Figure 2

Mapping-by-sequencing. (a) The frequency of the alternate allele relative to the Barke reference in the two capture pools is visualized along the integrated physical and genetic map of barley [23]. (b) Ten SNPs from the target intervals were converted to CAPS markers and genotyped on the entire F₂ mapping population. The number of recombinants between the markers (top axis) and marker positions in genetically anchored WGS assembly [24] (bottom axis) are indicated. Sequence contigs carrying large (>150 bp) putative deletions are shown as gray rectangles. (c) Read depth of MND (MLOC_64838.2) in the two capture pools. The positions of the two exons of MND in WGS contig 49382 are shown as green rectangles. At the bottom, the number of sequence reads per base position is shown for the mutant pool (red) and the wildtype pool (black). Because of a single heterozygous plant that was erroneously included in the mutant bulk, MND is also present at low read coverage in the mutant pool. Note that the highest coverage peak is in the short intron (130 bp) of MND due to a higher number of redundant capture probes at the ends of the two exons.