Runners from 318 plants representing 37 populations across the northern tier of US states, from Washington to New York, were collected and planted in two replications in a common greenhouse environment to assess morphological variation among octoploid strawberries (Fragaria chiloensis, F. virginiana spp. glauca and F. v. spp. virginiana). DNA was also extracted from these plants to determine molecular variation using RAPD's (Random Amplified Polymorphic DNA). Preliminary data suggest that the following morphological characters are useful traits in assessing diversity: flowering and runnering date; sex; petiole and peduncle hairs; petiole and peduncle color; leaf color, size, shape and density; and powdery mildew resistance. Preliminary RAPD data has revealed many useful molecular markers capable of detecting variability from the intrapopulation to interspecific level. Analysis of these data will determine relative genetic distances among the populations and provide a more complete understanding of the diversity available to the strawberry breeder in the octoploid taxa native to North America.
Richard E. Harrison, lames J. Luby, and Glenn R. Furnier
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.
Patrick J. Conner and Bruce W. Wood
Genetic variation among pecan [Carya illinoinensis (Wangenh.) K. Koch] cultivars was studied using randomly amplified polymorphic DNA (RAPD) markers. Using a combination of primers, a unique fingerprint was produced for each of the pecan genotypes studied. The genetic relatedness between 44 cultivars was estimated using more than 100 RAPD markers. Genetic distances based on the simple matching coefficient varied from 0.91 to 0.59. The phenetic dendogram developed from cluster analysis showed relatively weak grouping association. However, cultivars with known pedigrees usually grouped with at least one of the parents and genetic similarity estimates appear to agree with known genetic relationships. Using RAPD information in determining genetic relationships among pecan cultivars with unknown or questionable pedigrees and the integration of that knowledge into the breeding program is discussed.
Dapeng Zhang and Wanda Collins
To understand the prospects of applying the RAPD technique to assay genetic diversity in Ipomoea, four species (I. batatas, I. trifida, I. triloba, and I. ×leucantha) were analyzed for RAPD molecular markers. Six accessions of each species were used. Significant RAPD polymorphisms were detected within each species. Of 20 primers used, nine produced clear scorable polymorphic bands. The number of polymorphic bands produced per primer ranged from two to nine. Pair-wide genetic distance was calculated based on “band sharing”. The SAS-CLUSTER procedure was used to build a hierarchical species dendrogram. The four species were clearly separated by the clustering, which agrees with their existing taxonomic relationship. This study shows that RAPD analysis can be a powerful tool for identifying duplicates of germplasm acessions and for assessing genetic diversity. The procedures are relatively inexpensive and easy to perform and could be valuable in preliminary assessment of field genebank collections to separate species and indicate duplications in collected material.
Larry D. Knerr and Jack E. Staub
The available U. S. Cucumis sativus germplasm collection (754 Plant Introductions) was electrophoretically screened for genetic diversity using 39 enzymes representing a total of 57 loci. Polymorphisms were observed at 18 loci which included g2dh, gpi1, gpi2, gr1, gr2, idh, mdh1, mdh2, mdh3, mpi2, pep-la2, pep-pap2, per4, pgd1, pgd2, pgm1, pgm3, and skdh. Appropriate crosses were set up to verify the inheritance of and test linkages among these loci. Four allozyme linkage groups have currently been identified. Representative linkages and their genetic distances include: gpi1 - mdh3 (20); pgm1 - pgd1 (25); and g2dh - pgd2 (19). Additionally, crosses were made to marker stocks to test for linkages between some allozyme loci and loci coding for resistance to downy mildew and anthracnose, long hypocotyl, divided leaf, short petiole, glabrous, compact plant, determinate, little leaf, and bitter free (bi).
Margaret R. Pooler and John S. Hartung
Xylella fastidiosa is a fastidious gram-negative, xylem-limited leafhopper-transmitted bacterium that has proven to be the causal agent of many economically important horticultural plant diseases, including Pierce's disease of grapevine and citrus variegated chlorosis. Genetic relationships among 11 X. fastidiosa strains isolated from mulberry, almond, ragweed, grape, plum, elm, and citrus were determined using randomized amplified polymorphic DNA (RAPD). Twenty-two 10-base primers amplified a total of 77 discrete polymorphic bands. Phenetic analysis based on a similarity matrix corresponded well with previous reports on RFLP-based similarity relationships, indicating that RAPD-PCR amplification products can be used as a reliable indicator of genetic distance in X. fastidiosa. RAPD products have been cloned and sequenced, and pairs of 21-nucleotide PCR primers have been developed that detect X. fastidiosa in general and the causal agent of citrus variegated chlorosis specifically.
