A Partially Phase-Separated Genome Sequence Assembly of the Vitis Rootstock ‘Börner’ (Vitis riparia × Vitis cinerea) and Its Exploitation for Marker Development and Targeted Mapping

Abstract

Grapevine breeding has become highly relevant due to upcoming challenges like climate change, a decrease in the number of available fungicides, increasing public concern about plant protection, and the demand for a sustainable production. Downy mildew caused by Plasmopara viticola is one of the most devastating diseases worldwide of cultivated Vitis vinifera. In modern breeding programs, therefore, genetic marker technologies and genomic data are used to develop new cultivars with defined and stacked resistance loci. Potential sources of resistance are wild species of American or Asian origin. The interspecific hybrid of Vitis riparia Gm 183 x Vitis cinerea Arnold, available as the rootstock cultivar 'Börner,' carries several relevant resistance loci. We applied next-generation sequencing to enable the reliable identification of simple sequence repeats (SSR), and we also generated a draft genome sequence assembly of 'Börner' to access genome-wide sequence variations in a comprehensive and highly reliable way. These data were used to cover the 'Börner' genome with genetic marker positions. A subset of these marker positions was used for targeted mapping of the P. viticola resistance locus, Rpv14, to validate the marker position list. Based on the reference genome sequence PN40024, the position of this resistance locus can be narrowed down to less than 0.5 Mbp on chromosome 5.

Challenges of viticulture adaptation to global change: tackling the issue from the roots

“…Nevertheless, rootstock breeding often involves gathering together traits from highly diverse Vitis species comprising genome structural variation that is only being elucidated recently (Zhou et al 2019). Genome assembly has been useful to develop specific markers for resistance to downy mildew (Plasmopara viticola) in 'Börner', a hybrid of V. riparia Gm183 × V. cinerea Arnold rootstock cultivar (Holtgräwe et al 2020), while another assembly is available for the ancestral pure rootstock selection V. riparia cv. Gloire de Montpellier (Girollet et al 2019).…”

An improved assembly of the “Cascade” hop (Humulus lupulus) genome uncovers signatures of molecular evolution and refines time of divergence estimates for the Cannabaceae family

“…Cascade has a highly heterozygous genome, which can be desirable in the cultivation of new varieties [ 10 ]. Using short-read DNA sequencing, we estimated the heterozygosity of the hop genome to be approximately 5%, which is similar to the range of other heterozygous genomes, including potato (4.8%) [ 43 ], Vitis vinifera cultivar Börner (3.1%) [ 44 ], V. vinifera cultivar PN40024 (7%) [ 45 ], and sunflower (10%) [ 46 ]. Heterozygosity does present challenges in assembly and annotation related to distinguishing between haplotype and paralogous sequences, especially in the case of recent duplications.…”

A chromosome-level assembly of the “Cascade” hop (Humulus lupulus) genome uncovers signatures of molecular evolution and improves time of divergence estimates for the Cannabaceae family

“…Cascade has a highly heterozygous genome, which can be desirable in the cultivation of new varieties (Henning et al, 2004). Using short-read DNA sequencing, we estimated the heterozygosity of the hop genome to be approximately 5%, which is similar to the range of other heterozygous genomes, including potato (4.8%) (Leisner et al, 2018), Vitis vinifera cultivar Börner (3.1%) (Holtgräwe et al, 2020), Vitis vinifera cultivar PN40024 (7%) (Jaillon et al, 2007), and sunflower (10%) (Hübner et al, 2019). Heterozygosity does present challenges in assembly and annotation related to distinguishing between haplotype and paralogous sequences, especially in the case of recent duplications.…”