Analysis of genetic diversity among European and Asian fig varieties (<Emphasis Type="Italic">Ficus carica</Emphasis> L.) using ISSR,RAPD, and SSR markers

Nineteen fig varieties and lines from Europe and Asia have been fingerprinted by ISSR, RAPD, and SSR markers, respectively, using 13, 19, and 13 primer combinations. All primers produced 258 loci, with the highest number of loci (119) generated by RAPD (R _p: 48.42). Clustering analysis was applied to the three marker datasets to elucidate the genetic structure and relationships among these varieties. Mean genetic similarities were 0.787, 0.717, and 0.749, respectively, as determined using ISSR, RAPD, and SSR. Each marker system produced incompletely separated clusters, although a weak binding group based on race type appeared in the combined dataset. Comparisons of coefficients revealed no correlation between different similarity matrices; congruence was observed between similarity matrices and co-phenetic matrices in all markers. Analysis of molecular variance (AMOVA) showed that most of the total polymorphism was attributable to within-group variance (ISSRs + RAPDs, 97.41%; SSRs, 90.18%). These results suggest that the genetic diversity of this fig population is low and that multiple marker utilization is critical to estimate the relatedness of figs at the variety level. Additionally, it was presumed that ‘Houraihi’, the oldest variety in Japan, was disseminated independently of other foreign varieties in the 17th century or before then.     

Contrasted genetic diversity and differentiation among Mediterranean populations of <Emphasis Type="Italic">Ficus carica</Emphasis> L.: A study using mtDNA RFLP

Patterns of mitochondrial DNA (mtDNA) variation revealed by RFLP were investigated for 63 individuals of the common fig, Ficus carica L., in 15 supposedly natural populations throughout the Mediterranean basin. Fifteen haplotypes were detected using one restriction enzyme (HindIII) and four probes (atp, coxIII, nad3rpsl2 and rps12). Mitochondrial diversity within populations varied from monomorphic to entirely polymorphic and population differentiation was high (F_ST = 0.323, P < 10^–5). Seven groups of populations were defined on the basis of genetic and geographic proximity and lead to significant pairwise F_ST estimates except for the Corsican group which was similar to the Moroccan one. Fig populations were structured into three clusters: Balearic, West and East Mediterranean gene pools. The low diversity and strong differentiation of the Balearic populations strongly supports an ancient origin and the presence of natural populations in this area before domestication. Significant genetic differentiation between the West and East Mediterranean probably also reflects a diversification of the common fig over the Mediterranean basin preceding domestication. In contrast, Italian island populations seem to result from introduced cultivated fig since they present continental haplotypes. Our study represents a first mtDNA polymorphism survey and these indications should be confirmed by analysing local cultivated forms from the Baleares and from Italian islands and further natural populations from the East Mediterranean.     

Seasonal and diurnal photosynthetic behaviour of fig (Ficus carica L.) under semi-arid climatic conditions

Abstract

Diurnal and seasonal variations in net photosynthetic (P_N) and transpiration (E) rates and water use efficiency (WUE) of the fig tree (Ficus carica L.) were investigated under semi-arid climatic conditions. The two types of leaves from southern and northern parts of trees experienced natural air temperature and irradiance conditions, but differ particularly in water use efficiency. The obtained data reveal that leaf temperature, because of decrease in stomatal conductance, is the major factor limiting the gas exchange capacity of fig trees grown under rain-fed conditions. Stomatal conductance is the major control mechanism, particularly in the northern parts of the trees; however, P_N was most probably decreased by both stomatal and non-stomatal resistance mechanisms such as photoinhibition under severe drought and high irradiance conditions in the southern parts of the trees.     

