The Grapevine Genome: When DNA Becomes a Weapon Against Fungicides

⏱️ Reading time: 6 minutes

The grapevine is one of the most heavily treated crops in France — the second-largest consumer of plant-protection products, according to INRAE. The culprits: two fungi imported from North America in the nineteenth century, downy mildew (Plasmopara viticola) and powdery mildew (Erysiphe necator), against which Vitis vinifera, our European vine, is genetically defenceless. For nearly 150 years the response has been chemical: spray, and spray again. But since 2007 another path has opened — and it begins with reading the vine’s DNA.

IT ALL BEGINS BY READING THE DNA

Reading the grapevine’s DNA

In 2007, a French–Italian consortium led by INRA published the first grapevine genome in Nature. It was a world first for a fruit plant, only the fourth flowering plant to be sequenced. To ease the assembly, the researchers chose not a commercial variety but PN40024, a Pinot Noir–derived line made almost fully homozygous through successive self-fertilisations. The result: around 30,000 genes spread across 19 chromosomes.

That reference genome has been refined ever since. In 2023, an international team published a gapless “telomere-to-telomere” (T2T) version in Horticulture Research: 9,018 more genes than the previous version, and above all 377 gene clusters associated with complex traits — among them aroma and disease resistance. And that is the whole point: a complete genome is a map that makes it possible to locate resistance genes precisely and put them to use.

Rpv, Run, Ren: the resistance map

The crucial point: these genes don’t exist in Vitis vinifera. They come from wild American and Asian species that co-evolved with the fungi over millions of years — foremost among them Muscadinia rotundifolia, source of the famous Run1/Rpv1 pair located on chromosome 12, but also Vitis riparia, V. amurensis and V. labrusca.

Knowing the genome radically changes selection. Rather than waiting years to see whether a young plant resists infection, breeders read a DNA marker directly, as early as the seedling stage: this is marker-assisted selection (MAS). Better still, they can pyramid — stack at least two resistance genes targeting different mechanisms within a single variety. A fungus can mutate to get around one gene; to clear two or three locks it would have to mutate on several at once. This is the very principle of “durable resistance.”

CUTTING TREATMENTS TENFOLD

ResDur: cutting treatments tenfold

This is exactly the strategy of the INRAE-ResDur programme (for “durable resistance”), launched back in 2000 at Colmar under Didier Merdinoglu. The goal: to create wine-grape varieties resistant to downy and powdery mildew while keeping an oenological quality comparable to classic varieties. It takes an average of fifteen years of crossing and selection to produce a single variety.

The results are now in the vineyards. Four first varieties — Artaban and Vidoc (reds), Floreal and Voltis (whites), each carrying two downy-mildew and two powdery-mildew resistance genes — were entered in the Official Catalogue in 2018. Five more followed in 2021 (Coliris, Lilaro, Sirano, Selenor, Opalor), then three in 2024 (Calys, Exelys, Artys), fitted with new gene combinations to diversify the resistances. A ResDur3 series has been in the registration pipeline since 2025.

The agronomic gain is spectacular: 80 to 90% fewer fungicides than with a susceptible variety. One important nuance, often smoothed over in media shorthand: INRAE recommends keeping a minimum of two treatments per year. Not because the varieties are weak, but to keep pathogens from eroding the resistance — durability has to be protected. The OSCAR observatory (INRAE-IFV, created in 2017) monitors precisely these risks of resistance breakdown in growers’ plots.

On the ground, Floreal has become a best-seller — nearly 700 hectares on its own — thanks to an aromatic profile “strongly Sauvignon in character.” One major regulatory obstacle remains: long treated as hybrids, these varieties were recently attached to the Vitis vinifera taxon by the Community Plant Variety Office, an essential condition for one day laying claim to appellations. Christian Huyghe, INRAE’s scientific director for Agriculture, notes that “in France, there’s a trauma around hybrids” — even though the ResDur varieties kept nothing of Muscadinia but the resistance genes, everything else being vinifera.

ResDur varieties are obtained through conventional crossbreeding, accelerated by reading the genome. No in-vitro manipulation of the DNA: this is not a GMO.

Synthesis of INRAE–IFV work on resistant varieties

Tomorrow, CRISPR?

Conventional crossing has two limits: its slowness (fifteen years), and the fact that it reshuffles the entire genome. Crossing a Cabernet Sauvignon to add a resistance gene yields something other than a Cabernet. Genome editing promises the opposite: to modify a single gene within the existing variety, without touching its identity.

The most studied target in the vine is the MLO gene family (Mildew Locus O), which paradoxically makes the plant susceptible to powdery mildew. Deactivating them yields resistance through a “loss of susceptibility.” In 2025, Loredana Moffa’s team showed in The Plant Journal that a double CRISPR/Cas9 edit of the MLO6-7 genes confers resistance to powdery mildew, while editing the NPR3 gene increases tolerance to powdery mildew and downy mildew alike — via a cisgenic approach potentially free of any transgene. An honest scientific caveat: knocking out the MLO genes is sometimes accompanied by side effects (leaf necrosis, yield loss) that still have to be brought under control.

That leaves the regulatory lock, which has just been released. On 17 June 2026, the European Parliament gave final approval to the regulation on new genomic techniques (NGTs). It distinguishes two categories: NGT 1 plants (at most 20 modifications, “which could occur naturally or through conventional breeding”), largely exempt from GMO constraints, with no risk assessment; and NGT 2 plants, which remain regulated as GMOs. A historic shift: until now, these editing techniques were treated as GMOs, banned from cultivation in the EU.

The text remains divisive. Its defenders — rapporteur Jessica Polfjärd, INRAE — see it as a tool against climate change and disease. Its opponents — organic farming, environmental NGOs — denounce the absence of labelling, the risk of contaminating organic plots and the lack of risk assessment; France’s Anses agency itself recommended a “case-by-case” analysis in 2024. And the question of patents on living organisms remains wide open. One clarification is needed to avoid conflating everything: the ResDur varieties are not covered by this regulation — the debate concerns the next generation, that of vines edited gene by gene.

HOW FAR SHOULD WE MODIFY THE VINE TO SAVE IT?

The real divide is no longer scientific

In twenty years, genomics will have transformed the vine: from a passive victim of imported fungi, it has become a plant we can deliberately arm, gene by gene. Science now knows how to read the DNA, map the resistances, stack them and — soon — edit them. The real fault line has shifted: it no longer runs through the laboratory, but through society. How far are we prepared to modify the vine to save it?

And you — would you drink a wine from a resistant variety? A wine from a vine edited with CRISPR? Tell us in the comments.

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Sources: French–Italian Public Consortium for Grapevine Genome Characterization, Nature (2007); Shi et al., Horticulture Research — PN40024 T2T genome (2023); INRAE — ResDur programme releases (2018, 2021, 2024) and the OSCAR observatory; IFV — resistant varieties; Moffa et al., The Plant Journal — CRISPR/Cas9 editing of MLO6-7 and NPR3 (2025); European Parliament — regulation on new genomic techniques (17 June 2026); Anses — NGT opinion (2024); Réussir Vigne, Pleinchamp, Vitisphère. Data cross-checked in July 2026.