A set of universal primers for amplification of polymorphic non-coding regions of mitochondrial and chloroplast DNA in plants. Mol Ecol 4:129–131

    CAS  PubMed  Google Scholar 

  • Figueira AJ, Janick J, Goldsbrough P (1992) Genome size and DNA polymorphism in Theobroma cacao L. J Am Soc Hortic Sci 117:673–677

    CAS  Google Scholar 

  • Flament M-H, Kébé I, Clément D, Pierretti I, Risterucci AM, N’Goran JAK, Cilas C, Despréaux D, Lanaud C (2001) Genetic mapping of resistance factors to Phytophthora palmivora in cocoa. Genome 44:79–85

    Article  CAS  PubMed  Google Scholar 

  • Frary A, Nesbitt TC, Grandillo S, Knaap E, Cong B, Liu J, Meller J, Elber R, Alpert KB, Tanksley SD (2000) Fw2.2: a quantitative trait locus key to the evolution of tomato fruit size. Science 289:85–88

    Article  CAS  PubMed  Google Scholar 

  • Graham MA, Marek LF, Lohnes D, Cregan P, Shoemaker RC (2000) Expression and genome organization of resistance gene analogues in soybean. Genome 43:86–93

    CAS  PubMed  Google Scholar 

  • Graham MA, Marek LF, Shoemaker RC (2002) Organization, expression and evolution of a disease resistance gene cluster in soybean. Genetics 162:1961–1977

    Google Scholar 

  • Hammond-Kosack KE, Jones JD (1996) Resistance gene-dependent plant defence responses. Plant Cell 8:1773–1791

    CAS  PubMed  Google Scholar 

  • Holub EB, Jones JD (1998) Three genes of the Arabidopsis RPP1 complex resistance locus recognize distinct Peronospora parasitica avirulence determinants. Plant Cell 10:1847–1860

    CAS  PubMed  Google Scholar 

  • Jones PG, Allaway D, Gilmour DM, Harris C, Rankin D, Retzel ER, Jones CA (2002) Gene discovery and microarray analysis of cacao (Theobroma cacao L.) varieties. Planta 216:255–264

    Article  CAS  PubMed  Google Scholar 

  • Kuhn DN, Heath M, Wisser RJ, Meerow A, Brown JS, Lopes U, Schnell RJ (2003) Resistance gene homologues in Theobroma cacao as useful genetic markers. Theor Appl Genet 107:191–202

    Article  CAS  PubMed  Google Scholar 

  • Kunkel BN (1996) A useful weed put to work: genetic analysis of disease resistance in Arabidopsis thaliana. Trends Genet 12:63–69

    CAS  PubMed  Google Scholar 

  • Lahaye T, Shirasu K, Schulze-Lefert P (1998) Chromosome landing at the barley Rar1 locus. Mol Gen Genet 260:92–101

    Article  CAS  PubMed  Google Scholar 

  • Lanaud C, Hamon P, Duperray C (1992) Estimation of nuclear DNA content of Theobroma cacao L. by flow cytometry. Café Cacao Thé 36:3–8

  • Lanaud C, Risterucci AM, N’Goran J, Clément D, Flament M, Laurent V, Falque M (1995) A genetic linkage map of Theobroma cacao L. Theor Appl Genet 91:987–993

    CAS  Google Scholar 

  • Lanaud C, Motamayor JC, Sounigo O (1999) Le cacaoyer. In: Diversité génétique des plantes tropicales. Éditions CIRAD, Montpellier, pp 141–169

  • Lanaud C, Motamayor JC, Risterucci AM (2001) Implications of new insight into the genetic structure of Theobroma cacao L. for breeding strategies. In: Proceedings of the international workshop on new technologies and cocoa breeding. INGENIC, London, pp 89–107

