Enhancing grapevine breeding efficiency through genomic prediction and selection index.

Grapevine (Vitis vinifera) breeding reaches a critical point. New cultivars are released every year with resistance to powdery and downy mildews. However, the traditional process remains time-consuming, taking 20-25 years, and demands the evaluation of new traits to enhance grapevine adaptation to climate change. Until now, the selection process has relied on phenotypic data and a limited number of molecular markers for simple genetic traits such as resistance to pathogens, without a clearly defined ideotype, and was carried out on a large scale. To accelerate the breeding process and address these challenges, we investigated the use of genomic prediction, a methodology using molecular markers to predict genotypic values. In our study, we focused on 2 existing grapevine breeding programs: Rosé wine and Cognac production. In these programs, several families were created through crosses of emblematic and interspecific resistant varieties to powdery and downy mildews. Thirty traits were evaluated for each program, using 2 genomic prediction methods: Genomic Best Linear Unbiased Predictor and Least Absolute Shrinkage Selection Operator. The results revealed substantial variability in predictive abilities across traits, ranging from 0 to 0.9. These discrepancies could be attributed to factors such as trait heritability and trait characteristics. Moreover, we explored the potential of across-population genomic prediction by leveraging other grapevine populations as training sets. Integrating genomic prediction allowed us to identify superior individuals for each program, using multivariate selection index method. The ideotype for each breeding program was defined collaboratively with representatives from the wine-growing sector.

A genome-wide association and prediction study in grapevine deciphers the genetic architecture of multiple traits and identifies genes under many new QTLs.

To cope with the challenges facing agriculture, speeding-up breeding programs is a worthy endeavor, especially for perennial species such as grapevine, but requires understanding the genetic architecture of target traits. To go beyond the mapping of quantitative trait loci in bi-parental crosses, we exploited a diversity panel of 279 Vitis vinifera L. cultivars planted in 5 blocks in the vineyard. This panel was phenotyped over several years for 127 traits including yield components, organic acids, aroma precursors, polyphenols, and a water stress indicator. The panel was genotyped for 63k single nucleotide polymorphisms by combining an 18K microarray and genotyping-by-sequencing. The experimental design allowed to reliably assess the genotypic values for most traits. Marker densification via genotyping-by-sequencing markedly increased the proportion of genetic variance explained by single nucleotide polymorphisms, and 2 multi-single nucleotide polymorphism models identified quantitative trait loci not found by a single nucleotide polymorphism-by-single nucleotide polymorphism model. Overall, 489 reliable quantitative trait loci were detected for 41% more response variables than by a single nucleotide polymorphism-by-single nucleotide polymorphism model with microarray-only single nucleotide polymorphisms, many new ones compared with the results from bi-parental crosses. A prediction accuracy higher than 0.42 was obtained for 50% of the response variables. Our overall approach as well as quantitative trait locus and prediction results provide insights into the genetic architecture of target traits. New candidate genes and the application into breeding are discussed.

The Microvine, a plant model to study the effect of vine-shoot extract on the accumulation of glycosylated aroma precursors in grapes.

BACKGROUND: The Microvine plant model displays unique reproductive organ behavior and is suitable for grapevine fruit physiological studies, allowing one to undertake studies up to five times more rapidly than the current situation with grapevines. Recently, vine-shoot aqueous extracts, which have an interesting phenolic and aroma composition, have been proposed as viticultural biostimulants, since their post-veraison foliar application to grapevines impacts the wine aroma profile. Using Microvines, the aim of this study was to determine the effect of vine-shoot extract foliar application on 21 stages of grape development. The application was carried out from BBCH 53 (inflorescences clearly visible) to BBCH 85 (softening of berries) to reveal stage-specific responses of the accumulation of glycosylated aroma precursors at BBCH 89 (berries ripe for harvest), the phenological stage selected to study the treatment effect. RESULTS: Microvine use made it possible to carry out 15 sampling time points during 86 days of the experiment, which were established by the cumulative degree days (CDD) parameter. The results confirmed that vine-shoot extract treatment had a positive impact on total glycosylated compounds, especially aglycones such as alcohols, terpenes and C13 -norisoprenoids, with a higher effect when the treatment was applied during ripening. CONCLUSION: Extrapolation of the results to grapevines suggests that vine-shoot extract treatment could modulate the synthesis of grape glycosylated aroma precursors. © 2017 Society of Chemical Industry.