Genetic Diversity of Asian Cotton (Gossypium arboreum L.) in China Evaluated by Microsatellite Analysis

Asian cotton (Gossypium arboreum L.) was once widely cultivated in China. It has also been a valuable source of genetic variation in modern cotton improvement. In this study, the genetic diversity of selected G. arboreum accessions collected from different regions of China was evaluated by microsatellite (simple sequence repeats, SSRs) analysis. Of the 358 microsatellite markers analyzed, 74 primer pairs detected 165 polymorphic DNA fragments among 39 G. arboreum accessions examined. Twelve accessions could be fingerprinted with one or more SSR markers. With the exception of two accessions, DaZiJie and DaZiMian, genetic similarity coefficients among all accessions ranged from 0.58 to 0.87 suggesting high level of genetic variation in the G. arboreum collections. The UPGMA dendrogram constructed from genetic similarity coefficients revealed positive correlation between cluster groupings and geographic distances. In addition, comparison of the microsatellite amplification profiles of the diploid G. arboreum and tetraploid Gossypium hirsutum L. found that size distribution of amplified products in G. arboreum was dispersive and that of G. hirsutum was relatively concentrated. The information on the genetic diversity and SSR fingerprinting from this study is useful for developing mapping populations for constructing diploid cotton genetic linkage map and tagging economically important traits.Diqiu Liu, Xiaoping Guo: These two authors contributed equally to this work.     

AFLP Fingerprinting in Pigeonpea (Cajanus cajan (L.) Millsp.) and its Wild Relatives

Detection of DNA polymorphism in cultivated pigeonpea (Cajanus cajan) and two of its wild relatives Cajanus volubilis and Rhynchosia bracteata is reported here for the first time using amplified fragment length polymorphism (AFLP) fingerprinting. For this purpose, two EcoRI (three selective nucleotides) and 14 MseI (three selective nucleotides) primers were used. The two wild species shared only 7.15% bands with the pigeonpea cultivars, whereas 86.71% common bands were seen among cultivars. Similarly, 62.08% bands were polymorphic between C. volubilis and pigeonpea cultivars in comparison to 63.33% polymorphic bands between R. bracteata and pigeonpea cultivars, and 13.28% polymorphic bands among pigeonpea cultivars. The cluster analysis revealed low polymorphism among pigeonpea cultivars and very high polymorphism between cultivated pigeonpea and its wild relatives. The AFLP analysis also indicated that only one primer combination (EcoRI + ACT and MseI + CTG), at the most any four primer pair combinations, are sufficient for obtaining reliable estimation of genetic diversity in closely related cultivars like pigeonpea material analyzed herein. AFLP analysis may prove to be a useful tool for molecular characterization of pigeonpea cultivars and its wild relatives and for possible use in genome mapping.     

SSR fingerprinting of a German <Emphasis Type="Italic">Rubus</Emphasis> collection and pedigree based evaluation on trueness-to-type

Eighty-two genotypes of Rubus available in germplasm collections, nurseries and home gardens were collected and evaluated using a set of 16 simple sequence repeat (SSR) markers to estimate the level of genetic diversity and relatedness of the germplasm and for testing them on trueness-to-type. Each of the 16 SSRs was successful in amplifying alleles from most genotypes. Fifteen of the markers produced polymorphic bands, whereas marker RhM023 was monomorphic. The polymorphic information content among genotypes varied from 0.056 to 0.83 with an average of 0.348. A neighbor-joining analysis allocated the genotypes to four major clusters containing 11, 24, 39 and eight genotypes, respectively. Cluster I consists of floricane-fruiting cultivars originating from the Scottish and/or British breeding programs or cultivars which have those cultivars in their pedigree. Cluster II included cultivars that have ‘Autumn Bliss’ or ‘Tulameen’ in their pedigree. Cluster III consists of summer-bearing raspberry cultivars, some primocane-fruiting cultivars, and a few intermediate summer-fall-bearing types. Cluster IV consists of the blackberry ‘Navaho’ (R. fruticosus L.), the interspecific hybrid ‘Dorman Red’ and a few other raspberry varieties. A number of yellow fruited varieties was dispersed on three different clusters suggesting a convergent evolution of this trait. The pedigree of several genotypes could be confirmed using a Pedimap based approach, whereas other cultivars were found to be genetically identical. The results disclose the alarming narrow genetic base of Rubus resources in Germany. Broadening of this base is urgently needed.     

