New stable QTLs for berry weight do not colocalize with QTLs for seed traits in cultivated grapevine (Vitis vinifera L.)

International audienceBACKGROUND: In grapevine, as in other fruit crops, fruit size and seed content are key components of yield and quality; however, very few Quantitative Trait Loci (QTLs) for berry weight and seed content (number, weight, and dry matter percentage) have been discovered so far. To identify new stable QTLs for marker-assisted selection and candidate gene identification, we performed simultaneous QTL detection in four mapping populations (seeded or seedless) with various genetic backgrounds. RESULTS: For berry weight, we identified five new QTLs, on linkage groups (LGs) 1, 8, 11, 17 and 18, in addition to the known major QTL on LG 18. The QTL with the largest effect explained up to 31% of total variance and was found in two genetically distant populations on LG 17, where it colocalized with a published putative domestication locus. For seed traits, besides the major QTLs on LG 18 previously reported, we found four new QTLs explaining up to 51% of total variance, on LGs 4, 5, 12 and 14. The previously published QTL for seed number on LG 2 was found related in fact to sex. We found colocalizations between seed and berry weight QTLs only for the major QTL on LG 18 in a seedless background, and on LGs 1 and 13 in a seeded background. Candidate genes belonging to the cell number regulator CNR or cytochrome P450 families were found under the berry weight QTLs on LGs 1, 8, and 17. The involvement of these gene families in fruit weight was first described in tomato using a QTL-cloning approach. Several other interesting candidate genes related to cell wall modifications, water import, auxin and ethylene signalling, transcription control, or organ identity were also found under berry weight QTLs. CONCLUSION: We discovered a total of nine new QTLs for berry weight or seed traits in grapevine, thereby increasing more than twofold the number of reliable QTLs for these traits available for marker assisted selection or candidate gene studies. The lack of colocalization between berry and seed QTLs suggests that these traits may be partly dissociated

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Structure spatiale génétique et niveau de diversité intrapopulation chez les arbres forestiers

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Automatic Flower Number Evaluation in Grapevine Inflorescences Using RGB Images

International audienceA precise count of flower number per inflorescence is essential to characterize the reproductive behavior of a vine. Previous efforts to automatize this process by image-based technologies have failed in the development of a universal system that can be applied to multiple grapevine cultivars, or they have been tested in a set of inflorescences of narrow morphological diversity. Here, we have developed an alternative general method in FIJI for the non-destructive counting of visible flowers in RGB images, considering inflorescences from 45 different grapevine genotypes from three progenies segregating for inflorescence morphology. The algorithm, based on the segmentation of the image into regions of interest (ROIs) according to their color and morphology, provided counting results highly correlated to manual ones (R2 = 0.91). Similar results were obtained when validating this tool in an external dataset of 400 images of four grapevine cultivars. Counting values were used for actual flower number estimation by linear modelling using a subset of 45 images, considering a flower density factor to reduce the adverse effect of the variable number of hidden flowers. Our approach allowed the estimation of flower number with satisfactory results, providing useful information for grapevine breeding and research

Searching key regulatory genes at the origin of cell differentiation inside the pericarp

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Genetic architecture of water use efficiency in grapevine: a key role for night transpiration

National audienceImproving water use efficiency (WUE, the balance between biomass production and water costs) in crops becomes crucial to match increasing needs for food in a context of global change. Reduction of water loss at night could be a good strategy to limit waste of water without altering photosynthesis rate in the daytime. However, genetic and physiological bases of night transpiration and its contribution to WUE remain poorly documented. This study first aimed at deciphering the genetic determinants of WUE in grapevine, a woody crop of economic importance in drought prone areas. It further explored a possible role for night transpiration in WUE variability. A four-year experiment was run on a F1 progeny from a cross between Shiraz and Grenache. A greenhouse phenotyping facility (PhenoArch, Montpellier) was used to dissect determinants of WUE in potted plants and results were compared to those obtained in vineyard conditions under two soil water regimes. In PhenoArch, a high genetic variability was found and QTLs were detected for whole plant WUE under both watering regimes. Interestingly, these QTLs co-localized with those found for proxys of WUE (Δ13C in musts) measured in the field, highlighting the promising avenues offered by phenotyping facilities. Furthermore, a genetic control of water losses at night was detected and supported for the first time by QTL detection. Night transpiration could reach 30% of daytime one depending on genotype and conditions. Furthermore, we found common QTLs to WUE and night transpiration. This, together with significant negative correlations between both traits, strongly suggested that lower WUE relies, at least partly, on higher water losses at night. Through further physiological characterization of the determinants of night transpiration, we showed that both residual stomatal aperture and cuticle losses are genetically controlled. These results open new avenues to breed grapevine for lower water losses at night

