[show abstract][hide abstract] ABSTRACT: Flavonoids are secondary metabolites with multiple functions. In grape (Vitis vinifera), the most abundant flavonoids are proanthocyanidins (PAs), major quality determinants for fruit and wine. However, knowledge about the regulation of PA composition is sparse. Thus, we aimed to identify novel genomic regions involved in this mechanism. Expression quantitative trait locus (eQTL) mapping was performed on the transcript abun-dance of five downstream PA synthesis genes (dihydroflavonol reductase (VvDFR), leuco-anthocyanidin dioxygenase (VvLDOX), leucoanthocyanidin reductase (VvLAR1), VvLAR2 and anthocyanidin reductase (VvANR)) measured by real-time quantitative PCR on a pseudo F1 population in two growing seasons. Twenty-one eQTLs were identified; 17 of them did not overlap with known candidate tran-scription factors or cis-regulatory sequences. These novel loci and the presence of digenic epistasis support the previous hypothesis of a polygenic regulatory mechanism for PA biosyn-thesis. In a genomic region co-locating eQTLs for VvDFR, VvLDOX and VvLAR1, gene annotation and a transcriptomic survey suggested that VvMYBC2-L1, a gene coding for an R2R3-MYB protein, is involved in regulating PA synthesis. Phylogenetic analysis showed its high similarity to characterized negative MYB factors. Its spatiotemporal expression profile in grape coin-cided with PA synthesis. Its functional characterization via overexpression in grapevine hairy roots demonstrated its ability to reduce the amount of PA and to down-regulate expression of PA genes.
New Phytologist 02/2014; 201(3). · 6.74 Impact Factor
[show abstract][hide abstract] ABSTRACT: Grape diversity present in Morocco and the part of this diversity used nowadays are poorly documented. In order to choose
diversified genotypes, to select them so that their agronomic interest will be tested, a group of 21 autochthonous cultivars
preserved in the germplasm collections of SODEA and 18 Moroccan cultivars from “Domaine de Vassal” INRA grape collection was
compared to a group of cultivars from neighbouring countries (Algeria and Tunisia), and from a core collection optimizing
simple sequence repeat (SSR) allelic diversity of grape. Data from 20 nuclear and 3 chloroplastic SSR markers were obtained
for this set of 211 cultivars. A total of 156 alleles (mean of 7.8 alleles per locus) were detected for the nSSRs and 7 alleles
for the cpSSR in the Moroccan group. Chlorotype diversity in Moroccan and Algerian group were similar, but slightly lower
than in the Tunisian group and the core collection. Similarly, the nSSR diversity was high in the core collection and low
in the Moroccan and the Algerian groups compared to the two other groups. Clustering of cultivars based on nSSR data reflected
their geographical origin and, to a certain extent, the use of the cultivars. The specificity of the Moroccan plant material
was attested by the Bayesian analysis using Structure, while differences of the core collection were clearly revealed both
by the Bayesian and a multivariate analysis. These results confirm the differentiation of the material from Maghreb and more
specifically of Moroccan material, having evolved independently from Europe.
Tree Genetics & Genomes 08/2013; · 2.40 Impact Factor
[show abstract][hide abstract] ABSTRACT: Historical information and archaeological and palaeobotanical findings point Georgia, in the South Caucasus, as a cradle for grapevine (Vitis vinifera L.) domestication from its wild form (V. vinifera silvestris Beck.) and subsequent selection and development of varieties with characters suitable for human consumption. The hypothesis of Georgia being a center of domestication, combined with its distance from western countries and the importance of its viticulture and wine production, make Georgian grape germplasm particularly interesting to be investigated under the genetic point of view. Twenty nuclear microsatellite loci were used to genotype 112 Georgian grapevine accessions (V. vinifera sativa Beck.) from germplasm collections and 18 from spontaneous growing plants (V. vinifera silvestris Beck.) found in wild conditions and to compare them to a large international cultivar collection in France. Data analysis shows that Georgian grapevine germplasm has maintained distinctive traits despite arrival of international, foreign varieties and still conserve characteristics of local breeding linked to traditional wine production regions of the country. Results have identified alleles, overall loci, well represented in the Georgian germplasm (cultivated and wild) and absent or poorly represented in other countries, highlighting uniqueness and originality of traits of this viticulture. Moreover, the search for relationships between Georgian and foreign viticulture has evidenced few interesting cases linking the Georgian varieties with Western European ones and with neighboring Caucasian countries, helping to identify the real place of origin in some doubtful cases. In addition, populations or sparse individuals of wild grapevine still preserved in the Georgian natural environments present smaller genetic distances with local cultivars than in other European regions. Principal component analysis (PCA) has also identified special overlapping of the wild compartment with some cultivated varieties. This work provides a highly significant new contribution to applied aspects of Georgian grapevine genetic resources management and use. Uniqueness of the Georgian cultivated grapevine gene pool together with its close relatedness with the wild compartment makes this country a good candidate to address questions regarding domestication and grapevine genetic resource conservation.
