The aim of the present study was to develop a reliable reference database to discriminate between the major Greek olive (Olea europaea L.) cultivars and reveal their genetic relationships, since Greece is considered a secondary center of diversity. In order to establish genetic relationships among the 26 Greek and eight international cultivars, four amplified fragment length polymorphism (AFLP) primer pairs, 12 randomly amplified polymorphic DNA (RAPD) primers, along with measurements from 10 morphological traits, were used. A total of 576 AFLP and 113 RAPD markers were produced. Genetic similarities, estimated using the Jaccard algorithim, ranged from 0.45 to 0.83 for the AFLP data and 0.27 to 0.87 for the RAPD data. The cophenetic correlation coefficients between the genetic similarities and the unweighted pair group method of arithmetic averages (UPGMA) phenograms were 0.77 for the AFLPs, 0.81 for the RAPDs, and 0.69 for the morphological traits. However, limited clustering similarities among the phenograms derived from the three methods were observed. This was also reflected by the low correlation between the three genetic similarity matrices produced (AFLP and RAPD, r = 0.39; AFLP and morphological traits, r = 0.11; RAPD and morphological traits, r = 0.02). According to the molecular results, olive cultivars are clustered according to fruit size but not according to geographical origin. Three of the cultivars tested, `Vasilicada,' `Throumbolia', and `Lianolia Kerkiras', were found to branch distantly to the others, according to the AFLP results, and can be considered as ancient Greek cultivars.
Marianna Hagidimitriou, Andreas Katsiotis, George Menexes, Constantinos Pontikis, and Michael Loukas
A. del Rio, J.B. Bamberg, Z. Huaman, R. Hoekstra, A. Salas, and S.E. Vega
Effects of genebank seed increases on the genetic integrity and whether germplasm in the genebank still represents the in situ populations from which it was collected are major concerns of the recently formed Association of Potato Intergenebank Collaborators (APIC), a consortium of world potato genebank leaders. This cooperative APIC research used RAPDs and morphological markers 1) to establish genetic relationships between seed increased populations within accessions and (2) to measure genetic differentiation between diploid and tetraploid potato germplasm maintained for many years and current in situ populations from the same collection sites in the wild. Solanum jamesii Torrey (2n = 2x = 24) and S. fendleri A. Gray (2n = 4x = 48), two wild potato species native to North America, were used as plant material. These species represented two major breeding systems found among Solanum species: outcrossing diploids and inbreeding disomic tetraploids, respectively. Comparisons made between populations one generation apart and between sister populations generated from a common source indicated that there has been minimal loss of genetic diversity in captive germplasm using the genebank techniques standard at NRSP-6 and other world potato genebanks. RAPD markers also revealed that significant genetic differences were found between genebank-conserved and re-collected in situ populations for all diploid potato comparisons and for about half of the comparisons within tetraploid potato populations.
J. E. Staub and Jinsheng Liu
The genetic diversity among Cucumis sativus var. sativus (commercial cucumber) (1), var. anatolicus (2), var. cilicicus (3), var. europaeus (4), var. falcatus (5), var. indo-europaeus (6), var. irano-turanieus (7), var. izmir (8), var. sikkimensis (9), var. squamosus (10), var. testudaceus (11), var. tuberculatus (12), var. vulgatus (13), and var. hardwickii (14) were assessed using 7 morphological characteristics and 9 isozyme loci to determine their potential use for plant improvement. Results of morphological comparison below. Isozyme and morphological analysis did not result in similar dendrogram depictions. Varieties 13 and 3 might have potential in plant improvement based on yield performance.
J. Nienhuis, P. Skroch, M. Sass, S. Beebe, J. Tohme, and F. Pedraza
The number of Phaseolus vulgaris germplasm accessions numbers more than 30,000. While the large numbers of accessions increase the probability of preserving genetic variability they simultaneously limit the efficient and routine utilization of this resource. From the approximately 4000 P. vulgaris accessions in the C.I.A.T. whole collection that were collected in Mexico, a core collection of 400 accessions was developed based on variation for agronomic performance, ecological adaptation, and seed characteristics. Random samples of 90 accessions each were drawn from the core and whole collections and evaluated for 224 polymorphic RAPD bands. Based on analysis of the RAPD data there were no significant differences in genetic diversity between the two samples. The correlation of marker frequency for the two samples was 0.984 confirming that the two samples represent the same population.