Genetic diversity and relationships among safflower (<Emphasis Type="Italic">Carthamus tinctorius</Emphasis> L.) analyzed by inter-simple sequence repeats (ISSRs)

Genetic diversity and relationships among 48 safflower accessions were evaluated using 22 inter-simple sequence repeats (ISSR) primers. A total of 429 bands were amplified, and 355 bands (about 82.7%) were polymorphic. Five to forty-one polymorphic bands could be amplified by each primer, with an average of 16.1 polymorphic bands per primer. The results showed that the polymorphism of the safflower germplasm was higher at the DNA level. All the 48 accessions could be distinguished by ISSR markers and were divided into 9 groups based on ISSR GS by using UPGMA method. The genetic relationships among the accessions from different continents were closer. Comparatively, the genetic diversity of the accessions originated from Asia was higher, from Europe assembled. The results also showed that the genetic variation of accessions from Indian and Middle Eastern safflower diversity centers were relatively higher. ISSR is an effective and promising marker system for detecting genetic diversity among safflower and give some useful information on its phylogenic relationships.     

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.     

Comparative Analysis of Genetic Diversity in Two Tunisian Collections of Fig Cultivars Based on Random Amplified Polymorphic DNA and Inter Simple Sequence Repeats Fingerprints

This study characterized the genetic diversity of 18 Tunisian fig cultivars using random amplified polymorphic DNA (RAPD) and inter simple sequence repeats (ISSR). Both random and ISSR primers tested generated a total of 116 RAPD and 47 ISSR markers. Considerable genetic variation was observed among fig cultivars sampled from two regional Tunisian collections with an average diversity of 4.57. RAPD and ISSR banding patterns and genetic distances values reflected the high level of diversity among the collections and lower variability between the two collections. The correlation between the RAPD and ISSR similarity matrices computed for the 153 pairwise comparisons among the 18 varieties was lower and significant. An analysis of molecular variance showed that 92% of the total genetic diversity resided within collections, whereas only 8% between collections. The results indicated that in the local fig germ plasm the information provided by RAPD and ISSR is not analogous, most likely as a consequence of the fact that the two classes of markers explore, at least in part, different portions of the genome.     

Analysis of genetic diversity in Indian taro [Colocasia esculenta (L.) Schott] using random amplified polymorphic DNA (RAPD) markers

Taro [Colocasia esculenta (L.) Schott] germplasm accessions collected from different parts of India were subjected to RAPD (Random Amplified Polymorphic DNA) analysis to assess the genetic diversity prevalent and also to test the genetic basis of morphotypic classification. Thirteen random decamer primers out of the 22 tested were used to analyse 32 taro accessions belonging to 28 morphotypes. Three out of these thirteen primers analysed showed 100 per cent polymorphism. Per cent polymorphism varied from 60 to 100 among the polymorphic primers. High genetic diversity was revealed as the similarity coefficient values ranged from 0.50 to 0.98. No two accessions analysed in the present study showed a similarity coefficient value of one thereby indicating their distinctness and presence of high genetic diversity in Indian taro germplasm. Dendrogram obtained from UPGMA analysis grouped 32 accessions in four clusters and three accessions were placed as outliers. Clustering pattern did not show any strict relationship with geographical distribution, morphotype classification and genotypic diversity. Further, accessions classified, as belonging to the same morphotypic group did not always cluster together. Presence of a very close genepool of the wild, weedy and cultivated forms with extreme levels of phenotypic and genotypic variation is suggested as the reason for high genetic diversity reported. Usefulness of DNA markers such as RAPD in characterising and assessing the genetic diversity in Indian taro germplasm is hereby demonstrated.     

Genetic diversity in Tunisian perennial ryegrass revealed by ISSR markers

The genetic diversity in Tunisian perennial ryegrass (Lolium perenne) was examined by the help of inter-simple sequence repeats (ISSR). Starting from eighteen accessions, a large number of polymorphic ISSR markers were currently generated using appropriate primers (a total of 136, which average of 12.6 polymorphic bands/primer). These markers were considered to estimate the genetic distance among accessions and to draw phylogenetic trees. Our data provide evidence of a high degree of genetic diversity in Tunisian ryegrass. In addition, both cultivars and wild types present a high degree of divergence suggesting a complex domestication process in this crop. Moreover, spontaneous populations of Tunisian ryegrass have been identified as important ecotypes that are suitable in selection programs to improve grasslands.     

