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. 2023 May 30;6:580. doi: 10.1038/s42003-023-04938-4

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© The Author(s) 2023

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 3 — a A plot of linkage disequilibrium (LD) across chromosome 14, where darker colors represent higher levels of LD. The two dark squares on the diagonal include GWA peak 4 (on the left, from 0 to 7 Mb on the chromosome) and the GWA peak that corresponds to PdR1 (on the right, from 22 to 28 Mb on the chromosome). The two off-diagonal squares reflect LD between these two distinct regions. b A Manhattan plot of chromosome 14 indicating the locations of peak 4 and the PdR1 region. c An expanded representation of the PdR1 region showing the location of significant SNPs (red circles denote SNP significant with two GWA methods), significant kmers (green triangles) and CNVs (blue triangles). The dashed vertical lines represent the 361 kb region defined by SSR markers and the 106 kb region defined by the location of significant markers. The schematics below represent genes in PdR1 and a summary of gene expression results. Genes are denoted by rectangles and colored if they are related to R genes, with the category of R gene indicated by its color. Expression information shows expression, in transcripts per million (TPM) for leaves, for stems during four stages after infection and for mock controls.