Xianping Qu, Jiang Lu, and Olusola Lamikanra
Two morphologically distinct types of grapes belonging to the subgenera Euvitis and Muscadinia in the genus Vitis are cultivated in the United States. The former is commonly called bunch grapes while the latter is usually called muscadine. Genetic diversity among these grapes was investigated using RAPD markers. Sixteen grape cultivars, with parentage including V. rotundifolia Michx., V. vinifera L., and several American Vitis species, were used for the RAPD analysis. A total of 156 RAPD markers was produced from 19 random primers, over 90% of which was polymorphic among the muscadine and the bunch grapes. Polymorphisms were lower within each subgenus. Relationships between these two subgenera were estimated based on band-sharing and cluster analysis. The average genetic distance between the bunch and the muscadine grape cultivars was 0.45. The results based on DNA analysis agree with isozyme data obtained from a separate study, which demonstrated that muscadine grapes share very few common alleles with American bunch grapes and European grapes.
Jasmina Muminović, Andrea Merz, Albrecht E. Melchinger, and Thomas Lübberstedt
Twelve amplified fragment length polymorphism (AFLP) primer combinations and 10 inter-simple sequence repeat (ISSR) primers were applied to estimate genetic diversity among 68 varieties of cultivated radish (Raphanus sativus L.). The material consisted of open-pollinated varieties, inbred lines, diploid and a few tetraploid hybrid varieties of garden radish [R. sativus var. sativus DC. convar. radicula (DC.) Alef.] and black radish [R. sativus var. niger (Mill.) Pers.]. Two accessions of uncultivated relatives of radish that as weeds cause serious contamination during the process of hybrid radish production were added to the analyses. Polymorphic fragments were scored for calculation of Jaccard's coefficient of genetic similarity (GS). Substantial level of genetic variability (average AFLP-based GS = 0.70; average ISSR-based GS = 0.61) was detected in the available germplasm of cultivated radish. Cluster analyses separated two weedy species from the cultivated germplasm. Within cultivated material, black radish and french breakfast radish types formed separate clusters. Based on AFLP data, a principal coordinate analysis (PCoA) and model-based approach revealed the genetic structure within cultivated radish germplasm and indicated the existence of divergent pools. Although the model-based approach did not separate black radish from french breakfast radish varieties, it offered a clear sub-division within garden radish germplasm. The results of this study may be relevant for hybrid radish breeding.
N. Nikoloudakis, G. Banilas, F. Gazis, P. Hatzopoulos, and J. Metzidakis
Random amplified polymorphic DNA (RAPD) markers were used to study the genetic diversity and to discriminate among 33 Greek olive (Olea europaea L.) cultivars. Three feral forms from Crete and five foreign cultivars recently introduced into Greece were also included. Nineteen primers were selected which produced 64 reproducible polymorphic bands in the 41 olive genotypes studied, with an average of 3.4 informative markers per primer. The RAPD markers resulted in 135 distinct electrophoretic patterns, with an average of 7.1 patterns per primer. Based on either unique or combined patterns, all genotypes could be identified. Genetic similarities between genotypes were estimated using the Dice similarity index and these indicated that a high degree of diversity exists within the Greek olive germplasm. Using the unweighted pair-group method (UPGMA) most cultivars were clustered into two main groups according to their fruit size or commercial use (table or olive oil). However, poor correlation was detected between clustering of cultivars and their principal area of cultivation. RAPD marker data were subjected to nonmetric multidimentional scaling (NMDS) which produced results similar to those of the UPGMA analysis. The results presented here contribute to a comprehensive understanding of cultivated Greek olive germplasm and provide information that could be important for cultural purposes and breeding programs.