Analysis of genetic diversity in Turkish sesame (Sesamum indicum L.) populations using RAPD markers⋆

The genetic diversity of 38 cultivated populations of Sesamum indicum L. from four different regions of Turkey was estimated at the DNA level with the random amplified polymorphic DNA (RAPD) technique. Sixty-one bands were obtained for all populations 78% of which were polymorphic. Analysis of molecular variance (AMOVA) was used to investigate the genetic diversity of the populations which yielded highly significant differences among populations within regions (91.9% of the total genetic diversity). According to AMOVA and Shannon's index that were performed separately for each region, the highest value of genetic variation was observed among Northwest region populations (CV = 7.7; H₀ = 0.304) and lowest in the Southeast regions' populations (CV = 2.6; H₀ = 0.068). Nei and Li's similarity index was calculated and phylogenetic tree was established using the neighbor-joining algorithm. This phenetic analysis grouped 35 of 38 accessions in six groups leaving three highly diverse accessions outside. Wagner phylogenetic method was used to assess the phylogenetic relationships among the populations. In the majority-rule consensus tree, only 7 of the 32 forks showed above 60% occurrence. Using Principal Coordinate Analysis (PCO) of the RAPD data set, the groups were clearly separated along the first three axis. These results indicate that RAPD technique is useful for sesame systematics, and should be valuable for the maintenance of germplasm banks and the efficient choice of parents in breeding programs.     

Genetic Diversity among Syrian Cultivated and Landraces Wheat Revealed by AFLP Markers

Genetic diversity among some important Syrian wheat cultivars was estimated using Amplified Fragment Length Polymorphism (AFLP) markers. Five Triticum aestivum L. and 10 Triticum turgidum ssp. durum were analyzed with 11 EcoRI–MseI primer pair combinations. Of the approximately 525 detected AFLP markers, only 46.67% were polymorphic. Cluster analysis with the entire AFLP data divided all cultivars into two major groups reflecting their origins. The first one contained T. aestivum L. cultivars, and the T. turgidum ssp. durum cultivars and landraces were grouped in the second. Narrow genetic diversity among all cultivars was detected with an average genetic similarity of 0.884. The lowest similarity index (0.9) was found between Cham5 and Hamary (durum wheat), whereas this value was 0.93 between Salamony and Bouhouth 4 (T. aestivum L.). The narrow genetic diversity level indicates that these genotypes could be originated from the same source. AFLP analysis provides crucial information for studying genetic variation among wheat cultivars and provides important information for plant improvement.     

Genetic variability of Coffea arabica L. accessions from Ethiopia evaluated with RAPDs

The genetic diversity of 50 wild and semi-wild accessions of the Coffea arabica L. germplasm collection, gathered by the FAO and ORSTOM missions to Ethiopia, and maintained in Colombia by CENICAFE, was evaluated with RAPD markers. The evaluation was carried out in two phases: In phase one, the polymorphism of 8 Ethiopian accessions of different geographic origin, plus the cultivated variety 'Caturra' was assessed with the RAPD technique with forty-two 10-mer oligonucleotides. In phase two, 51 accessions were assessed with a set of 5 polymorphic primers that reproduced, with a correlation of 95%, the groups generated by the 24 polymorphic primers found in phase one. Principal Coordinate Analysis of molecular data revealed that a closely related group consisting of 86% of the Ethiopian C. arabica accessions evaluated are significantly different from the Caturra variety and could be used in a genetic breeding initiative to increase the variability of cultivated varieties. The results also indicate that a larger polymorphism is present in the Colombian replica of FAO Ethiopian coffee germplasm collection than previously reported.     

A-genome cotton as a source of genetic variability for Upland cotton (<Emphasis Type="Italic">Gossypium hirsutum</Emphasis>)

Since Upland cotton (Gossypium hirsutum) is known to have relatively low levels of genetic diversity, a better understanding of variation and relationships among possible sources of novel genes would be valuable. Therefore, analysis of genetic variation of the genus Gossypium, especially the diploids, which are the putative donors of the A and D genomes for the commercially important allotetraploid cottons (AADD), G. hirsutum and G. barbadense, could provide important information about the feasibility of using these genetic resources for cotton improvement. The primary objective of this study was to analyze the genetic diversity in A-genome diploid cotton species, G. herbaceum (A1) and G.␣arboreum (A2) by using microsatellite markers. Forty-one A-genome germplasm accessions were evaluated with 32 microsatellite loci. Genetic similarities between A1 and A2 ranged from 0.62 to 0.86 with a mean of 0.70. Within each A-genome species similarities ranged from 0.80 to 0.97 with a mean of 0.89 for A1 and from 0.82 to 0.98 with a mean of 0.89 for A2. A UPGMA tree and principal coordinate analysis based on genetic similarity matrices showed distinct clusters consistent with the genomic groups.     

