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. 2023 Feb 6;9(2):238–254. doi: 10.1038/s41477-022-01333-5

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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. 1 — a, Syntenic mapping between chromosomes, comparing gene density and repeat content. The orientation of chr. 9 (marked *) is reversed for visualization purposes. Chr. 7 and chr. 20 are duplicated with expanded axes to the right of the main plot to highlight the differences in repeat content. b, S. angustifolium recombination rate (calculated from the S. angustifolium genetic map) with putative centromere positions, denoted with red asterisks showing RLC5 cluster positions. Lines are coloured on the basis of y axis position to better highlight regions of low recombination (yellow) c, Zoomed in look at the RLC5 cluster region on chr. 7. Top panel shows recombination rate from the S. angustifolium genetic map (coloured by position on y axis), showing a drop in recombination coinciding with the RLC5 cluster. Bottom panel shows the recombination haplotypes (maroon and blue) within the F₁-haploid pedigree (n = 184; denoted on the y axis), finding no recombined haplotypes in the region overlapping with the RLC5 cluster. d, Recombination/LOD score heatmap for chr. 7 to show high recombination rate in pedigree and tight linkage among markers.

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