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Tree Genetics & Genomes

, 14:52 | Cite as

Assessment of genetic diversity and structure in cocoa trees (Theobroma cacao L.) in Côte d’Ivoire with reference to their susceptibility to Cocoa swollen shoot virus disease (CSSVD)

  • Boguinard S. H. B. Guiraud
  • Mathias G. Tahi
  • Olivier Fouet
  • Caudou I. Trebissou
  • Désiré Pokou
  • Ronan Rivallan
  • Xavier Argout
  • Kouamé K. Koffi
  • Boaké Koné
  • Bi I. A. Zoro
  • Claire Lanaud
Original Article
Part of the following topical collections:
  1. Population structure

Abstract

Resistance to Cocoa Swollen Shoot Virus disease (CSSVD) is becoming an increasingly important criterion for selection of new cocoa cultivars in Côte-d’Ivoire, where the disease resurfaced since 2003. This virus can seriously affect the yield of trees with a loss of 25%, 1 year after infection, to around 100% 3 years after. In order to find tolerant plant material, 337 farm accessions have been collected on fields affected by CSSVD, according to the status of accessions potentially tolerant (APT) or susceptible (APS). Both phenotypic groups were genotyped using 30 microsatellite markers (SSR) in the presence of representative clones of the ten genetic groups of cocoa. This study revealed 214 alleles with the set of primer pairs used. The number of alleles per locus was between 3 and 16 with an average of 7.13 alleles per locus. The results showed a high contribution of genetic diversity within population (Hs = 0.51) to the total genetic diversity (Ht = 0.53) for the two studied groups. There was no significant difference between tolerant and susceptible groups (Fst = 0.05). These results suggest that APT could be a potential genetic reservoir for other traits of interest associated with virus resistance. The phylogenetic tree, as the STRUCTURE analysis of Ivorian cocoa population, showed a distribution of individuals following four groups marked by a high contribution of group 4 (Nanay, Maranon, Guiana) followed by group 2 (Criollo), and group 1 (Amelonado), and a lower contribution of group 3 (Iquitos, Purus, Nacional, Curaray, Contamana).

Keywords

Diversity Microsatellites Theobroma cacao L. CSSVD Côte d’Ivoire 

Notes

Acknowledgements

Authors also thank the Nangui Abrogoua University of Abidjan (Côte d’Ivoire), the National Agricultural Research Centre in Côte d'Ivoire (CNRA), and the International Centre for Agricultural Research and Development of France (CIRAD) for provision of plant material and molecular genotyping platform availability.

Data archiving statement

The data has been submitted to public databases
  • List and characteristic of samples

  • Molecular SRR data

  • The main results of software’s (Darwin 6, Genetix 4.05; GeneAlex 6, Structure 2.4.3)

  • The new phylogenetic tree with the names of individuals (revealed by Darwin) and variable contribution (revealed by Structure)

Funding information

This work was funded by the AMRUGE-CI scholarship. Mars, Inc. also provided financial contribution to this work.

