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.     

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.     

Assessment of Genetic Diversity in Upland Cotton (<Emphasis Type="Italic">Gossypium hirsutum</Emphasis> L.) Breeding Lines by using Amplified Fragment Length Polymorphism (AFLP) Markers and Morphological Characteristics

Genetic diversity in 24 advanced breeding lines of cotton was studied by using six amplified fragment length polymorphism (AFLP) primer-pairs and 14 morphological characters. The six selected AFLP primer-pairs generated a total of 535 amplification products, of which 460 were found to be polymorphic resulting in 85.9% polymorphism. The observed genetic distances using AFLP markers ranged from 30% to 87% with an average of 34%. A wide range of variability was observed for all the morphological traits studied. The range in taxonomic distance was from 0.60 to 2.77. Most of the lines could be clustered in two major clusters in both the analyses. But the correlation coefficient between the pair-wise distances estimated from AFLPs and the average taxonomic distances estimated from morphological characters was found to be 0.04. UPGMA cluster analysis revealed inconsistencies in the clustering patterns, as the co-phenetic correlation coefficient between the dendrograms for morphological and AFLP data indicated a poor fit for the two data types. From combined information, genotypes ‘RST-12’, ‘H 1226’, ‘P 348’, ‘KDCAKD’, ‘CISV 24’ and ‘H1222’ were found to be distinct from rest of the material.     

Genetic Structure in Tunisian Apricot, Prunus armeniaca L., Populations Propagated by Grafting: A Signature of Bottleneck Effects and Ancient Propagation by Seedlings

In order to give insights into the origin and historical selection process of Tunisian apricot propagated by grafting, 31 cultivars from three areas presenting contrasting ecological conditions – Kairouan, Testour and Ras Jbel were compared to cultivars from Europe, North America, North Africa, Turkey, Iran and China, using 234 AFLP markers. The phenetic analysis allowed to distinguish 5 clusters, the four previously defined groups: – ‘diversification’, ‘geographically adaptable’, ‘continental European’ and ‘Mediterranean’ – groups and the Tunisian one. The partitioning of genetic diversity within and between cultivar groups assessed according to the Bayesian approach and assuming Hardy–Weinberg equilibrium, showed a loss of 21.81–38.49% of genetic diversity in Tunisian apricot compared to Mediterranean and diversification groups, respectively. Genetic variation occurred within Tunisian subgroups rather than among (F_ST = 0.060) evidencing a narrow genetic pool. Mediterranean and Tunisian groups were the least differentiated. Comparing them, 24 AFLP fragments discriminated the Mediterranean group from the Tunisian group but most of them where also shared by the other groups. Strongly differentiated gene pool and low genetic diversity are probably the result of bottleneck effects linked to the occurrence of propagation by seedlings rather than by grafting during the introduction periods in the North and the Centre of Tunisia. This study points at the propagation by seedlings as an important factor which should be taken into account to understand the evolution of apricot in South Mediterranean areas.     

Variation in morphology and seed production of snow clover [<Emphasis Type="Italic">Trifolium pratense</Emphasis> L. subsp. <Emphasis Type="Italic">nivale</Emphasis> (Koch) Arcang.] germplasm from the Rhaetian Alps,Italy

A recent approach to restoration of degraded mountain landscapes (e.g. ski slopes) recommend to sow seed mixtures including ‘site-specific’ species, i.e. native germplasm adapted to the prevailing conditions and ecologically compatible with the area of intervention. To better exploit the potential of these species and enhance their spread in revegetation projects, deeper knowledge is needed, however, on the existing variation in their germplasm, particularly for economically useful traits such as seed yield. Snow clover is one of the recommended ‘site-specific’ legumes. This study evaluated 12 populations of snow clover, collected in three valleys of the Rhaetian Alps, Italy, to assess their variation and highlight any promising material. The evaluation encompassed a mountain and a lowland site, to verify the behaviour of the germplasm also in one environment markedly different from that of origin. Differences among valleys were observed for flower colour, growth habit and type, flowering time and susceptibility to mildew, although the overall pattern of phenotypic diversity was similar among valleys. Some effect of the evaluation site on the expression of morphological and seed production traits, and on the overall diversity, was also evident. Furthermore, the lowland site experienced very high plant mortality towards the end of the first growing season. Individual populations proved a valuable source of variation for seed production. Some populations, in particular, were worth of attention for a possible selection of high-seed-yielding snow clover cultivars. An assessment of the mating system suggested a lack of self-tripping or an almost absolute self-incompatibility in snow clover.     

