<i>Vitis rotundifolia</i> Genes Introgressed with RUN1 and RPV1: Poor Recombination and Impact on <i>V. vinifera</i> Berry Transcriptome

Thanks to several <i>Vitis vinifera</i> backcrosses with an initial <i>V. vinifera</i> L. × <i>V. rotundifolia</i> (previously <i>Muscadinia rotundifolia</i>) interspecific cross, the MrRUN1/MrRPV1 locus (resistance to downy and powdery mildews) was introgressed in genotypes phenotypically close to <i>V. vinifera</i> varieties. To check the consequences of introgressing parts of the <i>V. rotundifolia</i> genome on gene expression during fruit development, we conducted a comparative RNA-seq study on single berries from different <i>V. vinifera</i> cultivars and <i>V. vinifera</i> × <i>V. rotundifolia</i> hybrids, including ‘G5’ and two derivative microvine lines, ‘MV102’ (resistant) and ‘MV32’ (susceptible) segregating for the MrRUN1/RPV1 locus. RNA-Seq profiles were analyzed on a comprehensive set of single berries from the end of the herbaceous plateau to the ripe stage. Pair-end reads were aligned both on <i>V. vinifera</i> PN40024.V4 reference genome, <i>V. rotundifolia</i> cv ‘Trayshed’ and cv ‘Carlos’, and to the few resistance genes from the original <i>V. rotundifolia</i> cv ‘52’ parent available at NCBI. Weighted Gene Co-expression Network Analysis (WGCNA) led to classifying the differentially expressed genes into 15 modules either preferentially correlated with resistance or berry phenology and composition. Resistance positively correlated transcripts predominantly mapped on the 4–5 Mb distal region of <i>V. rotundifolia</i> chromosome 12 beginning with the MrRUN1/MrRPV1 locus, while the negatively correlated ones mapped on the orthologous <i>V. vinifera</i> region, showing this large extremity of LG12 remained recalcitrant to internal recombination during the successive backcrosses. Some constitutively expressed <i>V. rotundifolia</i> genes were also observed at lower densities outside this region. Genes overexpressed in developing berries from resistant accessions, either introgressed from <i>V. rotundifolia</i> or triggered by these in the <i>vinifera</i> genome, spanned various functional groups, encompassing calcium signal transduction, hormone signaling, transcription factors, plant–pathogen-associated interactions, disease resistance proteins, ROS and phenylpropanoid biosynthesis. This transcriptomic insight provides a foundation for understanding the disease resistance inherent in these hybrid cultivars and suggests a constitutive expression of NIR NBS LRR triggering calcium signaling. Moreover, these results illustrate the magnitude of transcriptomic changes caused by the introgressed <i>V. rotundifolia</i> background in backcrossed hybrids, on a large number of functions largely exceeding the ones constitutively expressed in single resistant gene transformants.