Biology subjects

Duchene, E.

Publications and source records attributed to Duchene, E..

9 recordsLinked to original sources

bioRxiv2026

Genetic analysis of grapevine wood composition identifies glycosyltransferases involved in the biosynthesis of stilbene glycosides

Although wood extractives may play important roles in defense against pathogens, few studies have explored the genetic determinism of their accumulation. In this work, we have used a non-targeted metabolomic approach to perform a genetic analysis of grapevine (Vitis vinifera) wood extractive composition in a progeny from a cross between Riesling and Gewurztraminer. Metabolic quantitative trait loci (mQTL) analyses of cane and trunk wood extractives revealed a number of mQTLs. Analysis of one of these mQTL has led to the identification of a cluster of six UDP glycosyltransferase (UGT) genes linked to the accumulation of resveratrol-glucoside (piceid) in both canes and trunks. Detailed biochemical and structural characterization of these six UGTs highlighted a surprising functional diversity among this small gene family, as well as one UGT gene as a key determinant of the constitutive accumulation of piceid in lignified grapevine tissues. Molecular evolution analyses showed that the UGTs in this gene cluster were globally under strong purifying selection, suggesting important biological roles of the corresponding proteins. Moreover, the functional characterization showed that distinct UGT genes were involved in the biosynthesis of cis- and trans- isomers of piceid, suggesting that these isomers may play different biological roles in grapevine.

plant biology↗

bioRxiv2025

Comparative assessment of genomic, phenomic, and metabolomic prediction models in biparental grapevine breeding populations

Accelerating grapevine breeding for disease resistance and climate adaptation remains constrained by long generation cycles. We benchmarked genomic (SNP), phenomic (NIRS), and metabolomic (untargeted LC-MS) prediction for 24 agronomic traits in a biparental population phenotyped over three years. Seven statistical frameworks and four tissue x timepoint combinations (wood; vineyard leaves at budbreak and flowering; greenhouse leaves at flowering) were evaluated, together with feature-wise BLUPs across samples. Cross-year and cross-population analyses with two additional populations assessed temporal robustness and transferability. Genomic prediction was most accurate (up to r = 0.83), metabolomic prediction was intermediate (up to r = 0.59), and phenomic prediction was lowest (up to r = 0.39) despite its lower acquisition cost. Metabolite features were more heritable than NIR wavelengths, for which most unexplained variation remained residual under the fitted model. Multi-omics integration produced limited overall gains. These results support genomic selection as the primary approach, with metabolomic or phenomic screening considered only for traits and sampling designs that show reproducible predictive signal.

genomics↗

bioRxiv2025

Uncovering the genetic basis of agronomic traits in over 1,000 grapevine genotypes derived from a disease resistance breeding program

Breeding disease-resistant grapevines that retain agronomic performance under variable climates requires loci and predictions that transfer across related hybrid families. We analyzed 1,081 genotypes from 95 crosses within the French INRAE-ResDur breeding program for 13 phenology, yield and berry-composition traits evaluated at five sites from 2006 to 2024. We integrated within-family QTL mapping, kinship- and population-adjusted multiple-population QTL mapping in 772 progeny, and structure-aware GWAS in 899-968 individuals, depending on the trait, together with cross-environment, cross-trait and local genomic estimated breeding-value analyses. Genetic and phenotypic differentiation among families strongly affected locus detection. Of 76 family-QTL intervals, seven, representing six trait-region hypotheses, were locally concordant across all three mapping frameworks. The strongest recurrent evidence involved a chromosome-16 region for veraison and harvest date, where a localGEBV block at 14.69 Mb ranked first for veraison and second for harvest; chromosome-14 cluster traits and chromosome-1 compactness emerged as additional validation priorities. Cross-environment meta-analysis detected no common fixed-effect association at 5% FDR but revealed extensive heterogeneous evidence. Cross-trait analysis grouped 270 significant marker tests into 54 candidate multi-trait regions, without establishing biological pleiotropy. Population-adjusted localGEBV yielded a mean leave-one-population-out correlation of 0.470 between phenotypic BLUPs and genomic scores across traits. These results distinguish compact haplotype-validation targets from background- and environment-dependent signals, supporting a staged strategy that combines marker- assisted selection for validated recurrent regions with externally validated multi-trait, multi- environment genomic prediction for polygenic traits.

genetics↗

bioRxiv2025

Metabolic biomarker-based phenotyping unveils quantitative effects of plant resistance and pathogen aggressiveness in the grapevine (Vitis spp.) - downy mildew (Plasmopara viticola) pathosystem.

