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.
Highlights
Downy mildew of grapevine is caused by the oomycete Plasmopara viticola
We evaluated the average alignment depth” (AD) for the contigs in the assembly and classified the contigs with respect to the expected depth of aligned reads for paired contigs and contigs with merged sequences
For the development of molecular markers and to gain knowledge about genome regions as well as loci relevant for grapevine breeding, we analyzed the genome of the resistant interspecific hybrid ‘Börner’ (V. riparia x V. cinerea) by whole genome shotgun (WGS) sequencing
Summary
Downy mildew of grapevine is caused by the oomycete Plasmopara viticola. A number of resistance loci for downy mildew have been identified, and these have been localized within grapevine genomes. Other loci are less well characterized and are essentially known only from wild species (Marguerit et al, 2009; Blasi et al, 2011; Ochssner et al, 2016) To allow their application, these loci need to be introgressed into a favorable Vitis vinifera genetic background. These loci need to be introgressed into a favorable Vitis vinifera genetic background Such an introgression can be accelerated considerably by using marker-assisted selection or marker-assisted back crossing (Herzog et al, 2013). The discovery and development of this marker types by using NGS data has been successfully demonstrated for various plant species (Taheri et al, 2018)
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