Crop wild relative populations of Beta vulgaris allow direct mapping of agronomically important genes

Abstract

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.

Figure 1. A view of the wild beet population of Beta vulgaris subspecies maritima located along the coastal line of the Kalundborg fjord in Denmark.

The distribution of resistant and susceptible plants selected for MBS, after evaluation for rhizomania resistance, is shown. The exact position of all 189 collected plants used for seed production is presented in Supplementary Data 1. Distribution of susceptible and resistant plants (white and grey circles, respectively) was observed all over the coast.

Figure 2. The Rz2 region identified by MBS.

(a) Plot of delta-AFe values for BmChr3. The delta-AFe values, indicated by yellow dots, clearly show a skew in the AFe values of the two pools created from four and eight plants unequivocally identified as homozygous resistant and susceptible, respectively. The blue bar indicates the target region defined by genetic intervals from MBS. (b) Sketch of the 0.72 Mbp target region. Blue bars indicate genetic intervals identified by MBS. (c) Association analysis results after testing 189 families of the Kalundborg population. Black and white circles represent markers associated and not associated with resistance, respectively. Arrows indicate the number of recombinant plants identified. (d) Location of Bv3_jumg identified as Rz2 by recombinant analysis. (e) Structure of the Rz2 gene. Rz2_KD-R: allele identified in resistant plants in Kalundborg, rz2_KWS2320: allele present in the susceptible sugar beet genotype KWS2320; rz2_KD-S: allele identified in susceptible plants in Kalundborg. White box: location of conserved domains in the encoded protein sequence for three main domains of a CC-NB-LRR protein; grey box: transposon insertion location; number and letters: predicted amino acid changes.