Evolution of the VvMybA gene family, the major determinant of berry colour in cultivated grapevine (Vitis vinifera L.)

Pinot blanc and Pinot gris arose as independent somatic mutations of Pinot noir

Somatic mutation is a natural mechanism which allows plant growers to develop new cultivars. As a source of variation within a uniform genetic background, it also represents an ideal tool for studying the genetic make-up of important traits and for establishing gene functions. Layer-specific molecular characterization of the Pinot family of grape cultivars was conducted to provide an evolutionary explanation for the somatic mutations that have affected the locus of berry colour. Through the study of the structural dynamics along chromosome 2, a very large deletion present in a single Pinot gris cell layer was identified and characterized. This mutation reveals that Pinot gris and Pinot blanc arose independently from the ancestral Pinot noir, suggesting a novel parallel evolutionary model. This proposed 'Pinot-model' represents a breakthrough towards the full understanding of the mechanisms behind the formation of white, grey, red, and pink grape cultivars, and eventually of their specific enological aptitude.

Role of an esterase in flavor volatile variation within the tomato clade

Tomato flavor is dependent upon a complex mixture of volatiles including multiple acetate esters. Red-fruited species of the tomato clade accumulate a relatively low content of acetate esters in comparison with the green-fruited species. We show that the difference in volatile ester content between the red- and green-fruited species is associated with insertion of a retrotransposon adjacent to the most enzymatically active member of a family of esterases. This insertion causes higher expression of the esterase, resulting in the reduced levels of multiple esters that are negatively correlated with human preferences for tomato. The insertion was evolutionarily fixed in the red-fruited species, suggesting that high expression of the esterase and consequent low ester content may provide an adaptive advantage in the ancestor of the red-fruited species. These results illustrate at a molecular level how closely related species exhibit major differences in volatile production by altering a volatile-associated catabolic activity.

Association mapping in forest trees and fruit crops

Association mapping (AM), also known as linkage disequilibrium (LD) mapping, is a viable approach to overcome limitations of pedigree-based quantitative trait loci (QTL) mapping. In AM, genotypic and phenotypic correlations are investigated in unrelated individuals. Unlike QTL mapping, AM takes advantage of both LD and historical recombination present within the gene pool of an organism, thus utilizing a broader reference population. In plants, AM has been used in model species with available genomic resources. Pursuing AM in tree species requires both genotyping and phenotyping of large populations with unique architectures. Recently, genome sequences and genomic resources for forest and fruit crops have become available. Due to abundance of single nucleotide polymorphisms (SNPs) within a genome, along with availability of high-throughput resequencing methods, SNPs can be effectively used for genotyping trees. In addition to DNA polymorphisms, copy number variations (CNVs) in the form of deletions, duplications, and insertions also play major roles in control of expression of phenotypic traits. Thus, CNVs could provide yet another valuable resource, beyond those of microsatellite and SNP variations, for pursuing genomic studies. As genome-wide SNP data are generated from high-throughput sequencing efforts, these could be readily reanalysed to identify CNVs, and subsequently used for AM studies. However, forest and fruit crops possess unique architectural and biological features that ought to be taken into consideration when collecting genotyping and phenotyping data, as these will also dictate which AM strategies should be pursued. These unique features as well as their impact on undertaking AM studies are outlined and discussed.

Transposable elements are a major cause of somatic polymorphism in Vitis vinifera L

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.

