RAPD analysis of genetic diversity among and within Portuguese landraces of common white bean (Phaseolus vulgaris L.)

Seventeen landraces of common beans (Phaseolus vulgaris L.) sampled in the North and Centre of Portugal were analyzed at population level for 689 RAPD loci amplified by using forty random primers. The two different parameters used to estimate the genetic variability in and between samples indicate that the inter-population component of the genetic variability is mainly responsible for the diversity found, since only about a 10% would be of an intra-population nature. In addition, the gametic disequilibrium was estimated and reached an average value of 40% for the different combinations of pairs in the 689 loci studied taking the 17 samples as a whole population. Self-pollination, genetic drift and adaptation would thus be favouring the formation of multilocus associations. In addition, the fingerprinting study suggests that each landrace produced unique amplification products allowing it to be distinguished from the other tested genotypes, but, nevertheless, the landraces show a considerable genetic similarity (56% and 70.5% using two different methods). The Neighbour-Joining dendrogram did not show any relation between the geographical distribution of landraces and genetic distance. The results suggest that these Portuguese landraces conserved an important genetic diversity that can be useful to widen the genetic base of currently cultivated beans.     

Comparative analysis of genetic diversity in Tunisian apricot germplasm using AFLP and SSR markers

Eighty-one accessions representing apricot germplasm in Tunisia were collected from different areas of cultivation and fingerprinted using amplified fragment length polymorphism (AFLP) and microsatellites (SSR) markers. A total of 339 polymorphic markers were revealed using 5 AFLP primers combinations and 24 SSR loci. AFLP and SSR markers expressed a high level of polymorphism allowing the distinction of the accessions with an efficiency coefficient of discrimination of 100% for AFLP and 97% for SSR markers. Genetic diversity structure was assessed with AFLPs and SSRs markers separately then with combined matrix data by the help of hierarchical clustering elaborated using Wards method based on Nei and Li (1979) distances. Comparison of the obtained dendrograms revealed a phylogeographic structure into two major groups with significant conservation between the observed subgroups in relation with the geographic origin of the accessions. The relative efficiency of the markers in determining the genetic relationships among apricot accessions has been assessed and a combination of AFLPs and SSRs markers was the most effective. In addition, Mantel test based on genetic distances indicated highly significant correlation between AFLP-SSR data and each of the AFLP and SSR ones, with Pearson correlation values of r = 0.873 and r = 0.692, respectively, revealing the higher efficiency of the combination of both molecular techniques (AFLP and SSR) to estimate the levels of genetic variability among apricot germplasm.     

DNA fingerprinting of olive varieties in Istria (Croatia) by microsatellite markers

The Istria region, where olives have been cultivated for many centuries, is characterized by a considerable variety of microclimates. The study of varieties traditionally cultivated in Croatian Istria and their relationships with varieties in historically and geographically connected regions is very important in order to identify native olive germplasm, well adapted to local conditions, and to characterize the oil of regional origin. Twelve olive microsatellite markers were used for identification and differentiation of a set of 27 olive accessions grown in Istria (Croatia). Among the 27 accessions, 18 different SSR profiles were discriminated. All 12 microsatellite markers analysed were polymorphic, revealing a total of 81 alleles. The number of alleles per locus ranged from four to nine. This is the first molecular characterization of olive germplasm in Croatian Istria. The analysis clarified the genetic relationships of varieties native to Croatian Istria with introduced olive varieties, as well as with varieties in the neighbouring Slovene Istria region. Numerous varieties in neighbouring regions showed high similarity and a few cases of synonymy (‘Bilica’-‘Bjankera’; ‘Buga’-‘?rna’) and one Croatian-Slovenian homonymy (‘Bu?a’-‘Buga’) were observed. The results provide useful information for a native germplasm survey and can be used for the construction of a unique database comprising all olive varieties in the Istrian region of Croatia and Slovenia.     

Phenotypic variability and genetic structure in plum (Prunus domestica L.), cherry plum (P. cerasifera Ehrh.) and sloe (P. spinosa L.)