Supplementary material

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References

  1. Aikpokpodion PO, Motamayor JC, Adetimirin VO, Adu-Ampomah Y, Ingelbrecht I, Eskes AB, Schnell RJ, Kolesnikova-Allen M (2009) Genetic diversity assessment of sub-samples of cacao, Theobroma cacao L. collections in West Africa using simple sequence repeats marker. Tree Genet Genomes 5:699–711CrossRefGoogle Scholar
  2. Allegre M, Argout X, Boccara M, Fouet O, Roguet Y, Berard A, Thevenin JM, Chauveau A, Rivallan R, Clement D (2012) Discovery and mapping of a new expressed sequence tag-single nucleotide polymorphism and simple sequence repeat panel for large-scale genetic studies and breeding of Theobroma cacao L. DNA Res 19:23–35CrossRefPubMedGoogle Scholar
  3. Alverson WS, Whitlock BA, Nyffeler R, Bayer C, Baum DA (1999) Phylogeny of the core Malvales: evidence from ndhF sequence data. Am J Bot 86:1474–1486CrossRefPubMedGoogle Scholar
  4. Argout X, Salse J, Aury J-M, Guiltinan MJ, Droc G, Gouzy J, Allegre M, Chaparro C, Legrave T, Maximova SN, Abrouk M, Murat F, Fouet O, Poulain J, Ruiz M, Roguet Y, Rodier-Goud M, Babosa-Neto JF, Sabot F, Kudrna D, Ammiraju JSS, Schuster SC, Carlson JE, Sallet E, Schiex T, Dievart A, Kramer M, Gelley L, Shi Z, Bérard A, Viot C, Boccara M, Risterucci AM, Guignon V, Sabau X, Axtell MJ, Ma Z, Zhang Y, Brown S, Bourge M, Golser W, Xiang S, Clement D, Rivallan R, Tahi M, Akaza JM, Pitollat B, Gramacho K, D’Hont A, Brune D, Infante D, Kebe I, Costet P, Wing R, McCombie WR, Guiderdoni E, Quetier F, Panaud O, Wincker P, Bocs S, Lanaud C (2011) The genome of Theobroma cacao. Nat Genet 43(2):101–108CrossRefPubMedGoogle Scholar
  5. Argout X, Martin G, Droc G, Fouet O, Labadie K, Rivals E, Aury JM, Lanaud C (2017) The cacao Criollo genome v2.0: an improved version of the genome for genetic and functional genomic studies. BMC Genomics 18:730.  https://doi.org/10.1186/s12864-017-4120-9 CrossRefPubMedPubMedCentralGoogle Scholar
  6. Belkhir K, Borsa P, Chikhi L, Raufaste N, Bonhomme F (2004) GENETIX 4.05, logiciel sous Windows TM pour la génétique des populations, Laboratoire Genome, Populations, Interactions; CNRS UMR 5000; Université ́ Montpellier II, Montpellier (France).Google Scholar
  7. Besse J (1977) La sélection générative du cacaoyer en Côte d'Ivoire: bilan et orientation des recherches. In: Proc. 5th International Cocoa Research Conference. Ibadan, Nigeria, 95-103Google Scholar
  8. Bhattacharjee R, Kolesnikova-Allen M, Aikpokpodion P, Taiwo S, Ingelbrecht I (2004) A semi-automated rapid method of extracting genomic DNA for molecular marker analysis in cocoa, Theobroma cacao L. Plant Mol Biol Report 22:435a–435hCrossRefGoogle Scholar
  9. Bredemeijer GMM, Arens P, Wouters D, Visser D, Vosman B (1998) The use of semi-automated fluorescent microsatellite analysis for tomato cultivar identification. Theor Appl Genet 97:584–590CrossRefGoogle Scholar
  10. Brunt AA (1975) The effect of cocoa swollen shoot virus on the growth and yield of Amelonado and Amazon cocoa (Theobroma cacao L.) in Ghana. Ann Appl Biol 80:169–180CrossRefGoogle Scholar
  11. Chessman EE (1944) Notes on the nomenclature, classification and possible relationships of cocoa populations. Trop Agric 21:144–159Google Scholar
  12. Clement D, Risterucci AM, Motamayor JC, N’Goran J, Lanaud C (2003) Mapping QTL for yield components, vigor, and resistance to Phytophthora palmivora in Theobroma cacao L. Genome 46:204–212CrossRefPubMedGoogle Scholar
  13. Cope FW (1958) Incompatibility in Theobroma cacao. Nature 181:279CrossRefGoogle Scholar
