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R.J. Schnell, C.T. Olano, J.S. Brown, A.W. Meerow, C. Cervantes-Martinez, C. Nagai, and J.C. Motamayor

Commercial production of cacao in Hawaii is increasing, and this trend is expected to continue over the next several years. The increased acreages are being planted with seedlings from introduced and uncharacterized cacao populations from at least three initial introductions of cacao into the islands. Productive seedlings have been selected from a planting at Waialua, Oahu. The parents of these selections were believed to be the population at the Hawaii Agriculture Research Center (HARC) at Kunia; however, potential parental populations also exist at Univ. of Hawaii research stations at Waimanalo and Malama Ki. Using microsatellite markers, we analyzed the potential parental populations to identify the parents and determine the genetic background for 99 productive and 50 unproductive seedlings from the Waialua site. Based on 19 polymorphic microsatellite loci the parental population was identified as trees from Waimanalo and not trees from Malama Ki or Kunia. The Kunia and Malama Ki populations were very similar with low allelic diversity (A = 1.92) and low unbiased gene diversity (Hnb) of 0.311 and 0.329, respectively, and were determined to be Trinitario in type. The Waimanalo, productive seedling, and unproductive seedling populations had much higher levels of genetic diversity with Hnb of 0.699, 0.686, and 0.686, respectively, and were determined to be upper Amazon Forastero hybridized with Trinitario in type. An additional 46 microsatellite markers were amplified and analyzed in the Waimanalo parents, productive, and unproductive seedlings for a total of 65 loci. Seventeen loci contained alleles that were significantly associated with productive seedlings as determined by Armitage's trend test. Of these, 13 loci (76.4%) co-located with previously reported quantitative trait loci for productivity traits. These markers may prove useful for marker assisted selection and demonstrate the potential of association genetic studies in perennial tree crops such as cacao.

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Anna L. Hale, J. Creighton Miller Jr., K. Renganayaki, Alan K. Fritz, J.J. Coombs, L.M. Frank, and D.S. Douches

The objective of this study was to differentiate six intraclonal variants of the potato (Solanum tuberosum L.) cultivar Russet Norkotah. One-hundred-twelve AFLP primer combinations producing 3755 bands and 79 microsatellite primers producing over 400 bands failed to identify any reproducible polymorphisms among the intraclonal variants and `Russet Norkotah'. The inability to detect differences between clones underscores the degree of genetic similarity between them, despite differences in phenotypic expression. This inability could be due to the tetraploid nature of the clones and/or to epigenetic differences not detected by the utilized procedures.

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Maria Susana Lopes, Duarte Mendonça, Kristina M. Sefc, Fabíola Sabino Gil, and Artur da Câmara Machado

A collection of 130 olive samples, originating from diverse areas in Europe and corresponding to 67 different cultivars denominations, was genotyped at 14 microsatellite loci. In total, 135 alleles with a mean number of 9.6 alleles per locus were detected. All but 30 accessions showed unique genotypes. Several cases of synonymy listed in the FAO database of olive germplasm could not be confirmed, as different allelic profiles were obtained from putatively synonymous cultivars. The existence of homonyms or mislabeled samples in olive germplasm collections was evidenced by allele differences of up to 60% between samples of the same denomination. An allele-sharing phenogram of the analyzed genotypes revealed several cultivars with high levels of intra-varietal polymorphism, as well as cultivar families consisting of closely related cultivars with similar denominations. Our work shows that the current designations of olive cultivars fall short of describing the genetic variability among economically important plant material. A thorough investigation of the existing variability will prove of major importance for both management and economic production of olive trees.

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Raúl De la Rosa, Angjelina Belaj, Antonio Muñoz-Mérida, Oswaldo Trelles, Inmaculada Ortíz-Martín, Juan José González-Plaza, Victoriano Valpuesta, and Carmen R. Beuzón

visually to detect possible errors in the assignation of alleles. For the eight microsatellite primer pairs giving reproducible and readable peaks, number of alleles, observed (Ho) and expected (He) heterozygosity, polymorphism information content (PIC

Open access

Shanshan Cao, Stephen Stringer, Gunawati Gunawan, Cecilia McGregor, and Patrick J. Conner

molecular markers, simple sequence repeats (SSRs), also known as microsatellites, are characterized by high abundance, codominant inheritance, excellent reproducibility, and amenability to automated scoring with software, making them ideal markers for DNA

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Anne Frary, Hasan Özgür Şığva, Ayfer Tan, Tuncer Taşkın, Abdullah İnal, Sevgi Mutlu, Mehmet Haytaoğlu, and Sami Doğanlar

phylogenetic relationships in east and south Asian melons, Cucumis melo L. based on the analysis of five isozymes Euphytica 125 385 396 Danin-Poleg, Y. Reis, N. Tzuri, G. Katzir, N. 2001 Development and characterization of microsatellite markers in Cucumis

