Browsing by Author "Sue Mischke"

Now showing 1 - 5 of 5
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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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    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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    The relic Criollo cacao in Belize - genetic diversity and relationship with Trinitario and other cacao clones held in the International Cocoa Genebank, Trinidad
    (2010) Lambert A. Motilal; Oapeng Zhang; Pathmanathan Umaharan; Sue Mischke; Vishnarayan Mooleedhar; Lyndel W. Meinhardt