Abstract
A genetic linkage map of Theobroma cacao (cocoa) has been constructed from 131 backcross trees derived from a cross between a single tree of the variety Catongo and an F1 tree from the cross of Catongo by Pound 12. The map comprises 138 markers: 104 RAPD loci, 32 RFLP loci and two morphologic loci. Ten linkage groups were found which cover 1068 centimorgans (cM). Only six (4%) molecular-marker loci show a significant deviation from the expected 1∶1 segregation ratio.The average distance between two adjacent markers is 8.3 cM. The final genome-size estimates based on two-point linkage data ranged from 1078 to 1112 cM for the cocoa genome. This backcross progeny segregates for two apparently single gene loci controlling (1) anthocyanidin synthesis (Anth) in seeds, leaves and flowers and (2) self-compatibility (Autoc). The Anth locus was found to be 25 cM from Autoc and two molecular markers co-segregate with Anth. The genetic linkage map was used to localize QTLs for early flowering, trunk diameter, jorquette height and ovule number in the BC1 generation using both single-point ANOVA and interval mapping. A minimum number of 2–4 QTLs (P<0.01) involved in the genetic expression of the traits studied was detected. Coincident map locations of a QTL for jorquette height and trunk diameter suggests the possibility of pleiotropic effects in cocoa for these traits. The combined estimated effects of the different mapped QTLs explained between 11.2% and 25.8% of the phenotypic variance observed in the BC1 population.
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References
Allen JB (1988) Geographical variation and population biology in wild Theobroma cacao. PhD thesis, University of Edinburgh
Anonymous (1995) Quarterly bulletin of cocoa statistics, 21:29. ICCO, London
Arumuganathan K, Earle ED (1991) Nuclear DNA content of some important plant species. Plant Mol Biol Rep 9:208–219
Beckmann JS, Soller M (1983) Restriction fragment length polymorphisms in genetic improvement: methodologies, mapping and costs. Theor Appl Genet 67:35–43
Bekele FL, Kennedy AJ, McDavid C, Lauckner FB, Bekele I (1994) Numerical taxonomic studies on cacao (Theobroma cacao L.) in Trinidad. Euphytica 75:234–240
Carlson JE, Tulsieram LK, Glaubitz JC, Luk VWK, Kauffeldt C, Rutledge R (1991) Segregation of random amplified DNA markers in F1 progeny of conifers. Theor Appl Genet 83:194–200
Cheesman EE (1944) Notes on the nomenclature, classification and possible relationships of cacao populations. Trop Agric (Trinidad) 21:144–159
Cope FW (1962) The mechanism of pollen incompatibility in Theobroma cacao L. Heredity 17:157–182
Cope FW (1976) Theobroma cacao (Sterculiaceae). In: Simmonds NW (ed) Evolution of crop plants. Longman, London, pp 285–289
Couch J, Zintel HA, Fritz P (1993) The genome of the tropical tree Theobroma cacao L. Mol Gen Genet 237:123–128
Darvasi A, Weinreb A, Minke V, Weller JI, Soller M (1993) Detecting marker-QTL linkage and estimating QTL gene effect and map location using a saturated genetic map. Genetics 134:943–951
Devey ME, Jermstad KD, Tauer CG, Neale DB (1991) Inheritance of RFLP loci in a loblolly pine three-generation pedigree. Theor Appl Genet 83:238–242
Doebley J, Stec A (1993) Inheritance of the morphological differences between maize and teosinte: comparison of results for two F2 populations. Genetics 134:559–570
Doerge RW (1995) The relationship between the LOD score and the analysis of variance F-statistic when detecting QTLs using single markers. Theor Appl Genet 90:980–981
Edwards MD, Stuber CW, Wendel JF (1987) Molecular-marker-facilitated investigations of quantitative trait loci in maize. I. Numbers, genomic distribution and types of gene action. Genetics 116:113–125