Genetic diversity and differentiation in Ethiopian populations of Phytolacca dodecandra as revealed by AFLP and RAPD analyses

Amplified fragment length polymorphism (AFLP) and random amplified polymorphic DNA (RAPD) analyses were performed on six populations (a total of 89 individuals) of Phytolacca dodecandra (endod) collected in Ethiopia. The populations were selected based on our previous investigation to represent two altitude groups: lowland/central-highland (1600–2500 m) and highland (2501–3000 m). A total of 197 AFLP and 68 RAPD markers were scored from 5 primer pairs and 12 random primers, respectively. The overall patterns obtained for AFLPs and RAPDs from diversity, cluster and principal component analyses were very comparable. However, the moderate correlation (r = 0.56) between AFLP and RAPD similarity matrices as well as the discrepancies in diversity estimates between the two techniques in some populations and in the lowland/central-highland plants could be due to differences in sensitivity of reaction conditions, bias in scoring of bands, number of markers used for analyses, and/or parts of the genome surveyed. For both AFLP and RAPD, the lowland/central-highland populations showed higher polymorphism and Shannon information measure (H) than the highlands. Cluster and principal component analyses performed for both marker types have also clearly demonstrated the differentiation of all the lowland/central highland plants from those of the highlands, in agreement with our previous conclusion. Markers scored from any of the five AFLP primer pairs were sufficient to clearly distinguish the two altitude groups; with RAPD, selection of about 8 informative markers produced by seven random primers was needed for the same purpose.     

Relationship of European persimmon (Diospyros kaki Thunb.) cultivars to Asian cultivars, characterized using AFLPs

Sixty one persimmon (Diospyros kaki Thunb.) selections, including 17 Italian, 11 Spanish, 13 Japanese, six Korean, five Chinese, one Israeli, and eight of unknown origin, were evaluated for genetic differences by AFLP analysis. Relationships among cultivars were evaluated by UPGMA clustering, Neighbor Joining, and MultiDimensional Scaling. While similarities among groups were generally less than 0.60, both UPGMA and Neighbor Joining separated European and Asian cultivars. Spanish and Italian cultivars were not separated by any of the analyses, suggesting that they share a common gene pool, while Japanese, Chinese and Korean cultivars formed distinct clusters. Diversity within groups was greater than diversity between groups. Most cultivars were quite polymorphic (only 0.60–0.80 similarity between cultivars). In addition, the presence of several Japanese cultivars in the European group and a group of European cultivars nested between Chinese and Korean groups suggest that similar, but different progenitors were used in the development of the present European cultivars. ‘Kaki Tipo’ selections from different sources were clearly different by AFLP analysis, indicating that they are separate cultivars.     

Relationships among different geographical groups,agro-morphology,fatty acid composition and RAPD marker diversity in Safflower (<Emphasis Type="Italic">Carthamus tinctorius</Emphasis>)