  • Lanaud C, Flament M-H, Nyassé S, Risterucci AM, Fargeas D, Kébé I, Motilal L, Thévenin J-M, Paulin D, Ducamp M, Clement D, N’Goran JAK, Cilas C (2002) Synthesis of studies on genetic basis of cocoa tree resistance to Phytophthora using molecular markers. Proceedings of the 13th international cocoa research conference, October 9–14, Kota Kinabalu, Malaysia, pp 127–136

  • Lanaud C, Risterucci AM, Pieretti I, N’Goran JAK, Fargeas D (2004) Characterization and genetic mapping of resistance and defence gene analogues in cocoa (Theobroma cacao L.). Mol Breed (in press)

  • Leister D, Kurth J, Laurie DA, Yano M, Sasaki T, Devos K, Graner A, Schulze-Lefert P (1998) Rapid reorganization of resistance gene homologues in cereal genomes. Proc Natl Acad Sci USA 95:370–375

    CAS  PubMed  Google Scholar 

  • Marek LF, Mudge J, Darnielle L, Grant D, Hanson N, Paz M, Huihuang Y, Denny R, Larson K, Foster-Hartnett D, Cooper A, Danesh D, Larsen D, Schmidt T, Staggs R, Crow JA, Retzel E, Young ND, Shoemaker RC (2001) Soybean genomic survey: BAC-end sequences near RFLP and SSR markers. Genome 44:572–581

    Article  CAS  PubMed  Google Scholar 

  • Meyers BC, Dickerman AW, Michelmore RW, Sivaramakrishnan S, Sobral BW, Young ND (1999) Plant disease resistance genes encode members of an ancient and diverse protein family within the nucleotide-binding superfamily. Plant J 20:317–332

    Article  CAS  PubMed  Google Scholar 

  • Meyers BC, Morgante M, Michelmore RW (2002) TIR-X and TIR-NBS proteins: two new families related to disease resistance TIR-NBS-LRR proteins encoded in Arabidopsis and other plant genomes. Plant J 32:77–92

    Article  CAS  PubMed  Google Scholar 

  • Michelmore RW, Meyers BC (1998) Clusters of resistance genes in plants evolve by divergent selection and a birth-and-death process. Genome Res 8:1113–1130

    CAS  PubMed  Google Scholar 

  • Paradis L (1979) Le cacao précolombien: Monnaies d’échange et breuvage des dieux. J Agric Trad Bot Appl 26:3–4

    Google Scholar 

  • Penuela S, Danesh D, Young ND (2002) Targeted isolation, sequence analysis, and physical mapping of non-TIR NBS-LRR genes in soybean. Theor Appl Genet 104:261–272

    Article  Google Scholar 

  • Pflieger S, Lefebvre V, Caranta C, Blattes A, Goffinet B, Palloix A (1999) Disease resistance gene analogues as candidates for QTLs involved in pepper-pathogen interactions.Genome Res 42:1100–1110

    Article  CAS  Google Scholar 

  • Pound FJ (1945) A note of the cocoa population of South America. Arch Cocoa Res 1:93–97

    Google Scholar 

  • Pugh T, Fouet O, Risterucci AM, Brottier P, Deletrez C, Courtois B, Clément D, Abouladze M, Larmande P, N’Goran JNK, Lanaud C (2004) A new codominant markers-based cocoa linkage map: development and integration of 201 new microsatellites markers. Theor Appl Genet (in press)

  • Queiroz VT, Guimarães CT, Anhert D, Schuster I, Daher RT, Pereira MG, Miranda VRM, Loguercio LL, Barros EG, Moreira MA (2003) Identification of a major QTL in cocoa (Theobroma cacao L.) associated with resistance to witches broom disease. Plant Breed 122:268–272

    Article  CAS  Google Scholar 

  • Riely BK, Martin GB (2001) Ancient origin of pathogen recognition specificity conferred by the tomato disease resistance gene Pto. Proc Natl Acad Sci USA 98:2059–2064

    Article  CAS  PubMed  Google Scholar 

  • Risterucci AM, Grivet L, N’Goran JAK, Pieretti I, Flament M-H, Lanaud C (2000) A high-density linkage map of Theobroma cacao L. Theor Appl Genet 101:948–955