Engels JM (1992) The use of botanical descriptors for cocoa characterization: CATIE experiences. In: International workshop on conservation, characterisation and utilisation of cocoa genetic resources in the 21 st century. Port-of-Spain, Trinidad. 13–17th September 1992. The Cocoa research Unit, The University of the West Indies, pp 69–76
Figueira A, Janick J, Goldsbrough P (1992) Genome size and DNA polymorphism in Theobroma cacao. J Am Soc Hort Sci 117:673–677
Figueira A, Janick J, Morris L, Goldsbrough P (1994) Re-examining the classification of Theobroma cacao L. using molecular markers. J Am Soc Hort Sci 119:1073–1082
Glicenstein L, Fritz P (1989) Ploidy level in Theobroma cacao. J Hered 80:464–467
Grattapaglia D, Sederoff RR (1994) Genetic linkage maps of Eucalyptus grandis and E. urophylla using a pseudo-testcross mapping strategy and RAPD markers. Genetics 137:1121–1137
Grattapaglia D, Chaparro J, Wilcox P, McCord S, Werner D, Amerson H, McKeand S, Bridgewater F, Whetten R, O'Malley D, Sederoff R (1992) Mapping in woody plants with RAPD markers: application to breeding in forestry and horticulture. Proc Symp Appl RAPD Technol to Plant Breed, November 1, 1992, Minneapolis, Minnesota, pp 37–40
Hemmat M, Weeden NF, Manganaris AG, Lawson DM (1994) Molecular marker linkage map for apple. J Hered 85:4–11
Hulbert SH, Ilott TW, Legg EJ, Lincoln SE, Lander ES, Michelmore RW (1988) Genetic analysis of the fungus, Bremia lactucae, using restriction fragment length polymorphisms. Genetics 120:947–958
Knight R, Rodgers HH (1955) Incompatibility in Theobroma cacao. Heredity 9:69–77
Kosambi DD (1944) The estimation of map distances from recombination values. Ann Eugen 12:172–175
Kubisiak TL, Nelson CD, Nance WL, Stine M (1995) RAPD linkage mapping in a longleaf pinexslash pine F1 family. Theor Appl Genet 90:1119–1127
Lanaud C (1986) Utilisation des marqueurs enzymatiques pour l'étude génétique du cacaoyer: Theobroma cacao L. II. Etude du polymorphisme de six systèmes enzymatiques. Café Cacao Thé 30:271–276
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 AKJ, Clement D, Flament MH, Laurent V, Falque M (1995) A genetic linkage map of Theobroma cacao L. Theor Appl Genet 91:987–993
Lander ES, Botstein D (1989) Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121:185–199
Lander ES, Green P, Abrahamson J, Barlow A, Daly MJ, Lincoln SE, Newburg L (1987) MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1:174–181
Lange K, Boehnke M (1982) How many polymorphic genes will it take to span the human genome? Am J Hum Genet 34:842–845
Laurent V, Risterucci AM, Lanaud C (1994) Genetic diversity in cocoa revealed by cDNA probes. Theor Appl Genet 88:193–198
Lockwood G (1977) Studies on the effects of cross-incompatibility on the cropping of cocoa in Ghana. J Hort Sci 52:113–126
Lockwood G (1985) Genetic resources of the cocoa plant. Span 28:14–16
Lockwood G, End M (1992) History, technique and future needs for cocoa collecting. In: International workshop on conservation, characterisation and utilisation of cocoa genetic resources in the 21st century. Port-of-Spain, Trinidad, 13–17th September 1992. The Cocoa research Unit, The University of the West Indies, pp 1–14
Morera J, Paredes A, Mora A (1991) Germoplasma de cacao en el CATIE entre 1947 y 1991. In: CATIE/IICA.a II: generacion y transferencia de technologia. San Jose, Costa Rica, pp 49
Munoz JMO (1948) Estudios cromosomicos en el genero Theobroma L. MAg thesis, CATIE/IICA, Turrialba, Costa Rica
Nelson CD, Nance WL, Doudrick RL (1993) A partial genetic linkage map of slash pine (Pinus elliottii Engelm var. elliottii) based on random amplified polymorphic DNAs. Theor Appl Genet 87:145–151
