Additional file1: Table S1. Detailed information on the code number, name, grain color, pedigree, year of release, origin and wheat zone for the 326 winter wheat cultivars. Table S2 Functional markers associated with pre-harvest sprouting resistance in wheat. Table S3 Analysis of variance for germination index (GI) in the 326 winter wheat cultivars across three years. Table S4 Allelic variations of 10 genes associated with pre-harvest sprouting resistance and germination index (GI) in the 326 winter wheat cultivars. Fig. S1. The daily average temperature (a), relative humidity (b) and rainfall (c) of the three cropping seasons during 2017–2018, 2018–2019, and 2019–2020. Fig S2. Distribution of germination index (GI) in the 326 wheat cultivars (a) and comparison of GI in different wheat zones (b), provinces (c) and grain colors (d). NWWZ, Northern Winter Wheat Zone; YHWZ, Yellow and Huai River Valleys Winter Wheat Zone; SWWZ, Southwestern Winter Wheat Zone; MLWZ, Middle and Lower Yangtze River Valleys Winter Wheat Zone. Different letters in individual year and mean value indicate significant differences of GI at P < 0.05. Fig. S3. Correlation analysis of germination index between years. * and **, significant at P < 0.05 and P < 0.01, respectively. a Correlation between 2018 and 2019; b Correlation between 2018 and 2020; c Correlation between 2019 and 2020. Fig. S4. Distribution of germination index in the Lunxuan 13 × Bainong 3217 F2 (a) and F3 (b) populations.