Biology subjects

Wiedemann-Merdinoglu, S.

Publications and source records attributed to Wiedemann-Merdinoglu, S..

4 recordsLinked to original sources

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

Breeding for durable resistance in crops: defeated loci may act as Trojan horses compromising the effectiveness of major resistance genes.

Resistance breeding offers invaluable perspectives for environment-friendly crop protection, but its success may be limited by the breakdown of plant resistance by pathogen strains. This threat is particularly acute for perennial crops, which may be cultivated for several decades. With the increasing use of new varieties carrying multiple major resistance loci, grapevine (Vitis spp.) represents a distinctive model to investigate the broad agreement that combining several resistance genes (pyramiding) enhances both resistance efficacy and durability. To this end, grapevine progenies segregating for four resistance loci against Plasmopara viticola (Rpvs) were used to evaluate the efficiency of single and pyramided major loci when confronted to naive and Rpv-breaking pathogen strains. In the context of polygenic resistance, both undefeated and defeated Rpvs provided significant quantitative effects. However, interactions between pyramided Rpvs were either beneficial, neutral or detrimental to the level of resistance, depending on the loci combination and pathogen strain. In particular, the fact that the presence of defeated resistance loci may compromise the resistance provided by functional major loci has important implications for crops resistance breeding. Thorough phenotypic investigations of pyramiding breeding schemes emerge as a critical step for the effective and durable management of genetic resistances and plant diseases.

plant biology↗

bioRxiv2025

Rpv2 is part of a cluster of NLRs specific to Vitis rotundifolia and confers extreme resistance to grapevine downy mildew.

Downy mildew caused by the oomycete Plasmopara viticola is one of the most important diseases affecting grapevine. Resistant varieties are an environmentally-friendly tool to control grapevine downy mildew. Efficient breeding for durable resistance requires knowledge of the underlying mechanisms. Here we aimed at identifying the molecular basis of Rpv2, a gene for extreme resistance to downy mildew derived from Vitis rotundifolia, and at characterizing its effect on pathogen development. Individuals from two populations segregating for Rpv2 were evaluated for resistance to downy mildew and genotyped. Following genetic mapping, markers flanking Rpv2 were used to screen new populations and identify recombinant individuals. Sequencing of recombinants and in silico chromosome painting was used to reduce the interval containing Rpv2. Comparative genomics inside the Vitaceae, involving de novo assembly of the V. rotundifolia Regale genome, allowed narrowing-down the list of candidate genes. We restrict Rpv2 to a 250 kb genomic region that contains two resistance genes of the NLR type. Comparative genomics analyses could not find orthologs of both NLRs in the other Vitis species studied. We also show that Rpv2-mediated resistance leads to pathogen arrest early in the infection cycle. Our results show that Rpv2 belongs to the NLR family of resistance genes, contributing thus to understand the potential and risks of its use in breeding programs and suggesting that combining NLR-type genes may lead to durable resistance KEY MESSAGEThe Rpv2 locus for extreme resistance to grapevine downy mildew is mapped to a 250 kb genomic region containing two NLR-type genes specific to V. rotundifolia.

plant biology↗