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. 2021 Jan 12;22:23. doi: 10.1186/s13059-020-02217-7

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© The Author(s) 2021

Open AccessThis 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/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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Fig. 4 — Identification of the candidate gene FtAP2YT1 associated with 1000-grain weight. a Manhattan plot for GWAS on 1000-grain weight (GW). The dashed line indicates the threshold −logP = 5. The red arrow indicates the SNP in FtAP2YT1. b Structure of FtAP2YT1 genomic sequence containing only one exon that is represented by a box. The non-synonymous SNP at 226 bp is marked by a black line. Hap1, haplotype 1; Hap2, haplotype 2. c Box plots show GW in two haplotypes (Hap.). ***P < 0.001, Student’s t test. d Protein structure model of FtAP2YT1. Compared with site Pro76, Ala76 enlarged the β-sheet length, which functions in binding to the DNA. e Y1H analysis of the activity of FtAP2YT1^Pro and FtAP2YT1^Ala binding to GCC-box and mGCC-box. Data are mean ± SD. ***P < 0.001, Student’s t test. f–h Expression of genes containing GCC-box that are potential targets of FtAP2YT1 in different accessions carrying Hap.1 and Hap.2, respectively