Patterns of geographical diversity, and the relationship between agro-morphological traits and fatty acid composition were assessed for 193 safflower (Carthamus tinctorius) accessions representing forty countries. Accessions were assigned to eight groups based on geographical proximity. Cluster and Principal Component analyses were performed to assess patterns of diversity among the accessions and to select the most distant accessions from each of eight groups for analysis of randomly amplified polymorphic DNA (RAPD) markers. There was a large amount of diversity for agro-morphological traits, fatty acid composition, and RAPD markers. Most correlations among different traits were rather low. Plant height showed a positive correlation with days to flowering (r = 0.63**). Palmitic acid was positively correlated with stearic acid and oleic acid values, and negatively correlated with linoleic acid (P < 0.01). Oleic acid and linoleic acid showed a strong negative correlation (r = −0.89**). The first three principal components together explained 59% of the variation, however, neither principal component analysis (PCA) nor marker analysis revealed a clear relationship between diversity pattern and geographical origin. Accessions from some geographical regions tended to group together, such as accessions from South Western Asia, Central Western Europe, and the Mediterranean region. The correlation between the morphological matrix and the genetic matrix based on RAPD markers was not significant (r = 0.027). Wide diversity in safflower germplasm indicates a considerable potential for improving this crop for both agronomic and quality traits.     

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.     

Intra-varietal genetic diversity of the grapevine (<Emphasis Type="Italic">Vitis vinifera</Emphasis> L.) cultivar ‘Nero d’Avola’ as revealed by microsatellite markers

The Sicilian grape cultivar ‘Nero d’Avola’ is among the oldest and most cultivated in the island, taking part in the production of several red wines exported worldwide, including DOC wines (Etna Rosso and Cerasuolo di Vittoria). Due to the ancient origin and repeated clonally propagation of the cultivar, phenotypic variability has been observed. Clone identification in this important cultivar has so far relied on phenotypic and chemical traits analyses, often affected by environmental conditions. Genetic markers, such as microsatellites, are particularly useful for cultivar identification, parentage testing, pedigree reconstruction and population structure studies. In the present paper, microsatellites were used to analyze the intra-varietal genetic diversity among 118 plants of ‘Nero d’Avola’, collected in 30 vineyards displaced in different areas of Sicily. Out of 22 microsatellites, 11 showed polymorphism among samples and 15 different phylogenetic groups were identified. Results show that ‘Nero d’Avola’ actually comprises different genetic profiles, although most of clones share a common origin.     

Genetic diversity of prolamines in Agropyron mongolicum Keng indigenous to northern China

Genetic variability, based on prolamines, was studied among 40 populations of Agropyron mongolicum Keng that were collected from the extensive geographic areas of northern China. A high level of genetic diversity was detected in these A. mongolicum populations. In total, 81 electrophoretic bands were observed following acid polyacrylamide gel electrophoresis (A-PAGE), among which 20, 16,␣10, and 35 allelic variants were separated into α-, β-, γ-, and ω-fractions of prolamine. Each A. mongolicum population had unique electrophoretic pattern, which exhibited enough genetic diversity for identification and classification of populations in A. mongolicum. The proportion of diversity among and within geographic regions from which the populations of A. mongolicum originated indicated that 52.1% of the total variation was found within regions, and 47.9% among regions. According to the dentrogram based on the Nei’ genetic distance matrix, the A. mongolicum populations from different regions were distinctly clarified. At Nei’s distance of 0.75, the populations of A. mongolicum were divided into two groups. The UPGMA phenogram and the principal coordinate analysis (PCA) indicated that the populations from similar eco-geographical situations were clustered together.     

Exploration of intra- and inter-population genetic diversity in <Emphasis Type="Italic">Hedysarum coronarium</Emphasis> L. by AFLP markers

Amplified fragment length polymorphism (AFLP) markers were used to characterize the genetic diversity within and among natural populations and cultivars of Hedysarum coronarium. Twelve populations within Tunisia were evaluated with three AFLP primer combinations. A total of 207 reproducible bands was detected of which 178 (86%) were polymorphic. The great discriminative power of AFLP markers and their ability to represent genetic relationships among Hedysarum plants was demonstrated. Genetic diversity within and among populations was assessed through Principal Component Analysis (PCA) and cluster analysis by using the Neighbor-joining clustering algorithm. AFLP technology has provided evidence of a high degree of intra- and inter-population genetic diversity in H. coronarium. AFLP banding patterns provided molecular markers correlated with the plants’ geotropism. In addition, AFLP markers can differentiate wild accessions from cultivars. Moreover, geographical origins did not correspond to population clustering.     

