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Genetic diversity assessment of sub-samples of cacao, Theobroma cacao L., collections in West Africa using simple sequence repeat markers

Peter O Aikpokpodion, Juan C Motamayor, Victor O Adetimirin, Yaw Adu-Ampomah, Ivan Ingelbrecht, Albertus B Eskes, Raymond J Schnell and Maria Kolesnikova-Allen (2009) TREE GENETICS & GENOMES. 5(4). p.699-711
abstract
Knowledge of genebank and on-farm genetic diversity, particularly in an introduced crop species, is crucial to the management and utilization of the genetic resources available. Microsatellite markers were used to determine genetic diversity in 574 accessions of cacao, Theobroma cacao L., representing eight groups covering parental populations in West Africa, genebank, and farmers' populations in Nigeria. From the 12 microsatellite markers used, a total of 144 alleles were detected with a mean allelic richness of 4.39 alleles/locus. The largest genetic diversity was found in the Upper Amazon parent population (H (nb) = 0.730), followed by the 1944 Posnette's Introduction (H (nb) = 0.704), and was lowest in the Local parent population (H (nb) = 0.471). Gene diversity was appreciably high in the farmers' populations (H (nb) = 0.563-0.624); however, the effective number of alleles was lower than that found in the genebank's Posnette's population. Fixation index estimates indicated deficiency of heterozygotes in the Upper Amazon and the Local parent populations (F (is) = 0.209 and 0.160, respectively), and excess of heterozygotes in the Trinitario parent population (F (is) = -0.341). The presence of inbreeding in the Local parent populations and substructure (Wahlund effect) in the Upper Amazon were suggested for the deficiency of heterozygotes observed. Non-significant genetic differentiation observed between the genebank's and farmers' populations indicated significant impact of national breeding programs on varieties grown in farmers' plantations. From this study, we showed that appreciable genetic diversity was present in on-farm and field genebank collections of cacao that can be exploited for crop improvement in West Africa. Suggestions for future conservation of on-farm genetic diversity and local landraces are further discussed.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
Gene diversity, Cacao, Allelic diversity, Rarefaction, Hardy-Weinberg equilibrium, POPULATION-STRUCTURE, MICROSATELLITE MARKERS, LINKAGE MAP, COCOA, RFLP, GERMPLASM, ALLELES, NUMBER, TESTS, GHANA
journal title
TREE GENETICS & GENOMES
Tree Genet. Genomes
volume
5
issue
4
pages
699 - 711
Web of Science type
Article
Web of Science id
000269436200013
JCR category
FORESTRY
JCR impact factor
2.018 (2009)
JCR rank
4/46 (2009)
JCR quartile
1 (2009)
ISSN
1614-2942
DOI
10.1007/s11295-009-0221-1
language
English
UGent publication?
no
classification
A1
copyright statement
I have transferred the copyright for this publication to the publisher
id
1982070
handle
http://hdl.handle.net/1854/LU-1982070
date created
2012-01-10 16:25:47
date last changed
2016-12-19 15:39:20
@article{1982070,
  abstract     = {Knowledge of genebank and on-farm genetic diversity, particularly in an introduced crop species, is crucial to the management and utilization of the genetic resources available. Microsatellite markers were used to determine genetic diversity in 574 accessions of cacao, Theobroma cacao L., representing eight groups covering parental populations in West Africa, genebank, and farmers' populations in Nigeria. From the 12 microsatellite markers used, a total of 144 alleles were detected with a mean allelic richness of 4.39 alleles/locus. The largest genetic diversity was found in the Upper Amazon parent population (H (nb) = 0.730), followed by the 1944 Posnette's Introduction (H (nb) = 0.704), and was lowest in the Local parent population (H (nb) = 0.471). Gene diversity was appreciably high in the farmers' populations (H (nb) = 0.563-0.624); however, the effective number of alleles was lower than that found in the genebank's Posnette's population. Fixation index estimates indicated deficiency of heterozygotes in the Upper Amazon and the Local parent populations (F (is) = 0.209 and 0.160, respectively), and excess of heterozygotes in the Trinitario parent population (F (is) = -0.341). The presence of inbreeding in the Local parent populations and substructure (Wahlund effect) in the Upper Amazon were suggested for the deficiency of heterozygotes observed. Non-significant genetic differentiation observed between the genebank's and farmers' populations indicated significant impact of national breeding programs on varieties grown in farmers' plantations. From this study, we showed that appreciable genetic diversity was present in on-farm and field genebank collections of cacao that can be exploited for crop improvement in West Africa. Suggestions for future conservation of on-farm genetic diversity and local landraces are further discussed.},
  author       = {Aikpokpodion, Peter O and Motamayor, Juan C and Adetimirin, Victor O and Adu-Ampomah, Yaw and Ingelbrecht, Ivan and Eskes, Albertus B and Schnell, Raymond J and Kolesnikova-Allen, Maria},
  issn         = {1614-2942},
  journal      = {TREE GENETICS \& GENOMES},
  keyword      = {Gene diversity,Cacao,Allelic diversity,Rarefaction,Hardy-Weinberg equilibrium,POPULATION-STRUCTURE,MICROSATELLITE MARKERS,LINKAGE MAP,COCOA,RFLP,GERMPLASM,ALLELES,NUMBER,TESTS,GHANA},
  language     = {eng},
  number       = {4},
  pages        = {699--711},
  title        = {Genetic diversity assessment of sub-samples of cacao, Theobroma cacao L., collections in West Africa using simple sequence repeat markers},
  url          = {http://dx.doi.org/10.1007/s11295-009-0221-1},
  volume       = {5},
  year         = {2009},
}

Chicago
Aikpokpodion, Peter O, Juan C Motamayor, Victor O Adetimirin, Yaw Adu-Ampomah, Ivan Ingelbrecht, Albertus B Eskes, Raymond J Schnell, and Maria Kolesnikova-Allen. 2009. “Genetic Diversity Assessment of Sub-samples of Cacao, Theobroma Cacao L., Collections in West Africa Using Simple Sequence Repeat Markers.” Tree Genetics & Genomes 5 (4): 699–711.
APA
Aikpokpodion, P. O., Motamayor, J. C., Adetimirin, V. O., Adu-Ampomah, Y., Ingelbrecht, I., Eskes, A. B., Schnell, R. J., et al. (2009). Genetic diversity assessment of sub-samples of cacao, Theobroma cacao L., collections in West Africa using simple sequence repeat markers. TREE GENETICS & GENOMES, 5(4), 699–711.
Vancouver
1.
Aikpokpodion PO, Motamayor JC, Adetimirin VO, Adu-Ampomah Y, Ingelbrecht I, Eskes AB, et al. Genetic diversity assessment of sub-samples of cacao, Theobroma cacao L., collections in West Africa using simple sequence repeat markers. TREE GENETICS & GENOMES. 2009;5(4):699–711.
MLA
Aikpokpodion, Peter O, Juan C Motamayor, Victor O Adetimirin, et al. “Genetic Diversity Assessment of Sub-samples of Cacao, Theobroma Cacao L., Collections in West Africa Using Simple Sequence Repeat Markers.” TREE GENETICS & GENOMES 5.4 (2009): 699–711. Print.