Browsing by Author "Raymond J. Schnell"
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Item Ambiguous genetic relationships among coconut (Cocos nucifera L.) cultivars: the effects of outcrossing, sample source and size, and method of analysis(2010) Margarita Mauro-Herrera; Alan W. Meerow; Lalith Perera; Joanne Russell; Raymond J. Schnell;A prior analysis of eight coconut cultivars with 15 microsatellite (SSR) markers drew unexpected relationships between two of the out-crossing tall cultivars evaluated: ‘Atlantic Tall’ and ‘Panama Tall’. We further investigated the relationships between these eight cultivars by increasing the number of individuals studied (particularly for ‘Atlantic Tall’ and ‘Panama Tall’), by including 28 more molecular markers, and by adding two other cultivars to our analysis. Our results show that five to ten coconut individuals do not represent a dependable sample to withdraw conclusions regarding cultivar/variety relationships, particularly when studying out-crossing genotypes. As suggested in the prior study, a high level of hybridization was observed between the ‘Atlantic Tall’ and ‘Panama Tall’ cultivars. However, at this time we were able to identify distinct groups for each one of these two cultivars. The two clustering methods used (Neighbor Joining, NJ and Unweighted Pair Group Method with Arithmetic mean, UPGMA) produced dendrograms that resolved contrasting cultivar relationships, especially for the ‘Atlantic Tall’ and ‘Panama Tall’ cultivars. We discuss the implications of our results in regard to current scenarios of coconut domestication and future considerations when assessing genetic relationships among different varieties.Item Analysis of genetic diversity and population structure within Florida coconut (Cocos nucifera L.) germplasm using microsatellite DNA, with special emphasis on the Fiji Dwarf cultivar(2003) Alan W. Meerow; Randall J. Wisser; Steven Brown, J.; David N. Kuhn; Raymond J. Schnell; Timothy K. BroschatUsing 15 simple sequence repeat (SSR) microsatellite DNA loci, we analyzed genetic variation within Cocos nucifera germplasm collections at two locations in south Florida, representing eight cultivars. The loci were also used in a parentage analysis of progeny of the ‘Fiji Dwarf’ variety at both locations. A total of 67 alleles were detected, with eight the highest number at any one locus. These loci identified 83 of the 110 individual palms. Gene diversity of the 15 loci ranged from 0.778 to 0.223, with a mean of 0.574. ‘Fiji Dwarf’, ‘Malayan Dwarf’, ‘Green Niño’ and ‘Red Spicata’ cultivars resolve as distinct clusters in a neighbor joining tree using modified Rogers distance, while the tall varieties form two aggregates. The highest gene diversity was found in the tall cultivars (Hˆ = 0.583 cumulatively), and the lowest in the ‘Malayan Dwarf’ (Hˆ = 0.202). After the tall coconuts, the ‘Fiji Dwarf’ was most genetically diverse (Hˆ = 0.436), and had the largest number of unique alleles. Genetic identity is highest among the ‘Malayan Dwarf’ phenotypes, and between the tall varieties. The ‘Red Malayan Dwarf’ is genetically distinct from the ‘Green’ and ‘Yellow Malayan Dwarf’ phenotypes, which cannot be distinguished with the SSR loci used. Off-type ‘Malayan Dwarf’ phenotypes (putative hybrids with talls) can be identified genotypically. Parentage analyses of 30 ‘Fiji Dwarf’ progeny propagated from five adults surrounded by other cultivars estimate that only 20% of the progeny were out-crossed to the other varieties, while 40–46% were possible selfs. This suggests that a seed-production orchard of the variety maintained at reasonable distance from other varieties, will likely yield only ‘Fiji Dwarf’ genotypes. Our data are discussed in the context of hypotheses of coconut dissemination around the world.Item 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. SchnellMisidentification 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.Item 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 ZhangPopulation 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 cacaoItem Ten informative markers developed from WRKY sequences in coconut in coconut (Cocos nucifera)(Blackwell Publishing Ltd, 2006) Margarita Mauro-Herrera; Alan W. Meerow; James W. Borrone; David N. Kuhn; Raymond J. SchnellCoconut ( Cocos nucifera L.) WRKY sequences containing single nucleotide polymorphisms (SNPs) and one microsatellite repeat were used to develop 10 informative markers. These markers were evaluated in 15 genotypes representing six coconut cultivars. SNP-containing alleles were detected by single-strand conformation polymorphism (SSCP) analysis. The number of detected alleles ranged from two to four. Five pairs of loci were in linkage disequilibrium in the test population. These markers are currently being evaluated in more individuals/ cultivars to determine their value in estimating the genetic diversity of this species.