Browsing by Author "Elizabeth S. Johnson"

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    Field Guide efficacy in the identification of reallocated clonally propagated accessions of cacao
    (Springer Science+Business Media B.V., 2007) Elizabeth S. Johnson; Antonio Mora; Raymond J. Schnell
    Misidentification is a major constraint to the conservation and utilization of cacao genetic resources. One solution for rapid and accurate identification is to produce a Field Guide for each recognized cacao early generation original population. Each Field Guide in this series of compendia would be comprised of pod digital images with complementary morphological descriptors, molecular fingerprint data with kinship analyses and agronomic data useful to cacao cultivar development. This Field Guide Concept culminated in the production of the first compendium entitled, Field Guide to the ICS Clones of Trinidad. In the current study, this Field Guide was used to verify the identity of 69 trees representing a possible 15 ICS clone genotypes introduced nearly 50 years ago to Costa Rica. Phase one of this study involved identity verification of the trees in Costa Rica using the pod digital image and morphological descriptor data in the Field Guide to the ICS Clones of Trinidad. The error rate was 3.5% for misidentification in the field in Costa Rica. In the second and final phase, SSR fingerprint data were generated for each of the 69 trees and analyzed for verification to the original ICS genotype in the Field Guide. Misidentification was reduced to 0% with the addition of SSR fingerprint analyses. The 69 trees in this study clustered into two groups or sub-populations clearly differentiated by Discriminant analyses with six SSR primers. A 46% cost reduction in SSR fingerprinting of the ICS clones was realized by combining use of the pod image and morphological descriptor data in the Field Guide with genetic diversity estimates derived from these six primers. A Field Guide approach to the identification of reference genotypes for cacao germplasm is discussed.
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    Molecular characterization of an international cacao collection using microsatellite markers
    (2009) Elizabeth S. Johnson; Dapeng Zhang; Sue Mischke; Lyndel Meinhardt; Wilbert Phillips-Mora
    Plant 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 collection
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    Population Structure and Genetic Diversity of the Trinitario Cacao (Theobroma cacao L.) from Trinidad and Tobago
    (2009) Qijian Song; Elizabeth S. Johnson; Frances L. Bekele; Steven J. Brown; Raymond J. Schnell; Lyndel W. Meinhardt; Dapeng Zhang
    Population structure of the old Trinitario cacao (Theobroma cacao L.) in Trinidad was evaluated from the 35-microsatellite multilocus profi le of 32 relict clones from abandoned cocoa estates in Trinidad (TRD) and 88 Imperial College selections (ICS) clones conserved in the International Cocoa Genebank, Trinidad. Ancestry was derived by comparison to 34 representative genotypes of Criollo, Central American, and Lower and Upper Amazon origin. The 154 individuals separated into four populations in this study, labeled Population 1—Upper Amazon; Population 2—Ecuadorian; Population 3—Lower Amazon; and Population 4—Trinitario. Over 90% of the individuals demonstrated 70 to 99% membership to their respective populations. The ICS and TRD clones formed a genetically homogenous group, 84% of which clustered in Population 4 with clones of pure Criollo descent. Another 10% clustered in Population 1 containing clones of Upper Amazon descent. The cacao population of Trinidad is genetically different from clones of Ecuadorian and Lower Amazon descent, Populations 2 and 3, respectively. The 10 most discriminating loci for each population were different as shown by polymorphism information content values for each of the 35 microsatellite loci. This is the fi rst report to provide a strong genetic basis for the industry fl avor distinction of Trinitario and Ecuadorian cacaos. These fi ndings signifi cantly impact germplasm fi ngerprinting and curatorship and maintenance of industry fl avor classes while breeding for disease resistance in cacao