N'goran JAK, Laurent V, Risterucci AM, Lanaud C (1994) Comparative genetic diversity studies of Theobroma cacao L. using RFLP and RAPD markers. Heredity 73:589–597
Paterson AH, De Verna JW, Lanini B, Tanksley SD (1990) Fine mapping of quantitative trait loci using selected overlapping recombinant chromosomes, in an interspecies cross of tomato. Genetics 124:735–742
Paterson AH, Damon S, Hewitt JD, Zamir D, Rabinowitch HD, Lincoln SE, Lander SE, Tanksley SD (1991) Mendelian factors underlying quantitative traits in tomato: comparison across species, generations, and environments. Genetics 127:181–197
Penner GA, Bush A, Wise R, Kim W, Domier L, Kasha K, Laroche A, Scoles G, Molnar SL, Fedak G (1993) Reproducibility of random amplified DNA, RAPD analysis among laboratories. PCR Methods Applic 2:341–345
Rajapakse S, Belthoff LE, He G, Estager AE, Scorza R, Verde I, Ballard RE, Baird WV, Callahan A, Monet R, Abbot AG (1995) Genetic linkage mapping in peach using morphological, RFLP and RAPD markers. Theor Appl Genet 90:503–510
Ronning CM, Schnell RJ (1994) Allozyme diversity in a collection of Theobroma cacao L. J Hered 85:291–295
Ronning CM, Schnell RJ, Kuhn DN (1995) Inheritance of random amplified polymorphic DNA (RAPD) markers in Theobroma cacao L. J Am Soc Hort Sci 120:681–686
Russel JR, Hosein F, Johnson E, Waugh R, Powell W (1993) Genetic differentiation of cocoa (Theobroma cacao L.) populations revealed by RAPD analysis. Mol Ecol 2:89–97
Snyder T (1994) Isolation and characterization of a genomic chitinase clone from Theobroma cacao. PhD thesis, The Pennsylvania State University
Spencer ME, Hodge R (1991) Cloning and sequencing of the cDNA encoding the major albumin of Theobroma cacao. Identification of the protein as a member of the Kunitz protease inhibitor family. Planta 183:528–535
Stuber CW, Lincoln SE, Wolff DW, Helentjaris T, Lander ES (1992) Identification of genetic factors contributing to heterosis in a hybrid from two elite maize inbred lines using molecular markers. Genetics 132:823–839
Suiter K, Wendel JF, Case JS (1983) Linkage-1 a Pascal computer program for the detection and analysis of genetic linkage. J Hered 74:203–204
Tanksley SD, Ganal MW, Prince JP, de Vincente MC, Bonierbale MW, Broun P, Fulton TM, Giovanonni JJ, Grandillo S, Martin GB, Messeguer R, Miller JC, Miller L, Paterson AH, Pineda O, Röder MS, Wing RA, Wu W, Young ND (1992) High-density molecular-linkage maps of the tomato and potato genomes: biological inferences and pratical applications. Genetics 132:1141–1160
Tai H, McHenry L, Fritz P, Furtek D (1991) Nucleic-acid sequence of a 21 -kDa cocoa seed protein gene with homology to the soybean trypsin inhibitor (Kunitz) family of protease inhibitors. Plant Mol Biol 16:913–915
Tulsieram LK, Glaubitz JC, Kiss G, Carlson JE (1992) Single-tree genetic linkage analysis in conifers using haploid DNA from megagametophytes. Bio/Technol 10:686–690
Warren J (1994) Isozyme variation in a number of populations of Theobroma cacao L. obtained through various sampling regimes. Euphytica 72:121–126
Warren J, Misir S, Kalai (1995) Isozyme markers for self-compatibility and yield in Theobroma cacao (cacao). Heredity 74:354–356
Williams J, Kubelik A, Livak K, Rafalski J, Tingey S (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res 18:6531–6535
Wood G, Lass R (1985) Cocoa, 4th edn, Longman Scientific and Technical, Essex, England
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Communicated by J. W. Snape
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Crouzillat, D., Lerceteau, E., Petiard, V. et al. Theobroma cacao L.: a genetic linkage map and quantitative trait loci analysis. Theoret. Appl. Genetics 93, 205–214 (1996). https://doi.org/10.1007/BF00225747
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DOI: https://doi.org/10.1007/BF00225747