Search Results

You are looking at 41 - 50 of 215 items for :

  • "DNA fingerprint" x
  • Refine by Access: All x
Clear All
Free access

Donglin Zhang, Michael A. Dirr, and Robert A. Price

The correct identification of horticultural taxa becomes more and more important for intellectual property protection and economic reasons. Traditionally, morphological characteristics have been used to differentiate among the horticultural taxa. However, the morphological characteristics may vary with plant age, cultural conditions, and climate. Modern technologies, such as DNA markers, are now employed in the identification of horticultural taxa. Currently, technologies of DNA sequencing (gene sequences) and DNA fingerprinting (RAPD, RFLP, SSR, and AFLP) are available for distinguishing among horticultural taxa. The literature and our personal experience indicate that the application of each technique depends on the taxon and ultimate goal for the research. DNA sequencing of a variety of nuclear or chloroplast encoded genes or intergenic spacers (rbcL, ndhF, matK, ITS) can be applied to distinguish different species. All DNA fingerprinting technologies can be used to classify infraspecies taxa. AFLP (the most modern technique) is the better and more-reliable to identify taxa subordinate to the species, while RAPDs can be employed in clonal or individual identification. Techniques of RFLP and SSR lie between AFLP and RAPD in their effectiveness to delineate taxa. Mechanics, laboratory procedures, and inherent difficulties of each technique will be briefly discussed. Application of the above technologies to the classification of Cephalo taxus will be discussed in concert with the morphological and horticultural characteristics. Future classification and identification of horticultural taxa should combine DNA technology and standard morphological markers.

Free access

Lili Zhou, Frank Kappel, Cheryl Hampson, Paul A. Wiersma, and Guus Bakkeren

Amplified fragment length polymorphisms (AFLPs) were used to analyze the relationships between sweet cherry (Prunus avium L.) cultivars and selections from the breeding program at the Pacific Agri-Food Research Centre in Summerland, Canada. Six pairs of preselected primers were used for the analysis of a total of 67 cultivars and selections. Scoring the absence and presence of 118 polymorphic DNA fragments produced a unique binary code for each cultivar and selection. Two phylogenetic trees were constructed using these 118 polymorphic fragments, one tree for 55 related cultivars and selections from the Summerland breeding program and the other for 23 self-incompatible cultivars of differing origins. The reliability of AFLP DNA fingerprints was confirmed by correlating relationships revealed by AFLP profiles with known genetic relationships of some sweet cherry cultivars and by a blind test for cultivar identification. Results indicate that AFLP analysis is a good technique to evaluate genetic distance and relationships in a sweet cherry breeding population.

Free access

Guenhwa Jung, Dale T. Lindmen, and Dermot P. Coyne

Eight species and 57 selections/cultivars of Penstemon were compared for genetic variability using Random Amplified Polymorphic DNAs (RAPDs). The RAPD technique was used to help understand the genetic relationships in species and cultivars in the genus Penstemon. Ten RAPD primers (from Operon) were screened to identify polymorphisms among these eight species and 57 selections. More than 100 RAPD polymorphic bands were obtained. A principle component analysis was used to study genetic relationships. Variation among species was greater than variation among selections/cultivars within species. RAPD markers distinguished differences between most cultivars tested. DNA fingerprints generated by RAPDs should be useful to distinguish cultivars of Penstemon, as well as to assist in determining genetic relationships between species.

Free access

Nicholi Vorsa, Richard Novy, and Kim Patten

WA State bogs of the cultivar `McFarlin' exhibit highly variable productivity. Yield and various fruiting characteristics were sampled in 14 WA `McFarlin' bogs, representing two growing areas. Significant differences were found for yield, fruit number/area, percent fruit set, flowers/upright, fruit/upright, fruit weight and seed number/fruit. The variable, flowers/upright, accounted for 69% and 75% of the observed variation for yield and fruit number/area, respectively. A multivariate analysis model accounted for 93% of the variation for yield with 3 variables: flowers/upright (69%), fruit weight (20%), and seed number (4%). Principal component analysis identified three `groups' based on fruiting characteristics. DNA fingerprinting suggests, that variability in yield and fruiting characteristics, has a genetic component.