Molecular Markers for the Classification of Switchgrass (Panicum virgatum L.) Germplasm and to Assess Genetic Diversity in Three Synthetic Switchgrass Populations

Information regarding the amount of genetic diversity is necessary to enhance the effectiveness of breeding programs and germplasm conservation efforts. Genetic variation between 21 switchgrass genotypes randomly selected from two lowland (‘Alamo’ and ‘Kanlow’) and one upland (‘Summer’) synthetic cultivars were estimated using restriction fragment length polymorphism (RFLP) markers. Comparison of 85 RFLP loci revealed 92% polymorphism between at least two genotypes from the upland and lowland ecotypes. Within ecotypes, the upland genotypes showed higher polymorphism than lowland genotypes (64% vs. 56%). ‘Kanlow’ had a lower percent of polymorphic loci than ‘Alamo’ (52% vs. 60%). Jaccard distances revealed higher genetic diversity between upland and lowland ecotypes than between genotypes within each ecotype. Hierarchical cluster analysis using Ward's minimum variance grouped the genotypes into two major clusters, one representing the upland group and the other the lowland group. Phylogenetic analysis of chloroplast non-coding region trnL (UAA) intron sequences from 34 switchgrass accessions (6 upland cultivars, 2 lowland cultivars, and 26 accessions of unknown affiliation) produced a neighbor-joining dendrogram comprised of two major clusters with 99% bootstrap support. All accessions grouped in the same cluster with the lowland cultivars (‘Alamo’ and ‘Kanlow’) had a deletion of 49 nucleotides. Phenotypic identification of greenhouse-grown plants showed that all accessions with the deletion are of the lowland type. The deletion in trnL (UAA) sequences appears to be specific to lowland accessions and should be useful as a DNA marker for the classification of upland and lowland germplasm.     

Inter-Simple Sequence Repeat fingerprints to assess genetic diversity in Tunisian fig (Ficus carica L.) germplasm

The genetic diversity of 18 Tunisian fig cultivars was investigated at the DNA level using the Inter Simple Sequence Repeat (ISSR) associated with the Polymerase Chain Reaction (PCR). Using a set of primers, the most informative ones were selected that were characterized by an important Resolving power value of 29.6. A total of 47 discernible fragments were scored from samples, with a mean of 11.7 fragments per primer. The 90.4% of sample that were polymorphic were scored as molecular markers to examine the Tunisian fig germplasm polymorphism at DNA level. A large genetic diversity as related to ISSR patterns was found within the local Tunisian fig germplasm. An UPGMA dendrogram exhibits the unstructured variability in this crop. Moreover, the principal component analysis shows that the observed diversity was typically continuous. Our data provide a large number of ISSR markers that are useful in the fingerprinting of Ficus carica L. cultivars, and in the understanding of the genetic relationships among these accessions.     

Genetic diversity of Pakistan wheat germplasm as revealed by RAPD markers

Wheat breeding in Pakistan started in 1930s before partition in the United India and so far has released more than 68 cultivars, but no systematic analyses of the genetic diversity of Pakistan wheat have been made. Twenty Pakistan wheat cultivars released from 1933 to 2002 were examined for genetic diversity and relationships using random amplified polymorphic DNA (RAPD) markers. Forty-two RAPD primers were applied and 184 polymorphic bands were generated for each cultivar. Most of the cultivars were genetically interrelated, although six of them displayed some genetic distinctness. The RAPD variation observed among these cultivars was low. Only 40.7% of the total scorable bands were polymorphic, and 26.1% of the polymorphic bands were observed most frequently (f = 0.95) among the 20 cultivars. The proportions of polymorphic bands for each cultivar ranged from 0.67 in ‘Yecora’ to 0.84 in ‘C-250’ with an average of 0.76. About 1.4% of the RAPD variation might have been fixed over the 69 years of wheat breeding, but such fixation was not statistically significant. These results are significant for future improvement and conservation of Pakistan wheat.     

