Genetic diversity of introduced and local Spanish persimmon cultivars revealed by RAPD markers

Persimmon culture has become an alternative for fruit growers in Italy, Israel and Spain. However, there is some confusion concerning cultivar identification in non-Asian countries were the species was introduced. Authenticating the identity of germplasm resources of persimmon would be a great value for breeding. Due to the floral biology of the persimmon species the expected genetic variability is high. RAPD markers were chosen for this study of persimmon germplasm resources in Spain. Nineteen markers were obtained from 8 primers. The average of 2.4 markers/primer was higher than that obtained in other woody fruit species. The availability of data referenced from isozymes and pomological traits revealed complete agreement among groups identified by RAPDs, isozymes and pomological traits. Results suggest that RAPD technology is adequate for fingerprinting persimmon and the data is consistent with persimmon's hypothetical origins, adaptation history and previous classification by isozymes or pomological traits. Many synonyms have been identified, mostly in cultivars from local surveys, suggesting that a few new genotypes arose in Spain since the species was introduced to Europe. By means of RAPD markers, a better identification of the European persimmon germplasm is available.     

Genetic Relationships of some PCNA Persimmons (Diospyros kaki Thunb.) from China and Japan revealed by SRAP analysis

Sequence-related amplified polymorphism (SRAP) marker was employed to analyze genetic relationships of 10 Chinese, 11 Japanese varieties of persimmon and its 6 relatives. Twenty out of 72 primer combinations could amplify clearly and consistently. Just only one primer set could discriminate all the genotypes used in this study. The genetic relationships were analyzed using unweighted pair-group method of arithmetic average cluster analysis (UPGMA) and principal coordinated analysis (PCOA). The results showed: Chinese varieties were grouped into two clusters, while the Japanese varieties were grouped into one cluster with two subgroups. The persimmon relatives were clustered together. Probably, Chinese and Japanese Pollination-constant and Non-astringent (PCNA) persimmons had different genetic background. ‘Eshi No.1’ from Hubei province was close to Male type 6. ‘Xiangxitianshi’ from Xiangxi municipality, Hunan province, had a high similarity coefficient with ‘Maekawa-Jirou’ and was clustered in the Japanese varieties group, indicating that ‘Xiangxitianshi’ maybe close to the Japanese variety in terms of genetic background. The Chinese Pollination-constant and Astringent (PCA) and PCNA persimmons were not distinctly distinguished implying that the non-astringent trait of Chinese PCNA type might result from the PCA type.     

Genetic relationships and diversity among Brazilian cultivars and landraces of common beans (Phaseolus vulgaris L.) revealed by AFLP markers

The genetic variation and relationships among 31 accessions of Phaseolus vulgaris L., and two representatives of Vigna unguiculata L., were evaluated by AFLP analysis. A total of 263 DNA fragments across all materials were scored using nine primer combinations, averaging 32 per primer. More than 95% of the amplification products showed polymorphism, indicating high variation at the DNA level among these accessions. Pair-wise genetic similarity (Jaccard's coefficient) ranged from 0.553 to 0.840, with a mean of 0.765. Twenty-three accessions (70%) clustered into three groups. A majority of the commercial cultivars (91%) clustered within a single group, whereas the landraces were distributed along all the variation. An apparent correlation with phaseolin types was detected. Results of this study suggest that Brazilian landraces truly represent the overall genetic variability of Phaseolus vulgaris, confirming the multiple origins of these materials, and their potential as a source of variation for breeding programs.     

Assessing genetic diversity of sweet potato (Ipomoea batatas (L.) Lam.) cultivars from tropical America using AFLP

The sweet potato genebank at the International Potato Center (CIP) maintains 5,526 cultivated I. batatas accessions from 57 countries. Knowledge of the genetic structure in this collection is essential for rational germplasm conservation and utilization. Sixty-nine sweet potato cultivars from 4 geographical regions (including 13 countries) of Latin America were randomly sampled and fingerprinted using AFLP markers. A total of 210 polymorphic and clearly scorable fragments were generated. A geographic pattern of diversity distribution was revealed by mean similarity, multidimensional scaling (MDS), and analysis of molecular variance (AMOVA). The highest genetic diversity was found in Central America, whereas the lowest was in Peru-Ecuador. The within-region variation was the major source of molecular variance. The between-regions variation, although it only explains 10.0% of the total diversity, is statistically significant. Cultivars from Peru-Ecuador, with the lowest level of within region diversity, made the most significant contribution to the between region differentiation. These results support the hypothesis that Central America is the primary center of diversity and most likely the center of origin of sweet potato. Peru-Ecuador should be considered as a secondary center of sweet potato diversity.     

