Identification of novel QTLs for black rot resistance derived from Vitis rotundifolia in grapevine pseudo-backcross populations

Abstract

Grapevine black rot, caused by the ascomycete Phyllosticta ampelicida (Engelm.), formerly known as Guignardia bidwellii, is re-emerging as a major disease in European vineyards. This resurgence is particularly pronounced in low-input production systems andin varieties carrying resistance to downy and powdery mildew, where fungicide use is reduced.

Despite its increasing agronomic importance, the genetic basis of black rot resistance remains poorly characterized, with only three quantitative trait loci (QTLs) reported to date, located on chromosomes 14 and 16. The limited number and moderate effects of these loci constrain the development of grapevine cultivars with durable resistance, underscoring the need to identify additional resistance sources.

This study aimed to identify new black rot resistance loci derived from Vitis rotundifolia and to characterize their effects under vineyardconditions. A pseudo-backcross 2 population, derived from the muscadine accession ‘22-8-78’ crossed with Vitis vinifera cv. Syrah, was evaluated under natural infection in an untreated vineyard over three consecutive seasons. The population was genotyped using genotyping-by-sequencing (GBS)-derived SNP markers and subjected to QTL mapping. Amajor and highly significant QTL wasconsistently detected on chromosome 9, explaining up to 47% of the phenotypic variance for leaf resistance. This locus exhibited stable effects across years, observation dates, and plant organs. The resistance allele originated from V. rotundifolia and was associated with a marked reduction in symptom severity on both leaves and berries. Additional minor QTLs were identified on chromosomes 15 and 18, showing more limited and environment-dependent effects.

The major chromosome 9 locus, designated Rgb4, represents a previously undescribed source of black rot resistance, distinct fromknown loci on chromosome 14. These results demonstrate that V. rotundifolia remains a valuable reservoir of genetic variation for black rot resistance and confirm the relevance of vineyard-based phenotyping for identifying stable resistance factors. Rgb4 constitutes a strong candidate for marker-assisted selection and for pyramiding with other resistance loci to enhance the durability of grapevine cultivars in sustainable viticulture systems.

Acknowledgements

This work has been funded by the European Union through the Horizon Europe Research and Innovation Programme project GrapeBreed4IPM (grant number 101132223). Views and opinions expressed are, however, those of the authors only. Neither the European Union nor the granting authority nor the European Commission can be held responsible for them. GrapeBreed4IPM has also received funding from the Swiss State Secretariat for Education, Research and Innovation (SERI) Nr. 24.00152.