AFLP similarities among historic Danish cultivars of fodder beet (<Emphasis Type="Italic">Beta vulgaris</Emphasis> L. subsp. <Emphasis Type="Italic">vulgaris</Emphasis>var. <Emphasis Type="Italic">rapacea</Emphasis> Koch)

Dead seeds of a fodder beet cultivar ‘Elvetham’ stored under ambient conditions since 1880 were compared to a homonymous sample preserved in an on-farm situation in Denmark. DNA was isolated from single seeds and successfully applied to Amplified Fragment Length Polymorphism (AFLP) analysis of the accessions. Six primer pairs were used to determine the similarity between the two accessions based on 112 polymorphic bands. Furthermore, similarity among seven cultivars of fodder beets representing the main types used in Scandinavia at the end of the 19th century was determined. This analysis was based on 152 polymorphic bands. Differentiation among the seven cultivars was determined to a mean G _ST value of 0.438, while G _ST between the two ‘Elvetham’ accessions was 0.266. A principal coordinate analysis based on jaccards similarity index illustrates that the two ‘Elvetham’ accessions are different from each other. The differentiation is higher than the value found between two separate ‘Eckerndorfer’ accessions. The results indicate that the cultivated accession has changed. Additionally, the value of applying old dead seed material for documentation in gene banks is demonstrated. During the analysis it was found that DNA isolated from seeds and leaves behaved differently in the AFLP process, however, the two fractions assigned to their common accession.     

Genetic diversity of wild banana (<Emphasis Type="Italic">Musa balbisiana</Emphasis> Colla) in China as revealed by AFLP markers

Wild banana Musa balbisiana Colla is one of the progenitors of cultivated bananas and plantains. It is native to Southeast Asia and the western Pacific. South China represents the northern limit of its distribution range. The genetic diversity of Musa balbisiana was assessed by the amplified fragment length polymorphism (AFLP) fingerprinting in 15 populations of China. Four primer pairs produced 199 discernible loci. High levels of genetic diversity were detected, with P = 78.5%, H _E = 0.241, and H _pop = 0.3684 at population level, and P = 100%, H _T = 0.3362 and H _sp = 0.5048 at species level. Significant genetic differentiation among populations was detected based on Hickory’s analysis (27.6%), Shannon’s diversity index (27.0%) and AMOVA (27.1%). The AFLP results are discussed and compared with data obtained by microsatellites method. The estimates of genetic diversity and differentiation between each pair of populations computed with microsatellites and AFLP markers were not significantly correlated. Conservation strategies for Musa balbisiana in China are proposed.     

Genetic Diversity and Relationships of Japanese Peach (<Emphasis Type="Italic">Prunus persica</Emphasis> L.) Cultivars Revealed by AFLP and Pedigree Tracing

To evaluate the genetic diversity and to clarify the genetic relationships of Japanese peach cultivars, we analyzed the amplified fragment length polymorphism (AFLP) and traced the pedigree of 17 Japanese commercial peach cultivars and six traditional accessions. Sixteen AFLP primer combinations produced a total of 837 fragments and 146 polymorphic bands with a polymorphism percentage of 17.5%. All of the peach accessions could be identified from differences in at least 10 polymorphic bands. A cluster analysis showed that all the Japanese commercial peach cultivars, except ‘Kiyomi’ and ‘Jichigetsuto’, formed a major group consisting of three sub-groups. Of the six traditional accessions, four were genetically distant from the Japanese commercial peach cultivars while two accessions from China were classified into the Japanese commercial peach cultivars group. Both the AFLP analysis and pedigree tracing suggested that Japanese commercial peach cultivars are mainly derived from ‘Shanhai Suimitsuto’, one of the traditional accessions from China. Although the genetic relationships revealed by AFLP were generally in agreement with those shown by the pedigree information, some contradictions were found. Combining the AFLP results and pedigree information can provide a better understanding of the genetic relationships of Japanese peach cultivars.     