Inter Simple Sequence Repeat (ISSR) Analysis of Diploid Coffee Species and Cultivated Coffea arabica L. from Tanzania

Inter simple sequence repeat (ISSR) markers were used to evaluate levels of genetic similarity among Coffea arabica L. accessions from Tanzania and to estimate levels of genetic similarities in C. arabica and diploid coffee species. The six ISSR primers used generated a total of 82 fragments and the dissimilarity values ranged from 0.21 to 1. Mean dissimilarity values between provenances (0.56–0.85) were higher than within provenances (0.37–0.68). Cluster analysis based on Nei’s genetic distances showed C. arabica provenances grouping based on geographical origin. Two major clusters were formed that constituted of provenances from Kilimanjaro and Arusha in one sub-cluster; Tanga and Morogoro in the other; the second cluster had Mbeya provenances and diploid species, respectively. The implication is that Mbeya provenances are different from the rest of Tanzanian C. arabica. A principal coordinate analysis (PCA), whose first three coordinates explained 43% of the variation, showed similar groupings as in the cluster analysis. A separate cluster analysis of diploid species showed a distinct separation of the three species used. ISSR data gave results similar to previous findings from random amplified polymorphic DNA(RAPD) analysis. The results also confirm the limited diversity present in cultivated C. arabica 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.     

Genetic Relationship and Diversity of Four MangiferaSpecies Revealed through AFLP Analysis

We used AFLP analysis to explore the genetic relationship and diversity between and within 4 Mangifera species. We analyzed 35 accessions comprising 8 cultivars and 3 landraces of M. indica L., 11 landraces of M. odorata Griff., 7 landraces of M. foetida Lour., and 6 landraces of M. caesia Jack. Using 8 primer combinations produced a total of 518 bands, 499 (96.3%) of which were polymorphic among the 35 accessions. Clustering analysis showed that all 35 accessions were basically classified into 4 groups corresponding to the 4 Mangifera species. Our results indicate that the genetic relationship of these 4 Mangifera species based on AFLP analysis is in good agreement with their classification by classic methods. In addition, it was clearly revealed the genetic diversity between and within 4 Mangifera species. The findings obtained in this study are useful for the breeding in Mangifera species.     

DNA fingerprinting sheds light on the origin of introduced mulberry (Morus spp.) accessions in Italy

Mulberries are members of the genus Morus L., a taxonomic group showing a great genetic variability and adaptability to different environmental conditions. This study deals with the use of AFLP-based fingerprints as a tool for estimating genetic variability within as well as among three different mulberry species (i.e., M. alba L., M. latifolia Poir. and M. bombycis Koidz.). A high level of polymorphism (72.2) was found over all the 48 accessions analyzed. Genetic similarity (GS) within single Morus species ranged from 0.845 (M. bombycis) to 0.884 (M. alba) being intermediate in M. latifolia (0.869). The between-species mean genetic similarity estimates based on pair-wise AFLP marker fingerprint comparison were very similar ranging from 0.861 to 0.874. The partition of the genetic variation over the three Morus species was unexpected a proportion of the among-species genetic diversity as low as GST= 0.084 pointed out that about 92% of the total genetic diversity found among Morus accessions is due to DNA polymorphisms within a species, while only 8% of the total variation was highlighted among species. Our data indicate that some of the introduced accessions showing distinctive phenotypes, clearly differentiated from those revealed in the original habitat where they have been selected and adapted, hide an identical genotype.     

Genetic diversity of some accessions of Cucurbita maxima from Spain using RAPD and SBAP markers

Increasing the knowledge of the molecular diversity of a crop is essential for extending its genetic base, identifying cultivars and selecting parental varieties for breeding programs. In this sense, Cucurbita maxima Duch. is poorly characterised. Nineteen accessions of this species and 8 related Cucurbita accessions were included in a genetic diversity analysis. For this purpose, Random Amplified Polymorphic DNA markers (RAPDs), which analyse neutral variability, and Sequence-Based Amplified Polymorphism (SBAPs), which preferentially amplify coding regions of the genome, were used. While the UPGMA cluster and the principal coordinates analysis obtained using RAPDs did not group the different accessions according either to fruit morphological criteria or to passport data (origin and agro-climatic conditions), the principal coordinates analysis obtained using SBAPs grouped the different pumpkin accessions fundamentally according to the type of use (human consumption, animal fodder or ornamental). This passport trait is reported to be associated with agronomic breeding characters of interest. The usefulness of both types of markers for discriminating accessions of breeding interest is discussed.     

