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 FtAP2YT1Pro and FtAP2YT1Ala 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