Abundant genetic diversity in cultivated <Emphasis Type="Italic">Codonopsis pilosula</Emphasis> populations revealed by RAPD polymorphisms

Genetic diversity of seven cultivated populations of Codonopsis pilosula Nannf. from Longxi County, Gansu Province of China was estimated using randomly amplified polymorphic DNA (RAPD) markers. The 17 selected RAPD primers amplified 205 polymorphic bands out of a total of 235 (87.2%). Nei’s gene-diversity statistics and population differentiation parameters based on AMOVA analysis indicated that the cultivated C. pilosula populations remained a high level of genetic diversity with Hs = 0.299 and I = 0.450. A greater proportion of genetic diversity was found within (77%) rather than among (23%) the populations. In addition, we also detected that populations from different altitudes had a considerable genetic differentiation after 40 years of cultivation at the same site. Populations from higher altitude had lower genetic diversity than those from lower altitude. Our results suggested that irregular and sparse cultivation practices, i.e., random collecting, preserving, and planting seeds of the medicinal species without deliberate selection, might be an efficient way to conserve genetic resources of medicinal plants, in addition to their effective uses.     

Assessment of genetic diversity in cultivars and wild accessions of Luohanguo (<Emphasis Type="Italic">Siraitia grosvenorii</Emphasis> [Swingle] A. M. Lu et Z. Y. Zhang), a species with edible and medicinal sweet fruits endemic to southern China,using RAPD and AFLP markers

Genetic variation of wild populations and cultivars of Luohanguo (Siraitia grosvenorii), a plant species endemic to southern China, was assessed using random amplified polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP) markers. Based on the results for 130 individuals from seven populations, a high level of genetic diversity of Luohanguo was observed at the species level. The percentage of polymorphic loci (P) was 89.4%, Nei’s gene diversity (H _e) was 0.239, and Shannon’s information index (H _o) was 0.373 based on the combined AFLP and RAPD data. There was a high degree of genetic differentiation, with 45.1% of the genetic variation attributed to differences between the populations. The genetic diversity of the Luohanguo cultivars is much lower than that of wild populations (P = 41.8%, H _e = 0.141, H _o = 0.211), and a distinct genetic differentiation is observed between the cultivars and wild accessions. The pool of genetic variation in the wild populations provides an excellent gene resource for Luohanguo breeding.     

Relationships Among <Emphasis Type="Italic">Brassica napus</Emphasis> (L.) Germplasm from Spain and Great Britain as Determined by RAPD Markers

The genetic diversity and the relationships among a collection of Brassica napus L. European populations were evaluated using random amplified polymorphic DNA markers. The study included 33 accessions of B. napus collected from Galicia (northwestern Spain) and 18 British cultivars, 16 accessions of B. napus and two accessions of Brassica oleracea L. used as controls. DNA from 25 individuals per population was analyzed using 18 decamer primers. One hundred thirty-eight amplification products were scored of which 105 were polymorphic. These bands ranged in size from 350 to 2500 base pairs. Similarity coefficients and cluster analysis were computed and six groups were obtained. Cluster I was the largest and included all the landraces from northwestern Spain, except two accessions that grouped separately into Clusters III and IV, respectively. A low level of genetic variability was detected among the B. napus Spanish genotypes, while considerable diversity was present among the British ones, which grouped into three groups, two main clusters and one group formed by one accession. Cluster II included all commercial varieties grown in Great Britain whereas Cluster V grouped local varieties maintained by the growers for many years. Cluster VI was a singularity formed by one entry. British accessions of B. oleracea had the greatest dissimilarity with all the other populations and grouped separately in Clusters VII and VIII. As conclusion, B. napus landraces used in northwestern Spain as leafy-green vegetable probably have an independent origin from B. napus crops grown in other European regions. Besides, separate domestication in northwestern Spain and Great Britain for a different end use might have led to two distinct gene pools.     

Molecular phylogeny of banana cultivars from Thailand based on HAT-RAPD markers

Musa acuminata Colla (AA genomes) and Musa balbisiana Colla (BB genomes) are the wild progenitors of the cultivated banana, they are highly variable in Thailand. The genetic system is relatively unknown and complicated due to interspecific hybridization, heterozygosity and polyploidy, which are common in most clones. These factors make identification of closely related banana cultivars difficult, especially when sterile. The high annealing temperature-random amplified polymorphic DNA (RAPD) technique was used to estimate the genetic relationship between 22 selected banana cultivars, utilizing 14 random primers. Phylogenetic relationship was determined by unweighted pair group method with arithmetical averages cluster analysis. The dendrogram constructed from the similarity data showed that all the 22 cultivars analysed were closely related with a narrow genetic base. There were sufficient RAPD polymorphisms that were collectively useful in distinguishing the cultivars. The dendrogram grouped all the AA, BB, AAA, AAB and ABB genomes into a major cluster. Several subgroups are recognized within the major clade. As expected, Ensete glauca Roxb. (Musaceae) and Strelitzia reginae Banks (Strelitziaceae) were clearly differentiated from the analysed edible bananas. Our study showed that RAPD markers are sufficiently abundant to classify and readily dissect genetic differences between the closely related Musa germplasm and provide a basis for the selection of parents for improvement of this germplasm.     