Tree Genetics & Genomes 08/2013; 9(3). · 2.40 Impact Factor
[show abstract][hide abstract] ABSTRACT: Expression quantitative locus (eQTL) mapping was proposed as a valuable approach to dissect the genetic basis of transcript variation, one of the prime causes of natural phenotypic variation. Few eQTL studies have been performed on woody species due to the difficulty in sample homogenisation. Based on previous knowledge on berry colour formation, we performed eQTL mapping in field experimentation of grapevine with appropriate sampling criteria. The transcript level of VvUFGT, a key enzyme for anthocyanin synthesis was measured by real-time qRT-PCR in grape berry on a 191-individual pseudo-F1 progeny, derived from a cross between Syrah and Grenache cultivars. Two eQTLs were identified: one, explaining 20%, of genotypic variance and co-locating with VvUFGT itself (cis-eQTL), was principally due to the contrast between Grenache alleles; the other, explaining 35% of genotypic variance, was a trans-eQTL due to Syrah allelic contrast and co-located with VvMYBAs, transcription factors known to activate the expression of VvUFGT. This study assessed and validated the feasibility of eQTL mapping approach in grapevine and offered insights and new hypotheses on grape skin colour formation.
[show abstract][hide abstract] ABSTRACT: Proanthocyanidins (PA) play a major role in plant protection against biotic and abiotic stresses. Moreover these molecules are known to be beneficial for human health and are responsible for astringency of foods and beverages such as wine and thus have a great impact on the final quality of the product. Genes playing a role in the PA pathway are only partially known. The amount of available transcriptomic and genetic data to select candidate genes without a priori knowledge from orthologous function increases every day. However, the methods used so far generate so many candidate genes that it is impossible to validate all of them. In this study, we used an integrative strategy based on different screening methods to select a reduced list of candidate genes. We have crossed results from different screening methods including QTL mapping and three transcriptomic studies to select 20 candidate genes, located in QTL intervals and fulfilling at least two transcriptomic screenings. This list includes three glucosyltransferases, already suspected to have a role in the PA biosynthetic pathway. Among the 17 remaining genes, we selected three genes to perform further analysis by association genetic studies. For each of these genes, we found a polymorphism linked to PA variation. The three genes (VvMybC2-L1, VvGAT-like and VvCob-like), not previously known to play a role in PA synthesis, are promising candidates for further molecular physiology studies.
Plant Physiology and Biochemistry 04/2013; · 2.78 Impact Factor
[show abstract][hide abstract] ABSTRACT: BACKGROUND: Grapevine (Vitis vinifera subsp. vinifera) is one of the most important and ancient horticultural plants in the world. Domesticated about 8--10,000 years ago in the Eurasian region, grapevine evolved from its wild relative (V. vinifera subsp. sylvestris) into very diverse and heterozygous cultivated forms. In this work we study grapevine genetic structure in a large sample of cultivated varieties, to interpret the wide diversity at morphological and molecular levels and link it to cultivars utilization, putative geographic origin and historical events. RESULTS: We analyzed the genetic structure of cultivated grapevine using a dataset of 2,096 multi-locus genotypes defined by 20 microsatellite markers. We used the Bayesian approach implemented in the STRUCTURE program and a hierarchical clustering procedure based on Ward's method to assign individuals to sub-groups. The analysis revealed three main genetic groups defined by human use and geographic origin: a) wine cultivars from western regions, b) wine cultivars from the Balkans and East Europe, and c) a group mainly composed of table grape cultivars from Eastern Mediterranean, Caucasus, Middle and Far East countries. A second structure level revealed two additional groups, a geographic group from the Iberian Peninsula and Maghreb, and a group comprising table grapes of recent origins from Italy and Central Europe. A large number of admixed genotypes were also identified. Structure clusters regrouped together a large proportion of family-related genotypes. In addition, Ward's method revealed a third level of structure, corresponding either to limited geographic areas, to particular grape use or to family groups created through artificial selection and breeding. CONCLUSIONS: This study provides evidence that the cultivated compartment of Vitis vinifera L. is genetically structured. Genetic relatedness of cultivars has been shaped mostly by human uses, in combination with a geographical effect. The finding of a large portion of admixed genotypes may be the trace of both large human-mediated exchanges between grape-growing regions throughout history and recent breeding.