Genetic diversity in the Lima bean (Phaseolus lunatus L.) as revealed by chloroplast DNA (cpDNA) variations

Genetic diversity in the Lima bean (P. lunatus L.) was assessed bymeans of two chloroplast DNA probes. Based on data obtained from 152accessions including wild forms and landraces, the two separateMesoamerican and Andean groups were confirmed and a transition poolof genetic diversity was observed in the two botanical formsconsistent with their distribution range. Three primary centres ofgenetic diversity and one secondary diversification spot are proposedfor the wild Lima bean whereas only two domestication sites areunderlined for the landraces. The importance of human intervention inwidening the distribution range and the genetic diversity inlandraces is discussed.     

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 Survey of Chinese and Swedish Oilseed Rape (Brassica napus L.) by Simple Sequence Repeats (SSRs)

Eleven Chinese and twelve Swedish rapeseed (Brassica napus) genotypes were analysed by PCR with 41 microsatellite primers, generating a total of 50 loci. For these 50 loci, the number of alleles ranged from 1 to 14, and the average number of alleles per loci was 2.7. As an example of simple sequence repeat (SSR) scoring in Metaphor agarose gel, a single marker could distinguish 14 different DNA profiles. Based on cluster analysis (UPGMA), the dendrogram clearly distinguished three clusters, a cluster with exclusively Swedish genotypes, and two clusters with Chinese genotypes. The genetic diversity within the Chinese genotypes was broad compared to the genetic diversity within the Swedish material. The genetic similarity within the Swedish breeding lines ranged from 69.5 to 95.6%, while that of Chinese genotypes ranged from 57.1 to 81.6%. The results in this report will permit to establish a set of microsatellite primers that can be used for selecting appropriate parents for Brassica napus hybrids and for monitoring hybridity level.     

Genetic diversity in sweetpotato [Ipomoea batatas (L.) Lam.] in relationship to geographic sources as assessed with RAPD markers

Available evidence shows that sweetpotato originated from either Central or South American lowlands with subsequent dispersal to North America, Europe, Africa, Asia and the pacific islands. A total of 71 polymorphic RAPD molecular markers were used to assess the genetic relationships amongst 74 sweetpotato varieties originating from a total of 23 sweetpotato producing countries within six geographical regions, namely, South America, Central America/Caribbean, United States of America (USA), East Africa, Asia and Oceania. An Analysis of Molecular Variance (AMOVA) indicated that 93.4% of the total variance was due to the differences between genotypes within regions. The difference between regions was significant (P < 0.001) but only contributed 6.6% to the variance. Genetic distance (PhiST) calculated with AMOVA and multidimensional scaling (MDS) revealed that the South American and the Central American/Caribbean genotypes formed two separate clusters. East African varieties, which have unique characteristics from other traditional varieties, were distinct from other traditional varieties from South America and Oceania. These results support the reported hypothesis of the origin and dispersal of the sweetpotato and indicate that the primary centre of diversity probably has two distinct genepools. It is proposed that the dispersal of the sweetpotato from its origin may have mainly involved varieties from Central America/Caribbean as opposed to varieties from South America. There is an indication that new genepools may be evolving in Africa and Asia due to hybridisation and adaptation to the local environments.     

The major Italian landraces of lentil (<Emphasis Type="Italic">Lens culinaris</Emphasis> Medik.): Their molecular diversity and possible origin

The eleven most known landraces from central and southern Italy were analysed using ISSR markers on 15 randomly chosen individuals for each landrace, with the aim of assessing genetic variation within and among landraces and possibly ascertaining their origin and genetic relationships. A total of 164 loci were observed, 128 of which (78.05%) were polymorphic. Gene diversity over all landraces was I = 0.3759. The highest within-landrace diversity was observed in samples from the Apennine ridge and for one Sicilian landrace; on the other hand, samples from the small Sicily islands were less variable. Principal Component Analysis and AMOVA allowed the discrimination of groups of landraces with higher similarity. Analyses indicate that the small Sicily islands landraces are very closely related to one another and seem to be derived from the peninsular material; moreover, they help disclose relationships among geographically close landraces. The knowledge so acquired can, therefore, contribute to elaborate strategies for increasing the economical value of élite landraces and to protect producers from frauds.     