Anfu Hou, James R. McFerson, and Warren F. Lamboy
Molecular DNA markers based on the RAPD (random amplified polymorphic DNA) assay are gaining use in germplasm assessment. RAPD markers are simple, relatively inexpensive, and highly informative. We used five primers to assess 26 Brassica oleracea breeding lines from the IVF and nine accessions from the PGRU. The test array included eight subspecies of B. oleracea. We generated 90 RAPD markers and were able to unambiguously discriminate among all 35 test entries, but could not separate subspecies within B. oleracea. Genetic similarity between subspecies ranged from 0.629 to 0.738. Average similarity within accessions was 0.96, confirming the suspected homogeneity of breeding lines. Nevertheless, significant genetic diversity was found among kohlrabi, broccoli, and cabbage accessions. Similarity analysis of breeding lines and hybrids confirmed their pedigree relationships. Interestingly, B. o. subsp. costata `Couve Nabica' showed closer similarity to B. napus subsp. oleifera `Jet Neuf' than to other B. o. materials and B. o. subsp. italica `Packman' showed higher similarity to some cabbages than to other broccolis. Results provide further evidence that diversity assessment using RAPDs is broadly applicable and useful in germplasm conservation and utilization.
R.J. Schnell, J.S. Brown, C.T. Olano, A.W. Meerow, R.J. Campbell, and D.N. Kuhn
Mango (Mangifera indica L.) germplasm can be classified by origin with the primary groups being cultivars selected from the centers of diversity for the species, India and Southeast Asia, and those selected in Florida and other tropical and subtropical locations. Accessions have also been classified by horticultural type: cultivars that produce monoembryonic seed vs. cultivars that produce polyembryonic seed. In this study we used 25 microsatellite loci to estimate genetic diversity among 203 unique mangos (M. indica), two M. griffithii Hook. f., and three M. odorata Griff. accessions maintained at the National Germplasm Repository and by Fairchild Tropical Botanic Garden in Miami, Fla. The 25 microsatellite loci had an average of 6.96 alleles per locus and an average polymorphism information content (PIC) value of 0.552 for the M. indica population. The total propagation error in the collection (i.e., plants that had been incorrectly labeled or grafted) was estimated to be 6.13%. When compared by origin, the Florida cultivars were more closely related to Indian than to Southeast Asian cultivars. Unbiased gene diversity (Hnb) of 0.600 and 0.582 was found for Indian and Southeast Asian cultivars, respectively, and both were higher than Hnb among Florida cultivars (0.538). When compared by horticultural type, Hnb was higher among the polyembryonic types (0.596) than in the monoembryonic types (0.571). Parentage analysis of the Florida cultivars was accomplished using a multistage process based on introduction dates of cultivars into Florida and selection dates of Florida cultivars. In total, 64 Florida cultivars were evaluated over four generations. Microsatellite marker evidence suggests that as few as four Indian cultivars, and the land race known as `Turpentine', were involved in the early cultivar selections. Florida may not represent a secondary center of diversity; however, the Florida group is a unique set of cultivars selected under similar conditions offering production stability in a wide range of environments.
Raymond Schnell, J. Steven Brown, Cecile Olano, Alan Meerow, Richard Campbell, and David Kuhn
Mangifera indica L. germplasm can be classified by origin with the primary groups being cultivars selected from the centers of diversity for the species, India and Southeast Asia, and those selected in Florida and other tropical and subtropical locations. Accessions have also been classified by horticultural type: cultivars that produce monoembryonic seed vs. cultivars that produce polyembryonic seed. In this study, we used 25 microsatellite loci to estimate genetic diversity among 203 accessions. The 25 microsatellite loci had an average of 6.96 alleles per locus and an average PIC value of 0.552. The total propagation error in the collection, i.e., plants that had been incorrectly labeled or grafted, was estimated to be 6.13%. When compared by origin, the Florida cultivars were more closely related to Indian than to Southeast Asian cultivars. Unbiased gene diversity (Hnb) of 0.600 and 0.582 was found for Indian and Southeast Asian cultivars, respectively, and both were higher than Hnb among Florida cultivars (0.538). When compared by horticultural type, Hnb was higher among the polyembryonic types (0.596) than in the monoembryonic types (0.571). Parentage analysis of the Florida cultivars was accomplished using a multistage process based on introduction dates of cultivars into Florida and selection dates of Florida cultivars. Microsatellite marker evidence suggests that as few as four Indian cultivars, and the land race known as `Turpentine', were involved in the early cultivar selections. Florida may not represent a secondary center of diversity; however, the Florida group is a unique set of cultivars selected under similar conditions offering production stability in a wide range of environments.