Fig. 6: Natural variation in GNP3 modulates grain number.

a Comparison of GNP between accessions carrying GNP3^Hap-G and GNP3^Hap-T in aromatic rice (n = 41/48/38/48 plants). HN-R1: accessions cultivated in Sanya, Hainan province (replicated 1);  HN-R2: accessions cultivated in Sanya, Hainan province (replicated 2). b, c Phylogenetic tree (b) and minimum spanning network (c) of GNP3 haplotypes across eight rice subgroups: Or-I, Or-II, Or-III, indica (ind), temperate japonica (tej), tropical japonica (trj), aus, and aromatic (aro). d, e Representative panicles (d) and GNP (e) of WT, gnp3-1, GNP3^Hap-G-CM, and GNP3^Hap-T-CM plants grown in Nanning (n = 19/19/16/15 plants). f, g Representative panicles (f) and grain number per panicle (g) of WT, gnp3-1, GNP3^Hap-G-OE, and GNP3^Hap-T-OE plants grown in Beijing (n = 20/15/17/20 plants). h Frequency of GNP3 alleles in improved varieties (IMP) and landraces (LAN). i, j Representative panicles (i) and GNP (j) of NIL-GNP3^Nip and NIL-GNP3⁹³¹¹ (n = 30 plants). Scale bar, 2 cm (d, f, i). In (a, j), asterisks indicate statistical significance by two-tailed Student’s t tests (*P < 0.05, **P < 0.01). In (a, e, g, j), the center line indicates the median, the box edges represent the first and third quartiles, and the whiskers extend to the minima and maxima. Lowercase letters denote significant differences (one-way ANOVA with Tukey multiple-range test, P < 0.05). Source data are provided as a Source Data file.