Collection of Lupinus angustifolius L. Germplasm and Characterisation of Morphological and Molecular Diversity

Lupinus angustifolius L. is a Mediterranean species, domesticated in the 20th century, representing an important grain legume crop in Australia and other countries. This work is focused on the collection of wild germplasm and on the characterisation of morphological and molecular diversity of germplasm accessions. It reports the collection of 81 wild L. angustifolius accessions from the South and Centre of Portugal, available at the ‘Instituto Superior de Agronomia Gene Bank’, with subsequent morphological and molecular characterisation of a selection of these and other accessions. A multivariate analysis of morphological traits on 88 L. angustifolius accessions (including 59 wild Portuguese accessions, 15 cultivars and 14 breeding lines) showed a cline of variation on wild germplasm, with plants from Southern Portugal characterised by earlier flowering, higher vegetative development and larger seeds. AFLP and ISSR molecular markers grouped modern cultivars as sub-clusters within the wider diversity of wild germplasm, revealing the narrow pool of genetic diversity on which domesticated accessions are based. The importance of preserving, characterising and using wild genetic resources for L. angustifolius crop improvement is outlined by the results obtained.     

Level and Transmission of Genetic Heterozygosity in Apricot (Prunus armeniaca L.) Explored Using Simple Sequence Repeat Markers

In this study, 17 peach simple sequence repeat (SSR) sequences were used in the exploration of the genetic heterozygosity level of several apricot cultivars from Spain, France, Greece, and the USA, and 23 descendants. The genotypes can be classified in three groups as a function of their genetic heterozygosity (1) local cultivars from Murcia (Spain) (‘Gitanos’ and ‘Pepito del Rubio’) and several descendants from crosses among these cultivars, with very low genetic heterozygosities (less than 0.30); (2) cultivars from France and Spain (‘Moniquí’, ‘Currot’ and ‘Bergeron’) and several descendants, with intermediate levels of genetic heterozygosity (around 0.45); and (3) cultivars ‘Orange Red’ and ‘Goldrich’ from North America and ‘Lito’ from Greece, with the remaining descendants, having genetic heterozygosities higher than 0.50. The results showed the high increase of genetic heterozygosity in the case of descendants from complementary crosses. The use of cultivars from North America could increase greatly the genetic heterozygosity in the Spanish apricot breeding programs, enlarging the genetic variability of the local cultivars. On the other hand, in the case of transgressive crosses among local Spanish cultivars, the increase of genetic heterozygosity was much lower.     

Genetic diversity of 38 spinach (<Emphasis Type="Italic">Spinacia oleracea</Emphasis> L.) germplasm accessions and 10 commercial hybrids assessed by TRAP markers

Target region amplification polymorphism (TRAP) markers were used to assess genetic variability among 38 germplasm accessions and 10 commercial hybrids of spinach (Spinacia oleracea L.), an economically important leafy vegetable crop in many countries. Germplasm accessions with different geographic origins and 10 commercial hybrids were examined. For assessing genetic diversity within accessions, DNA was extracted from 12 individual seedlings from six germplasm accessions and two hybrids. A relatively high level of polymorphism was found within accessions based on 59 polymorphic TRAP markers generated from one fixed primer derived from the Arabidopsis-like telomere repeat sequence and two arbitrary primers. For evaluating interaccession variability, DNA was extracted from a bulk of six to 13 seedlings of each accession. Of the 492 fragments amplified by 12 primer combinations, 96 (19.5%) were polymorphic and discriminated the 48 accessions from each other. The average pair-wise genetic similarity coefficient (Dice) was 57.5% with a range from 23.2 to 85.3%. A dendrogram indicated that the genetic relationships among the accessions were not highly associated with the geographic locations in which the germplasms were collected. The seven commercial hybrids were grouped in three separate clusters, suggesting that the phenotype-based breeding activities tended to reduce the genetic variability. This preliminary study demonstrated that TRAP markers are effective for fingerprinting and evaluating genetic variability among spinach germplasms. Mention of trade names or commercial products in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the US Department of Agriculture. The U.S. Government's right to retain a non-exclusive, royalty-free license in and to any copyright is acknowledged.     

