Abstract
A sample of 94 accessions of Theobroma cacao L. (cacao), representing four populations from the Brazilian Amazon (Acre, Rondônia, lower Amazon and upper Amazon) were analyzed using microsatellite markers to assess the genetic diversity and the natural population structure. From the 19 microsatellite loci tested, 11 amplified scorable products, revealing a total of 49 alleles, including two monomorphic loci. The Brazilian upper Amazon population contained the largest genetic diversity, with the most polymorphic loci, the highest observed heterozygosity; and the majority of rare alleles, thereby this region might be considered part of the center of diversity of the species. The observed heterozygosity for all the Brazilian populations (Ho = 0.347) was comparable with values reported for other similar upper Amazon Forastero cacao populations, with the Acre and Rondônia displaying the lowest values. The lower Amazon population, traditionally defined as highly homozygous, presented an unexpectedly high observed heterozygosity (Ho = 0.372), disclosing rare and distinct alleles, with large identity with the upper Amazon population. It was hypothesized that part of the lower Amazon population might derive from successive natural or intentional introduction of planting material from other provenances, mainly upper Amazon. Most of the loci exhibited a lower observed heterozygosity than expected, suggesting that self-pollination might be more common than usually assumed in cacao, but excess of homozygotes might also derive from sub-grouping (Wahlund effect) or from sampling related individuals. Most of the gene diversity was found to occur within groups, with small differentiation between the four Brazilian Amazon populations, typical of species with high gene flow.
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Abbreviations
- AFLP:
-
amplified fragment length polymorphism
- bp:
-
base pairs
- CAB:
-
Cacao Amazon Brazil
- cDNA:
-
complementary DNA
- CIRAD:
-
“Centre de Cooperation Internationale en Recherche Agronomique pour le Developpement”
- CTAB:
-
hexadecytrimethyl ammonium bromide
- dNTPs:
-
deoxyribonucleotides
- EDTA:
-
ethylenediaminetetraacetic acid
- ERJOH:
-
“Estação de Recursos Genéticos do Cacau José Haroldo”
- RAPD:
-
random amplified polymorphic DNA
- rDNA:
-
ribosomal DNA
- RFLP:
-
restriction fragment length polymorphism
References
Allen JB (1987) London Cocoa Trade Amazon Project. Final Report Phase 2. Cocoa Growers’ Bul. 39, 94 pp. Cadbury Limited, Birmingham, UK.
CMVC Almeida CFG Almeida (1987) ArticleTitleColeta de cacau silvestre no estado de Rondônia Rev. Theobroma 17 IssueID2 65–92
Almeida CMVC, Barriga JP, Machado PFR, Bartley BGD (1987) Evolução do programa de conservação dos recursos genéticos de cacau na Amazônia Brasileira. Boletim Técnico no. 5. Ministério da Agricultura. Comissão Executiva do Plano da Lavoura Cacaueira, Belém, Pará.
Almeida CMVC, Machado PFR, Barriga JP, Silva FCO (1995) Coleta de cacau (Theobroma cacao L.) da Amazônia brasileira: uma abordagem histórica e analítica. Ministério de Agricultura e Reforma Agrária. Comissão Executiva do Plano da Lavoura Cacaueira, 92 pp. Belém, Para, Brasil.
WS Alverson BA Whitlock R Nyffeler C Bayer DA Baum (1999) ArticleTitlePhylogeny of the core Malvales: evidence from ndhF sequence data Am J Bot. 86 1474–1486 Occurrence Handle1:CAS:528:DyaK1MXntlaku7c%3D Occurrence Handle10523287
Baker RED, Cope FW, Holliday PC, Bartley BGD, Taylor J (1953) The Anglo-Colombian cacao collecting expedition. Report Cacao Research. St. Augustine, Trinidad. In: Reprint Archives of Cocoa Research (Ed. Toxopeus H), vol. 1, pp. 127–154. American Cocoa Research Institute, USA.
J Barrau (1979) ArticleTitleSur l’origine du cacaoyer, Theobroma cacao Linne, Sterculiacées. J. d’Agr. Trad. Bot. Appl. 26 IssueID3–4 171–180
Bartley BGD, Machado PFR, Ahnert D, Barriga JP, Almeida CMVC (1987). Descrição de populações de cacau da Amazônia brasileira. I- Observações preliminares sobre populações de Alenquer, Pará. In: 10th International Cocoa Research Conference, Santo Domingo, Dominican Republic, pp. 665–672. Cocoa Producers’ Alliance, Lagos, Nigeria.
