Haplotype-resolved genomics reveals structural variation and parental haplotypes in global grapevine rootstocks

Abstract

Grapevine rootstocks remain the primary defence against phylloxera and soil-borne stresses in viticulture. However, increasing climaticvariability and emerging environmental constraints demand the development of improved, climate-resilient rootstock varieties. Conventional rootstock breeding is slow due to long generation times and complex hybrid backgrounds, highlighting the need forgenomics-assisted strategies. Despite their importance, genomic resources for rootstocks remain limited compared with scion cultivars.

Rootstocks are predominantly derived from wild Vitis species and interspecific hybrids, resulting in high heterozygosity, complexancestry and extensive structural variation. To capture this diversity, we analysed a panel of 27 grapevine rootstock cultivars used acrossthe globe, including two newly developed rootstock lines from the Department of Plant Breeding, HGU. All genotypes were sequenced using Oxford Nanopore long reads (> 100 × coverage) and assembled into haplotype-resolved genomes. The assemblies achieved anaverage N50 of ~ 26 Mb across 54 haplotypes with mean assembly sizes of ~ 529 Mb, enabling high-resolution comparison of both inter-cultivar and intra-cultivar haplotypic variation.

Initial comparative analyses indicate substantial structural variation and haplotypic divergence among rootstocks, including largepresence-absence variants and introgressed haplotype blocks derived from distinct Vitis parental lineages. This framework enables the assessment of how structural variants, introgressed segments and haplotype blocks of parental origin are inherited, reshaped, or lost across F1-derived clonal generations. Ongoing analyses aim to quantify the gain, loss and rearrangement relative to gene space. These results and analytical approaches will be presented and discussed.

Using these new genomic resources, we are constructing a graph-based rootstock pangenome, which will also be presented as a developing framework for haplotype-guided breeding. By enabling direct haplotype-aware marker development and the targeted selection of structurally conserved or variable genomic regions relevant for rootstock breeding this work will provide a foundation for the development of molecular tools to accelerate the design of rootstocks adapted to future environmental challenges.