Molecular characterization of an international cacao collection using microsatellite markers

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dc.contributor.authorElizabeth S. Johnson
dc.contributor.authorDapeng Zhang
dc.contributor.authorSue Mischke
dc.contributor.authorLyndel Meinhardt
dc.contributor.authorWilbert Phillips-Mora
dc.date.accessioned2014-04-16T05:41:16Z
dc.date.available2014-04-16T05:41:16Z
dc.date.issued2009
dc.description.abstractPlant germplasm collections invariably contain varying levels of genetic redundancy, which hinders the efficient conservation and utilization of plant germplasm. Reduction of genetic redundancies is an essential step to improve the accuracy and efficiency of genebank management. The present study targeted the assessment of genetic redundancy and genetic structure in an international cacao (Theobroma cacao L.) collection maintained in Costa Rica. A total of 688 cacao accessions maintained in this collection were genotyped with 15 simple sequence repeat (SSR) loci, using a capillary electrophoresis genotyping system. The SSR markers provided a high resolution among the accessions. Thirty-six synonymously labeled sets, involving 135 accessions were identified based on the matching of multilocus SSR profiles. After the elimination of synonymous sets, the level of redundancy caused by closely related accessions in the collection was assessed using a simulated sampling scheme that compared allelic diversity in different sample sizes. The result of the simulation suggested that a random sample of 113 accessions could capture 90% of the total allelic diversity in this collection. Principal Coordinate Analysis revealed that the Trinitario hybrids from Costa Rica shared a high similarity among groups as well as among individual accessions. The analysis of the genetic structure illustrated that the within-country/within-region difference accounted for 84.6% of the total molecular variation whereas the among-country/among-region difference accounted for 15.4%. The Brazilian germplasm contributed most to this collection in terms of total alleles and private alleles. The intercountry/interregion relationship by cluster analysis largely agreed with the geographical origin of each germplasm group and supported the hypothesis that the Upper Amazon region is the center of diversity for cacao. The results of the present study indicated that the CATIE International Cacao Collection contains a high level of genetic redundancy. It should be possible to rationalize this collection by reducing redundancy and ensuring optimal representation of the genetic diversity from distinct germplasm groups. The results also demonstrated that SSR markers, together with the statistical tools for individual identification and redundancy assessment, are technically practical and sufficiently informative to assist the management of a tropical plant germplasm collectionen_US
dc.identifier.citationTree Genetics & Genomes (2009) 5:1–10en_US
dc.identifier.urihttp://hdl.handle.net/123456789/390
dc.language.isoenen_US
dc.subjectTheobroma cacao L.en_US
dc.subjectCacaoen_US
dc.subjectGenetic diversityen_US
dc.subjectPopulation structureen_US
dc.subjectConservationen_US
dc.subjectSSR molecular markersen_US
dc.subjectGenebanken_US
dc.subjectCATIEen_US
dc.subjectCosta Ricaen_US
dc.titleMolecular characterization of an international cacao collection using microsatellite markersen_US
dc.typeArticleen_US

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