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. 2020 Oct 22;11:569876. doi: 10.3389/fpls.2020.569876

FIGURE 6.

FIGURE 6

Genomic analysis of the RLK cluster DM4.1.2, indicating structural variation. (A) Predicted gene models of genes in the RLK cluster within the interval of subQTL DM4.1.2. Black boxes indicate predicted exons and lines represent predicted introns. Arrowheads indicate the orientation of the reading frame. Physical locations on chromosome 4 of the cucumber reference genome (Chinese Long 9930 v2) are indicated. (B) Whole genome sequencing reads of NIL DM4.1 aligning to predicted gene Csa4M410860 are visualized using the Integrative Genomics Viewer (IGV). A coverage graph is given above the aligned reads. Reads pairs with larger than expected or smaller than expected insert sizes are indicated in dark red and dark blue, respectively. (C) PCR was performed using primers designed to amplify the predicted gene Csa4M410860 on DNA samples isolated from the partially resistant NIL DM4.1.1/.2 and the susceptible recurrent parent HS279. (D) RNAseq reads from P. cubensis inoculated NIL DM4.1.1/.2 were re-aligned to the RLK cluster including the 551 bp insertion found in the predicted gene Csa4M410860. Gene models of CsLRK10L1 (Csa4M410830) and CsLRK10L2 (novel gene consisting of both Csa4M410850 and Csa4M410860) are indicated above, including the 551 bp insertion in red. Numbers indicate physical location on chromosome 4 of the cucumber reference genome (Chinese Long 9930 v2).