Genetic Structure of Wild and Domesticated Populations of Capsicum annuum (Solanaceae) from Northwestern Mexico Analyzed by RAPDs

Levels of genetic variation and genetic structure of 15 wild populations and three domesticated populations of Capsicum annuum were studied by RAPD markers. A total of 166 bands (all of them polymorphic) and 126 bands (125 of them polymorphic) were amplified in wild and domesticated populations, respectively. Mean percentage of polymorphism was 34.2% in wild populations and 34.7% in domesticated populations. Mean and total genetic diversity were 0.069 and 0.165 for wild populations and 0.081 and 0.131 for domesticated populations. Parameters of genetic diversity estimated from 54 bands with frequencies ≥1 − (3/n) (n = sample size) showed that 56.7% of the total variation was within and 43.3% among wild populations, whereas 67.8% of the variation was within and 32.2% among domesticated populations. AMOVA indicated that total genetic diversity was equally distributed within (48.9 and 50.0%) and among (50.0 and 51.1%) populations in both wild and domesticated samples. Wild and domesticated populations were clearly resolved in a UPGMA dendrogram constructed from Jaccard’s distances (average GD = 0.197), as well as by AMOVA (17.2% of variance among populations types, p = 0.001) and by multidimensional scaling analysis. Such differentiation can be associated with domestication as well as different origin of gene pools of the wild (Northwestern Mexico) and cultivated (more probably Central Mexico) samples analyzed. The considerable genetic distances among cultivars (average GD = 0.254) as well as the high number of diagnostic bands per cultivar (33 out of 126 bands), suggest that genetic changes associated with domestication could have resulted from artificial selection intervening in different directions, but the inclusion of more domesticated samples might clarify the nature of distinctions detected here.     

Genetic Variation of Ethiopian Mustard (Brassica carinata A. Braun) Germplasm in Western Canada

Information on genetic diversity and genetic relationships among genotypes of Brassica carinata is currently limited. The objectives of this study were to evaluate patterns and levels of genetic diversity in B. carinata based on amplified fragment length polymorphisms (AFLP) as compared with Brassica juncea and Brassica nigra, and to evaluate agronomic and seed quality data for plants grown in the field in western Canada. A total of 296 AFLP bands were generated from four primer pair combinations and scored for presence/absence in 66, 20 and 7 accessions of B. carinata, B. juncea and B. nigra, respectively. B. carinata was less genetically diverse than the other two species. Differences in diversity were evident in the proportion of polymorphic loci within each species: 23, 35 and 50% for B. carinata, B. nigra and B. juncea, respectively. Pair-wise similarity measures based on the Jaccard coefficient were highest among accessions of B. carinata and showed the narrowest range: 0.911 (0.810–0.981) compared to B. nigra: 0.569 (0.438–0.660) and B. juncea: 0.715 (0.345–0.951). AFLP-based genetic distance information can be used by plant breeders to select diverse genotypes. AFLPs are also useful for fingerprinting cultivars and two primer pair combinations were sufficient to uniquely identify all the accessions of B. carinata. More variation among accessions was identified in the agronomic trial than had previously been described in studies of B. carinata in western Canada, but the data were too limited to draw conclusions regarding specific accessions. Overall, the findings were in agreement with other published work describing the favourable agronomic potential of this species.     

