Surveys of Magnaporthe oryzae genotypes in breeding stations and commercial rice fields in Arkansas, Louisiana, and Puerto Rico from 2017 to 2019

Major resistance (R) gene mediated resistance to rice blast fungus Magnaporthe oryzae is often overcome by the fungus due to the occurrences of new races with altered corresponding avirulence (AVR) genes. In this study, blast diseased rice tissue samples were collected from breeding stations and commercial rice fields in Arkansas, Louisiana, and Puerto Rico during 2017-2019 to determine the efficacy of major R genes, Pi-ta, Pik, Pizt, Pi9, and Pi33. A total of 185 blast isolates were isolated from the diseased tissue samples to examine the existence of AVR genes AVR-Pita1, AVR-Pib, AVR-Pik, AVR-Pizt, AVR-Pi9 and ACE1. Genotyping of the isolates were conducted using 10 simple sequence repeat (SSR) markers. AVR-Pizt and AVR-Pita1 were found in all isolates suggesting that major R genes Pizt and Pi-ta are still effective to prevent infections by these isolates. Among the 185 isolates, 117 contained all the 6 AVR genes and 68 contained 3-5 AVR genes suggesting various degrees of race shift in these isolates. The SSR data revealed endemicity in genetic backgrounds among Arkansas isolates, whereas migration in isolates between Louisiana and Puerto Rico. Structure analysis of the SSR data suggested three major clusters with 46 combinations. The Arkansas isolates showed a high genetic diversity, but one genotype dominated. The Louisiana isolates were also genetically diversified without any obvious predominant group. The Puerto Rico isolates had the lowest heterozygosity. These data reveal contemporary genetic changes of the rice blast fungus and are useful for guiding the deployment of major R genes in these regions.