A Combination of Phenotyping, Genetic and Physiological Approaches to Guide Breeding for Efficient Water Use in Grapevine

International audienceWater scarcity associated with climate change particularly threatens the sustainability of viticulture in most cultivated, drought prone areas. Breeding grapevine for reduced water use and maintained production (that is high water-use efficiency) is therefore of major interest. This requires a comprehensive knowledge of the physiological impacts of drought which are the most influential on yield and quality. Special attention should be paid to those mechanisms involved in the regulation of water status in plant tissues as the primary parameter affected by drought. Transpiration rate, which has major influence on plant water status, together with water-use efficiency, therefore require special attention in breeding programs. To progress on the determinism of transpiration rate and water-use efficiency in grapevine, we used a F1 progeny made of 188 genotypes from a cross between two widespread cultivars, Syrah and Grenache, well-known for their contrasted water use. We showed the benefits of combining quantitative genetics (for QTL detection) and physiological experiments to study this population both in the vineyard and on potted plants. On the one hand, we developed an original experimental design in the field coupled to geostatistical modelling to take into account the spatial variability of soil water status inherent to vineyard conditions. This helped to identify significant genetic variability for the traits of interest. On the other hand, we combined powerful phenotyping tools on potted plants (high-throughput platform and controlled chambers) to control water deficit conditions and improve QTL detection. First, we found evidence that a dual physiological mechanism controls the decline of leaf water status under drought with a key role for plant hydraulic conductance beside that of stomatal control of transpiration. Contrasted combination of these two controls may lead to more or less efficient maintenance of leaf water status in response to soil drying (i.e. iso- or an isohydric behaviour). An indirect role of abscisic acid on stomatal conductance was also identified, mediated by the downregulation of leaf hydraulic conductance, with a genetic variability which correlated with genetic variation in iso- or aniso-hydric behaviour. We then revealed wide genetic variations in nocturnal transpiration, which correlated with variations in whole plant water-use efficiency (WUE), and identified corresponding genetic and physiological determinants. Lastly, we showed some consistency between QTLs detected for daytime WUE in pots and in the vineyard. Beyond the potential interest of the QTLs detected in this study for breeding prospects, this work demonstrated the interest of quantitative genetics to shed light on ecophysiological and physiological processes

New insight into the genetics of color in grape

Grapes may either be white or colored, ranging from the lightest pink to the darkest purple tone depending on the quantity and composition of anthocyanins accumulated in the berry skin. QTL mapping on cross-derived progeny and association mapping on natural diversity were combined to decipher the genetic architecture of anthocyanin content and composition in berry skin, a crucial trait for both wine quality and human nutrition. For the total anthocyanin content in the skin of mature berries on a segregating population of 191 progenies, we identified 2 QTLs accounting for 62% and 7.1% of the total variation. Further studying candidate genes from these QTL intervals on a core collection of natural resources (141 individuals), we identified Myb genes highly associated with total content of anthocyanins. Using a multivariate regression method, we demonstrated that four polymorphisms accounted for 86% of the observed variation, with all these polymorphisms leading to structural changes in the MYB proteins. Skin color tones are not only due to the overall pigment concentration but also to variation in pigment composition, mostly due to hydroxylation, methylation and acylation differences. For all these variations, the major QTL on LG2 played a key role. In addition, specific QTLs were found for each of the composition variable: on LG6, explaining 13% of the hydroxylation variation, on LG1, explaining up to 17% of the methylation variation and on LG7 and LG13, explaining 11 and 7% of the variation in p-coumaric acylation. For the hydroxylation level, the specific QTL on LG6 co-localized with candidate VvF3' 5' H genes and two genic SNPs within two of those genes were identified as associated to the variation. For the methylation variation, the specific QTL on LG1 co-localized with a cluster of O-methyltransferase genes among which VvAOMT3.2 showed a strong association