In the present study, phenotypic variability of 80 plum (Prunus domestica L.) varieties maintained in the French National Plum Collection was evaluated with 19 quantitative traits. In addition, genetic diversity and genetic structure was studied in three plum species (P. domestica L., Prunus cerasifera Ehrh. and Prunus spinosa L.) using chloroplast DNA (cpDNA) markers and five single sequence repeat (SSR) loci. Based on phenotypic traits, some varieties, such as mirabelle plums, grouped together. Bayesian structure analysis was used to identify different genetic groups, whereby damson plums were clearly distinguished from greengage plums. When examining the three species together, a higher level of cpDNA allelic richness was found in P. cerasifera and in P. spinosa than in P. domestica where only five cpDNA haplotypes were detected in the national plum collection, with one main haplotype that accounted for 80% of the varieties studied. P. domestica cpDNA haplotypes tended to group together with P. cerasifera haplotypes whereas most of P. spinosa haplotypes formed a separate cluster. SSR markers were somewhat able to distinguish the three species. These results provide some clues as to the origin of plum and the various plum varieties. Our results also provide useful information for the management of plum genetic resources.     

Assessment of genetic diversity of Latvian and Swedish sweet cherry (Prunus avium L.) genetic resources collections by using SSR (microsatellite) markers

Three previously described highly polymorphic SSR (microsatellite) primer pairs were tested on 126 sweet cherry (Prunus avium L.) accessions to adapt a fast, reliable method for preliminary screening of sweet cherry germplasm collections and to compare two sweet cherry germplasm collections: at the Latvia State Institute of Fruit-Growing, Dobele (LIFG-Dobele) and at the Division of Horticultural Genetics and Plant Breeding at Balsgård, Department of Crop Sciences, Swedish University of Agricultural Sciences (SLU-Balsgård). The SSR loci were highly polymorphic with 4–10 different alleles and 5–18 genotypes. Heterozygosity values ranged from 0.431 to 0.809, gene diversity (PIC) values ranged from 0.400 to 0.753, and the discriminating power of each locus varied from 0.631 to 0.894. The combined discriminating power of all loci was highly effective (0.996). Sixteen identical accession groups with the same allele profile were discovered in both collections. This study demonstrated that SSR fingerprinting with the three primer pairs tested, can be used for preliminary characterization of sweet cherry germplasm collections.     

SSR markers reveal the uniqueness of olive cultivars from the Italian region of Liguria

Twenty-three important Ligurian olive accessions corresponding to 16 cultivars were studied using 12 SSR markers and 40 Mediterranean cultivars were included in the study in order to investigate the relationships between Ligurian and Mediterranean germplasm. All SSRs produced polymorphic amplifications. One hundred and forty-nine alleles were found in the 63 accessions analysed. Twenty-two alleles were specific to germplasm from Liguria and of these 12 were unique to single cultivars. Heterozygosity and discriminating power calculated in this regional germplasm were high on average (0.70 and 0.74) and not so much lower than the values in the total sample that includes cultivars from different Mediterranean countries (0.77 and 0.88 respectively). No cases of genetic identities were found between Ligurian and Mediterranean accessions. Several cases of homonyms and synonyms within the Ligurian germplasm were explained. Cluster analysis generally revealed a clear discrimination of the profiles from Liguria and Italy with respect to the cultivars from other Mediterranean countries. Only one Ligurian cultivar, “Negrea”, appeared to have a different origin, grouping with the Mediterranean cultivars.     

黄瓜种质资源遗传多样性及其亲缘关系的AFLP分析

 采用AFLP分子标记技术,对中国黄瓜种质资源遗传多样性及其与外来种质的关系进行了分析, 结果表明8对AFLP引物在70份黄瓜种质中共扩增出425条带,多态性带的比例为66％。供试黄瓜种质的平 均期望杂合度为0．376,中国种质的平均期望杂合度为0．387,明显高于国外种质的n 291。西双版纳黄瓜和印度野生黄瓜具有一些栽培种质没有的特异位点,中国栽培种质的特异位点多于外来栽培种质,后者也有一些中国栽培种质没有的特异位点。聚类分析将70份种质分为三大组群,即西双版纳黄瓜(Cucumis sativus L.vaF．xishuangbannanesis Qi et Yuan)组群,e sativus var．hardwickii野生黄瓜组群和栽培黄瓜组群。西双版纳黄瓜与栽培黄瓜的距离最远,与野生黄瓜次之。按一定的遗传距离可以将中国和外来栽培种质分开。大多数 华南型和华北型种质归属于不同的亚组。这些结果有助于有目的地利用这些变异拓宽育种材料的遗传背景。     

