Fig. 3

TaSPL17-A (TraesCS7A02G246500) is associated with spike morphology traits. a Local Manhattan plot and pairwise LD analysis showing the association between 20 markers and spike morphology trait in the region between 225,328,984 and 225,737,586 bp on chromosome 7A. Green dots indicate SNPs above the significance threshold (-log₁₀[P value] = 5.00). Blue lines in the heatmap highlight strong LD with the significant variants. b Relative transcript levels for the three genes (TraesCS7A02G246500, TraesCS7A02G246400, TraesCS7A02G246300) within the associated region at six developmental stages: inflorescence meristem stage (ZM1), spikelet meristem stage (ZM2), glume primordium stage (ZM3), floral meristem stage (ZM4), stamen and pistil primordium stage (ZM5), and floral organ stage (ZM6). c Schematic diagram of TraesCS7A02G246500. Green rectangles and black lines indicate exons and introns, respectively. The gene is located on the reverse strand. d, e Spikes (d) and spikelets (e) of wild type (WT) and KO lines in the field. Scale bars = 4.00 cm (d) and 0.50 cm (e). f Grain width and length of WT and KO lines in the field. Scale bars = 1.00 cm and 5.00 mm for grain width and grain length, respectively. g–m Spike length (g), spikelet number per spike (h), grain number per spikelet (i), grain number per spike (j), grain width(k), grain length (l), and thousand grain weight (TGW) (m) in WT and KO lines in the field. Data are shown as means ± SD (n = 20). Triple KO line, KO-ABD; double KO line (TraesCS7A02G246500 and TraesCS7D02G245200 KO line), KO-AD; double KO line (TraesCS7A02G246500 and TraesCS7B02G144900 KO line), KO-AB; double KO line (TraesCS7B02G144900 and TraesCS7D02G245200 KO line), KO-BD; single KO line (TraesCS7A02G246500 KO line), KO-A; single KO line (TraesCS7B02G144900 KO line), KO-B; single KO line (TraesCS7D02G245200 KO line), KO-D. Different lowercase letters indicate significant differences (P < 0.05), as determined by ANOVA