Ali Ergül

Multiple origins of cultivated grapevine (Vitis vinifera L. ssp. sativa) based on chloroplast DNA polymorphisms.

The domestication of the Eurasian grape (Vitis vinifera ssp. sativa) from its wild ancestor (Vitis vinifera ssp. sylvestris) has long been claimed to have occurred in Transcaucasia where its greatest genetic diversity is found and where very early archaeological evidence, including grape pips and artefacts of a ‘wine culture’, have been excavated. Whether from Transcaucasia or the nearby Taurus or Zagros Mountains, it is hypothesized that this wine culture spread southwards and eventually westwards around the Mediterranean basin, together with the transplantation of cultivated grape cuttings. However, the existence of morphological differentiation between cultivars from eastern and western ends of the modern distribution of the Eurasian grape suggests the existence of different genetic contribution from local sylvestris populations or multilocal selection and domestication of sylvestris genotypes. To tackle this issue, we analysed chlorotype variation and distribution in 1201 samples of sylvestris and sativa genotypes from the whole area of the species’ distribution and studied their genetic relationships. The results suggest the existence of at least two important origins for the cultivated germplasm, one in the Near East and another in the western Mediterranean region, the latter of which gave rise to many of the current Western European cultivars. Indeed, over 70% of the Iberian Peninsula cultivars display chlorotypes that are only compatible with their having derived from western sylvestris populations.

Characterizing the Grape Transcriptome. Analysis of Expressed Sequence Tags from Multiple Vitis Species and Development of a Compendium of Gene Expression during Berry Development

We report the analysis and annotation of 146,075 expressed sequence tags from Vitis species. The majority of these sequences were derived from different cultivars of Vitis vinifera, comprising an estimated 25,746 unique contig and singleton sequences that survey transcription in various tissues and developmental stages and during biotic and abiotic stress. Putatively homologous proteins were identified for over 17,752 of the transcripts, with 1,962 transcripts further subdivided into one or more Gene Ontology categories. A simple structured vocabulary, with modules for plant genotype, plant development, and stress, was developed to describe the relationship between individual expressed sequence tags and cDNA libraries; the resulting vocabulary provides query terms to facilitate data mining within the context of a relational database. As a measure of the extent to which characterized metabolic pathways were encompassed by the data set, we searched for homologs of the enzymes leading from glycolysis, through the oxidative/nonoxidative pentose phosphate pathway, and into the general phenylpropanoid pathway. Homologs were identified for 65 of these 77 enzymes, with 86% of enzymatic steps represented by paralogous genes. Differentially expressed transcripts were identified by means of a stringent believability index cutoff of ≥98.4%. Correlation analysis and two-dimensional hierarchical clustering grouped these transcripts according to similarity of expression. In the broadest analysis, 665 differentially expressed transcripts were identified across 29 cDNA libraries, representing a range of developmental and stress conditions. The groupings revealed expected associations between plant developmental stages and tissue types, with the notable exception of abiotic stress treatments. A more focused analysis of flower and berry development identified 87 differentially expressed transcripts and provides the basis for a compendium that relates gene expression and annotation to previously characterized aspects of berry development and physiology. Comparison with published results for select genes, as well as correlation analysis between independent data sets, suggests that the inferred in silico patterns of expression are likely to be an accurate representation of transcript abundance for the conditions surveyed. Thus, the combined data set reveals the in silico expression patterns for hundreds of genes in V. vinifera, the majority of which have not been previously studied within this species.

Genetic characterization and relationships of traditional grape cultivars from Transcaucasia and Anatolia

We present here the first large-scale genetic characterization of grape cultivars from Transcaucasia and Anatolia. These regions where wild grapes still grow in nature have been cultivating wine and table grapes for thousands of years and are considered the cradles of viticulture. Using 12 nuclear microsatellite markers, we genotyped 116 accessions of traditional grape cultivars from Armenia, Georgia and Turkey and we detected 17 identical genotypes and six homonymy cases, mainly within each national germplasm. Neighbour-joining analysis of genetic distance showed that each germplasm could have multiple origins and although they are now separated, they might have some common ancestors. In addition, four varieties from Western Europe included as outgroups turned out to be more related to Georgian cultivars than other germplasms, suggesting a possible ancient origin in Georgia. This work represents a first step towards germplasm management of this rich ampelographic heritage.