[show abstract][hide abstract] ABSTRACT: a b s t r a c t The NAC gene family encodes a large plant-specific transcription factors that play diverse roles in plant development and stress regulation. In this study, nucleotide variation at gene NAC4 was surveyed by sequencing a sample of 50 wild grapevine accessions and 73 cultivars of Vitis vinifera L. A total of 11 bi-allelic single nucleotide polymorphisms were detected in the studied gene resulting in an average of 1 SNP every 63 bp. Among the 11 detected SNPs, 2 SNPs were located in the coding region, SNP R373 results in a change in the encoded amino acid (Val ⇒ Ile) and the second is synonymous. The detected SNPs combine to 10 haplotypes with frequency varying from 0.4% to 53.3%. Genetic diversity level recorded for cultivated grapevine gene pools (11 SNP, 9 haplo, Hd = 0.735 ± 0.028, Pi = 0.00492 ± 0.00024) was higher than for wild germplasms (9 SNPs, 8 haplo, Hd = 0.526 ± 0.051, Pi = 0.00236 ± 0.00026). A search for selection signatures highlighted non deviations from the standard neutral model for this gene in wild sample. However patterns of nucleotide diversity were consistent with a balancing selection in cultivated gene pool which may provide evidence for adaptation at the molecular level and help elucidate genotype phenotype relationships. The presence of SNPs resulting in the change in the encoded amino acid in the studied gene can be interesting to highlight contribution of SNP in the evolution of candidate genes coding for functional trait in plants and can be a base for further genetic association studies.
[show abstract][hide abstract] ABSTRACT: This study provides the first analysis of the level and patterns of nucleotide polymorphism of the NCED1 gene in grapevine (Vitis vinifera L.). A total of 123 sequences of the gene were analyzed to give a sample of 50 wild accessions and 73 cultivars. A high single nucleotide polymorphism and haplotype diversity was revealed in the cultivars studied, especially Tunisian germplasms which present an important and diverse reservoir of genetic diversity for grape breeding and conservation. The haplotype distribution highlights two origins of the cultivars studied: one may be related to primary grapevine gene pool domestication while the second seems to be more recent. Thus, besides domestication, gene introgression has also played a role in shaping the current varietal landscape of grape cultivars. Higher nucleotide and haplotype polymorphism was recorded for cultivars. This was accompanied by a higher recombination rate in cultivated grapevines for this gene, a recent selective sweep in wild samples and a balancing selection in cultivars. The conservation of genetic diversity of the endangered wild germplasm is important to ensure that the wild population can be used in future breeding programs of the domesticated cultivars. The high number of alleles discovered can be used as a valuable source for association studies between allele frequencies and phenotypic variations in this gene. In addition to natural selection, molecular evidence shows that genetic variation in this locus appears to be shaped by a combination of mutation and recombination events.