Characterization of Tunisian pomegranate (Punica granatum L.) cultivars using amplified fragment length polymorphism analysis

The amplified fragment length polymorphism (AFLP) analysis of DNA was used to characterize 34 pomegranate cultivars. By using a combination of six primers, a total of 327 markers were scored with a mean of 57.5. The high percentage of polymorphic bands (ppb) of 94.7 and the resolving power (R_p) collective rate value of 129.14 were scored. Data proved that the tested primers were informative to discriminate among cultivars and to survey the genetic diversity in this fruit crop. It has been assumed that the local pomegranate germplasm is characterized by a typically continuous genetic diversity. The derived dendrogram proved that cultivars are clustered independently from their geographical origin and their denomination. In addition, AFLP permitted the generation of a nearly unlimited number of molecular markers that are reliable in differentiating the cultivars and/or the polyclonal varieties.     

生长调节物质对高温下菜豆叶片水分的调节作用

在实验室控制高温条件下,分别用不同浓度的外源ＧＡ３和６－ＢＡ涂抹菜豆叶片,探讨它们对高温下菜豆叶片水分的调节作用及菜豆高温伤害状况,结果表明：在短期高温胁迫条件下,两种生长调节物质明显地提高了菜豆叶片细胞间的孔隙度,降低了高气温下植株的叶温,减缓了叶片细胞膜伤害;但是从总体上看两种调节物质处理后对叶片气体扩散阻力影响不大。     

Modelling salt accumulation by a bean crop grown in a closed hydroponic system in relation to water uptake

Four different NaCl concentrations in the irrigation water, 0.8, 3, 6 and 9 mol m⁻³, were applied as experimental treatments to beans (Phaseolus vulgaris L.) grown in completely closed hydroponic systems in a greenhouse. Initially, the Na and Cl concentrations increased rapidly in the root zone, as indicated by the values measured in the drainage water, and this resulted in corresponding increases in the Na/water and Cl/water uptake ratios. However, as these ratios approached equilibrium with the NaCl/water ratios in the irrigation water, the Na and Cl concentrations in the root zone converged to maximal levels, which depended on the treatment. The highest Na and Cl concentrations in the root zone and the corresponding NaCl concentrations in each treatment were used to establish relationships between the external NaCl concentration and the Na/water or Cl/water uptake ratios, which proved to be exponential for Na but linear for Cl. These relationships were then used in a previously established model [Savvas, D., Kotsiras, A., Meletiou, G., Margariti, S., Tsirogiannis, I., 2005a. Modeling the relationship between water uptake by cucumber and NaCl accumulation in a closed hydroponic system. HortScience 40, 802–807] to enable the prediction of the Na and Cl concentrations in the root zone in relation to the cumulative water uptake. The curves predicted by the model followed a convex pattern, with an initially rapid increase in Na and Cl concentrations in the root zone followed by a gradual levelling out as the cumulative water consumption rose. The measured Na and Cl concentrations in the drainage water were more accurately predicted at the higher NaCl concentrations in the irrigation water, although those predicted at 0.8 mol m⁻³ of NaCl were considered acceptable for use in commercial practice. Bean showed a high efficiency of Na exclusion from the upper leaves, while Cl was readily translocated to the young leaves as the external Cl concentration rose. Plant growth decreased with increasing salinity in a way similar to that reported for beans constantly exposed to comparable salinity levels.     

Molecular polymorphism of cytoplasmic DNA in Ficus carica L.: Insights from non-coding regions of chloroplast DNA

