Using Oxford Nanopore sequencing in grapevine breeding

Abstract

Traditional grapevine varieties like Merlot, Pinot noir, or Riesling are all exclusively propagated via cuttings. Due to this, a high level of genomic and epigenomic variation has developed in each of these varieties over the course of hundreds of years of vegetative propagation. Furthermore, due to both haplotypes of the genome mutating independently, grapevine varieties are highly heterozygous. The use of Oxford Nanopore long-read sequencing technology enables us to better understand the underlying mechanisms by creating chromosome-scale assemblies of different subclones in each variety to get comprehensive overview of the amount of intravarietal variation. In addition, the use of ultra-long nanopore reads enables completely phasing chromosomes in both haplotypes. Besides this, the nanopore direct RNA sequencing and cDNA sequencing methods are also being used for grapevine virus research. Since plant viruses occur exclusively as RNA viruses and minus-strand viruses cannot be easily reverse transcribed, direct RNA sequencing enables us to study these viruses and still get full-length virus genomes without the need of further assembly.

Biography

Maximilian Schmidt started his PhD in 2014 at RWTH Aachen University, Germany, in the group of Professor Björn Usadel. There, he was part of the team that sequenced and assembled the Solanum pennellii genome as the first eukaryotic genome that was sequenced and assembled with Oxford Nanopore technology. In 2020, Max moved to the Research Center Juelich with Professor Usadel to continue working on plant de novo genomics. In 2022, he moved to the group of Professor Kai Voss-Fels in the Institute of Grapevine Breeding at Geisenheim University where he is currently working on setting up the sequencing infrastructure to introduce new methods into grapevine breeding approaches.