Analysis of genetic diversity in a sweet potato (Ipomoea batatas L.) germplasm collection from Tanzania as revealed by AFLP

Sweet potato (Ipomoea batatas L.) is the fifth most important crop in the developing countries after rice, wheat, maize and cassava. The amplified fragment length polymorphism (AFLP) method was used to study the genetic diversity and relationships of sweet potato accessions in the germplasm collection of Sokoine University of Agriculture, Morogoro and Sugarcane Research Institute, Kibaha, Tanzania. AFLP analysis of 97 sweet potato accessions using ten primer combinations gave a total of 202 clear polymorphic bands. Each one of the 97 sweet potato accessions could be distinguished based on these primer combinations. Estimates of genetic similarities were obtained by the Dice coefficient, and a final dendrogram was constructed with the un-weight pair-group method using arithmetic average. AFLP-based genetic similarity varied from 0.388 to 0.941, with a mean of 0.709. Cluster analysis using genetic similarity divided the accessions into two main groups suggesting that there are genetic relationships among the accessions. Principal Coordinate analysis confirmed the pattern of the cluster analysis. Analysis of molecular variance revealed greater variation within regions (96.19%) than among regions (3.81%). The results from the AFLP analysis revealed a relatively low genetic diversity among the germplasm accessions and the genetic distances between regions were low. A maximally diverse subset of 13 accessions capturing 97% of the molecular markers diversity was identified. We were able to detect duplicates accessions in the germplasm collection using the highly polymorphic markers obtained by AFLP, which were found to be an efficient tool to characterize the genetic diversity and relationships of sweet potato accessions in the germplasm collection in Tanzania.     

Assessment of genetic relationships among Pyrus species and cultivars using AFLP and RAPD markers

Twenty-five Pyrus communis L. cultivars including eight traditional Portuguese pears, and four commercial Pyrus pyrifolia (Burm.) Nak. (Japanese pear or `nashi') cultivars were analysed by RAPD and AFLP techniques focusing on their molecular discrimination and the assessment of their genetic relatedness. Twenty-five primers generated 324 RAPD markers, among which 271 (84%) were polymorphic. The AFLP technique, using seven primer combinations, revealed a similar level of molecular polymorphisms (87%), representing 418 polymorphic bands among a total of 478 scored in autoradiographs. The high reproducibility of RAPD and AFLP techniques was confirmed comparing DNA samples from different extractions and different digestions of DNA from the same plant. Three genetic similarity matrices and respective dendrograms were elaborated on using RAPD, AFLP or joint RAPD and AFLP data. Both molecular marker techniques proved their reliability to assess genetic relationships among pear cultivars. P. pyrifolia cultivars exhibit a closer genetic relatedness, clustering apart from P. communis cultivars. Within P. communis, `William's', as well as `Doyenne du Comice', cluster close to their hybrids. Most of the Portuguese cultivars tend to cluster together, indicating to constitute a relatively independent genetic pool, which can be of interest in pear breeding programs.     

Assessing the Genetic Diversity in the International Cocoa Genebank,Trinidad (ICG,T) using Isozyme Electrophoresis and RAPD

Random amplified polymorphic DNA (RAPD) and isozyme electrophoresis (IE) techniques were used to estimate the level of genetic diversity in a sample of cacao germplasm existing at the International Cocoa Genebank, Trinidad. Twenty-six cocoa populations represented by 459 cocoa genotypes were analysed using IE and 22 populations represented by 353 cocoa genotypes were analysed using RAPD. Despite few differences in the classification of the populations, both techniques revealed three major groups: the indigenous trees, the cultivated Trinitario and the cultivated trees from Ecuador. Two-thirds of the partitioned diversity were found within populations and one-third between the populations, with both techniques.     

Evaluation of genetic diversity in Turkish melons (<Emphasis Type="Italic">Cucumis melo</Emphasis> L.) based on phenotypic characters and RAPD markers

The genetic relationships among 56 melon (Cucumis melo L.) genotypes collected from various parts of Turkey were determined by comparing their phenotypic and molecular traits with those of 23 local and foreign melon genotypes to investigate the taxonomic relationships and genetic variation of Turkish melon germplasm. Sixty-one phenotypic characters and 109 polymorphic RAPD markers obtained from 33 primers were used to define the genetic similarity among the melon genotypes by dendrograms or two and three dimensional scaling. There were high correlations (r ≥ 0.97) among the four resulting matrices used in molecular characterization. The correlations between phenotypic (Euclidean) and molecular Euclidean, Jaccard, Simple matching, and Nei analyses were r = 0.41, r = −0.40, r = −0.43 and r = −0.40, respectively. Related genotypes or genotypes collected from similar regions were partitioned to similar clusters. Both analyses (phenotypic and molecular) indicated that non-sweet melon types were dissimilar from sweet types and diversity of Turkish melon genotypes was higher than that of sweet foreign cultivars examined, but similar to that of the reference accessions employed. It was also observed that sweet Turkish melon genotypes belonging to groups inodorus and group cantalupensis were highly variable and could have intermated or have crossed with other non-sweet types.