Grapevine resistance to downy mildew has been primarily associated with major "Resistance to Plasmopara viticola" (Rpv) loci, which are extensively used in breeding programs. Resistant varieties represent an effective solution to mitigate the environmental impact of fungicide application in viticulture, but P. viticola strains able to overcome major Rpv have become a main threat to their cultivation. Pyramiding resistance loci in the same variety enhances plant resistance, but interactions involving stacked and defeated Rpv and different P. viticola strains are poorly documented. Investigation of these interactions may uncover new information for the development of efficient breeding strategies, the optimal exploitation of Rpv, and the building of durable resistance. In the present study, a grapevine offspring carrying single and pyramided Rpv1, Rpv3.1 and Rpv10 was phenotyped in laboratory conditions for the resistance to P. viticola using a naive strain and a strain virulent towards Rpv10. By using a high-resolution phenotyping strategy based on P. viticola metabolic biomarkers, we demonstrated that the efficacy of Rpv combinations and aggressiveness of P. viticola strains can be quantified in the early phase of infection and were often related to sporulation outcome. Furthermore, we described how a limited residual effect of a defeated Rpv may become significant in pyramiding. In conclusion, in addition to providing the keys to streamlining resistance utilization in grapevine, our research presents a distinctive case study that provides valuables information for breeding new resistant varieties, thanks to an innovative "omic"-based phenotyping approach, which may be adapted to other plant pathosystems.

plant biology↗

bioRxiv2025

Impact of the introgression of resistance loci on agro-oenological traits in grapevine interspecific hybrids

O_LIA major aim in modern grapevine (Vitis vinifera L.) breeding programs is the introgression of disease resistance genes along with desired cultural and nological traits. Understanding the genetic links between resistance genes and agro-nological traits is a crucial issue for grapevine breeders. C_LIO_LIWe studied the genetic determinism of a wide range of agro-oenological traits in a complex interspecific hybrid population and identified two cases of colocalizations with disease resistance quantitative trait loci (QTL). C_LIO_LIThe species of origin of chromosomal regions in the off-springs were determined thanks to in silico chromosome painting. The linkage drag around resistance genes from primary gene pool was assessed as low due to a good recombination rate with V. vinifera. C_LIO_LIWe established that wild Vitis species are, apart from their interest in disease resistance, essential resources for improving the cultural characteristics of grapevine. C_LI

plant biology↗

bioRxiv2023

Discovery of a locus associated with susceptibility to esca dieback in grapevine

Esca is the most destructive and predominant grapevine trunk diseases. The chronic infections and vine mortality caused by esca syndrome lead to huge economic losses and threatens the sustainability of vineyards worldwide. Although shown as associated with the presence of wood fungi, the etiology of esca remains still unclear and putatively involves multifactorial causes, which makes the development of effective control methods challenging. As differences in esca susceptibility had already been observed among grapevine varieties, we investigated in a biparental population the presence of genetic factors that can explain theses variations. Thanks to the destructive phenotyping of a 16-year-old vineyard plot, we discovered that the Gewurztraminer variety carries on chromosome 1 a locus linked to variations in trunk necrosis associated with esca, which we have named ENS1. Our study also suggests that there is a partial link between trunk vigor and necrosis due to esca. To our best knowledge, ENS1 is the first instance of genetic factor identified as involved in the limitation of necrosis associated to grapevine esca. While the identification of ENS1 alone may not provide a complete resolution of the esca issue, this discovery represents nonetheless a first step towards a genetic solution and paves the way for broader genetic investigations in the future.

genetics↗

bioRxiv2022

An improved reference of the grapevine genome supports reasserting the origin of the PN40024 highly-homozygous genotype

