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. 2023 May 17;14:2824. doi: 10.1038/s41467-023-38527-0

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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 PZ size estimates (corrected) in F2 RILs (n = 70, assayed across six experimental blocks) and parental lines, JU1200 (red), and JU751 (blue) (see Supplementary Note 5 for details). b Generation and analysis of F2 RILs. Dotted line: hypothetical QTL. c Single-QTL scans identify two QTL (QII and QV). Horizontal lines: LOD threshold based on permutation tests. x-axis: genetic map for each chromosome. Green line: naïve scan results. Magenta line: results of a scan where marker M13 (peak, magenta curve) is included as a covariate. d Two-QTL scan results. Top half: LOD scores (LOD_a) comparing additive to null model. Bottom half: LOD scores comparing additive to single-QTL model (LOD_av1). LOD_av1 scores above threshold (white, determined by permutation testing) indicate improvement in fit over single-QTL model. e Interaction plot for markers in the peak in panel D, bottom half (chr V, M1; chr II, M14). f Approximate locations and sizes of the QTL on II and V. g Two-QTL scan allowing opposing effects. Top half: LOD scores (LOD_i) comparing a full two-QTL model to the additive model. Bottom half: LOD scores comparing the full model (allowing for interactions) with the single-QTL model (LOD_fv1). LOD_i scores above threshold (white) indicate evidence for an interaction, whereas LOD_fv1 scores above the threshold indicate an improvement in fit over the single-QTL model. h Interaction plot for markers in the significant peak in the top half of panel G (chr I, M14 and chr X, M2). i Approximate locations and sizes of candidate QTL on chromosomes I and X. j Representation of multi-QTL model selection. Nodes represent candidate QTL (QII = chrII@35 cM, QV = chr V@0 cM, QI = chrI@23 cM, QXa = chrX@16 cM, QXb = chrX@2.5 cM) and spokes represent interactions. Penalized LOD scores (below each model) above zero indicate better performance than the global null (zero QTL). See Methods, Supplementary Fig. 1, and Supplementary Note 6 for more detail. Y-axes in panels a, e, and h are scaled to μm²/1000 (0.1008 μm²/pixel). Data are provided as a Source Data file.