Extended Data Fig. 5: Genome-wide association analysis (GWAS) of important agronomic traits in indica-indica hybrid population and segregating populations.
a-e, GWAS results of key agronomical traits in indica-indica hybrid population. (a) Physiological feature (heading date). (b) Morphological traits: I, leaf length; II, leaf width; III, tiller angle; IV, plant height. (c) Grain yield-related traits: I, full grain number per panicle; II, full grain number per plant; III, kilo-grain weight; IV, seed setting rate; V, yield per plant. (d) Grain cooking quality: I, amylose content; II, gel consistency. (e) Grain appearance quality: I, chalky grain percentage; II, chalkiness; III, grain translucency level; IV, grain shape (length to width ratio of polished grain). f-h, GWAS results of key agronomical traits in indica-indica segregating population. I-k, GWAS results of key agronomical traits in indica-japonica segregating population. (f and i) Physiological feature (heading date). (g and j) Morphological traits: I, leaf length; II, leaf width; III, tiller angle; IV, plant height. (h and k) Grain yield-related traits: I, full grain number per panicle; II, full grain number per plant; III, total grain number per panicle; IV, kilo-grain weight; V, seed-setting rate; VI, valid panicle number; VII, yield per plant. Negative log10(p) values (Y-axis) were plotted against SNP positions (X-axis) on each of 12 chromosomes. Association signals with the known genes located nearby were marked in red, and newly identified loci discussed in Fig. 3 were marked in black.