    CAS  Google Scholar 

  • Risterucci AM, Paulin D, Ducamp M, N’Goran JAK, Lanaud C (2003) Identification of QTL related to cocoa resistances to three species of Phytophthora. Theor Appl Genet 108:168–174

    CAS  PubMed  Google Scholar 

  • Shen KA, Meyers BC, Islam-Faridi MN, Chin DB, Stelly DM, Michelmore RW (1998) Resistance gene candidates identified by PCR with degenerate oligonucleotide primers map to clusters of resistance genes in lettuce. Mol Plant Microbe Interact 11:815–823

    CAS  PubMed  Google Scholar 

  • Shirasu K, Lahaye T, Tan MW, Zhou F, Azevedo C, Schulze-Lefert P (1999) A novel class of eukaryotic zinc-binding proteins is required for disease resistance signalling in barley and development in C. elegans. Cell 99:355–366

    CAS  PubMed  Google Scholar 

  • Soderlund C, Longden I, Mott R (1997) FPC: a system for building contigs from restriction fingerprinted clones. CABIOS 13:523–535

    CAS  PubMed  Google Scholar 

  • Strong SJ, Ohta Y, Litman GW, Amemiya CT (1997) Marked improvement of PAC and BAC cloning is achieved using electro-elution of pulsed-field gel-separated partial digests of genomic DNA. Nucleic Acids Res 25:3959–3961

    Article  CAS  PubMed  Google Scholar 

  • Wei F, Gobelman-Werner K, Morroll SM, Kurth J, Mao L, Wing R, Leister D, Schulze-Lefert P, Wise RP (1999) The Mla (powdery mildew) resistance cluster is associated with three NBS-LRR gene families and suppressed recombination within a 240 kb DNA interval on chromosome 5S (1HS) of barley. Genetics 153:1929–1948

    CAS  PubMed  Google Scholar 

  • Zhang H-B, Zhao X, Ding X, Paterson AH, Wing RA (1995) Preparation of megabase-size DNA from plant nuclei. Plant J 7:175–184

    CAS  Google Scholar 

  • Zhou F, Kurth J, Wei F, Elliott C, Vale G, Yahiaoui N, Keller B, Somerville S, Wise R, Schulze-Lefert P (2001) Cell-autonomous expression of barley Mla1 confers race-specific resistance to the powdery mildew fungus via a Rar1-independent signalling pathway. Plant Cell 13:337–350

    CAS  PubMed  Google Scholar 

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Acknowledgements

We thank USDA for their financial contribution to the contig analyses of RGA-containing BAC clones. We are grateful to CNRA (Centre National de Recherche Agronomique) of the Côte d’Ivoire for providing the Scavina-6 leaves and to the Montpellier Languedoc Roussillon Genopole for the robotic platform used to manage the BAC library.

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Authors and Affiliations

  1. TA 43/02, Centre de coopération internationale en recherche pour le développement (CIRAD), Avenue d’Agropolis, 34398 , Montpellier , Cedex 5, France

    D. Clément, C. Lanaud, X. Sabau, O. Fouet, L. Le Cunff, E. Ruiz, A. M. Risterucci, J. C. Glaszmann & P. Piffanelli

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  1. D. Clément
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  2. C. Lanaud
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  3. X. Sabau
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  4. O. Fouet
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  5. L. Le Cunff
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  6. E. Ruiz
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  7. A. M. Risterucci
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  8. J. C. Glaszmann
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  9. P. Piffanelli
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Correspondence to D. Clément.

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Communicated by J.W. Snape

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Clément, D., Lanaud, C., Sabau, X. et al. Creation of BAC genomic resources for cocoa (Theobroma cacao L.) for physical mapping of RGA containing BAC clones. Theor Appl Genet 108, 1627–1634 (2004). https://doi.org/10.1007/s00122-004-1593-0

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  • DOI: https://doi.org/10.1007/s00122-004-1593-0

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