Effect of single resistance genes and their pyramid on the diversity of Xanthomonas oryzae pv. oryzae population under field conditions as revealed by insertion sequence-polymerase chain reaction (IS-PCR)

Knowledge of plant-pathogen interaction and pathogen population structure can contribute to sustainable manipulation and deployment of host resistance in disease control. A molecular technique that is reliable but simpler than other methods such as RFLP was used to study population structure of Xanthomonas oryzae pv. oryzae (Xoo), which causes bacterial blight, a worldwide destructive disease of rice, particularly serious in Asia. IS-PCR using primer I3 designed based on the endogenous high-copy insertion sequences IS 1112 isolated from the pathogen was able to identify Xoo from other pathovars, detect polymorphisms between Xoo strains and differentiate the two genetic lineages of the pathogen population. This simple technique when combined with virulence analysis constitutes a good tool to study population of Xoo especially in differentiating the four-groups of race 9 in the contemporary pathogen population in the Philippines. Analyses of 249 bacterial isolates collected during two consecutive years from near-isogenic rice lines IRBB5 (xa5), IRBB7 (Xa7), gene pyramid IRBB61 (Xa4 + Xa5 + Xa7) and the recurrent parent IR24 (susceptible) deployed in rice fields at Calauan and Santa Cruz (Philippines) showed that lineage C, composed of races 3 and 9, dominated the indigenous Xoo population (98.8%), with race 9 constituting 94.8%. In contrast, Lineage B, represented by race 2 diminished (1.2%). It appears that race 3C is the source of variability observed in the pathogen population. Being under host selection pressure for a longer time (10 years), the Xoo population in Calauan was shown to be more diverse compared to that in Santa Cruz (2 years). However, the pathogen populations at these two locations had similar tendency for genetic diversification over two years. This tendency confirmed adaptation of Xoo to virulence on rice with Xa7 associated with a fitness penalty in the pathogen population. Although some single resistance genes were shown to be durable, especially where the effect of fitness penalty was present, gene pyramid with three-gene combination revealed enhanced resistance and was predicted to have a better durability. It is suggested that, aside from simply deploying resistance in the fields, the diversity of the effective resistqnce gene to which the pathogen population is exposed should be taken into consideration to improve resistance durability.