[show abstract][hide abstract] ABSTRACT: Inheritance of nuclear microsatellite markers (nSSR) has been proved to be a powerful tool to verify or uncover the parentage of grapevine cultivars. The aim of the present study was to undertake an extended parentage analysis using a large sample of Vitis vinifera cultivars held in the INRA "Domaine de Vassal" Grape Germplasm Repository (France). A dataset of 2,344 unique genotypes (i.e. cultivars without synonyms, clones or mutants) identified using 20 nSSR was analysed with FAMOZ software. Parentages showing a logarithm of odds score higher than 18 were validated in relation to the historical data available. The analysis first revealed the full parentage of 828 cultivars resulting in: (1) 315 original full parentages uncovered for traditional cultivars, (2) 100 full parentages confirming results established with molecular markers in prior papers and 32 full parentages that invalidated prior results, (3) 255 full parentages confirming pedigrees as disclosed by the breeders and (4) 126 full parentages that invalidated breeders' data. Second, incomplete parentages were determined in 1,087 cultivars due to the absence of complementary parents in our cultivar sample. Last, a group of 276 genotypes showed no direct relationship with any other cultivar in the collection. Compiling these results from the largest set of parentage data published so far both enlarges and clarifies our knowledge of the genetic constitution of cultivated V. vinifera germplasm. It also allows the identification of the main genitors involved in varietal assortment evolution and grapevine breeding.
Theoretical and Applied Genetics 09/2012; · 3.66 Impact Factor
[show abstract][hide abstract] ABSTRACT: Fertility (number of inflorescences per shoot) is a trait of major importance for grapevine breeding. We present and compare
the results of quantitative trait locus (QTL) detection for fertility in two table grape progenies, MTP3140 and MTP3234. Novel
parental and consensus maps were built for MTP3140. We found a main QTL on linkage group (LG) 5 in both progenies, which was
also the most stable one across years. It explained up to 18.5% of the total intra-cross phenotypic variance. Three other
QTLs, one on LG 5 and two on LG 14, were repeated over years but were found in a single progeny. Our results suggest that
QTLs effect was mainly additive. The prospects for testing candidate genes are discussed as well as the potential interest
of these results for marker-assisted selection.
Tree Genetics & Genomes 04/2012; 6(3):413-422. · 2.40 Impact Factor
[show abstract][hide abstract] ABSTRACT: Ampelographic descriptions, a set of 20 nuclear microsatellite loci (nuSSR), five chloroplast microsatellites (cSSR), as well
as historical references have been used to identify 66 accessions of Vitis vinifera L. The plant material included major and minor varieties under risk of extinction, collected in the Balearic Islands, and
now conserved in two germplasm repositories site in Spain. The 66 samples analyzed corresponded to 32 different genotypes,
several unique genotypes were found, three of them remaining unknown. Some synonyms and homonyms were found in the Mediterranean
basin, highlighting that the dispersal of some varieties are related with historical human movements and migrations occurred
in three several periods, (1) around seventh century related to Islam expansion, (2) around thirteen to fifteenth centuries
and (3) in the nineteenth century related to phylloxera crisis. Some parentages were identified, being the cultivar Callet
Cas Concos a key variety in several crosses, confirming the high value of unknown varieties for parentage analysis. Several
grouping methods confirm the existence of two gene pools.
KeywordsChlorotype–Genetic structure–Minor varieties–Nuclear microsatellite–Parentage analysis–
[show abstract][hide abstract] ABSTRACT: Proanthocyanidins (PAs), or condensed tannins, are flavonoid polymers, widespread throughout the plant kingdom, which provide protection against herbivores while conferring organoleptic and nutritive values to plant-derived foods, such as wine. However, the genetic basis of qualitative and quantitative PA composition variation is still poorly understood. To elucidate the genetic architecture of the complex grape PA composition, we first carried out quantitative trait locus (QTL) analysis on a 191-individual pseudo-F1 progeny. Three categories of PA variables were assessed: total content, percentages of constitutive subunits and composite ratio variables. For nine functional candidate genes, among which eight co-located with QTLs, we performed association analyses using a diversity panel of 141 grapevine cultivars in order to identify causal SNPs.
Multiple QTL analysis revealed a total of 103 and 43 QTLs, respectively for seed and skin PA variables. Loci were mainly of additive effect while some loci were primarily of dominant effect. Results also showed a large involvement of pairwise epistatic interactions in shaping PA composition. QTLs for PA variables in skin and seeds differed in number, position, involvement of epistatic interaction and allelic effect, thus revealing different genetic determinisms for grape PA composition in seeds and skin. Association results were consistent with QTL analyses in most cases: four out of nine tested candidate genes (VvLAR1, VvMYBPA2, VvCHI1, VvMYBPA1) showed at least one significant association with PA variables, especially VvLAR1 revealed as of great interest for further functional investigation. Some SNP-phenotype associations were observed only in the diversity panel.