Free access

A. Levi and L.J. Rowland

Fifteen highbush (or highbush hybrid) blueberry cultivars (Vaccinium corymbosum Linnaeus), two rabbiteye blueberry cultivars (V. ashei Reade), and one southern lowbush (V. darrowi Camp) selection from the wild were examined using seventeen 10-base RAPD and seven 15- to 18-base SSR-anchored primers (primers comprised of SSR motifs) in polymerase chain reactions (PCRs). Fifteen RAPD and three SSR markers resulting from these reactions were chosen to construct a DNA fingerprinting table to distinguish among the genotypes included in this study. Similarity values were calculated based on 132 RAPD and 51 SSR bands, and a dendrogram was constructed based on the similarity matrix. The V. ashei cultivars and V. darrowi selection grouped out separately from the V. corymbosum cultivars as expected. However, estimates of relative genetic similarity between genotypes within the V. corymbosum group did not agree well with known pedigree data and, thus, indicated that RAPD and SSR data did not accurately assess the genetic relationships of cultivars within this species.

Free access

Peter Boches, Nahla V. Bassil, and Lisa Rowland

Sixty-nine accessions representing wild and domesticated highbush blueberry (Vaccinium corymbosum L.) germplasm were genotyped using 28 simple sequence repeats (SSRs). A total of 627 alleles was detected and unique fingerprints were generated for all accessions. Suspected duplicate accessions of `Coville' and `Ivanhoe' had DNA fingerprints that were identical to `Coville' and `Ivanhoe', respectively. Genetic similarity measures placed wild and cultivated blueberries in separate groups. Northern highbush blueberries grouped among ancestral clones that were used extensively in blueberry breeding such as `Rubel' and `Stanley'. Southern highbush blueberries formed a separate group from northern highbush blueberries. The microsatellite markers used here show excellent promise for further use in germplasm identification, in genetic studies of wild Vaccinium L. populations, and for constructing linkage maps.

Free access

Lisa J. Rowland, Anik L. Dhanaraj, James J. Polashock, and Rajeev Arora

Expressed sequence tag-polymerase chain reaction (EST-PCR) markers for DNA fingerprinting and mapping in blueberry (Vaccinium sp.) had previously been developed from expressed sequence tags (ESTs) produced from a cDNA library, derived from RNA from floral buds of cold acclimated plants. Because EST-PCR markers are derived from gene coding regions, they are more likely to be conserved across populations and species than markers derived from random regions of DNA, such as randomly amplified polymorphic DNA (RAPD) or amplified fragment length polymorphism (AFLP) markers. In this study, we tested whether many of the EST-PCR primer pairs developed for blueberry are capable of amplifying DNA fragments in other members of the family Ericaceae. In addition, we cloned and sequenced a selection of 13 EST-PCR fragments to determine if they showed homology to the original blueberry cDNA clones from which the EST-PCR primer pairs were derived. Closely related cranberry genotypes (two wild selections of V. oxycoccus L. and two cultivars of V. macrocarpon Aiton, `Early Black' and `Stevens') and more distantly related rhododendron genotypes (one wild selection each of Rhododendron arboreum Marsh, R. maximum L., and R. ponticum L. and three complex species hybrids, `Sonata', `Grumpy Yellow', and `Roseum elegans') were used. Of 26 primer pairs tested in cranberry, 23 (89%) resulted in successful amplification and eight of those (35%) amplified polymorphic fragments among the cranberry genotypes. Of 39 primer pairs tested in rhododendron, 29 (74%) resulted in successful amplification and 21 of those (72%) amplified polymorphic fragments among the rhododendron genotypes. Approximately 50% of the 13 sequenced EST-PCR fragments were found to be homologous to the original blueberry cDNA clones. These markers should be useful for DNA fingerprinting, mapping, and assessing genetic diversity within cranberry and rhododendron species. The markers which are shown to be homologous to the blueberry cDNA clones by DNA sequencing should also be useful for comparative mapping and genetic diversity studies between some genera of the family Ericaceae.