Determining Sources of Diversity in Cultivated and Wild <Emphasis Type="Italic">Lablab purpureus</Emphasis> Related to Provenance of Germplasm by using Amplified Fragment Length Polymorphism

To improve understanding of diversity of Lablab purpureus and establish relationships among 103 germplasm accessions collected from diverse geographic origins, amplified fragment length polymorphism markers were used. Four primer sets selected out of 16 produced 289 clear, repeatable polymorphisms. UPGMA analysis of similarity data clustered the accessions according to their subspecific taxonomic organization, i.e., subsp. purpureus and subsp. uncinatus, as well as to cultivated and wild forms. The well-represented landraces from Africa and Asia, belonging predominantly to subsp. purpureus, displayed moderate genetic diversity. Wild forms from Africa showed far greater levels of diversity that would justify taxonomic re-assessment of the wild subsp. uncinatus. The molecular analysis identified forms that were collected in the wild in India but were genetically placed intermediate between wild and cultivated forms. As these plant types did not exist among the African accessions, it is suggested that they might represent escapes from early attempts of domestication. These results support the suggested pathway of domestication and distribution of L. purpureus from Africa to Asia. Additional members to a previously published core collection of the species are proposed.     

Diversity of Nordic Landrace Potatoes (<Emphasis Type="Italic">Solanum tuberosum</Emphasis> L.) Revealed by AFLPs and Morphological Characters

The management of genebank collections of cultivated potato is costly due to the need for in vitro maintenance and virus eradication. Therefore, it is important to set up conservation strategies, which prevent duplicates entering the collections. In this study, 32 Nordic potato landraces were studied for 57 morphological traits and analysed for amplified fragment length polymorphism (AFLP). Most landraces could be distinguished based on the morphological characters, except five accessions. Using five primer combinations to generate 114 reproducible AFLPs, of which 63 (55%) were polymorphic, the five morphologically indistinguishable accessions were placed into two groups with identical AFLP patterns, suggesting that some of the accessions were redundant for long-term preservation. The AFLP data showed that the Nordic collection of potato landraces is composed of genetically different clones, and morphological analysis revealed a wide range of variability. This variability seems to be distributed randomly over the Nordic region since the cluster analysis based on AFLPs and morphological traits revealed no grouping based on the country of origin. Principal component analysis suggests that fewer morphological traits than used in this study will be sufficient to discriminate between different genotypes of cultivated potato (Solanum tuberosum L.). Future possibilities for rationalising potato collections are discussed.     

AFLP Analysis of the Phenetic Organization and Genetic Diversity in the Sugarcane Complex, Saccharum and Erianthus

Amplified fragment length polymorphism (AFLP) markers were evaluated for determining the phylogenetic relationships, and the diversity in the Saccharum complex using 30 clones belonging to S. officinarum, S. robustum, S. spontaneum, S. barberi, S. sinense and the related genus Erianthus. The phenetic tree of the species clones based on AFLP data was consistent with the known taxonomical relationships. AFLP gave higher resolution of closely related species into discrete groups than that by RAPD and RFLP markers, reported earlier. The levels of diversity within the various Saccharum species were also found to be higher than those obtained previously with the same set of clones using RAPD markers. The intraspecies similarity in S. barberi and S. sinense was much higher than interspecies similarity suggesting a clear separation of the two, which are considered ‘horticultural species’. The genetic similarity matrix derived from a single primer combination highly correlated (r = 0.980) with that obtained from all the 12 primer combination used in the study, thus highlighting the efficiency of a single primer combination in delineating species relationships. All the primer combinations could identify markers that are specific to each of the species and the genus Erianthus. Among the species, specific markers were highest in S. spontaneum followed by S. robustum, S. barberi, S. officinarum and S. sinense. Erianthus had a distinct profile with 30% of the total amplified fragments being specific to it. This offers great scope for identifying intergeneric hybrids, which has been very difficult using morphological traits and RAPD markers. High degree of correspondence between the results from the cluster analysis based on Jaccard's similarity index, Neighbour Joining tree based on Sokal and Michener distance matrix and AFTD (Analyses Factorielle on Table of Distances) analysis clearly demonstrated that AFLP markers would be an appropriate tool in providing better information about the relationships among the species, estimation of diversity, and in revealing species and genus specific markers that could be directly applied in sugarcane breeding programmes.     