This study presents the first QTL analysis on grape berry PA composition with a comparison between skin and seeds, together with an association study. Our results suggest a complex genetic control for PA traits and different genetic architectures for grape PA composition between berry skin and seeds. This work also uncovers novel genomic regions for further investigation in order to increase our knowledge of the genetic basis of PA composition.
[show abstract][hide abstract] ABSTRACT: a b s t r a c t Twenty highly polymorphic nuclear microsatellite markers were used to assess genetic relationships among 181 grapevine accessions traditionally grown in different geographical region of the species' range and 21 wild Tunisian samples. A total of 330 alleles were detected and extensive genetic polymorphisms were recorded either in the cultivated or in the wild compartment. A genetic structure according to accessions taxonomic status and cultivars geographical origin was revealed by multivariate analysis and F st values. However, a considerable overlap was observed in the majority of distinguished groups. The highest level of differentiation between wild and cultivated accessions is recorded between Tunisian wild accessions and North African cultivars which are confirmed by multivariate analysis. Thus the occurrence of local domestication event of grapevines in the North African region is unlikely. North African cultivars do not derive directly from local wild populations but could mostly correspond to imported materials introduced probably from East region or derived from crosses between them. A genetic affinity between wild gene pool and cultivars of West Europe was brought to light by multivariate and F st analysis. Pattern structure of genetic diversity in the analyzed material presents an additional proof of the occurrence of secondary grapevine domestication events in West Europe region which contributed to the evolution of the species, a hypothesis supported by recent archeobiological and molecular studies.
Scientia Horticulturae 01/2012; 141:53-60. · 1.40 Impact Factor
[show abstract][hide abstract] ABSTRACT: In this study, two gene fragments corre-sponding to the VvMYBA1 and VvMYBA2 loci were sequenced on a sample of grapes including cultivated and wild accessions originating from Tunisia, Germany and France. A total of 42 SNPs were detected in the sequenced fragments giving an average of 1 SNP every 33 bp. High level of polymorphism was observed in the samples either in cultivated or wild accessions. Pattern of nucleotide diversity indi-cates a non departure from neutrality expectations for wild grapevine sample for gene VvMYBA1 and VvMYBA2 and for cultivated sample for gene VvMYBA1. However, a linkage to a selective sweep was revealed for cultivated grapevine gene pool in gene VvMYBA2. A genetic structure of the studied sample according to accession taxonomic status was revealed by the UPGMA clustering with a consider-able overlap. This result was confirmed by significant but low genetic differentiation values between culti-vated and wild sample. The number of migrants Nm based on sequence data information between Tunisian cultivars and Tunisian wild accessions showed a low level of gene flow between those germplasms. This finding indicates that Tunisian cultivars do not derive directly from local wild populations but could mostly correspond to imported materials introduced during historical times. However, the possibility that some cultivars derived from ancestral events of local domestication or cross hybridization with native wild plants was not completely excluded for Tunisian grapevine accessions.
Genetic Resources and Crop Evolution 01/2012; · 1.59 Impact Factor
[show abstract][hide abstract] ABSTRACT: Through multiple vegetative propagation cycles, clones accumulate mutations in somatic cells that are at the origin of clonal phenotypic diversity in grape. Clonal diversity provided clones such as Cabernet-Sauvignon N°470, Chardonnay N° 548 and Pinot noir N° 777 which all produce wines of superior quality. The economic impact of clonal selection is therefore very high: since approx. 95% of the grapevines produced in French nurseries originate from the French clonal selection. In this study we provide the first broad description of polymorphism in different clones of a single grapevine cultivar, Pinot noir, in the context of vegetative propagation. Genome sequencing was performed using 454 GS-FLX methodology without a priori, in order to identify and quantify for the first time molecular polymorphisms responsible for clonal variability in grapevine. New generation sequencing (NGS) was used to compare a large portion of the genome of three Pinot noir clones selected for their phenotypic differences. Reads obtained with NGS and the sequence of Pinot noir ENTAV-INRA® 115 sequenced by Velasco et al., were aligned on the PN40024 reference sequence. We then searched for molecular polymorphism between clones. Three types of polymorphism (SNPs, Indels, mobile elements) were found but insertion polymorphism generated by mobile elements of many families displayed the highest mutational event with respect to clonal variation. Mobile elements inducing insertion polymorphism in the genome of Pinot noir were identified and classified and a list is presented in this study as potential markers for the study of clonal variation. Among these, the dynamic of four mobile elements with a high polymorphism level were analyzed and insertion polymorphism was confirmed in all the Pinot clones registered in France.
