Browsing by Author "Dapeng Zhang"

Now showing 1 - 7 of 7
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    Association mapping of seed and disease resistance traits in Theobroma cacao L
    (2016) Lambert A. Motilal; Dapeng Zhang; Sue Mischke; Lyndel W. Meinhardt; Michel Boccara; Olivier Fouet; Claire Lanaud; Pathmanathan Umaharan
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    A computer simulation study on the number of loci and trees required to estimate genetic variability in cacao (Theobroma cacao L.)
    (2006) Cuauhtemoc Cervantes-Martinez; J. Steven Brown; Raymond Schnell; Juan C. Motamayor; Alan W. Meerow; Dapeng Zhang
    Current methods for measures of genetic diversity of populations and germplasm collections are often based on statistics calculated from molecular markers. The objective of this study was to investigate the precision and accuracy of the most common estimators of genetic variability and population structure, as calculated from simple sequence repeat (SSR) marker data from cacao (Theobroma cacao L.). Computer simulated genomes of replicate populations were generated from initial allele frequencies estimated using SSR data from cacao accessions in a collection. The simulated genomes consisted of ten linkage groups of 100 cM in length each. Heterozygosity, gene diversity and the F statistics were studied as a function of number of loci and trees sampled. The results showed that relatively small random samples of trees were needed to achieve consistency in the observed estimations. In contrast, very large random samples of loci per linkage group were required to enable reliable inferences on the whole genome. Precision of estimates was increased by more than 50% with an increase in sample size from one to five loci per linkage group or 50 per genome, and up to 70% with ten loci per linkage group, or equivalently, 100 loci per genome. The use of fewer, highly polymorphic loci to analyze genetic variability led to estimates with substantially smaller variance but with an upward bias. Nevertheless, the relative differences of estimates among populations were generally consistent for the different levels of polymorphism considered.
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    Genomics of Theobroma cacao, "the Food of the Gods"
    (2008) Joseph Verica; Mark J. Guiltinan; Dapeng Zhang; Antonio Figueira
    Theobroma cacao, the chocolate tree. is an important tropical tree-cropthat provides sustainable economic and environmental benefits to some of the poor-est and most ecologically sensitive areas of the world. Recent progress in thedevelopment of genomics tools for cacao is reviewed. These include a referencemolecular genetic map, simple sequence repeats and other molecular markers, twogermplasm databases with microsatellite DNA fingerprints and other moleculardata, many quantitative trait loci mapping projects which have identified disease re-sistance and yield component loci, several expressed sequence tag resources, a cacaomicroarray, bacterial artificial chromosome libraries, and a genetic transformationsystem. The evolutionary relatedness of cacao with other important crops and modelplant systems positions cacao genomics to play a significant role in translationalplant genomics. The future prospects for the contribution of cacao genomics to im-provement of this crop for sustainable cacao production and as a tool for povertyalleviation and environmental stabilization are discussed.
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    Increasing Accuracy and Throughput in Large-Scale Microsatellite Fingerprinting of Cacao Field Germplasm Collections
    (2009) Lambert A. Motilal; Dapeng Zhang; Pathmanathan Umaharan; Sue Mischke; Stephen Pinney; Michel Boccara
    In this study we report on increasing the rate and accuracy of microsatellite fingerprinting of accessions in Theobroma cacao L. field germplasm collections with a medium-throughput capillary sequencing system. We examined the use of a reduced number of microsatellite loci to decrease the time and materials required for fingerprinting and determined the best available microsatellite loci for accurately separating accessions. A subset of nine informative loci that could separate sixty accessions into the same genetic groupings as a complete set of 37 loci was found. Stringent probability of identity values (i.e. chance of unique accession) was highly influenced (r=−0.996; P<0.001) by the number of alleles utilised in the fingerprinting set but the composition of the primer set was more important when choosing discriminatory loci. DNA pooling to reduce the number of samples was also investigated. There was a relatively high level of mixture within plots (59% of 54 plots examined) of the field genebank, which opposed the use of a pooling strategy to fingerprint the multiple trees of an accession plot in the collection
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    Microsatellite variation and population structure in the ‘‘Refractario’’ cacao of Ecuador
    (2008) Dapeng Zhang; Michel Boccara; Lambert Motilal; David R. Butler; Sue Mischke; Lyndel Meinhardt
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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