Studies on the rice blast pathogen, resistance genes, and implication for breeding for durable blast resistance in Colombia

Rice blast disease caused by Pyricularia grisea, the anamorph of Magnaporthe grisea, is the main rice production constraint in Latin America. Development of resistant cultivars has been the preferred means of controlling this disease; however, blast resistance is defeated by the pathogen shortly after cultivar release, affecting both leaves and panicles of the plant and reducing yields severely. Major efforts are being made at CIAT to understand the high pathogen variation observed, often reported as the main cause of resistance breakdown. We have analyzed extensively the genetic structure of blast pathogen populations using MGR-DNA and rep-PCR fingerprinting techniques and studied the avirulence gene diversity using a set of rice differentials with known resistance genes. The blast pathogen in Colombia has been found to be mainly clonal exhibiting few genetic lineages. At present, there are three lineages predominating in the pathogen population and their frequencies depend upon the susceptibility and planted area of the commercial rice cultivars by farmers. In general, a single haplotype predominates within each lineage. These three genetic lineages exhibit broad spectrum of virulence and together defeat all known blast resistance genes. However, some resistance genes are effective against all members of a lineage, suggesting an association of avirulence genes and genetic groups in the pathogen. Avirulence genes vary in frequency in the pathogen population and some are highly frequent in several genetic lineages of the fungus. This suggests that these avirulence genes could play an important role in the pathogen or be associated with pathogenic fitness and then the corresponding resistance genes could be more relevant in breeding for durable resistance. Despite this high virulence diversity, breeders at CIAT have been able to develop durable blast resistant cultivars, indicating that combinations of these resistance genes may confer suitable and durable resistance to the pathogen. Evaluation and selection of breeding lines are routinely carried out under "hot spot" conditions favoring high pathogen pressure and diversity. Our studies are allowing us to identify and predict the durability of resistance gene combinations based on avirulence gene frequencies and the possible association of avirulence genes with pathogenic fitness. We have inferred the possible resistance genes present in our blast susceptible rice cultivars and initiated a backcrossing program to incorporate the desired resistance gene combinations into Latin American rice cultivars through marker assisted selection using mainly microsatellite and scar markers. Rice lines carrying the combination of the resistance genes Pi-1, Pi-2 and Pi-33 are then tested under controlled greenhouse conditions as well as our "hot spot" screening site using a spreader row technique to maintain a high and diverse population of the pathogen in the field. Resistant plants are then selected based on other desirable traits for their distribution to national programs in Latin America. (Résumé d'auteur