Fig. 3
Genetic details and phenotypic associations of the three loci controlling NIS to M. oryzae in temperate japonicas. Three loci were identified after GWAS analysis of disease levels against CD203 isolate: RRobN1 locus (23,9 Mpb − 24,2Mpb on chromosome 6; a), NIS2 locus (27.55–27.96 Mb on chromosome 5; b) and NIS3 locus (18,4 Mpb-19,2Mpb on chromosome 11; c). For each locus, the figure on the left represents the physical position of the QTL on their respective chromosome. Heatmaps show the extent of Linkage Desiquilibrium established by R2 calculation between each SNPs. The QTL is established for an entire LD block containing significant SNPs. For A and B, the points show the SNPs p-value of the GWAS for blast susceptibility. Black dots represent p-values obtained in the N0 condition and blue for the N1 condition. For C, the dots show p-values for SNPs identified in the GWAS for the NIS index phenotype. The figures in the middle show susceptibility to CD203 strain for each haplotype of each QTL, in each of the two nitrogen conditions. Each black point corresponds to the Lsmean of the number of rice blast lesions in one genotype. In white, N0 corresponds to the low nitrogen condition, in grey N1 corresponds to the high nitrogen condition. Red diamonds corresponds to the mean Lsmean for each treatment. The red arrow indicates the value of the increased susceptibility in case of significant effect of nitrogen condition. Statistical groups are determined from a pairwise comparison with Tukey adjustment based on a model with Trials and genotypes as covariate. The figures on the right represent the NIS index depending of each QTL haplotype. Although this Index was only used for the identification of NIS3, we also displayed it for RRobN1 and NIS2 for comparison. Each point corresponds to the NIS Index for each genotypes. Red diamonds correspond to Lsmeans of each haplotype. P-Values were obtained from Wilcoxon test for a and b, and a Student Test after a logarithmic transformation for c