The genome sequence assembly of the diploid and highly homozygous V. vinifera genotype PN40024 serves as the reference for many grapevine studies. Despite several improvements of the PN40024 genome assembly, its current version PN12X.v2 is quite fragmented and only represents the haploid state of the genome with mixed haplotypes. In fact, despite the PN40024 genome is nearly homozygous, it still contains various heterozygous regions. Taking the opportunity of the improvements that long-read sequencing technologies offer to fully discriminate haplotype sequences and considering that several Vitis sp. genomes have recently been assembled with these approaches, an improved version of the reference, called PN40024.v4, was generated. Through incorporating long genomic sequencing reads to the assembly, the continuity of the 12X.v2 scaffolds was highly increased. The number of scaffolds decreased from 2,059 to 640 and the number of N bases was reduced by 88%. Additionally, the full alternative haplotype sequence was built for the first time, the chromosome anchoring was improved and the amount of unplaced scaffolds were reduced by half. To obtain a high-quality gene annotation that outperforms previous versions, a liftover approach was complemented with an optimized annotation workflow for Vitis. Integration of the gene reference catalogue and its manual curation have also assisted in improving the annotation, while defining the most reliable estimation to date of 35,230 genes. Finally, we demonstrate that PN40024 resulted from selfings of cv. Helfensteiner (cross of cv. Pinot noir and Schiava grossa) instead of a single Pinot noir. These advances will help maintaining the PN40024 genome as a gold-standard reference also contributing in the eventual elaboration of the grapevine pangenome.

genomics↗

bioRxiv2021

The grape MYB24 mediates the coordination of light-induced terpene and flavonol accumulation in response to berry anthocyanin sunscreen depletion

The presence of naturally-occurring color mutants in plants has permitted the identification of many regulatory genes implicated in the synthesis of discrete metabolic compounds, mostly anthocyanins and carotenoids. Conversely, transcription factors that coordinate more than one specialized metabolic pathway seem challenging to screen from a forward genetics perspective. We explored the relationship between different branches of the phenylpropanoid and isoprenoid pathways while examining an infrequent berry skin color variegation in grapevine. Red and white berry skin sections were compared at the genetic, transcriptomic and metabolomic levels showing that, as in most cultivated white grape varieties, the uncolored skin section convened the non-functional alleles of the anthocyanin regulators MYBA1 and MYBA2, explaining the lack of pigments. In contrast, light-responsive flavonols and monoterpenes increased in anthocyanin-depleted areas. We disclosed an enrichment of the flavonol, terpene and carotenoid pathways among up-regulated genes from white-skin sections, accompanied by increased expressions of flavonol regulators and the still uncharacterized MYB24 gene. We used DAP-seq to examine the in vitro binding of affinity-purified MYB24 protein to genomic DNA and demonstrated its binding in the promoter regions of terpene (22) and carotenoid (6) genes, in addition to more than 30 photosynthesis and light-response genes, including the flavonol-regulator HY5 homologue (HYH). We confirmed the activation of TPS35 and HYH promoter:luciferase reporters in the presence of MYB24 and the grape bHLH MYC2, all of which correlate in their higher expression in white skin variegated sections. The integration of several datasets allowed to define a list of high confidence targets, suggesting MYB24 as a modulator of light responses including the synthesis of flavonoids (flavonols) and isoprenoids (terpenes, and putatively carotenoids). The correspondence between MYB24 and monoterpenes in all conditions surveyed implies that this regulatory network is broadly triggered towards berry ripening, and that the absence of anthocyanin sunscreens accelerates its activation most likely in a dose-dependent manner due to increased radiation exposure.

plant biology↗

bioRxiv2020

The wild grape genome sequence provides insights into the transition from dioecy to hermaphroditism during grape domestication

Grapevine has a major economical and cultural importance since antiquity. A key step in domestication was the transition from separate sexes (dioecy) in wild Vitis vinifera ssp. sylvestris (V. sylvestris) to hermaphroditism in cultivated Vitis vinifera ssp. vinifera. While the grapevine sex locus is known to be small, its precise boundaries, gene content and the sex-determining genes are unknown. Here we obtained a high-quality de novo reference genome for V. sylvestris and whole-genome resequencing data of a cross. Studying SNP segregation patterns, gene content and expression in wild and cultivated accessions allowed us to build a model for sex determination in grapevine. In this model, up- and down-regulation of a cytokinin regulator is sufficient to cause female sterility and reversal to hermaphroditism, respectively. This study highlights the importance of neo-functionalization of Y alleles in sex determination and provides a resource for studying genetic diversity in V. sylvestris and the genomic processes of grapevine domestication.

plant biology↗