Identifying and selecting for genetic diversity in Papua New Guinea sweetpotato Ipomoea batatas (L.) Lam. germplasm collected as botanical seed

A total of 141 Ipomoea batatas (L.) Lam. accessionsderived from botanical seed originally collected from 26 sites in 4 Provinces inPapua New Guinea, a secondary center of genetic diversity for sweetpotato, weregenetically analyzed. Two hundred Amplified Fragment Length Polymorphism (AFLP)markers were identified and utilized in the analysis. Relatedness amongaccessions was estimated by analyzing the AFLP data using the Dice coefficientof similarity and UPGMA methods. The molecular analysis revealed relativelylimited genetic diversity within and between sites. Genotypes collected in agiven region often displayed molecular marker variability similar to thatobserved over the entire sampled area. However, a subset of 14 genotypes derivedfrom seed collected from New Ireland island differed from genotypes collected onNew Guinea island. Estimates of genetic diversity-based similarity valuescalculated from the AFLP data indicated a moderate level of diversity (0.767mean coefficient of similarity) across all plant materials analyzed. Threemethods of selection were evaluated for their efficacy in capturing themolecular marker diversity within the plant materials in the form of a subset.They were random, stratified-random (geographic based), and marker-assistedselection (MAS). MAS was the most efficient. A Maximally Diverse Subset (MDS) of12 genotypes capturing 92% of the molecular marker diversity was identified.     

Assessing phenotypic,biochemical, and molecular diversity in coriander (<Emphasis Type="Italic">Coriandrum sativum</Emphasis> L.) germplasm

Our goals for this research were to elucidate phenotypic and biochemical diversity in coriander (Coriandrum sativum L.) populations maintained at the North Central Regional Plant Introduction Station in Ames, IA, and examine relationships between amplified fragment length polymorphism (AFLP) markers and patterns of phenotypic and biochemical diversity. Phenotypic and biochemical traits were evaluated, and analyses of variance and mean comparisons were performed on the resulting data sets. Euclidean distances from phenotypic (PD) and biochemical (BD) data were estimated, and modified Rogers’ distances (RD) were estimated for 80 polymorphic AFLP markers. These data were subjected to cluster analyses (CA) and principal components analyses (PCA), to reveal patterns among populations, and to analyses of molecular variance (AMOVA) for grouping patterns from PD and BD by using the 80 polymorphic AFLP markers. Resulting phenotypic, biochemical, and molecular distance matrices were also compared by applying Mantel tests. Our results describe significant differences among populations for all the phenotypic traits, and dendrograms obtained from PD and BD revealed complex phenetic patterns, as did groups from PCA. The primary seed essential oils and nearly all fatty-acid components were identified and their abundance measured; the primary chemical constituents of corresponding PCA groups are described herein. Molecular evidence supported phenotypic and biochemical subgroups. However, variation attributed among subgroups and groups was very low (∼4–6%), while variation among populations within groups was intermediate (∼24–26%), and that within populations was large (∼69–70%), reflecting weak differentiation among subgroups and groups, which was confirmed by values for fixation indices. Phenotypic subgroups described in this study differed somewhat from previous infraspecific classifications. Weak correlations were found between the phenotypic and biochemical matrices and between the biochemical and AFLP matrices. No correlation was found between the phenotypic and AFLP matrices. These results may be related to coriander’s phenotypic plasticity, its wide range in lifecycle duration, its predominantly allogamous reproductive biology, a human-selection process focused on special traits that may be controlled by few genes, and the widespread trade of coriander seeds as a spice, which may result in dynamic, poorly differentiated molecular variation, even when phenotypic and biochemical differentiation is easily documented. The U. S. Government’s right to retain a non-exclusive, royalty-free license in and to any copyright is acknowledged.     