Belkhir K (2001) GENETIX, logiciel sous WindowsTM pour la génétique des populations. Laboratoire Génome et Populations, CNRS UPR 9060, Université de Montpellier II, Montpellier (France).
EE Cheesman (1944) ArticleTitleNotes on the nomenclature, classification and possible relationships of cocoa populations. Trop. Agric. 21 IssueID8 144–159
FW Cope (1962) ArticleTitleThe mechanism of pollen incompatibility in Theobroma cacao Heredity 17 157–182
FW Cope (1976) Cacao, Theobroma cacao NW Simmonds (Eds) Evolution of Crop Plants Longman London 285–289
JJ Doyle JL Doyle (1990) ArticleTitleIsolation of plant DNA from fresh tissue Focus 12 IssueID1 13–15
A Figueira J Janick M Levi P Goldsbrough (1994) ArticleTitleReexamining the classification of Theobroma cacao L. using molecular markers J. Amer. Soc. Hort. Sci. 119 1073–1082 Occurrence Handle1:CAS:528:DyaK2MXhsl2it7c%3D
DR Glendinning (1960) ArticleTitleSelfing of self-incompatible cocoa Nature 187 IssueID4732 170
JL Hamrick M Godt (1990) Allozyme diversity in plant species AHD Brown MT Clegg AL Kahler BS Weir (Eds) Plant Population, Genetics, Breeding and Genetic Resources Sinauer Associates Sunderland 43–63
JL Hamrick MJ Godt SL Sherman-Broyles (1992) ArticleTitleFactors influencing levels of genetic diversity in woody plant species New Forest 6 95–124 Occurrence Handle10.1007/BF00120641
R Knight H Rogers (1955) ArticleTitleIncompatibility in Theobroma cacao Heredity 9 67–69
Lanaud C (1987) Nouvelles donnes sur la biologie du cacaoyer (Theobroma cacao L): diversité des populations, systéme d’incompatibilité, haploides spontanées. Leurs consequence pour l’amelioration genetique de cette espece. D. Sc. Thesis, Université de Paris Sud, Centre d’Orsay, France.
C Lanaud AM Risterucci I Pieretti M Falque A Bouet PJL Lagoda (1999) ArticleTitleIsolation and characterization of microsatellites in Theobroma cacao L Mol. Ecol. 8 2141–2143 Occurrence Handle10.1046/j.1365-294x.1999.00802.x Occurrence Handle1:CAS:528:DC%2BD3cXpvF2lug%3D%3D Occurrence Handle10632866
C Lanaud O Sounigo YK Amefia D Paulin P Lachenaud D Clement (1987) ArticleTitleNouvelles données sur la fonctionement du systéme d’incompatibilité du cacaoyer et ses consequences pour la selection Café Cacao Thé 31 IssueID4 267–277
V Laurent AM Risterucci C Lanaud (1993) ArticleTitleVariability for nuclear ribosomal genes within Theobroma cacao Heredity 71 96–103 Occurrence Handle1:CAS:528:DyaK3sXlvF2ksr8%3D
V Laurent AM Risterucci C Lanaud (1994) ArticleTitleGenetic diversity in cocoa revealed by cDNA probes Theor. Appl. Genet. 88 193–198 Occurrence Handle10.1007/BF00225897 Occurrence Handle1:CAS:528:DyaK2cXmvFOgsrY%3D
E Lerceteau T Robert V Pétiard D Crouzillat (1997) ArticleTitleEvaluation of the extent of genetic variability among Theobroma cacao accessions using RAPD and RFLP markers Theor. Appl. Genet. 95 10–19 Occurrence Handle10.1007/s001220050527 Occurrence Handle1:CAS:528:DyaK2sXlvVakt7k%3D
JM Marita J Nienhuis JL Pires WM Aitken (2001) ArticleTitleAnalysis of genetic diversity in Theobroma cacao with emphasis on witches’ broom disease resistance Crop Sci. 41 1305–1316
KF Martius Particlevon (1930) ArticleTitleSur le cacao et les espéces du genre Theobroma Rev. Bot. Appl. D’agric trop. 110 184–192
JC Motamayor AM Risterucci PA Lopez CF Ortiz A Moreno C Lanaud (2002) ArticleTitleCacao domestication I: the origin of the cacao cultivated by the Mayas Heredity 89 308–386 Occurrence Handle10.1038/sj.hdy.6800156
M Nei (1972) ArticleTitleGenetic distance between populations Am. Nat. 106 283–292 Occurrence Handle10.1086/282771