  14. Da Silva MR, Clément D, Gramacho KP, Monteiro WR, Argout X, Lanaud C, Lopes UV (2016) Genome-wide association mapping of sexual incompatibility genes in cacao (Theobroma cacao L.). Tree Genet Genomes 12(3):62 13 p.  https://doi.org/10.1007/s11295-016-1012-0 CrossRefGoogle Scholar
  15. Dzahini-Obiatey H, Ameyaw GA, Ollennu LA (2006) Control of cocoa swollen shoot disease by eradicating infected trees in Ghana: a survey of treated and replanted areas. Crop Prot 25:647–652CrossRefGoogle Scholar
  16. Efombagn IBM, Sonigo O, Nyassé S, Manzanares-Dauleux M, Cilas C, Eskes MAB, Kolesnikova-Allen (2006) Genetic diversity in cocoa germplasm of southern Cameroon revelead by simple sequences repeat (SSRs) markers. Afr J Biotechnol 5(16):1441–1449Google Scholar
  17. Efombagn IBM, Motamayor JC, Sounigo O, Eskes AB, Nyassé S, Cilas C, Schnell R, Manzanares-Dauleux MJ, Kolesnikova-Allen M (2008) Genetic diversity and structure of farm and GenBank accessions of cacao (Theobroma cacao L.) in Cameroon revealed by microsatellite markers. Tree Genet Genomes 4:821–831CrossRefGoogle Scholar
  18. Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611–2620CrossRefPubMedGoogle Scholar
  19. Fouet O, Allegre M, Argout X, Jeanneau M, Lemainque A, Pavek S, Boland A, Risterucci AM, Loor G, Tahi GM (2011) Structural characterization and mapping of functional EST-SSR markers in Theobroma cacao. Tree Genet Genomes 7:799–817CrossRefGoogle Scholar
  20. Goudet J (1995) FSTAT (1.2): A computer program to calculate F-Statistics. J Hered 86(6):485–486CrossRefGoogle Scholar
  21. Hoffman K, Sackey ST, Maiss E, Adomako D, Vetten HJ (1997) Immunocapture polymerase chain reaction for the detection and characterization of cocoa swollen shoot virus 1A isolates. J Phytopathol 145:205–2012CrossRefGoogle Scholar
  22. International Cocoa Organization (ICCO) (2017) Quarterly bulletin of cocoa statistics, Vol. XLIII, No. 3, Cocoa year 2016/2017Google Scholar
  23. Knight R, Rogers HH (1955) Incompatibility in Theobroma cacao. Heredity 9:69–77CrossRefGoogle Scholar
  24. Kouakou K (2014) Diversité molécualaire du CSSV (Cocoa swollen shoot virus) et épidémiologie de la maladie du swollen shoot du cacaoyer (Theobroma cacao L.) en Côte d’Ivoire. Thèse de doctorat-Phytovirologie, Université Félix Houphouet Boigny, Abidjan (Côte d’Ivoire) 141 pages.Google Scholar
  25. Kouakou K, Kébé BI, Kouassi N, Anno AP, Aké S, Muller E (2011) Impact de la maladie virale du swollen shoot du cacaoyer sur la production de cacao en milieu paysan à Bazré (Côte d’Ivoire). J Appl Biosci 43:2947–2957Google Scholar
  26. Kouakou K, Kébé BI, Kouassi N, Aké S, Cilas C, Muller E (2012) Geographical distribution of Cocoa swollen shoot virus molecular variability in Côte d’Ivoire. Plant Dis 96:1445–1450CrossRefGoogle Scholar
  27. Lachenaud P, Fouet O, Couturier C, Lanaud C (2016) Cacao trees (Theobroma cacao L.) of the “Guiana” genetic group: “Tanpok 2012” survey. Genet Resour Crop Evol 63(5):781–790CrossRefGoogle Scholar
  28. Lanaud C (1986) Utilisation des marqueurs enzymatiques pour l’étude génétique du cacaoyer: Theobroma cacao L. I. Contrôle génétique et “linkage” de neuf marqueurs génétiques. Café, Cacao, Thé 30(4):259–270Google Scholar
  29. Lanaud C, Hamon P, Duperray C (1992) Estimation of nuclear DNA content of Theobroma cacao L. by flow cytometry. Café, Cacao, Thé 36:3–8Google Scholar
  30. Lanaud C, Risterucci AM, Pieretti I, Falque M, Bouet A, Lagoda PJL (1999) Isolation and characterization of microsatellites in Theobroma cacao L. Mol Ecol 8:2141–2143CrossRefPubMedGoogle Scholar