Identification of tissue-specific, abiotic stress-responsive gene expression patterns in wine grape (Vitis vinifera L.) based on curation and mining of large-scale EST data sets

BackgroundAbiotic stresses, such as water deficit and soil salinity, result in changes in physiology, nutrient use, and vegetative growth in vines, and ultimately, yield and flavor in berries of wine grape, Vitis vinifera L. Large-scale expressed sequence tags (ESTs) were generated, curated, and analyzed to identify major genetic determinants responsible for stress-adaptive responses. Although roots serve as the first site of perception and/or injury for many types of abiotic stress, EST sequencing in root tissues of wine grape exposed to abiotic stresses has been extremely limited to date. To overcome this limitation, large-scale EST sequencing was conducted from root tissues exposed to multiple abiotic stresses.ResultsA total of 62,236 expressed sequence tags (ESTs) were generated from leaf, berry, and root tissues from vines subjected to abiotic stresses and compared with 32,286 ESTs sequenced from 20 public cDNA libraries. Curation to correct annotation errors, clustering and assembly of the berry and leaf ESTs with currently available V. vinifera full-length transcripts and ESTs yielded a total of 13,278 unique sequences, with 2302 singletons and 10,976 mapped to V. vinifera gene models. Of these, 739 transcripts were found to have significant differential expression in stressed leaves and berries including 250 genes not described previously as being abiotic stress responsive. In a second analysis of 16,452 ESTs from a normalized root cDNA library derived from roots exposed to multiple, short-term, abiotic stresses, 135 genes with root-enriched expression patterns were identified on the basis of their relative EST abundance in roots relative to other tissues.ConclusionsThe large-scale analysis of relative EST frequency counts among a diverse collection of 23 different cDNA libraries from leaf, berry, and root tissues of wine grape exposed to a variety of abiotic stress conditions revealed distinct, tissue-specific expression patterns, previously unrecognized stress-induced genes, and many novel genes with root-enriched mRNA expression for improving our understanding of root biology and manipulation of rootstock traits in wine grape. mRNA abundance estimates based on EST library-enriched expression patterns showed only modest correlations between microarray and quantitative, real-time reverse transcription-polymerase chain reaction (qRT-PCR) methods highlighting the need for deep-sequencing expression profiling methods.

Genetic characterization of green bean (Phaseolus vulgaris) genotypes from eastern Turkey.

Green bean genotypes collected from eastern Turkey were characterized using simple sequence repeat (SSR) markers and morphological traits. Among 12 SSR markers, 10 produced successful amplifications and revealed DNA polymorphisms that were subsequently used to assess genetic relatedness of the genotypes. Based on the number of alleles generated and the probability of identity values, the most informative SSR loci were PVGLND5, PVMEIG, PV-ag001, and PV-ag004. Probably, due to the inbreeding nature of beans, the heterozygosity observed within genotypes was low at most of the SSR loci. The UPGMA dendrogram constructed based on the SSR data yielded two major clusters. The overall genetic distance was around 98%, among the genotypes. This information can be used to help select Turkish green bean lines.

Genetic diversity in Anatolian wild grapes ( Vitis vinifera subsp. sylvestris ) estimated by SSR markers

Anatolia (Asia Minor) is considered to be the cradle of viticulture, but wild grape accessions from this region have not been subjected to any genetic analysis. We present the first genetic characterization of wild grapes ( Vitis vinifera subsp. sylvestris ) from this region. Using 15 nuclear microsatellites, we genotyped 84 wild grape accessions collected from three Anatolian locations. The unweighted pair group method with arithmetic mean analysis revealed four genetic clusters that partially separated Anatolian wild grape populations. In general, accessions from geographically closer locations showed higher genetic similarities than those from more distant locations. In some cases, accessions from one population showed close genetic relationships to accessions from a different population. The genetic diversity between natural populations from both ends of the Mediterranean basin has shown higher genetic diversity in the Anatolian Peninsula than peripheral populations, suggesting that this area could be one centre of diversity of the species. The genetic relationship between wild and cultivated grapevine from Anatolian Peninsula indicated a clear separation between them. However, we cannot discarded a local genetic contribution. Overall, this study reveals useful information for management and potential utilization of Anatolian wild grape germplasm.

Genetic analysis of Anatolian apples (Malus sp.) by simple sequence repeats

The apple is one of the most important fruit species in the world. Turkey has a diverse and ancient apple germplasm that have played a major role in the domestication of the Malus genus. However, so far locally grown Anatolian apple germplasm has largely been uncharacterized. In this study, 171 local apple (M. domestica Borkh.) accessions originated from eco‐geographically diverse regions of Anatolia were studied using 16 SSR (simple sequence repeat) loci, which generated 254 alleles. Of the SSR markers used, the CH04g10 locus showed the highest allele diversity. Relatively high genetic similarities were found between some accessions. The factorial correspondence analysis did not clearly separate different all apple accession groups, suggesting that Anatolian apple accessions are highly intermixed. However, most apple accessions were grouped according to their collection sites in structure analyses. In addition, reflecting the richness of the Anatolian apple germplasm, low numbers of synonymous, and identical accessions were identified among the germplasm. Finally, using the publically available SSR data generated in other studies, we investigated genetic relationships between Anatolian accession groups and European apple accession groups. Our results reported here provide a useful base for future studies aimed at investigating the genetic diversity of wild and cultivated apples from Anatolia and the surrounding regions.

