Discovery and genome-guided mapping of REN12 from Vitis amurensis, conferring strong, rapid resistance to grapevine powdery mildew

Novel loci associated with resistance to downy and powdery mildew in grapevine

Among the main challenges in current viticulture, there is the increasing demand for sustainability in the protection from fungal diseases, such as downy mildew (DM) and powdery mildew (PM). Breeding disease-resistant grapevine varieties is a key strategy for better managing fungicide inputs. This study explores the diversity of grapevine germplasm (cultivated and wild) from Caucasus and neighboring areas to identify genotypes resistant to DM and PM, based on 13 Simple Sequence Repeat (SSR) loci and phenotypical (artificial pathogen inoculation) analysis, and to identify loci associated with DM and PM resistance, via Genome-Wide Association Analysis (GWAS) on Single Nucleotide Polymorphism (SNP) profiles. SSR analysis revealed resistant alleles for 16 out of 88 genotypes. Phenotypic data identified seven DM and 31 PM resistant genotypes. GWAS identified two new loci associated with DM resistance, located on chromosome 15 and 16 (designated as Rpv36 and Rpv37), and two with PM resistance, located on chromosome 6 and 17 (designated as Ren14 and Ren15). The four novel loci identified genomic regions rich in genes related to biotic stress response, such as genes involved in pathogen recognition, signal transduction and resistance response. This study highlights potential candidate genes associated with resistance to DM and PM, providing valuable insights for breeding programs for resistant varieties. To optimize their utilization, further functional characterization studies are recommended.

Non-Destructive Monitoring of Foliar Fungicide Efficacy with Hyperspectral Sensing in Grapevine

Frequent fungicide applications are required to manage grapevine powdery mildew (Erysiphe necator). However, this practice is costly and has led to widespread fungicide resistance. A method of monitoring in-field fungicide efficacy could help growers maximize spray-interval length, thereby reducing costs and the rate of fungicide resistance emergence. The goal of this study was to evaluate if hyperspectral sensing in the visible to shortwave infrared range (400 to 2,400 nm) can quantify foliar fungicide efficacy on grape leaves. Commercial formulations of metrafenone, Bacillus mycoides isolate J (BmJ), and sulfur were applied on Chardonnay grapevines in vineyard or greenhouse settings. Foliar reflectance was measured with handheld hyperspectral spectroradiometers at multiple days post-application. Fungicide efficacy was estimated as a proxy for fungicide residue and disease control measured with the Blackbird microscopy imaging robot. Treatments could be differentiated from the untreated control with an accuracy of 73.06% for metrafenone, 67.76% for BmJ, and 94.10% for sulfur. The change in spectral reflectance was moderately correlated with the cube root of the area under the disease progress curve for metrafenone- and sulfur-treated samples (R2 = 0.38 and 0.36, respectively) and with sulfur residue (R2 = 0.42). BmJ treatment impacted foliar physiology by enhancing the leaf mass/area and reducing the nitrogen and total phenolic content as estimated from spectral reflectance. The results suggest that hyperspectral sensing can be used to monitor in-situ fungicide efficacy, and the prediction accuracy depends on the fungicide and the time point measured. The ability to monitor in-situ fungicide efficacy could facilitate more strategic fungicide applications and promote sustainable grapevine protection. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Boosting grapevine breeding for climate-smart viticulture: from genetic resources to predictive genomics

The multifaceted nature of climate change is increasing the urgency to select resilient grapevine varieties, or generate new, fitter cultivars, to withstand a multitude of new challenging conditions. The attainment of this goal is hindered by the limiting pace of traditional breeding approaches, which require decades to result in new selections. On the other hand, marker-assisted breeding has proved useful when it comes to traits governed by one or few genes with great effects on the phenotype, but its efficacy is still restricted for complex traits controlled by many loci. On these premises, innovative strategies are emerging which could help guide selection, taking advantage of the genetic diversity within the Vitis genus in its entirety. Multiple germplasm collections are also available as a source of genetic material for the introgression of alleles of interest via adapted and pioneering transformation protocols, which present themselves as promising tools for future applications on a notably recalcitrant species such as grapevine. Genome editing intersects both these strategies, not only by being an alternative to obtain focused changes in a relatively rapid way, but also by supporting a fine-tuning of new genotypes developed with other methods. A review on the state of the art concerning the available genetic resources and the possibilities of use of innovative techniques in aid of selection is presented here to support the production of climate-smart grapevine genotypes.

A multitiered haplotype strategy to enhance phased assembly and fine mapping of a disease resistance locus

Fine mapping of quantitative trait loci (QTL) to dissect the genetic basis of traits of interest is essential to modern breeding practice. Here, we employed a multitiered haplotypic marker system to increase fine mapping accuracy by constructing a chromosome-level, haplotype-resolved parental genome, accurate detection of recombination sites, and allele-specific characterization of the transcriptome. In the first tier of this system, we applied the preexisting panel of 2,000 rhAmpSeq core genome markers that is transferable across the entire Vitis genus and provides a genomic resolution of 200 kb to 1 Mb. The second tier consisted of high-density haplotypic markers generated from Illumina skim sequencing data for samples enriched for relevant recombinations, increasing the potential resolution to hundreds of base pairs. We used this approach to dissect a novel Resistance to Plasmopara viticola-33 (RPV33) locus conferring resistance to grapevine downy mildew, narrowing the candidate region to only 0.46 Mb. In the third tier, we used allele-specific RNA-seq analysis to identify a cluster of 3 putative disease resistance RPP13-like protein 2 genes located tandemly in a nonsyntenic insertion as candidates for the disease resistance trait. In addition, combining the rhAmpSeq core genome haplotype markers and skim sequencing-derived high-density haplotype markers enabled chromosomal-level scaffolding and phasing of the grape Vitis × doaniana 'PI 588149' assembly, initially built solely from Pacific Biosciences (PacBio) high-fidelity (HiFi) reads, leading to the correction of 16 large-scale phasing errors. Our mapping strategy integrates high-density, phased genetic information with individual reference genomes to pinpoint the genetic basis of QTLs and will likely be widely adopted in highly heterozygous species.