  31. Lanaud C, Fouet O, Clement D, Boccara M, Risterucci AM, Surujdeo-Maharaj S, Legrave T, Xavier A (2009) A meta-QTL analysis of disease resistance traits of Theobroma cacao L. Mol Breed 24(4):361–374.  https://doi.org/10.1007/s11032-009-9297-4 CrossRefGoogle Scholar
  32. Lanaud C, Fouet O, Legavre T, Lopes U, Sounigo O, Eyango MC, Mermaz B, DaSilva MR, Solorzano RGL, Xavier A, Gyapay G, Ebaiarrey HE, Colonges K, Sanier C, Rivallan R, Mastin G, Cryer N, Boccara M, Verdeil JL, Ives Bruno Efombagn IBM, Gramacho KP, Clement D (2017) Deciphering the Theobroma cacao self-incompatibility system: from genomics to diagnostic markers for self-compatibility. J Exp Bot 68:2–16.  https://doi.org/10.1093/jxb/erx293 CrossRefGoogle Scholar
  33. Laurent V, Risterucci AM, Lanaud C (1994) Genetics diversity in cocoa revealed by cDNA probes. Theor Appl Genet 88:193–198CrossRefPubMedGoogle Scholar
  34. Lot H, Djiekpor E, Jacquemond M (1991) Characterization of the genome of Cocoa swollen shoot virus. J Genet Virol 72:1735–1739CrossRefGoogle Scholar
  35. Mafu N, Naidoo R, Fato P, Danson J, Derera J, Laing MD (2014) Genetic diversity of maize germplasm lines and implications for breeding maize streak virus resistant hybrids. S Afr J Plant Soil 31:77–86CrossRefGoogle Scholar
  36. Moose SP, Mumm RH (2008) Molecular plant breeding as the foundation for 21st century crop improvement. Plant Physiol 147:969–977CrossRefPubMedPubMedCentralGoogle Scholar
  37. Motamayor JC, Risterucci AM, Lopez PA, Ortiz CF, Moreno A, Lanaud C (2002) Cacao domestication I: the origin of the cacao cultivated by the Mayas. Heredity 89:380–386CrossRefPubMedGoogle Scholar
  38. Motamayor JC, Risterucci AM, Heath M, Lanaud C (2003) Cacao domestication II progenitor germplasm of the Trinitario cacao cultivar. Heredity 9:322–330CrossRefGoogle Scholar
  39. Motamayor JC, Lachenaud P, da Silva E Mota JW, Loor R, Kuhn DN, Brown JS, Schnell RJ (2008) Geographic and genetic population differentiation of the Amazonian chocolate tree (Theobroma cacao L). PLoS ONE 3:e3311CrossRefPubMedPubMedCentralGoogle Scholar
  40. Muller E, Sackey S (2005) Molecular variability analysis of five new complete cacao swollen shoot virus genomic sequences. Arch Virol 150:53–66CrossRefPubMedGoogle Scholar
  41. N’goran JAK, Laurent V, Risterucci AM, Lanaud C (2000) The genetic structure of cocoa populations (Theobroma cacao L.) revealed by RFLP analysis. Euphytica 115:83–90CrossRefGoogle Scholar
  42. Nei M (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89:583–590PubMedPubMedCentralGoogle Scholar
  43. N'goran JAK, Laurent V, Risterucci AM, Lanaud C (1994) Comparative genetic diversity studies of Theobroma cacao L. using RFLP and RAPD markers. Heredity 73:589–597CrossRefGoogle Scholar
  44. Opoku SY, Bhattacharjee R, Kolesnikova-Allen M, Motamayor JC, Schnell R, Ingelbrecht I, Enu-Kwesi L, Adu-Ampomah Y (2007) Genetic diversity in cocoa (Theobroma cacao L.) germplasm collection from Ghana. J Crop Improv 20:73–87CrossRefGoogle Scholar
  45. Ouédraogo M, Maquet M, Baudoin JP (2005) Etude comparative de la diversité et de la structure génétique de populations sauvages de Phaseolus lanatus L. à l’aide des marqueurs enzymatiques et microsatellites. J Appl Biosci 43:2947–2957Google Scholar
  46. Peakall R, Smouse PE (2012) GenAlEx 6.5 Genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinformatics 28:2537–2539CrossRefPubMedPubMedCentralGoogle Scholar
  47. Perrier X, Jacquemoud-Collet JP (2006) Darwin software http://darwin.cirad.fr accessed on http://darwin.cirad.fr/product.php