Profiling of proteasome activity in Alyssum species on serpentine soils in Turkey reveals possible insight into nickel tolerance and accumulation

In crops and most plants, nickel induces oxidative stress resulting in oxidized and misfolded proteins. Proteasomes maintain cellular homeostasis during stress by removing these damaged proteins. Although mild stress tolerance is mediated by proteasomal proteolysis of misfolded and oxidized proteins, previous studies have observed that severe nickel stress decreases proteasome activity in nickel-sensitive plants. Whether or not proteasome function is impaired in nickel-tolerant plants is not know. Therefore, we tested the hypothesis that proteasome activity is elevated in nickel-tolerant Alyssum species capable of accumulating nickel to unusually high levels. Our field studies examined Alyssum sibiricum and Alyssum caricum, a moderate nickel accumulator and hyper-accumulator respectively, growing on their native serpentine soil in Turkey. A. sibiricum had higher proteasome activity on serpentine soil compared to non-serpentine soil; these plants also had elevated levels of nickel accumulation and higher proteasome activity compared to other low accumulating plants in the genus Festuca or Astragalus. In A. caricum, proteasome activity was very weakly correlated with nickel soil bioavailability or accumulation in leaf tissue, suggesting that proteasome function was not impaired in plants that accumulated the highest concentration of nickel. We discuss if maintained proteasome activity might underpin nickel tolerance and the unique ecophysiology of nickel hyper-accumulation in plants.

Amplified fragment length polymorphism analysis of grapevine rootstock genotypes in Turkey.

Amplified fragment length polymorphism (AFLP) technique was used to assess genetic relationships among 20 grapevine rootstocks in Turkey. Discrimination of the rootstocks with 10 primer combinations yielded 1366 bands on AFLP gels; 65% of them were polymorphic. The rootstocks revealed two main clusters; one of them comprised two (Malégue and Harmony) and the other 18 genotypes. The Ber x Rip hybrids Cosmo 2 and Cosmo 10 formed a group with a high internal similarity ratio (0.909); they also formed a group with other Ber x Rip hybrids, 5C, 8B, SO4, and 420A Mgt, with a similarity ratio higher than 0.690 (subcluster II). Rootstock 5BB was placed in another subcluster (subcluster III). Among five Ber x Rup rootstocks, 110R-99R (0.853) and 1103P-140Ru (0.837), which were located in different subclusters, formed a dual group, as expected. Rootstock 779P, which had almost 0.800 similarity with the dual group of 110R-99R, formed another group. The 44-53 Malégue and Harmony rootstocks formed a group with the lowest similarity ratio (0.668) (subcluster I) and 41B-Fercal formed another dual group with a high similarity ratio (0.813). The distinction capacity of single- and double-EcoRI-MseI primers was evaluated; primers AC/CTA, TC/CAC, AG/CTC, and AG/CAG discriminated the 20 rootstocks, with a similarity value below 0.910. The best primers for discrimination of rootstock varieties were AG/CAG and AG/CTC, while the primers TC/CAC and AC/CTA could also be useful for clonal discrimination of genotypes.

In vitro multiplication of wild relatives in genus Beta conserves the invaluable threatened germplasms

Conservation of threatened plant genetic resources is vital for food security and biodiversity maintenance. Wild species of genus Beta are invaluable germplasm which could be utilized for beet breeding programs. In this study, in vitro multiplication and genotypic responses of different species in the section Beta and Corollinae were compared in presence of plant growth regulators. Following the surface sterilization, seeds were cultivated in vitro. Cotyledonary node explants were excised from the germinated young seedlings and treated with BAP, GA3 and TDZ. The obtained results demonstrated a significant difference between the genotypes in terms of in vitro shoot proliferation efficiency when subjected to BAP and GA3. Among the applied growth regulators, effect of BAP on number of multiplied shoots was the highest. Moreover, the genotypic variation in rooting was also evident when the shoots were subjected to IAA and IBA. This study is the first report of in vitro multiplication of wild species in genus Beta that could be exploited in future germplasm maintenance, gene transformation and breeding studies.