Free access

Riaz Ahmad, Louise Ferguson, and Stephen M. Southwick

A genomic DNA library enriched for dinucleotide (CT)n and (CA)n and trinucleotide (CTT)n microsatellite motifs has been developed from `Kerman' pistachio (Pistacia vera L.). The enrichment method based on magnetic or biotin capture of repetitive sequences from restricted genomic DNA revealed an abundance of simple sequence repeats (SSRs) in the pistachio genome which were used for marker development. After an enrichment protocol, about 64% of the clones contained (CT)n repeats while 59% contained (CA)n for CT and CA enriched libraries, respectively. In the (CT)n enriched library, compound sequences were 45% while for (CA)n it was 13.5%. In both dinucleotide enriched libraries, about 80% of the clones having microsatellites have a repeat length in the range of 10 to 30 units. A library enriched for trinucleotide (CTT)n contained <19% of the clones with (CTT)n repeats. Of the clones that contained microsatellites, 62% had sufficient flanking sequence for primer design. An initial set of 25 pairs of primers was designed, out of which 14 pairs amplified cleanly and produced an easily interpretable PCR product in the commercially important American, Iranian, Turkish, and Syrian pistachio cultivars. The efficient DNA extraction method developed for pistachio kernels and shells (roasted and nonroasted) yielded DNA of sufficient quality to use PCR to create DNA fingerprints. In total, 46 alleles were identified by 14 primer pairs and a dendrogram was constructed on the basis of that information. The SSR markers distinguished most of the tested cultivars from their unique DNA fingerprint. An UPGMA cluster analysis placed most of the Iranian samples in one group while the Syrian samples were the most diverse and did not constitute a single distinct group. The maximum number of cultivar specific markers were found in `Kerman'(4), the current industry standard in the United States, and the Syrian cultivar Jalab (5). The technique of using extracted DNA from pistachio kernal or shell coupled with the appropriate marker system developed here, can be used for analyses and measurement of trueness to type.

Free access

Karen L. Burgher, Andrew R. Jamieson, and Xuewen Lu

Twenty-six genotypes of lowbush blueberry (Vaccinium angustifolium Aiton) representing four geographical zones (Maine, United States; New Brunswick, northern Nova Scotia, and western Nova Scotia, Canada) were selected to obtain DNA fingerprints and to estimate genetic similarity by randomly amplified polymorphic DNA analysis. The genotypes were either native accessions or selections from crosses involving native accessions as parents or grandparents. Thirty 10-base RAPD primers were initially screened; 11 proved to be polymorphic, resulting in 73 consistent RAPD bands. All 26 genotypes could be distinguished by their unique RAPD banding patterns and three unlabeled samples were correctly identified. The RAPD band data set was analyzed with Genstat5 to calculate similarity and distance matrices. Average similarity across all genotypes was 56%. Results from average linkage cluster analysis were used to construct a dendogram which demonstrated six main clusters with an average similarity linkage of 70%. The selection `Fundy' and its parent `Augusta' clustered at 77% similarity. The corresponding principal coordinate analysis supported the clusters and identified two distinct outliers. There was a small association by geographic grouping for five genotypes from Maine. It was concluded that RAPD analysis is a useful tool for genotypic identification and estimates of genetic similarity in lowbush blueberry.

Free access

Andrey Sabitov, Kim E. Hummer, and Tom Davis

A plant-collecting expedition to Iturup and Sakhalin Islands, Russian Federation, occurred between 21 July and 12 Sept. 2003. Actinidia, Rubus, Ribes, and Vaccinium, as well as seven accessions of strawberries, Fragaria L., were collected. Among them, a wild strawberry, Fragaria iturupensis Staudt, was collected on the eastern slope of Atsonupuri Volcano, Iturup Island, at 630 and 650 m elevation. This species was similar in habit, leaf color and overall appearance to the American strawberry species F. virginiana Mill. Fruits were bright red, oblate spherical, about 1.4 cm in diameter, and had exerted achenes. The native distribution of this species was limited to the middle elevation of the slope of this volcano, and only on Iturup Island. Chromosome counts indicated that these plants were octoploid. Initial DNA fingerprinting aligned this sample with other octoploid species. In addition to this species, samples of F. yezoensis H. Hara (syn. F. nipponica Makino) were collected on Kuibyshewskii Bay of Cape Otlivnoy, Iturup, and near Ujno-Sakhalinsk City, Sakhalin Island. F. iinumae Makino was observed in Ogon'ki Village, Sakhalin Island. This report confirmed the existence of F. iturupensis, the only known native Asian octoploid strawberry, and documented its limited range. Seeds of these strawberry species are available for research by request from the U.S. Department of Agriculture, Agricultural Research Service, National Clonal Germplasm Repository in Corvallis.