Uncovering the genomic diversity of global grapevine rootstocks

Abstract

Rootstocks continue to serve as the first line of defence against phylloxera in viticulture; however, to mitigate the impacts of climate change, future viticulture will require novel, improved rootstock varieties. As conventional rootstock breeding is extremely time-consuming, modern genomics-assisted approaches are urgently needed. Yet, the genomic resources that could serve as a foundation for such efforts remain highly limited. Therefore, our aim is to explore the genomic diversity in a diverse panel of grapevine rootstocks as a basis to develop modern breeding tools and accelerate rootstock improvement.

Unlike scion cultivars, most rootstocks are selections of wild Vitis species or interspecific hybrids, making them genetically diverse and structurally complex. To investigate this diversity, we selected 26 grapevine rootstock cultivars commonly used worldwide, including both single-species genotypes and multi-species hybrids. Two newly bred rootstock lines from our department were also included in the panel.

Each genotype was subjected to long-read sequencing using Oxford Nanopore Technology at over 100× coverage and assembled into haplotype-resolved genomes using Hifiasm. The resulting assemblies had an average N50 of ~26 Mb across 52 haplotypes and an average total contig length of ~529 Mb. These haplotype-level assemblies enable high-resolution comparison of both inter-cultivar and inter-haplotype (intra-cultivar) genomic variation.

Bioinformatic analyses aimed at uncovering haplotypic divergence, structural variants, and species-derived genomic segments are currently in progress. Initial findings that offer new perspectives on the genetic architecture of rootstocks will be presented.

By generating high-quality, phased genome assemblies for a diverse panel of rootstocks, this work establishes a valuable resource for rootstock genomics and lays the foundation for development of a rootstock pangenome. Such resources can be leveraged in breeding programs to identify and utilize genomic variation underlying key traits, such as biotic and abiotic stress resistance and adaptability.