Genetic diversity in wild Tunisian populations of Mentha pulegium L. (Lamiaceae)

The allozyme variation of 15 Tunisian wild populations of Mentha pulegium L. threatened by human activities (clearing, hard-grazing, ploughing, traditional uses) was surveyed by the analysis of 14 isozyme loci using horizontal gel starch electrophoresis. The species exhibited a high level of genetic variation within populations (the mean Ap = 2.20, P = 72%, Ho = 0.349 and He = 0.229), which indicates a predominately outcrossing mating system and the recruitment of new genotypes via dispersal seeds. The genetic structure analysis of the populations using F statistics indicates no inbreeding, and showed an excess of heterozygosity for few loci. The moderate differentiation of populations (F_ST = 0.110) and the low rate of gene flow between them (Nm = 2.02) might been caused by recent isolation of the populations through biotope disturbances. The value of Nei's genetic identity varied from 0.839 to 0.999 reflecting a relatively low genetic divergence between populations. Cluster analysis using UPGMA method and Nei's genetic identity values, showed that populations geographically close didn't always cluster together. However, populations within the same bioclimatic stage generally subclustered together indicating that differentiation between bioclimatic regions occurred.     

Studying the extent of genetic diversity among Gossypium arboreum L. genotypes/cultivars using DNA fingerprinting

Genetic diversity is an area of concern for sustaining crop yield. Information on genetic relatedness/diversity among Gossypium arboreum L. cultivars/genotypes is scanty. We have used random amplified polymorphic DNA (RAPD) analysis to assess the genetic divergence/relationship among 30 genotypes/cultivars of G. arboreum. Of 45 primers surveyed, 63% were polymorphic. Out of the total number of loci amplified, 36% were polymorphic. The calculated genetic similarity between the cultivars/genotypes was in the range of 47.05–98.73%. Two genotypes, HK-244 and Entry-17, were the most distantly related. The average genetic relatedness among all the genotypes was 80.46%. However, most of the cultivated varieties showed a close genetic relationship, indicating a narrow genetic base in comparison to the non-cultivated germplasm. The calculated coefficients were used to construct a dendrogram using the unweighted pair group of arithmetic means (UPGMA) algorithm, which grouped the genotypes/cultivars into two major and three smaller clusters. The study is the first comprehensive analysis of the genetic diversity of G. arboreum germplasm and identifies cultivars that will be useful in extending the genetic diversity of cultivated varieties and future genome mapping projects.     

Genetic diversity of Syrian pistachio (<Emphasis Type="Italic">Pistacia vera</Emphasis> L.) varieties evaluated by AFLP markers

Pistachio (Pistacia vera L.) is a strategic nut tree species in the Middle East which holds comparative advantage over other fruit trees in view of its hardiness, income generation opportunities and benefits for the ecosystem. Yet pistachio cultivation depends on a very narrow genetic base, in spite of the existence of many varieties still marginally exploited. Syria is an important center of diversity for pistachio. A country wide ecogeographic survey in this country was carried out to determine the extent of pistachio genetic diversity and its use. As a whole, 114 accessions were collected from 37 farms to assess diversity at morphological and molecular level. Molecular evaluation was carried out using Amplified Fragment Length Polymorphism (AFLP) technique and performed using seven primer pair combinations. Results from the studies allowed the identification of 25 pistachio female varieties in Syria, some of which unique and described for the first time. Three groups of pistachio diversity were identified by cluster analysis which provides useful information about the distribution of genetic diversity in Syria for enhanced use and sustainable conservation.