PLoS ONE 01/2012; 7(3):e32973. · 3.73 Impact Factor
[show abstract][hide abstract] ABSTRACT: Plant color variation is due not only to the global pigment concentration but also to the proportion of different types of pigment. Variation in the color spectrum may arise from secondary modifications, such as hydroxylation and methylation, affecting the chromatic properties of pigments. In grapes (Vitis vinifera L.), the level of methylation modifies the stability and reactivity of anthocyanin, which directly influence the color of the berry. Anthocyanin methylation, as a complex trait, is controlled by multiple molecular factors likely to involve multiple regulatory steps.
In a Syrah × Grenache progeny, two QTLs were detected for variation in level of anthocyanin methylation. The first one, explaining up to 27% of variance, colocalized with a cluster of Myb-type transcription factor genes. The second one, explaining up to 20% of variance, colocalized with a cluster of O-methyltransferase coding genes (AOMT). In a collection of 32 unrelated cultivars, MybA and AOMT expression profiles correlated with the level of methylated anthocyanin. In addition, the newly characterized AOMT2 gene presented two SNPs associated with methylation level. These mutations, probably leading to a structural change of the AOMT2 protein significantly affected the enzyme specific catalytic efficiency for the 3'-O-methylation of delphinidin 3-glucoside.
We demonstrated that variation in methylated anthocyanin accumulation is susceptible to involve both transcriptional regulation and structural variation. We report here the identification of novel AOMT variants likely to cause methylated anthocyanin variation. The integration of QTL mapping and molecular approaches enabled a better understanding of how variation in gene expression and catalytic efficiency of the resulting enzyme may influence the grape anthocyanin profile.
[show abstract][hide abstract] ABSTRACT: High-throughput re-sequencing, new genotyping technologies and the availability of reference genomes allow the extensive characterization of Single Nucleotide Polymorphisms (SNPs) and insertion/deletion events (indels) in many plant species. The rapidly increasing amount of re-sequencing and genotyping data generated by large-scale genetic diversity projects requires the development of integrated bioinformatics tools able to efficiently manage, analyze, and combine these genetic data with genome structure and external data.
In this context, we developed SNiPlay, a flexible, user-friendly and integrative web-based tool dedicated to polymorphism discovery and analysis. It integrates:1) a pipeline, freely accessible through the internet, combining existing softwares with new tools to detect SNPs and to compute different types of statistical indices and graphical layouts for SNP data. From standard sequence alignments, genotyping data or Sanger sequencing traces given as input, SNiPlay detects SNPs and indels events and outputs submission files for the design of Illumina's SNP chips. Subsequently, it sends sequences and genotyping data into a series of modules in charge of various processes: physical mapping to a reference genome, annotation (genomic position, intron/exon location, synonymous/non-synonymous substitutions), SNP frequency determination in user-defined groups, haplotype reconstruction and network, linkage disequilibrium evaluation, and diversity analysis (Pi, Watterson's Theta, Tajima's D).Furthermore, the pipeline allows the use of external data (such as phenotype, geographic origin, taxa, stratification) to define groups and compare statistical indices.2) a database storing polymorphisms, genotyping data and grapevine sequences released by public and private projects. It allows the user to retrieve SNPs using various filters (such as genomic position, missing data, polymorphism type, allele frequency), to compare SNP patterns between populations, and to export genotyping data or sequences in various formats.
