A meta-QTL analysis of disease resistance traits of Theobroma cacao L

Molecular Breeding

Volumn 24, Issue 4, 2009, Pages 361-374

  Lanaud, C ^a   Fouet, O ^a   Clement D ^a   Boccara, M ^a   Risterucci, A M ^a   Surujdeo Maharaj, S ^a   Legavre, T ^a   Argout, X ^a  

^a CIRAD   (France)

Author keywords

Disease resistance; Genetic map; Meta analysis; Phytophthora resistance; QTL; Theobroma cacao

Indexed keywords

COCOA;

CONFIDENCE INTERVAL; DISEASE RESISTANCE; GENETIC MAP; MARKER-ASSISTED SELECTION; META-ANALYSIS; PHYTOPHTHORA; PHYTOPHTHORA RESISTANCE; QTL; QTL MAPPING; THEOBROMA CACAO;

MAPPING;

PHYTOPHTHORA; THEOBROMA CACAO;

EID: 70350702577     PISSN: 13803743     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11032-009-9297-4     Document Type: Article

References (67)

1. Akaike H (1973) Information theory and an extension of the maximum likelihood principle. 2nd International Symposium on Information Theory: 267-281.
2. Akaike H (1992) Information theory and an extension of the maximum likelihood principle. In: Kotz S, Johnson NL (eds) Breakthroughs in statistics, vol 1. Springer-Verlag, London, pp 610-624.
3. Albuquerque PSB, Figueira A (2004) Genetic mapping and identification of genomic regions associated with witches' broom resistance, derived from alternative sources from the Brazilian Amazon (CAB genotypes). INGENIC Newsl 9:39-42.
4. Allison DB, Heo M (1998) Meta-analysis of linkage data under worst-case conditions: a demonstration using the human OB region. Genetics 148:859-865.
5. APG II (2003) An update of the angiosperm phylogeny group classification for the orders and families of flowering plants. Bot J Linn Soc 141:399-436. doi:10.1046/j.1095-8339.2003.t01-1-00158.x.
6. Arcade A, Labourdette A, Falque M, Mangin B, Chardon F, Charcosset A, Joets J (2004) BioMercator: integrating genetic maps and QTL towards discovery of candidate genes. Bioinformatics 20(14):2321-2326. doi:10.1093/bioinformatics/bth230.
7. Argout X, Fouet O, Wincker P, Gramacho K, Legavre T, Sabau X, Risterucci AM, Da Silva C, Cascardo J, Allegre M, Kuhn D, Verica J, Courtois B, Loor G, Babin R, Sounigo O, Ducamp M, Guiltinan M, Ruiz M, Alemanno L, Machado R, Phillips W, Schnell R, Gilmour M, Rosenquist E, Butler D, Maximova S, Lanaud C (2008) Towards the understanding of the cocoa transcriptome: production and analysis of an exhaustive dataset of ESTs of Theobroma cacao L. generated from various tissues and under various conditions. BMC genomics 9:512.
8. Argout X, Ruiz M, Rouard M, Turnbull C, Lanaud C, Rosenquist E, Courtois B (2006) Cocoagen db: a web portal for crossing cocoa phenotypic, genetic and genomic data from ICGD and Tropgene db database. 15th International Cocoa Research Conference, Oct. 2006, San Jose (Costa Rica).
9. Belsky JM, Seibert S (2003) Cultivating cacao: implications of sun-grown cacao on local food security and environmental sustainability. Agric Human Values 20:277-285. doi:10.1023/A:1026100714149.
10. Borrone JW, Kuhn DN, Schnell RJ (2004) Isolation, characterization, and development of WRKY genes as useful markers in Theobroma cacao. Theor Appl Genet 109:495-507. doi:10.1007/s00122-004-1662-4.
11. Bowers JH, Bailey BA, Hebbar PK, Sanogo S, Lumsden RD (2001) The impact of plant diseases on world chocolate production. Online. Plant Health Prog. doi:10.1094/PHP-2001-0709-01-RV.
12. 2 population using SSR markers and candidate genes. J Am Soc Hortic Sci 130:366-373.
13. Brown JS, Phillips-Mora W, Power EJ, Krol C, Cervantes-Martinez C, Motamayor JC, Schnell RJ (2007) Mapping QTLs for resistance to frosty pod and black pod diseases and horticultural traits in Theobroma cacao. Crop Sci 47:1851-1858. doi:10.2135/cropsci2006.11.0753.
