Intraspecific recurrent selection in V. vinifera is an effective method for grape breeding with high quality and disease resistance. The core theory of this method is the substitution accumulation of multi-genes with low disease resistance. The discovery of multi-genes for disease resistance in V. vinifera may provide a molecular basis for breeding for disease resistance in V. vinifera. In this study, resistance to downy mildew was identified, and genetic analysis was carried out in the intraspecific crossing population of V. vinifera (Ecolly × Dunkelfelder) to screen immune, highly resistant and disease-resistant plant samples; transcriptome sequencing and differential expression analysis were performed using high-throughput sequencing. The results showed that there were 546 differential genes (194 up-regulated and 352 down-regulated) in the immune group compared to the highly resistant group, and 199 differential genes (50 up-regulated and 149 down-regulated) in the highly resistant group compared to the resistant group, there were 103 differential genes (54 up-regulated and 49 down-regulated) in the immune group compared to the resistant group. KEGG analysis of differentially expressed genes in the immune versus high-resistance group. The pathway is mainly concentrated in phenylpropanoid biosynthesis, starch and sucrose metabolism, MAPK signaling pathway–plant, carotenoid biosyn-thesis and isoquinoline alkaloid biosynthesis. The differential gene functions of immune and resistant, high-resistant and resistant combinations were mainly enriched in plant–pathogen interaction pathway. Through the analysis of disease resistance-related genes in each pathway, the potential minor resistance genes in V. vinifera were mined, and the accumulation of minor resistance genes was analyzed from the molecular level.

Cold resistance is an important characteristic of sustainable development in the grape industry. The intraspecific recurrent selection in the Vitis vinifera (V. vinifera) method uses high-quality varieties as breeding materials and the substitution and accumulation of minor resistance genes, breeding high-quality grapes with cold resistance. This study was conducted to identify and genetically analyse the cold resistance of a V. vinifera hybrid population (Ecolly × Dunkelfelder), screen for highly resistant and sensitive plant samples, and use high-throughput sequencing to perform transcriptome sequencing and related differential gene expression analysis on each sample. The results revealed that the cold resistance of the hybrid offspring population was characterised by continuous quantitative trait inheritance, with 38 differentially expressed genes (7 upregulated genes and 31 downregulated genes) between the high resistance and high-sensitivity types. Analysis of genes related to various pathways, related to cold resistance, revealed that CYP76F10, Dxs, GERD, NMT, GDE1, glgC, and DHQ-SDH, as well as transcription factor MYB, HB, and MADS family genes, are key candidate genes for V. vinifera cold resistance research. Real-time fluorescence quantitative polymerase chain reaction (RT-qPCR) was used to investigate the expression characteristics of the six genes that were differentially expressed genes, the results of which were essentially consistent with the results of RNA-seq. Specifically, NMT may enhance cold resistance by enhancing membrane lipid stability. The synergistic expression pattern of CYP76F14 and Dxs suggests its key role in terpene synthesis. By exploring potential genes related to micro effects, a theoretical foundation for further exploration of new high-quality cold-resistant grape varieties has been provided.