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. 2023 Nov 18;14:7501. doi: 10.1038/s41467-023-43077-6

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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 licence, and indicate if changes were made. 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/4.0/.

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Fig. 7 — a Correlations of SPP with cis-EC (left) and trans-EC (right) of OsMADS17. The colors of the dots represent different genotypes of the OsMADS17-V1 variant: reference type (orange), 11-bp deletion type (blue), and 39-bp deletion type (purple). The error bands indicate 95% confidence intervals. b Correlations of SDT expression with cis-EC (left) and trans-EC (right) of OsMADS17. The colors of the dots represent different genotypes of OsMADS17-V1, as in (a). c Regional association plots of GWAS using linear mixed model for SPP (top), SDT expression (middle) and OsMADS17 expression (bottom) in a 200-kb region centered on OsMADS17. d Schematic diagram of the effector and reporter constructs used for transient transcriptional activity assay in (e). Firefly luciferase gene LUC, driven by the 4-kb and 4.6-kb promoters of SDT as well as dOCR (4.2–4.4 kb upstream of SDT, as shown in Fig. 6f), was used as the reporter. e Transient transcriptional activity assay showing that OsMADS17 transactivates SDT transcription and this transactivation requires the dOCR upstream of SDT. All data are means ± SEM (9 biologically independent samples for OsMADS17 + control and 3 for the others). f Panicle morphologies of CR-osmads17 mutant and WT. WT wild-type. Scale bar, 2 cm. g–i Quantification of the number of primary branches (g), number of secondary branches (h), and spikelets per panicle (i) in the main panicle of CR-osmads17 mutant and WT. Data are means ± SEM. Comparisons are made by two-tailed Student’s t test. j Gene regulatory networks constructed using cis- and trans-ECAS. The SPP TWAS-significant genes (FDR <0.01) were used as e-traits, and the network centered on SDT and OsMADS17 (SDT and OsMADS17 as regulatory genes) is shown. The color of the nodes indicates the regulatory direction of genes for SPP: light salmon for positive correlation and blue for negative correlation. The size of each node circle indicates the number of nodes it connects to. Solid lines represent the regulatory relationships validated in this study and those previously reported. Source data underlying (a, b, e, g–i) are provided as a Source Data file.