14. Chardon F, Virlon B, Moreau L, Falque M, Joets J, Decousset L, Murigneux A, Charcosset A (2004) Genetic architecture of flowering time in maize as inferred from quantitative trait loci meta-analysis and synteny conservation with the rice genome. Genetics 168:2169-2185. doi:10.1534/genetics.104.032375.
15. Cilas C, Despreaux D (eds) (2004) Improvement of cocoa tree resistance to Phytophthora diseases. Collection repères, CIRAD, pp 171-174.
16. Clément D, Risterucci AM, Motamayor JC, N'Goran J, Lanaud C (2003a) Mapping QTLs for yield components, vigor and resistance to Phytophthora palmivora in Theobroma cacao L. Genome 46:204-212. doi:10.1139/g02-125.
17. Clément D, Risterucci AM, Motamayor JC, N'Goran J, Lanaud C (2003b) Mapping quantitative trait loci for bean traits and ovule number in Theobroma cacao L. Genome 46:103-111. doi:10.1139/g02-118.
18. Crouzillat D, Lercetau E, Pétiard V, Morera J, Rodríguez H, Walker D, Phillips W, Ronning C, Schnell R, Osei J, Fritz P (1996) Theobroma cacao L: a genetic linkage map and quantitative trait loci analysis. Theor Appl Genet 93:205-214.
19. Crouzillat D, Ménard B, Mora A, Phillips W, Pétiard V (2000a) Quantitative trait loci analysis in Theobroma cacao L. using molecular markers. Euphytica 114:13-23. doi:10.1023/A:1003892217582.
20. Crouzillat D, Phillips W, Fritz PJ, Pétiard V (2000b) 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. doi:10.1023/A:1003994212394.
21. Crouzillat D, Rigoreau M, Cabigliera M, Alvarez M, Bucheli P, Pétiard V (2003) QTL studies carried out for agronomic, technological and quality traits of cacao in Ecuador. 14th International Cocoa Conference, 13-18 October, Accra, Ghana: Cocoa Producers, Alliance.
22. Darvasi A, Soller M (1997) A simple method to calculate resolving power and confidence interval of QTL map location. Behav Genet 27:125-132. doi:10.1023/A:1025685324830.
23. Djiekpor EK, Goka K, Lucas P, Partiot M (1981) Brown rot of cocoa pod due to Phytophthora species in Togo, evaluation and control strategy. Cafe, Cacao, The (Paris) 25:263-268.
24. Etzel C, Guerra R (2003) Meta-analysis of genetic-linkage of quantitative trait loci. Am J Hum Genet 71:56-65. doi:10.1086/341126.
25. Evans HC (2002) Invasive neotripical pathogens of tree crops. Vol 2 micromycetes. In: Watling R, Frankland J, Ainsworth M, Isaac S, Robinson C (eds) Tropical mycology. CABI Publishing, Wallingford, pp 83-112.
26. Evans HC (2007) Cacao diseases-the trilogy revisited. Phytopathology 97:1640-1643. doi:10.1094/PHYTO-97-12-1640.
27. Faleiro FG, Queiroz VT, Lopes UV, Guimarães CT, Pires JL, Yamada MM, Araújo IS, Pereira MG, Souza Filho GA, Brown JS, Schnell R, Ferreira CF, Barros EG, Moreira MA (2006) Mapeamento genético molecular do cacaueiro (Theobroma cacao L.) e QTLs associados à resistência à vassoura-de-bruxa. Euphytica 149:227-235. doi:10.1007/s10681-005-9070-7.
28. Figueira A, Paulo S, Albuquerque B, Gildemberg A Leal Jr (2006) Genetic mapping and differential gene expression of Brazilian alternative resistance sources to witches' broom (causal agent Crinipellis perniciosa). 15th International Cocoa Research Conference, October. 2006, San Jose, Costa Rica: Cocoa Producers, Alliance (in Press).
29. Flament MH (1998) Cartographie génétique de facteurs impliqués dans la résistance du cacaoyer (Theobroma cacao L.). à. Phytophthora megakarya et à Phytophthora palmivora.Thèse de doctorat soutenue le 21 décembre 1998. ENSAM- ED biologie intégrative, Montpellier.
30. Flament MH, Kébé I, Clément D, Pieretti I, Risterucci AM, N'Goran JAK, Cilas C, Despéux D, Lanaud C (2000) Genetic mapping of resistance factors to Phytophthora palmivora in cocoa. Genome 44:79-85. doi:10.1139/gen-44-1-79.
31. Fulton RH (1989) The cacao disease trilogy: black pod, monilia pod rot and witches' broom. Plant Dis 73:601-603. doi:10.1094/PD-73-0601.
32. Goffinet B, Gerber S (2000) Quantitative trait loci: a meta-analysis. Genetics 155:463-473.
