Extended Data Fig. 1: Nitrogen response of agronomic traits and expression analysis of three candidate genes.
From: Genomic basis of geographical adaptation to soil nitrogen in rice
a, PCA with genotype likelihoods in 110 accessions. Principal component 1 and principal component 2 divided 110 accessions into 4 groups: japonica, indica, aus and aromatic. b, Genome-wide linkage disequilibrium analysis of 110 Mini-Core accessions. c, d, Grain number per panicle (c) and 1,000-grain weight (d) of 110 accessions under low, moderate and high nitrogen conditions in the field. Dots represent individual data points of 110 accessions and lines connect the data points of the same accession under low, moderate and high nitrogen. Black diamonds represent means. For each individual data point, data are average (n = 5 plants). e, Nitrogen response of tiller number, grain number per panicle, and 1,000-grain weight from low to moderate nitrogen. f, TRN among different subgroups. g, The position of three candidate genes and the 15 most-significant SNPs that underlie the significant locus on rice chromosome 6. x axis, position; y axis, P value of the SNPs. Red dots, 15 SNPs. h, Expression analysis of three candidate genes by qRT–PCR in the roots of ZH11 plants grown in different nitrogen concentrations (NH4NO3). Data are mean ± s.d. (n = 3 biologically independent samples). i, Expression analysis of OsTCP19 under different nitrate and ammonium concentrations. Data are mean ± s.d. (n = 3 biologically independent samples). e, f, The bars in the violin plots represent 25th percentiles, medians and 75th percentiles. In c, d, f, h, i, letters indicate significant differences (P < 0.05, one-way ANOVA, Tukey’s HSD test). For P values, see Source Data.
