Figure 4.

Analysis of the candidate gene of Xa40. A, B, Haplotype analyses of LOC_Os11g46900 (A) and LOC_Os11g46890 (B). Both used four significant nonsynonymous SNPs in the coding regions based on the MSU v7 annotation of Nipponbare reference genome. Haplotypes with less than five accessions were not shown. Chi-square tests were used to compare haplotype frequencies among subpopulations, with “***” representing P < 0.001 and “NS” representing no significant difference. “–“ mean missing reads. The characters “W” and “Y” represent A/T and C/T heterozygous alleles. XI, Xian/indica; GJ, Geng/japonica C, D, Comparisons of the mean lesion lengths (caused by Xoo race P1 [PXO61]) vs. haplotypes of LOC_Os11g46900 (C) and LOC_Os11g46890 (D) in subpopulations. One-way ANOVA followed by Tukey’s honest significant difference (HSD) post hoc tests were used to detect the major effects. Different letters on the boxplots indicate statistically significant differences at P < 0.001 by Tukey’s HSD post hoc tests. Boxplots represent the interquartile range, the thick line in the middle of each box represents the median, and the whiskers represent 1.5 times the interquartile range. The data are based on two replications. The box in each column in (C) and (D) corresponds to the same haplotype (Hap) in (A) and (B), respectively. E, The CRISPR/Cas9 target sites of LOC_Os11g46890 in Wuyugeng20 (WYG20). The target sequence is marked in grey background and PAM motif (NGG) is marked by underline. F, Sequence at the target site of three T₁ mutants (JK143, JK150, and JK151) of LOC_Os11g46890. G–H, Reaction (G) and the lesion lengths (H) of wild-type WYG20 and three knockout T₁ plants inoculated with Xoo race C5 (GD1358). Data are presented as mean ± sd (n = 9). Asterisks indicate a significant difference compared with WYG20, with ***P < 0.001 by Student’s two-sided t test