Genetic and morphological variation in breadfruit (<Emphasis Type="Italic">Artocarpus altilis</Emphasis> (Park.) Fosberg) in the Western Ghats of India using AFLP markers

Artocarpus altilis (Park.) Fosberg is an important fruit vegetable tree grown in the homesteads of southern part of India. To provide reasoned scientific management practices and conservation measures, the pattern of morphological and genetic variation were investigated for six populations using Amplified Fragment Length Polymorphism (AFLP) markers and 15 morphological traits. The use of five selective primer combinations on 60 samples resulted a total of 414 bands in which 85% were polymorphic. The values of Nei’s genetic distance varied from 0.0044 (Palai–Palghat) to 0.3376 (Palghat–Mangalore). Analysis of molecular variance revealed most of the variation within populations (57.45%) than (42.55%) among populations. The genetic variation by AFLP data is not reflected in quantitative morphological variables. However, the genetic and geographical distances were positively correlated which were further well supported by the PCO analysis and Dollo-parsimony tree, both show the tendency of the individuals to group according to the geographical localities.     

Genetic diversity in cucumber (Cucumis sativus L.): II. An evaluation of selected cultivars released between 1846 and 1978

Genetic variation among 155 U.S. modern and heirloom cultivars was assessed from assays of 21 polymorphic isozyme loci. Four loci (Fdp-1, Mdh-1, Mpi-1 and Pgd-1) were monomorphic. Multivariate analyses partitioned cultivars into two distinct groups: those released before 1968, and those released after 1968. Cluster analysis produced a dendrogram with 14 nodes and 28 groups. Modern U.S. and European cultivars released after 1968 differed in isozyme frequencies. Isozymic profiles clearly discriminated some cultivars with unique attributes and/or pedigrees [e.g., Windermoor Wonder (USA), Gergana (The Netherlands), Seiram (The Netherlands), Fancy Pak (USA), Dasher 2 (USA), and WI 2757 (USA)].     

Genetic Analysis of Egyptian Date (<Emphasis Type="Italic">Phoenix dactylifera</Emphasis> L.) Accessions Using AFLP Markers

Forty-seven samples of date palm (Phoenix dactylifera L.) collected from eight locations in Egypt were studied using four sets of amplified fragment length polymorphism (AFLP) markers with near infrared fluorescence labeled primers. These samples belonged to 21 named accessions and 9 of unknown pedigrees. A total of 350 bands were scored and 233 (66.6%) were polymorphic. Twenty-seven Egyptian accessions and ‘Medjool’and ‘Deglet Noor’accessions from California could beclassified into the major cluster. This major cluster may represent a major group of date palm germplasm in North Africa. There were four other clusters, each containing one or two accessions. The variety ‘Halawy’and one accession of unknown provenance were most likely from hybridization between two clusters. Six groups of accessions of which had the same names, revealed similar but not identical AFLP profiles suggesting these accessions might derive from seedlings rather thanthrough clonal offshoot propagation.     

AFLP fingerprinting of sesame (<Emphasis Type="Italic">Sesamum indicum</Emphasis> L.) cultivars: identification,genetic relationship and comparison of AFLP informativeness parameters

Amplified fragments length polymorphism (AFLP) was used to distinguish 20 cultivars of sesame (Sesamum indicum L.) and to elucidate the genetic relationship among these genotypes. The data were also used to estimate the usefulness of parameters currently used to assess the informativeness of molecular markers. A total of 339 markers were obtained using 8 primer combinations. Of the bands, 91% were polymorphic. Five primer combinations were able to distinguish all 20 cultivars used. None of the remaining three primer combinations could distinguish all accessions if used alone, but using all three combinations reduced the probability of a random match to 5 × 10⁻⁵. Polymorphic information content (PIC), resolving power (Rp) and marker index (MI) of each primer combination failed to correlate significantly with the number of genotypes resolved. Jaccard’s similarity coefficients ranged from 0.31 to 0.78. Fifteen cultivars were grouped by four UPGMA-clusters supported by bootstrapping values larger than 0.70. The grouping pattern was similar to the grouping generated by principal coordinate analysis. The results demonstrated that AFLP-based fingerprints can be used to identify unequivocally sesame genotypes, which is needed for cultivar identification and for the assessment of the genetic variability of breeding stocks. We recommend to use the number of cultivars identified by a primer combination instead of PIC, Rp and MI; and to calculate the maximal, instead of average probability of identical match by chance in the assessment of the informativeness of a marker for cultivar identification.