Use of the VvMybA1 gene for non-destructive quantification of promoter activity via color histogram analysis in grapevine (Vitis vinifera) and tobacco

We report the development of a convenient plant-based reporter system to analyze promoters and facilitate selection of genetically engineered plants. The VvMybA1 gene of grapevine (Vitis vinifera L.) regulates the last metabolic step of anthocyanin biosynthesis and its ectopic expression leads to anthocyanin production in otherwise non-pigmented cells. To develop an anthocyanin-based quantitative reporter system, the VvMybA1 gene was isolated from V. vinifera 'Merlot' and placed under control of three promoters to test its ability to distinguish different activity levels. Promoters included a double enhanced CaMV35S (d35S) promoter, a double enhanced CsVMV (dCsVMV) promoter or a bi-directional dual promoter (BDDP), resulting in transformation vectors DAT, CAT and DEAT, respectively. These vectors were introduced into grapevine and tobacco via Agrobacterium-mediated transformation for transient and stable expression analysis. A linear relationship between the mean red brightness (MRB) and optical density (OD) values with a 0.99 regression coefficient was identified in a dilution series of anthocyanin, thus allowing the use of histogram data for non-destructive and real-time assessment of transcriptional activity. Results of histogram-based analysis of color images from transformed grapevine somatic embryos (SE) and various tissues of transgenic tobacco showed a consistent six to sevenfold promoter activity increase of DEAT over DAT. This expression increase was verified by spectroscopic measurement of anthocyanin concentrations in sepal tissue of transgenic tobacco plants. These results were congruent with previously findings of promoter activity derived from GUS fluorometric assay, thus demonstrating for the first time that the VvMybA1 gene could offer a simple, versatile and reliable plant-based alternative for quantitative promoter analysis in plants.

Haplotype composition at the color locus is a major genetic determinant of skin color variation in Vitis × labruscana grapes

Skin color is one of the most important fruit traits in grape, and has become greatly diversified due to hybridization and human selection. Many studies concerning the genetic control of grape color in European species (Vitis vinifera L.), especially the role of MYB-related genes, have been reported. On the other hand, there have been few studies of the MYB-related genes in grapes belonging to V. ×labruscana L.H. Bailey, a subgroup of grapes that originated from the hybridization of V. labrusca with V. vinifera. In the present study, we found a novel functional haplotype, HapE2 (consisting of the genes VlMYBA2 and VlMYBA1-3), in diploid V. ×labruscana. Moreover, we developed a method to determine the haplotype compositions of tetraploid grapes by means of quantitative real-time PCR, and investigated the relationship between haplotype composition and skin color. The color locus in V. ×labruscana grapes usually consists of functional haplotypes (HapE1 and/or HapE2), and non-functional haplotype HapA. The number of functional haplotypes in the genome was found to be correlated with the level of anthocyanin in the skin. Anthocyanin contents of grapes that contained HapE2 were significantly higher than those containing HapE1. These results suggest that the number and kind of functional haplotypes at the color locus are the major genetic factors that determine skin color variation. These findings provide new knowledge about the unique genetic control of color in V. ×labruscana grapes, and should contribute to development of new cultivars that have the desired color and anthocyanin content.

Genetic structure and domestication history of the grape

The grape is one of the earliest domesticated fruit crops and, since antiquity, it has been widely cultivated and prized for its fruit and wine. Here, we characterize genome-wide patterns of genetic variation in over 1,000 samples of the domesticated grape, Vitis vinifera subsp. vinifera, and its wild relative, V. vinifera subsp. sylvestris from the US Department of Agriculture grape germplasm collection. We find support for a Near East origin of vinifera and present evidence of introgression from local sylvestris as the grape moved into Europe. High levels of genetic diversity and rapid linkage disequilibrium (LD) decay have been maintained in vinifera, which is consistent with a weak domestication bottleneck followed by thousands of years of widespread vegetative propagation. The considerable genetic diversity within vinifera, however, is contained within a complex network of close pedigree relationships that has been generated by crosses among elite cultivars. We show that first-degree relationships are rare between wine and table grapes and among grapes from geographically distant regions. Our results suggest that although substantial genetic diversity has been maintained in the grape subsequent to domestication, there has been a limited exploration of this diversity. We propose that the adoption of vegetative propagation was a double-edged sword: Although it provided a benefit by ensuring true breeding cultivars, it also discouraged the generation of unique cultivars through crosses. The grape currently faces severe pathogen pressures, and the long-term sustainability of the grape and wine industries will rely on the exploitation of the grape's tremendous natural genetic diversity.