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D. Struss, M. Boritzki, R. Karle, and A.F. Iezzoni

Two rootstocks from the Giessen (GiSelA) series of dwarfing cherry (Prunus sp.) rootstocks, GiSelA (GI) 5 (syn. 148/2) and GI 6 (syn. 148/1), are becoming commercially important and five other Giessen cherry rootstocks are being evaluated for horticultural traits. Since GI 5 and GI 6 are morphologically similar, a DNA fingerprinting project was undertaken to identify molecular markers that could be used by the nursery industry to differentiate these two rootstocks. The project was extended to include six additional Giessen rootstocks of varying pedigrees. Fourteen DNA primer pairs were tested for their ability to differentiate among the eight rootstocks. None of the primer pairs could differentiate all eight rootstock selections; however, three primer pairs could differentiate all but two selections. Two primer pairs, PMS 15 and PceGA59, were identified as the most suitable for high throughput screening of GI 5 and GI 6 due to the simplicity and the size of the base pair differences among the polymorphic fragments. These results demonstrate the utility of molecular markers to differentiate the Giessen cherry rootstocks.

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Zsolt Galli, Gábor Halász, Erzsébet Kiss, László Heszky, and Judit Dobránszki

A collection of 66 commercial apple (Malus ×domestica Borkh.) cultivars was screened with six previously described SSR (Simple Sequence Repeat) markers for molecular identification. In total, 55 polymorphic alleles were detected at the 6 SSR loci (average 9.2 alleles per locus) and the polymorphism information content (PIC) averaged 0.72. Successful differentiation of all apple genotypes except for somatic mutants was accomplished by using only four (CH03g07, CH04e03, CH05d11, and CH05e03) SSR markers. Sport mutants proved to be indistinguishable from each other and their progenitors. The cumulative probability of obtaining an identical SSR profile for two randomly chosen apple genotypes was 1.79 × 10–4, which confirms the high potential of simple sequence repeats (SSRs) for cultivar identification.

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Dror Sharon, Jossi Hillel, Samir Mhameed, Perry B. Cregan, Emanuel Lahav, and Uri Lavi

The detection of association between DNA markers and traits of interest in an outbred population is complicated and requires highly polymorphic markers. A genetic linkage map of avocado (Persea americana Mill.) recently generated consists of simple sequence repeat (SSR) markers as well as DNA fingerprint (DFP) and randomly amplified polymorphic DNA (RAPD) markers. These markers were used to detect putative quantitative trait loci (QTLs) of eight avocado fruit traits. Two statistical methods were used: one-way analysis of variance and interval mapping. Six traits were found to be associated with at least one of the 90 DNA markers. Based on the two statistical approaches, a putative QTL associated with the presence of fibers in the flesh, was found to be located on linkage group 3. This putative QTL was found to be associated with the SSR marker AVA04 having a high significant value (P = 4.4 × 10-8). The haplotype analysis of linkage group 3 showed a putative dominant interaction between the alleles of this locus.

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Claudio Cantini, Amy F. Iezzoni, Warren F. Lamboy, Manuela Boritzki, and Darush Struss

The U.S. Department of Agriculture (USDA), Agricultural Research Service (ARS) tetraploid cherry (Prunus L. sp.) collection at Geneva, N.Y., contains ≈75 accessions of sour cherry (P. cerasus L.), ground cherry (P. fruticosa Pall.), and their hybrids. Accurate and unambiguous identification of these accessions is essential for germplasm preservation and use. Simple sequence repeats (SSRs) are currently the markers of choice for germplasm fingerprinting because they characteristically display high levels of polymorphism. Recently SSR primer pairs from sweet cherry (P. avium L.), sour cherry, and peach [(P. persica L. Batsch (Peach Group)] have been reported. Ten SSR primer pairs were tested on 59 tetraploid cherry accessions to determine if they could differentiate among the accessions. Scorable SSR fragments were produced with all primer-accession combinations. The cherry accessions exhibited high levels of polymorphism with 4 to 16 different putative alleles amplified per primer pair. Most of the putative alleles were rare with frequencies <0.05. Heterozygosity values ranged from 0.679 to 1.00, while gene diversity values ranged from 0.655 to 0.906. The primer pairs differentiated all but two of the 59 cherry accessions. Based upon the ability of the SSR data to differentiate the cherry accessions and the high level of gene diversity, we propose that all the tetraploid cherry accessions in the USDA/ARS collection be fingerprinted to provide a mechanism to verify the identity of the individual accessions. The fingerprinting data are available on the World Wide Web (http://www.ars-grin.gov/gen/cherry.html) so that other curators and scientists working with cherry can verify identities and novel types in their collections and contribute to a global database.