M Nei (1973) ArticleTitleAnalysis of gene diversity in subdivided populations Proc. Natl. Acad. Sci. USA 70 3321–3323 Occurrence Handle1:STN:280:CSuD2MrkvVM%3D Occurrence Handle4519626
M Nei (1987) Molecular Evolutionary Genetics Columbia University Press New York 190
M Nei RK Chesser (1983) ArticleTitleEstimation of fixation indexes and gene diversities Ann. Hum. Genet. 47 253–259 Occurrence Handle6614868
JAK N’Goran V Laurent AM Risterucci C Lanaud (1994) ArticleTitleComparative genetic diversity studies of Theobroma cacao L. using RFLP and RAPD markers Heredity 73 589–597
JAK N’Goran V Laurent AM Risterucci C Lanaud (2000) ArticleTitleThe genetic structure of cocoa populations (Theobroma cacao L.) revealed by RFLP analysis Euphytica 115 83–90 Occurrence Handle1:CAS:528:DC%2BD3cXntFOjsLo%3D
Pires JL, Luz EDMN, Lopes UV, Bartley BGD (1994) Incidência natural de podridão parda em clones de cacaueiro na Bahia, Brasil. In: Proc. of the 11th International Cocoa Research Conference, Yamoussoukro, Cote d‘Ivoire, pp. 871–877. Cocoa Producers’ Alliance, Lagos, Nigeria.
JL Pires JCM Cascardo SV Lambert A Figueira (1998) ArticleTitleIncreasing cocoa butter yield through genetic improvement of Theobroma cacao L: seed fat content variability, inheritance, and association with seed yield Euphytica 103 115–121 Occurrence Handle10.1023/A:1018327411530
Pires JL, Monteiro WR, Luz EDMN, Silva SDVN, Pinto LRM, Figueira A (1999) Cocoa breeding for witches’ broom resistance at CEPEC, Bahia, Brazil. In: Proc. 2nd INGENIC International Workshop on Cacao Genetics, pp. 91–101. Salvador, Bahia, Brazil, November 24th–26th 1996.
FJ Pound (1943) Cacao and witches’ broom disease (Marasmius pernicious) H Toxopeus (Eds) Reprint Archives of Cocoa Research. American Cocoa Research Institute USA 73–92
LH Purdy RA Smith (1996) ArticleTitleStatus of cacao witches’ broom: biology, epidemiology, and management Annu. Rev. Phytopathol. 34 573–594 Occurrence Handle10.1146/annurev.phyto.34.1.573 Occurrence Handle1:CAS:528:DyaK28XlsFOhsbs%3D Occurrence Handle15012557
J Soria (1970) ArticleTitleThe latest cocoa expeditions to the Amazon basin Cacao 15 5–15
AM Risterucci L Grivet JAK N’Goran L Pieretti MH Flament C Lanaud (2000) ArticleTitleA high-density linkage map of Theobroma cacao L Theor. Appl. Genet. 101 948–955 Occurrence Handle10.1007/s001220051566 Occurrence Handle1:CAS:528:DC%2BD3cXosFygsrk%3D
CM Ronning RJ Schnell (1994) ArticleTitleAllozyme diversity in a germplasm collection of Theobroma cacao L J. Hered. 85 291–295
H Toxopeus (1987) Botany, types and populations GAR Wood RA Lass (Eds) Cocoa Longman London 11–37
JM Warren (1994) ArticleTitleIsozyme variation in a number of populations of Theobroma cacao L obtained through various sampling regimes Euphytica 72 121–126 Occurrence Handle10.1007/BF00023780
BS Weir CC Cockerham (1984) ArticleTitleEstimating F-statistics for the analysis of population structure Evolution 38 1358–1370
R Whitkus M Cruz Particlede la L Mota-Bravo A Gómez-Pompa (1998) ArticleTitleGenetic diversity and relationships of cacao (Theobroma cacao L.) in southern Mexico Theor. Appl. Genet. 96 621–627 Occurrence Handle10.1007/s001220050780
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Sereno, M.L., Albuquerque, P.S.B., Vencovsky, R. et al. Genetic Diversity and Natural Population Structure of Cacao (Theobroma cacao L.) from the Brazilian Amazon Evaluated by Microsatellite Markers. Conserv Genet 7, 13–24 (2006). https://doi.org/10.1007/s10592-005-7568-0
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DOI: https://doi.org/10.1007/s10592-005-7568-0