33. Guiltinan MJ, Verica J, Zhang D, Figueira A (2008) Genomics of Theobroma cacao, 'the food of the gods'. In: Moore PH, Ming R (eds) Genomics of tropical crop plants. Springer-Verlag, Berlin, Heidelberg, pp 145-170.
34. Guo B, Sleper DA, Lu P, Shannon JG, Nguyen HT, Arelli PR (2006) QTLs associated with resistance to soybean cyst nematode in soybean: meta-analysis of QTL locations. Crop Sci 46:595-602. doi:10.2135/cropsci2005.04-0036-2.
35. Iwaro AD, Butler DR, Eskes AB (2006) Sources of resistance to Phytophthora pod rot at the International Cocoa Genebank, Trinidad. Genet Resour Crop Evol 53:99-109. doi:10.1007/s10722-004-1411-1.
36. Jansen RC (1996) Complex plant traits: time for polygenic analysis. Trends Plant Sci 1:89-94. doi:10.1016/S1360-1385(96)80040-9.
37. Keane PJ (1992) Diseases and pests of cocoa: an overview. Cocoa pest and disease management in Southeast Asia and Australisia. FAO Plant Prot Prot Pap 112:1-12.
38. Kearsey M, Farquhar A (1998) QTL analysis in plants; where are we now? Heredity 80:137-142. doi:10.1046/j.1365-2540.1998.00500.x.
39. 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. doi:10.1007/s00122-003-1239-7.
40. Lanaud C, Kébé I, Risterucci AM, Clément D, N'Goran JKA, Grivet L, Tahi M, Cilas C, Pieretti I, Eskes A, Despréaux D (1999) Mapping quantitative trait loci (QTL) for resistance to Phytophthora palmivora in T. cacao L. 12th International Cocoa Research Conference, November 17-23. 99-105. Salvador, Bahía, Brazil: Cocoa Producers, Alliance.
41. Lanaud C, Boult E, Clapperton J, N'Goran JKA, Cros E, Chapelin M, Clément D, Petithugenin P (2003) Identification of QTLs related to fat content, seed size and sensorial traits in Theobroma cacao L. 14th International Cocoa Conference, 13-18 October, Accra, Ghana: Cocoa Producers, Alliance.
42. Lanaud C, Clément D, Flament MH, Risterucci AM, Kebe I, Nyasse S, Sounigo O, Motilal L, Thévenin JM, Paulin D, Ducamp M, N'Goran J, Fargeas D, Cilas C (2004a) Genetic mapping of quantitative trait loci for black pod resistance in cocoa. In: Cilas C, Despreaux D (eds) Improvement of cocoa tree resistance to Phytophthora diseases. Collection repères, Cirad, pp 147-164.
43. Lanaud C, Paulin D, Clément D, Ducamp M, Fouet O, Vezian-Bonnemayre K, Efron Y, Risterucci AM (2004b) Bulk segregant analyses of (17-3/1 × 36-3/1) progeny for resistance to Phytophthora- preliminary results. INGENIC meeting Univ, Reading.
44. Lanaud C, Risterucci AM, Pieretti I, N'Goran JAK, Fargeas D (2004c) Characterisation and genetic mapping of resistance and defence gene analogs in cocoa (Theobroma cacao L.). Mol Breed 13:211-227. doi:10.1023/B:MOLB.0000022515.23880.1b.
45. Lefebvre V, Palloix A (1996) Both epistatic and additive effects of QTLs are involved in polygenic induced resistance to disease: a case study, the interaction pepper-Phytophthora capsici Leonian. Theor Appl Genet 93:503-511. doi:10.1007/BF00417941.
46. Leonards-Schippers C, Gieffers W, Schiifer-Pregl R, Ritter E, Knapp SJ, Salamini F, Gebhardt C (1994) Quantitative resistance to Phytophthora infestans in potato. A case study for QTL Mapping in an allogamous plant species. Genetics 137:67-77.
47. Lohmueller KE, Pearce CL, Pike M, Lander ES, Hirschhorn JN (2003) Meta-analysis of genetic association studies supports a contribution of common variants to susceptibility to common disease. Nat Genet 33:177-182. doi:10.1038/ng1071.
48. Marcano M, Morales S, Hoyer MT, Courtois B, Risterucci AM, Fouet O, Pugh T, Cros E, Gonzalez V, Dagert M, Lanaud C (2009) A genomewide admixture mapping study for yield factors and morphological traits in a cultivated cocoa (Theobroma cacao L.) population. TGG 5:329-337.
49. Marcano M, Pugh T, Cros E, Morales S, Portillo Páez E, Courtois B, Glaszmann J, Engels M, Phillips W, Astorga C, Risterucci AM, Fouet O, González V, Rosenberg K, Vallat I, Dagert M, Lanaud C (2007) Adding value to coca Theobroma cacao L germplasm information with domestication history and admixture mapping. Theor Appl Genet 114:877-884. doi:10.1007/s00122-006-0486-9.