The trnL (UAA) intron and the intergenic spacer between the 3′ exon of trnL (UAA) and trnF (GAA) sequences were used as genetic markers for differentiating Ficus carica cultivars and establishing refined genetic relationships. The study was based on 20 fig cultivars, collected from south and centre of Tunisia. Since, the intron was thought to be more variable among close relatives than is the chloroplast spacer. The size of these non-coding regions varied from 554 to 589 and from 989 to 1022 bases pairs for the intron and the combined sequences correspondingly. The average of GC content was 33.9% and 34.6% in the intron and the combined intron and spacer respectively. High values of A + T contents were detected in both data sets and may explain the high proportions of transversions founded. The observed variation pattern of plastid DNA provides evidence of an important genetic diversity. The overall transition/transversion bias (R) was 0.202 in the intron and 0.27 in the combined regions. The RI index of 0.592 indicates that these combined sequences have clearly more homoplasy then the intron (RI = 0.705) and spacer (RI = 0.777) sequences separately. Phylogenetic trees were generated based on maximum parsimony (MP) and neighbor-joining (NJ) analysis of the chloroplast sequences data. Results proved that a typically continuous genetic diversity characterizes the local fig germplasm. In fact, relationships inferred from the cpDNA analysis suggest several clades, which do not show geographical or tree sex correspondence. Although the level of apparent diversity is considerable, we may conclude that non-coding regions of chloroplast genome provide a new and practical opportunity to evaluate genetic diversity and to discriminate fig cultivars. Revealed cytoplasmic DNA markers are reliable to elaborate a molecular data base to conduct management and breeding programs on local fig germplasm.     

Assessing Rosa persica genetic diversity using amplified fragment length polymorphisms analysis

The genetic diversity among 128 Iranian Rosa persica (R. persica) accessions in the different populations was analyzed. Amplified fragment length polymorphisms (AFLP) technique was used to produce 171 polymorphic fragments. The number of polymorphic loci ranged from 101 to 147 and the polymorphism information content (PIC) varied from 0.289 to 0.073, with an average of 0.16. This shows extreme variability and genetic diversity among the studied R. persica populations. An indirect estimate of the number of migrants per generation (Nm = 0.376) indicated that gene flow was relatively low among populations of the species. Cluster analysis using the UPGMA method grouped all accessions into six clusters. The results did not show relative agreement with the genotypes’ region of origin. Based on an analysis of molecular variance, 48% of the genetic variation of R. persica was within population and 52% was among populations. The present analysis revealed that Iranian R. persica genotypes are highly variable and genetically distinct from their origins. The apparent unique nature of the R. persica genotypes revealed by our results supports the case for the implementation of more intense characterization and conservation strategies, and provides useful information to address breeding programmes and germplasm resource management in Rosa spp.     

The risks of success in quality vegetable markets: Possible genetic erosion in Marmande tomatoes (Solanum lycopersicum L.) and consumer dissatisfaction

Following consumer complaints about the quality of modern varieties of tomato, landraces have strengthened their quality markets. In Spain, two tomato landraces, ‘Montserrat’ and ‘Pera Girona’, are grown in contiguous areas and have different market niches. We used amplified fragment length polymorphism (AFLP) to characterize 13 accessions of Montserrat, 14 accessions of Pera Girona, and 4 control varieties. We found a narrow genetic base for ‘Montserrat’ and ‘Pera Girona’ (8.5% of polymorphic loci) and no differences between the landraces. We studied agronomical and sensory traits to determine why the two landraces continue to have separate market niches. We found high variability among accessions within each landrace and overlapping among accessions of both landraces for all traits except fruit morphology. Consumers probably came to associate the organoleptic quality of these landraces with their external traits, but due to spontaneous crossings and introgressions these relations have been lost. Selection within landraces will be necessary to reestablish the link between morphology and sensory value and to consolidate these quality markets.     

Isolation and characteristics of eight novel polymorphic microsatellite loci from the genome of garlic (Allium sativum L.)

Here we characterized eight novel polymorphic SSR markers, developed from an enriched genomic library of garlic (Allium sativum L.). These SSRs produced a total of 64 alleles across 90 garlic accessions, with an average of 8 alleles per locus. Values for observed (H_O) and expected (H_E) heterozygosity ranged from 0.16 to 0.77 (mean = 0.44) and from 0.22 to 0.86 (mean = 0.65), respectively. Six loci deviated significantly (P < 0.05) from Hardy–Weinberg equilibrium (HWE). The averages of gene diversity and PIC values were 0.65 and 0.62, respectively. The mean genetic similarity coefficient was 0.4380, indicating that among garlic accessions existed wide genetic variation. Based on 64 alleles obtained by 8 SSRs, a phenogram was constructed to understand the relationships among the 90 accessions. These newly developed SSRs should prove very useful tools for genotypes identification, assessment of genetic diversity and population structure in garlic.