Grapevine (
Vitis vinifera L.) holds significant agricultural importance as the major species cultivated worldwide within the
Vitaceae family, with thousands of cultivars dedicated to wine grapes, table grapes, or raisins production [
1]. Grapevine industries face significant challenges due to the prevalence of fungal diseases, particularly powdery and downy mildews, caused by the biotrophic pathogen
Erysiphe necator and
Plasmopara viticola, respectively [
2]. These pathogens, imported from the New World in the 19th [
3], and transmitted to the susceptible Eurasian
vinifera, became major concerns for European viticulture, necessitating heavy reliance on fungicides for control, posing environmental and health concerns [
4]. Interspecific hybridization aims to combine the high-quality fruit characteristics of the Eurasian
V. vinifera with the disease resistances of wild
Vitis species from other continents, including the more distant
V. rotundifolia [
5,
6].
V. rotundifolia, also known as the muscadine grape, is native to the southeastern United States and has inherent resistance to many pests and diseases. Ongoing grape breeding programs now prioritize traits related to agronomy and production, such as yield, quality, and disease resistance. These characteristics are crucial in determining the acceptance of new grape varieties by farmers and the market value of the grapes [
7]. The enhancement of agronomic and production traits in grapes should be facilitated by a deeper understanding of their developmental and physiological characteristics. Over the past 25 years, numerous studies have been conducted to characterize grapevine fruit development at the molecular level. Transcriptomics was used for the characterization of varietal diversity between a cultivated grapevine variety and the PN40024 reference genome [
8,
9], to characterize the molecular response of berries to water deficit [
10,
11], temperature [
12], combined stress [
13], abscisic acid (ABA) [
14] and pathogens [
15], although these last ones are more frequently studied on leaves [
16,
17]. Comparative transcriptomic analysis between cultivated and wild species revealed the conservation of expressed genes [
18]. Recently, a study explored the genetic diversity of nucleotide-binding leucine-rich repeat receptor (NLR) genes between wild and domesticated grapevine populations [
19]. By analyzing 17 genotypes, they identified and classified these NLR genes into eight distinct types, discovering that wild populations generally possess a higher number of these genes compared to cultivated varieties. Additionally, gene ontology (GO) enrichment analysis indicated a reduction in programmed cell death associated gene families, a key immune response, in domesticated grapevines. This suggests that domestication may have led to a decrease in the pool of resistance-related genes, as observed in other crops like tomatoes [
20].
Genetic improvement through hybridization, particularly incorporating fungus-tolerance traits, is a key focus for developing new grapevine cultivars [
21,
22]. The MrRUN1/MrRPV1 locus proved very convenient to confer a high level of tolerance to powdery and downy mildews [
23,
24,
25,
26]. MrRUN1/MrRPV1 were introgressed in
vinifera according to a pseudo-backcrossing breeding scheme [
25,
27]. The ‘G5’, ‘G14’ and ‘Artaban’ genotypes, which were obtained after the fourth and fifth backcrosses of a
V. vinifera ×
M. rotundifolia hybrid with
V. vinifera exhibit a high level of tolerance against downy and powdery mildews [
7,
25,
28,
29]. A study reported the screening of a BAC library from a powdery mildew-resistant plant and narrowed down the Run1/Rpv1 locus to a ∼1 Mbp in the chromosome 12 [
25]. A cluster of 11 resistance gene analogs (RGAs) was identified within this locus including seven genes encoding full-length TIR-NBS-LRR resistance proteins. Sequencing of this region ruled out the presence of other kinds of resistance against fungal pathogens [
28]. A novel approach for multi-domain and multi-gene family identification provided insights into the evolutionary dynamics of disease resistance genes in core eudicot including grapevine, indicating that R-genes typically show an unusually high turnover rate due to strong selection to keep up in a biological arms race with plant pathogens [
30]. The QTL region is usually screened with microsatellites markers, however more than 900 total individuals from two additional progenies were required for the narrowing of this QTL suggesting that many genes outside the MrRUN1/MrRPV1 locus may frequently be also introgressed alongside this locus [
26].
In order to address the introgression of additional genes and its consequences on gene expression in ripening berries, we conducted a comprehensive transcriptomic study on 102 single-berries from non-resistant V. vinifera cultivars and resistant or non-resistant V. rotundifolia x V. vinifera derivative hybrids. Fruits were sampled across different stages of berry development. Following reads alignment on both V. vinifera PN400024.V4, V. rotundifolia var. ‘Carlos’ and ‘Trayshed’ genomes, Weighted Gene Co-expression Network Analysis (WGCNA) and Gene Ontology (GO) analysis allowed us to elucidate which LG12 region from V. rotundifolia was introgressed in the hybrids together with Run1 and Rpv1 genes. The multifaceted consequences of such introgression of M. rotundifolia genes on the transcriptome of the grapevine fruit are described.