A panel of 13 sugar beet lines and one genotype each of the Beta vulgaris cultivars red beet and Swiss chard, and B. vulgaris ssp. maritima were used to identify polymorphisms in alignments of genomic DNA sequences derived from 315 EST- and 43 non-coding RFLP-derived loci. In sugar beet lines, loci of expressed genes showed an average SNP frequency of 1/72 bp, 1 in 58 bp in non-coding sequences, increasing to 1/47 bp upon the addition of the remaining genotypes. Within analysed DNA fragments, alleles at different SNP positions displayed linkage disequilibrium indicative of haplotype structures. On average 2.7 haplotypes were found in sugar beet lines, and haplotype conservation in expressed genes appeared to exceed 500 bp in length. Seven different genotyping techniques including SNP detection by MALDI-TOF mass spectrometry, pyrosequencing and fluorescence scanning of labelled nucleotides were employed to perform 712 segregation analyses for 538 markers in three F(2) populations. Functions were predicted for 492 mapped sequences. Genetic maps comprised 305 loci covering 599.8 cM in population K1, 241 loci distributed over 636.6 cM in population D2, and 166 loci over 507.1 cM in population K2, respectively. Based on 156 markers common to more than one population an integrated map was constructed with 524 loci covering 664.3 cM. For 377 loci the genome positions of the most similar sequences from A. thaliana were identified, but little evidence for previously presented ancestral genome structures was found.

Rapid identification of agronomically important genes is of pivotal interest for crop breeding. One source of such genes are crop wild relative (CWR) populations. Here we used a CWR population of <200 wild beets (B. vulgaris ssp. maritima), sampled in their natural habitat, to identify the sugar beet (Beta vulgaris ssp. vulgaris) resistance gene Rz2 with a modified version of mapping-by-sequencing (MBS). For that, we generated a draft genome sequence of the wild beet. Our results show the importance of preserving CWR in situ and demonstrate the great potential of CWR for rapid discovery of causal genes relevant for crop improvement. The candidate gene for Rz2 was identified by MBS and subsequently corroborated via RNA interference (RNAi). Rz2 encodes a CC-NB-LRR protein. Access to the DNA sequence of Rz2 opens the path to improvement of resistance towards rhizomania not only by marker-assisted breeding but also by genome editing.

Field-grown sugar beets were analysed for morphological characters, sucrose content, and reproducible transcript profiles by macroarray analyses with 11,520 unique sugar-beet cDNA targets in two different years. Seasonal differences were partly compensated by expressing sampling dates as thermal time. During early beet development the number of cambial rings, root length, and sucrose concentration had already achieved >40% of their final values. Sucrose levels rose from 10% to 17% over the thermal time of 1300-1400 degrees Cd with only small changes later when lower concentrations were restricted to the exterior zone at the minimum of the spatial sucrose gradient through the beet. The number of leaves and root diameter followed the same temporal growth pattern, but mass increased until beet maturity at around 2000 degrees Cd. Cluster analysis identified 543 transcripts with reproducible preferential expression between 1300-1400 degrees Cd, and 170 showing the highest transcript levels later. In maturing beets, 373 transcripts were over-represented in the inner zone and 148 in the outer zone. During early development, genes involved in cytoskeletal reorganization and transport processes showed the highest transcript levels. Cell wall biogenesis-, defence-, stress-, and degradation-related transcripts were identified in all samples, and associated with pathogen attack during late development and in the outer zone. Candidates with potential roles in carbohydrate metabolism appeared to serve anaplerotic functions by converting excess intermediates to sucrose production. Transcripts preferentially occurring in sucrose-accumulating young beet cells and newly generated peripheral cells of mature beets are discussed as potential breeding targets to improve sink strength and growth.

Grapevine breeding becomes 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. Therefore, in modern breeding programs 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 V. 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 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.