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. 2024 Aug 14;633(8031):848–855. doi: 10.1038/s41586-024-07808-z

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© The Author(s) 2024

Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, 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 licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by-nc-nd/4.0/.

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Fig. 2 — a, Effect of assembly quality on association genetics. Significantly associated k-mers for resistance to Pgt race QTHJC mapped to two Ae. tauschii TA1662 assemblies (top, low-quality, contig N50 = 196 kb (ref. ¹⁴); bottom, high-quality, contig N50 = 58.21 Mb (this study)). The chromosome arm 1DS disequilibrium block contains the stem rust resistance gene SrTA1662 (renamed Sr66). b, Different Mla haplotypes²⁴ reflected by analysis of resistance gene analogues (RGA) in Ae. tauschii CPI 110799 (Sr33 donor), AUS 18913, AUS 18911 and TA1662 (SrTA1662 donor). Boxes indicates genes; + indicates pseudogenes. Alleles are indicated by matching colour and position. The locus is flanked by subtilisin-chymotrypsin inhibitor (CI, grey) and pumilio (Bpm, black) genes. Unrelated genes present in this region are omitted. Locus length and gene distribution are not drawn to scale. c, k-mer-based genome-wide association study (GWAS) with Pt race BBBDB mapped to the Ae. tauschii TA1675 assembly. The chromosome arm 2D peak corresponds to leaf rust resistance locus LR39. The diagram shows the LR39 interval delimited by bi-parental mapping, flanked by markers Csq21 and Csq22, and markers Csq8 and Csq25-Csq30 co-segregating with LR39. Arrows indicate candidate genes. d, Effects of VIGS on susceptibility to leaf rust. AL8/78, susceptible control; BSMV-γGFP, barley stripe mosaic virus (BSMV) expressing a GFP silencing construct (control); BSMV-γLrSi2, BSMV-γLrSi6 and BSMV-γLrSi7 are silencing constructs specific for the WTK gene. BSMV-γLrSi3 and BSMV-γLrSi8 are silencing construct specific for the NLR gene. Probe specificities were evaluated using the TA1675 assembly. Chlorosis in BSMV-γGFP controls represent virus symptoms. Scale bar, 1 cm. e, Gene structure of Lr39 (top) and domain architecture of the Lr39 protein (bottom). Grey boxes represent untranslated regions, orange boxes are exons and lines are introns. VIGS probes are indicated. R457I and C1023S indicate the two Lr39 amino acid changes between the TA1675 (resistant) and AL8/78 (susceptible) lines. MSP, major sperm protein domain.