(A) Midpoint rooted neighbor-joining dendrogram representing the proportion of shared microsatellite alleles among multilocus genotypes. Two hundred fourteen isolates (the prefix ‘CH’ visible in C was removed from A for clarity) were genotyped using 13 microsatellites. Only one representative of multilocus genotypes repeated multiple times was kept, and for each repeated multilocus genotype the corresponding isolates are listed at the tip of a branch (74 unique multilocus genotypes in total). Bootstrap supports are indicated by a black dot when >40% (1000 resamplings). Isolates harvested on japonica and indica rice are indicated in black and grey respectively. Six isolates (i.e. CH1180, CH1189, CH1195, and CH1317, collected on indica; CH1208 and CH1301, collected on japonica) that show in the dendrogram an intermediate position, were assigned to the IB group because of their pathogenicity phenotypes and their separation from the other JB genotypes in the DAPC (Figure 1—figure supplement 1). The isolates selected for (C) and Figure 3 are marked by a ‘*’ and a ‘+’ respectively. The cluster of Japonica-borne isolates (abbreviated JB; within the square with dashed lines) was defined following Discriminant Analysis of Principal Components; the remaining samples represent the cluster of Indica-borne (IB) isolates. (B) Distribution of the two clusters identified based on microsatellite variation (japonica borne ‘JB’ and indica borne ‘IB’) on japonica and indica hosts in the Yuanyang terraces. The fact that the distributions are largely non-overlapping (the JB and IB clusters are mostly found on Japonica and Indica hosts, respectively) suggests local adaptation of the pathogens to their respective hosts. The numbers of isolates are indicated above the bars. (C) Pathogenicity profiles of 30 isolates on two japonica and five indica varieties (‘R’ and ‘S’ stand for resistance and susceptibility, respectively). The 30 representative isolates were selected from the analysis presented in (A) and inoculated onto seven major rice varieties grown in Yuanyang (HPN: Huang Pi Nuo; NG: Nuo Guo; ZN: Zi Nuo; XG: Xiao Gu; LJG: Li Jiao Gu; AZG: Ai Zhe Gu; Acuce). HPN, NG and ZN are all glutinous rice varieties. The isolates marked with a ‘+’ in (A) and (C) are those used in Figure 3; all isolates included in (C) are marked with a ‘*’ in (A). The qualitative analysis of symptoms presented here suggests that japonica-borne (JB) isolates cannot attack indica rice whereas indica-borne (IB) isolates can attack japonica.