Biology subjects

This, P.

Publications and source records attributed to This, P..

5 recordsLinked to original sources

bioRxiv2024

Large gradient of susceptibility to esca disease revealed by long-term monitoring of 46 grapevine cultivars in a common garden vineyard

Grapevine (Vitis vinifera L.) is prone to many fungal diseases, including esca, a severe vascular disease threatening the wine sector and for which there is no cost-effective cure. Susceptibility to esca varies between cultivars in different infection conditions. It may therefore be possible to use the genetic diversity of grapevine cultivars to mitigate disease impact. However, the genetic component of esca susceptibility has rarely been investigated in the vineyard, and the specific mechanisms and varietal traits underlying esca susceptibility remain unknown. In this study, we monitored the incidence and severity of esca foliar symptoms and plant dieback (apoplexy and mortality) at plant level for seven years, on 46 cultivars planted in an experimental common garden, to separate the genetic component of esca susceptibility from the effects of environment and cropping practices. We observed a broad gradient of varietal susceptibility, with a mean incidence of 0 to 26% of vines expressing esca foliar symptoms depending on the variety. This gradient remained similar across years and, unlike the severity of foliar symptoms, the incidence of grapevine dieback was significantly correlated with that of foliar symptoms. We detected a significant but weak and very localised phylogenetic signal for the incidence of esca foliar symptoms in this panel of cultivars. We then explored the relationships between epidemiological metrics and ecophysiological and phenological traits phenotyped on the same plot. Esca disease incidence was negatively correlated with {delta}13C across cultivars, suggesting that varieties with higher water use efficiency are less prone to the expression of esca symptoms on leaves. Moreover, the least vigorous cultivars were among the least susceptible, although this relationship was not significant. By contrast, neither phenological stages nor nitrogen status were significantly predictive of cultivar susceptibility to the disease. Together, these results provide new insight into the potential of genetic resources for use in the sustainable management of grapevine trunk diseases and open up new perspectives for studying the pathological and physiological determinants of their incidence.

plant biology↗

bioRxiv2021

Interest of phenomic prediction as an alternative to genomic prediction in grapevine

Phenomic prediction has been defined as an alternative to genomic prediction by using spectra instead of molecular markers. A reflectance spectrum reflects the biochemical composition within a tissue, under genetic determinism. Thus, a relationship matrix built from spectra could potentially capture genetic signal. This new methodology has been successfully applied in several cereal species but little is known so far about its interest in perennial species. Besides, phenomic prediction has only been tested for a restricted set of traits, mainly related to yield or phenology. This study aims at applying phenomic prediction for the first time in grapevine, using spectra collected on two tissues and over two consecutive years, on two populations and for 15 traits. First, we characterized the genetic signal in spectra and under which condition it could be maximized, then phenomic predictive ability was compared to genomic predictive ability. We found that the co-inertia between spectra and genomic data was stable across tissues or years, but variable across populations, with co-inertia around 0.3 and 0.6 for diversity panel and half-diallel populations, respectively. Differences between populations were also observed for predictive ability of phenomic prediction, with an average of 0.27 for the diversity panel and 0.35 for the half-diallel. For both populations, there was a correlation across traits between predictive ability of genomic and phenomic prediction, with a slope around 1 and an intercept of -0.2, thus suggesting that phenomic prediction could be applied for any trait.

genetics↗

bioRxiv2021

Across-population genomic prediction in grapevine opens up promising prospects for breeding

Crop breeding involves two selection steps: choosing progenitors and selecting offspring within progenies. Genomic prediction, based on genome-wide marker estimation of genetic values, could facilitate these steps. However, its potential usefulness in grapevine (Vitis vinifera L.) has only been evaluated in non-breeding contexts mainly through cross-validation within a single population. We tested across-population genomic prediction in a more realistic breeding configuration, from a diversity panel to ten bi-parental crosses connected within a half-diallel mating design. Prediction quality was evaluated over 15 traits of interest (related to yield, berry composition, phenology and vigour), for both the average genetic value of each cross (cross mean) and the genetic values of individuals within each cross (individual values). Genomic prediction in these conditions was found useful: for cross mean, average per-trait predictive ability was 0.6, while per-cross predictive ability was halved on average, but reached a maximum of 0.7. Mean predictive ability for individual values within crosses was 0.26, about half the within-half-diallel value taken as a reference. For some traits and/or crosses, these across-population predictive ability values are promising for implementing genomic selection in grapevine breeding. This study also provided key insights on variables affecting predictive ability. Per-cross predictive ability was well predicted by genetic distance between parents and when this predictive ability was below 0.6, it was improved by training set optimization. For individual values, predictive ability mostly depended on trait-related variables (magnitude of the cross effect and heritability). These results will greatly help designing grapevine breeding programs assisted by genomic prediction.

genetics↗

bioRxiv2020

Harnessing multivariate, penalized regression methods for genomic prediction and QTL detection to cope with climate change affecting grapevine

Viticulture has to cope with climate change and decrease pesticide inputs, while maintaining yield and wine quality. Breeding is a potential key to meet this challenge, and genomic prediction is a promising tool to accelerate breeding programs, multivariate methods being potentially more accurate than univariate ones. Moreover, some prediction methods also provide marker selection, thus allowing quantitative trait loci (QTLs) detection and allowing the identification of positional candidate genes. We applied several methods, interval mapping as well as univariate and multivariate penalized regression, in a bi-parental grapevine progeny, in order to compare their ability to predict genotypic values and detect QTLs. We used a new denser genetic map, simulated two traits under four QTL configurations, and re-analyzed 14 traits measured in semi-controlled conditions under different watering conditions. Using simulations, we recommend the penalized regression method Elastic Net (EN) as a default for genomic prediction, and controlling the marginal False Discovery Rate on EN selected markers to prioritize the QTLs. Indeed, penalized methods were more powerful than interval mapping for QTL detection across various genetic architectures. Multivariate prediction did not perform better than its univariate counterpart, despite strong genetic correlation between traits. Using experimental data, penalized regression methods proved as very efficient for intra-population prediction whatever the genetic architecture of the trait, with accuracies reaching 0.68. These methods applied on the denser map found new QTLs controlling traits linked to drought tolerance and provided relevant candidate genes. These methods can be applied to other traits and species.

genetics↗

bioRxiv2020

Genome-wide association and prediction studies using a grapevine diversity panel give insights into the genetic architecture of several traits of interest

To cope with the challenges faced by agriculture, speeding-up breeding programs is a worthy endeavor, especially for perennials such as grapevine, but requires understanding the genetic architecture of target traits. To go beyond the mapping of quantitative trait locus (QTL) in bi-parental crosses, we exploited a diverse panel of 279 Vitis vinifera L. cultivars. This panel planted in five blocks in the vineyard 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 (SNPs) by combining an 18K microarray and genotyping-by-sequencing (GBS). The experimental design allowed to reliably assess the genotypic values for most traits. Marker densification via GBS markedly increased the proportion of genetic variance explained by SNPs, and two multi-SNP models identified QTLs not found by a SNP-by-SNP model. Overall, 489 reliable QTLs were detected for 41% more response variables than by a SNP-by-SNP model with microarray-only SNPs, many new ones compared to the results from bi-parental crosses. Prediction accuracy higher than 0.42 was obtained for 50% of the response variables. Our overall approach as well as QTL and prediction results provide insights into the genetic architecture of target traits. New candidate genes and the application in breeding are discussed.

genetics↗