Our experiments on grapevine genetic projects showed that SNiPlay allows geneticists to rapidly obtain advanced results in several key research areas of plant genetic diversity. Both the management and treatment of large amounts of SNP data are rendered considerably easier for end-users through automation and integration. Current developments are taking into account new advances in high-throughput technologies.SNiPlay is available at: http://sniplay.cirad.fr/.
[show abstract][hide abstract] ABSTRACT: a b s t r a c t Chloroplast microsatellite markers were used in this study to genotype 43 grapevines accessions grown in Tunisia. Size variation was observed for the three cpSSR loci, both in the sample of cultivars and in wild accessions. The seven alleles observed in the sample of cultivars for the three loci are present in wild accessions except that their distribution is different. Levels of genetic diversity obtained for the Tunisian grapevines either in wild or cultivated gene pools are high and comparable with values obtained with other studied samples of Vitis vinifera. The distribution of haplotypes within the two samples is differen-tial. Indeed, the chlorotype A is most abundant in the wild sample, whereas the chlorotype C is majority in the sample of cultivars. Haplotypes frequencies for cultivated grapevine distinguish haplotypes B and C as the most frequent (28% and 44% respectively) and haplotypes A and D as the least frequent (16% and 12% respectively). For wild grapevines, the seven alleles combined in three haplotypes, A, C and D. The haplotype A is the most frequent (44%) in the analyzed sample of wild accessions while haplotypes C and D show a frequency of 28%. Chlorotype distribution in Tunisian cultivars is comparable with that of cultivars in the Eastern Region representing the primary centre of domestication of the species. These results agree with the higher relevance of table grape cultivars in Tunisian viticulture and support an ori-ental origin of a large part of autochthons cultivars. Our results agree with other studies based in nuclear and chloroplast microsatellite markers and suggest independent domestication events for V. vinifera L. species.
[show abstract][hide abstract] ABSTRACT: Chloroplast microsatellite markers were used in this study to genotype 43 grapevines accessions grown in Tunisia. Size variation was observed for the three cpSSR loci, both in the sample of cultivars and in wild accessions. The seven alleles observed in the sample of cultivars for the three loci are present in wild accessions except that their distribution is different. Levels of genetic diversity obtained for the Tunisian grapevines either in wild or cultivated gene pools are high and comparable with values obtained with other studied samples of Vitis vinifera. The distribution of haplotypes within the two samples is differential. Indeed, the chlorotype A is most abundant in the wild sample, whereas the chlorotype C is majority in the sample of cultivars. Haplotypes frequencies for cultivated grapevine distinguish haplotypes B and C as the most frequent (28% and 44% respectively) and haplotypes A and D as the least frequent (16% and 12% respectively). For wild grapevines, the seven alleles combined in three haplotypes, A, C and D. The haplotype A is the most frequent (44%) in the analyzed sample of wild accessions while haplotypes C and D show a frequency of 28%. Chlorotype distribution in Tunisian cultivars is comparable with that of cultivars in the Eastern Region representing the primary centre of domestication of the species. These results agree with the higher relevance of table grape cultivars in Tunisian viticulture and support an oriental origin of a large part of autochthons cultivars. Our results agree with other studies based in nuclear and chloroplast microsatellite markers and suggest independent domestication events for V. vinifera L. species.
Scientia Horticulturae - SCI HORT-AMSTERDAM. 01/2011; 130(4):781-786.
[show abstract][hide abstract] ABSTRACT: In this study, we developed a nuclear DNA extraction protocol for Next Generation Sequencers (NGS).
We applied this extraction method to grapevines and coffee trees, which are known to contain many secondary metabolites. The nuclear DNA obtained was sequenced by the 454/GS-FLX method. We obtained excellent results, with less than 4% cytoplasmic DNA, in a similar way to a BAC (Bacterial Artificial Chromosome)-building protocol. We also compared our protocol with a classic DNA extraction using specific cytoplasmic DNA amplification. Results showed a lower cytoplasmic DNA contamination with the new protocol.
The method presented here is fast and economical. The DNA obtained is of high quality, with a low level of cytoplasmic DNA contamination, and very efficient for the construction of sequencing libraries.
American Journal of Botany 01/2011; 98(1):e13-5. · 2.59 Impact Factor