Pheno-morphological,agronomic and genetic diversity among natural populations of sulla (<Emphasis Type="Italic">Hedysarum coronarium</Emphasis> L.) collected in Sicily,Italy

Sulla (Hedysarum coronarium L.) is a short-lived perennial forage legume that plays a key role in cereal-based systems in semi-arid Mediterranean regions, particularly in organic production and low-input oriented agriculture. In Sicily, the species is widespread both as a wild and cultivated plant. The present study assessed the phenotypic and genetic variation among natural populations of sulla collected from different environments throughout Sicily and analysed how the patterns of phenotypic diversity varied according to the environmental parameters of each collection site. Two commercial varieties and two Sicilian agro-ecotypes were also included in the study as controls. Principal components analysis (PCA) was performed on the sites using geographic, climatic, and pedological data to assess the differences in types of collection sites. PCA was also performed on the accessions (using pheno-morphological and agronomic data) to establish the importance of different traits in explaining multivariate polymorphisms. The results showed a large degree of genetic diversity (based on ISSR markers) and variability in pheno-morphological and agronomic traits. PCA did not clearly differentiate the accessions according to their habitats of origin, but in some cases accessions from the same habitat had a tendency to group together. The agronomic attributes of several populations were more pronounced than those of the controls. The observed variability may be valuable when selecting for H. coronarium varieties suitable for various uses (e.g., hay production, grazing, soil protection).     

A study of variability in the Sicilian faba bean landrace ‘Larga di Leonforte’

In this paper molecular analysis, physical, technological, and chemical traits were used to estimate the level of variation on five accessions of a locally adapted Sicilian faba bean (Vicia faba L.) landrace named ‘Larga di Leonforte’. DNA analysis was performed using the Amplified Fragment Length Polymorphism (AFLP) molecular marker class and two other faba beans (cv. ‘Aguadulce Samba’—Spain—and landrace ‘Locale di Modica’—Sicily) were used as controls. Although the accessions of ‘Larga di Leonforte’ varied significantly for most of the agronomical and physical traits, this landrace generally had a heavy seed weight, short but large pods, and no more than two seeds per pod. This last characteristic allowed for erect pod angle attitude at maturity. Idratation data showed difference among accessions in seed weight at full hydration and in absorption rate at the very beginning of the hydration process, while any difference among accessions emerged in terms of cooking properties. The six AFLP Eco+3/Mse+3 different primer combinations applied in this research revealed different levels of polymorphism among the faba bean accessions and a total number of 346 amplicons were generated. Around 60% of amplicons displayed a polymorphic pattern among different accessions. Cluster analysis on morphological, technological, chemical and molecular data placed the all five ‘Larga di Leonforte’ accessions into a separated group, and the Sicilian material shares a fairly large amount of similarity with respect to the cultivar ‘Aguadulce Samba’ selected in Spain.     

Physiological,morphological, chemical and genomic diversities of different origins of thyme (<Emphasis Type="Italic">Thymus vulgaris</Emphasis> L.)

For the selection of donors with valuable characteristics for breeding, 39 thyme accessions were evaluated in three years according to a staggered schedule. The criteria investigated were: winter hardiness, beginning of flowering, growth height, yield of the dry herb, content of essential oil, composition of the essential oil, DNA content of cell nuclei and number of chromosomes. The most strongly varying traits between the populations were the yield of dry herb, the content of essential oil and the content of volatile phenols with coefficients of variation (CV) between CV 40% and 50%. The largest variation within a population was detected for the yield of dry herb (CV 25–46%) and the content of essential oil (CV 17–48%). The homogeneity of the populations was different. The minimal average coefficient of variation of all traits (CV 19%) was determined in the population of the cultivar ‘Varico II’ and in a population from Lithuania. The ploidy level of T. vulgaris was diploid (2n = 30).