S. Echeverrigaray, R.L. Cansian, A.P.L. Delamare, R.P. Silveira, and V. Barni
A collection of garlic (Allium sativum L.) germplasm, including 11 cultivars currently used in South Brazil, was evaluated using randomly amplified polymorphic DNA (RAPD) markers. Objectives were to assess genetic variations and relationships among cultivars and determine the potential of RAPD markers for the identification of garlic cultivars. One-hundred-twenty-two RAPD bands were scored from 12 oligonucleotide decamer primers selected from Operon Techn. kits B, X, and Y. Of these, 46 bands (37.6%) were polymorphic. Similarity indices between garlic entries were computed from RAPD data, and these range from 0.69 to 1.00. UPGMA cluster analysis of genetic distances showed three groups: one formed by nine cultivars and two formed by single entries. The nine cultivars that form group I had common origin, which explains the high similarity observed between them.
D.G. Ranamukhaarachchi, R.J. Henny, C.L. Guy, and Q.B. Li
Randomly amplified polymorphic DNA (RAPD) markers were utilized to determine the genetic relationships of nine morphologically similar pot plant cultivars of Anthurium sp. by developing DNA fingerprints (DFP). Of 25 arbitrary primers screened, nine generated DFPs that were used in computing the genetic distance (d) and similarity coefficient (C) values. All cultivars tested exhibited a high degree of genetic similarity. `Lady Ann' and `Lady Beth' possessed the closest relationship with d and C values of 0.06 and 0.98, respectively. The next closest genetic relationship was between `Red Hot' and `Southern Blush' (d = 0.33, C = 0.89). These two cultivars exhibited a more distant relationship to the other seven cultivars as indicated by higher `d' values. However, this study showed that the nine Anthurium cultivars examined were genetically closely related. These cultivars share specific DNA bands with three possible parental species (A. andraeanum Linden ex Andre, A. antioquens L., and A. amnicola Dressler) included in this study, which may indicate similarities in their pedigree. This study shows that RAPDs can be a useful tool to distinguish Anthurium pot plant cultivars as well as identify their genetic relationships.
Salih Kafkas and Rafael Perl-Treves
Phylogenetic relationships among nine species in the genus Pistacia were studied by randomly amplified polymorphic DNA (RAPD) analysis. The following species were included: P. atlantica, P. terebinthus, P. eurycarpa, P. vera, P. integerrima, P. mexicana, P. palaestina, P. lentiscus, and P. khinjuk. Genomic DNA was extracted from leaf tissue and RAPD analysis was performed using 20 primers. A total of 242 fragments were generated and 228 bands were polymorphic at the inter-specific level. Subjecting these data to phylogenetic analysis yielded a shortest cladogram that is 338 steps long, featuring two main groups. P. vera, P. khinjuk, P. eurycarpa, P. atlantica, and P. integerrima were included in one group, while P. terebinthus, P. palaestina, P. mexicana, and P. lentiscus formed the second group. The first group included species with single-trunked and big trees, whereas the species included in the second group mostly grow as shrubs or small trees. The cladogram showed that the closest pairs of species were P. terebinthus and P. palaestina, P. eurycarpa and P. atlantica, P. vera and P. khinjuk, and P. mexicana and P. lentiscus. We suggest that P. palaestina is in fact a variety of P. terebinthus in view of the small genetic distance between them. This study also showed that P. eurycarpa (syn. P. atlantica var. kurdica) is a distinct species from P. atlantica, rather than a variety within the same species.
Marilyn L. Warburton and Fredrick A. Bliss
Previous studies of peach germplasm using pedigree information and isozyme polymorphism data have shown limited diversity in the U.S. gene pool. To further investigate the genetic diversity among peach cultivars grown in different regions of the United States, 94 RAPD markers were used to estimate the genetic distances among 136 cultivars. Of the 12 clusters formed in a dendrogram, the 90 U.S. cultivars and breeding lines and most of those from Europe and Latin America grouped to only three clusters, while the 23 peach entries from India, Pakistan, Russia, Okinawa, and China, as well as the almond cultivar used as an outgroup, were distributed among the other nine clusters. Therefore, the genetic diversity within temperate U.S. peach germplasm is quite limited, and to expand the variability, additional germplasm should be obtained, especially from Asia. Comparison of genetic similarity based on inbreeding coefficients with similarity coefficients based on the RAPD data produced a correlation of 0.395, which is comparable to values in similar investigations in other crops. Thus, similar conclusions can be drawn from these two sources of information. RAPD data are useful particularly when pedigree information is incomplete, there has been substantial selection within breeding populations, and a high proportion of alleles are identical in state but not by descent.