Selection of P. oryzae isolates and rice genotypes for downstream analyses
To infer the population structure of P. oryzae in YYT and place the diversity observed in YYT in the global diversity of P. oryzae pathogens infecting rice, we analysed a set of 512 isolates sampled in YYT, along with 45 samples representing the main lineages observed at world scale (Gladieux et al., 2018; Saleh et al., 2014), which were all genotyped using 13 microsatellites (Adreit et al., 2007). Part of the microsatellite data was available from previous studies in the worldwide (Saleh et al., 2014; 45 isolates) and YYT (Liao et al., 2016; 215 isolates) contexts. To further characterize the genetic co-structure between hosts and pathogens, we analysed a subset of paired samples collected in 2015 and composed of 46 plants representative of the five most popular indica landraces in YYT, and their corresponding 46P. oryzae pathogens (i.e. one isolate per plant coming from rice blast lesions found on the plant).