50. Morais RC (2005) The genomes of cacao. In: Forbes (March 14) 110-112.
51. Motilal LA, Sounigo O, Thévenin JM, Risterucci AM, Pierretti I, Noyer JL, Lanaud C (2000) Theobroma cacao L; genome map and QTLs for Phytophthora palmivora resistance. 13th International Cocoa Research Conference, 9-14 October 2000. 111-117. Kota Kinabalu, Malaysia: Cocoa Producers, Alliance.
52. N'Goran JAK, Risterucci AM, Clément D, Sounigo O, Lorieux M, Lanaud C (2000) Identification of quantitative trait loci (QTL) in Theobroma cacao L. Agron Afr 9:55-63.
53. Paim VRLM, Luz EDMN, Pires JL, Silva SDVM, de Souza JT, Albuquerque PSB, Filho LPS (2006) Sources of resistance to Crinipellis perniciosa in progenies of cacao accessions collected in the Brazilian Amazon. Sci Agric (Piracicaba Braz) 63(6):572-578.
54. Phillips-Mora W, Wilkinson MJ (2007) Frosty pod of cacao: a disease with a limited geographic range but unlimited potential of damage. Phytopathology 97:1644-1647. doi:10.1094/PHYTO-97-12-1644.
55. Ploetz RC (2007) Cacao diseases: important threats to chocolate production worldwide. Phytopathology 97:1634-1639. doi:10.1094/PHYTO-97-12-1634.
56. Pugh T (2005) Etude du déséquilibre de liaison chez le cacaoyer appartenant aux groupes Criollo/Trinitario. Application au marquage génétique d'intérêt pour la sélection. Thèse Doctorat Ecole National Supérieur de Agriculture, Montpellier, France, p 107.
57. Pugh T, Fouet O, Risterucci AM, Brottier P, Deletrez C (2004) A new codominant markers based cocoa linkage map: development and integration of 201 new microsatellites markers. Theor Appl Genet 108:1151-1161. doi:10.1007/s00122-003-1533-4.
58. Queiroz VT, Guimaraes 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. doi:10.1046/j.1439-0523.2003.00809.x.
59. 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 108:168-174. doi:10.1007/s00122-003-1408-8.
60. Rong J, Feltus FA, Waghmare VN, Pierce GJ, Chee PW, Draye X, Saranga Y, Wright RJ, Wilkins TA, May OL, Smith CW, Gannaway JR, Wendel JF, Paterson AH (2007) Meta-analysis of polyploid cotton QTL shows unequal contributions of subgenomes to a complex network of genes and gene clusters implicated in lint fiber development. Genetics 76(4):2577-2588. doi:10.1534/genetics.107.074518.
61. Ruiz M, Rouard M, Turnbull CJ, Orain R, Ford C, Raboin LM, Lartaud M, Lanaud C, Clément D, Petithuguenin P, Wilkinson MD, Hadley P, Brown S, Rosenquist E, Courtois B (2003) A new international cocoa genetic database. 14th International Cocoa Conference, 13-18 October, Accra, Ghana: Cocoa Producers, Alliance.
62. Schnell RJ, Olano CT, Brown JS, Meerow AW, Cervantes-Martínez C (2005) Retrospective determination of the parental population of superior cacao (Theobroma cacao L) seedlings and association of microsatellite alleles with productivity. J Am Soc Hortic Sci 130(2):181-190.
63. Stam P (1993) Construction of integrated genetic linkage maps by means of a new computer package: joinmap. Plant J 3:739-744.
64. Surujdeo-Maharaj S (2008) Studies on the mechanisms of resistance in Theobroma cacao L. to witches' broom disease caused by Crinipellis perniciosa PhD Thesis, The University of The West Indies, St. Augustine, Trinidad and Tobago.
65. Thabuis A, Palloix A, Pflieger S, Daubeze AM, Caranta C, Lefebvre V (2003) Comparative mapping of Phytophthora resistance loci in pepper germplasm: evidence for conserved resistance loci across Solanaceae and for a large genetic diversity. Theor Appl Genet 106:1473-1485.
66. van Ooijen JW (2004) MapQTL V5, Software for the mapping of quantitative trait loci in experimental populations. Kyazma BV, Wageningen, Netherlands.
67. van Ooijen JW (2006) JoinMAP V4, software for the calculation of genetic maps in experimental populations. Kyazma BV, Wageningen, Netherlands.