  48. Pires JL, Monteiro WR, Luz EDMN, Silva SDVM, Pinto LRM, Figueria A, Ahnert DE, Bruggnerotto MIB (1998) CocoaBreeding for Witches’BroomResistance at CEPEC, Bahia, Brazil. Pages 91-101 In: Proc. International Workshop on the Contribution of Disease Resistance to Cocoa Variety Improvement. INGENIC, Bahia, BrazilGoogle Scholar
  49. Pokou ND, Motamayor JC, Tondo CL, Tahi M, Schnell R (2014) Molecular characterization of resistant accessions of cocoa (Theobroma cocoa L.) to Phytophtora pod rot selected on-farm in Côte d'Ivoire. Int J Agric Biosci 3(5):236–240Google Scholar
  50. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959PubMedPubMedCentralGoogle Scholar
  51. Risterucci AM, Paulin D, Ducamp M, N’Goran JAK, Lanaud C (2003) Identification of QTLs related to cocoa resistance to three species of Phytophthora. Theor Appl Genet 108(1):168–174CrossRefPubMedGoogle Scholar
  52. Royaert S, Phillips-Mora W, Arciniegas Leal AM (2010) Identification of marker-trait associations for self-compatibility in a segregating mapping population of Theobroma cacao L. Tree Genet Genomes 7:1159–1168CrossRefGoogle Scholar
  53. Saunders JA, Mischeke S, Leamy EA, Hemeida AA (2004) Selection of international molecular standards for DNA fingerprinting of Theobroma cacao. Theor Appl Genet 110(1):41–47CrossRefPubMedGoogle Scholar
  54. Sereno ML, Albuquerque PSB, Vencovsky R, Figueira A (2006) Genetic diversity and natural population structure of cacao (Theobroma cacao L.) from the Brazilian Amazon evaluated by microsatellite markers. Conserv Genet 7:13–24CrossRefGoogle Scholar
  55. Solorzano LRG, Fouet O, Lemainque A, Pavek S, Boccara M, Argout X, Amores F, Courtois B, Risterucci AM, Lanaud C (2012) Insight into the wild origin, migration and domestication history of the fine flavor nacional Theobroma cacao L. variety from Ecuador. PLoS ONE 7(11):e48438 1-11CrossRefGoogle Scholar
  56. Sonigo O, Umaharan R, Christopher Y, Sankar A, Ramdahin S (2005) Assessing the genetic diversity in the international Cocoa Genebank, Trinidad (IGG, T) using isozyme electrophoresis and RAPD. Genet Resour Crop Evol 52:1111–1120CrossRefGoogle Scholar
  57. Tahi GM, Lachenaud PH, N’Goran JAK, Kebe IA, Paulin D, N’Guessan KF, Cilas C and Eskes AB (2010) Second cycle de sélection récurrente du Cacaoyer (Theobroma cacao L.) en Côte d’Ivoire : bilan à mi-parcours et propositions de sorties variétales. 16 ème Conférence International sur la Recherche Cacaoyère, Bali, Indonésie : pp 3-12Google Scholar
  58. Takrama JF, Cervantes-Martinez C, Phillips-Mora W, Brown JS, Motamayor JC, Schnell RJ (2005) Determination of off-types in cocoa breeding programme using microsatellites. Ingenic Newsl 10:2–8Google Scholar
  59. Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38:1358–1370PubMedGoogle Scholar

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Boguinard S. H. B. Guiraud
    • 1
    • 2
    • 3
    • 4
  • Mathias G. Tahi
    • 2
  • Olivier Fouet
    • 3
    • 4
  • Caudou I. Trebissou
    • 2
  • Désiré Pokou
    • 2
  • Ronan Rivallan
    • 3
    • 4
  • Xavier Argout
    • 3
    • 4
  • Kouamé K. Koffi
    • 1
  • Boaké Koné
    • 2
  • Bi I. A. Zoro
    • 1
  • Claire Lanaud
    • 3
    • 4
  1. 1.UFR des Sciences de la Nature, Unité de Phytotechnie et Amélioration génétiqueUniversité Nangui Abrogoua d’Abidjan (UNA)AbidjanCôte d’Ivoire
  2. 2.Programme cacao, Opération Amélioration variétaleCentre National de Recherche Agronomique (CNRA)DivoCôte d’Ivoire
  3. 3.Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD),UMR AGAPMontpellierFrance
  4. 4.AGAPUniv Montpellier, CIRAD, INRA, Montpellier SupAgroMontpellierFrance

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