Population genomics of Vitis pseudoreticulata reveals the genetic basis of fungal resistance in grapevine

Grapevine cultivation is facing significant challenges from fungal diseases. Wild Vitis species exhibit extraordinary fungal resistance, offering valuable genetic resources for grapevine improvement, yet their genetic basis of fungal resistance remains largely unexplored. In this study, we assembled a haplotype-resolved, chromosome-level genome of Vitis pseudoreticulata, an East-Asian wild grapevine species known for its exceptional fungal resistance. The genome size for V. pseudoreticulata haplotype 1 and 2 were 520.32 and 511.58 Mb, with contig N50 values of 27.31 and 21.33 Mb, respectively. Fungal response genes were significantly expanded in this genome, accounting for 8.14% (252/3095) of the expanded genes and showing functional enrichment within these families, which provide a genetic foundation for its fungal resistance. Population genomic analyses identified genes under selection in V. pseudoreticulata were enriched for functions related to responses to fungus, auxin, heat, and salt stress, potentially contributing to the strong fungal resistance, rapid growth, and adaptation to hot and humid subtropical environment of this species. Key candidate genes, such as FER, TDX, and PAT10 exhibited low intraspecies genetic diversity and high interspecies genetic divergence, likely playing important roles in these processes. Over half (54.37%) of the genes under selection were specific to V. pseudoreticulata, highlighting the uniqueness of its resistance and adaptation. Notably, a 3.7 Mb homozygous inversion, specifically identified in V. pseudoreticulata, encompasses genes related to anther dehiscence and pollen acceptance, potentially contributing to its reproductive success. The reference genome, variation map, and candidate genes identified in this study provide valuable genetic resources for breeding grapevine cultivars and rootstocks with enhanced fungal resistance.