Screening of Fast-Neutron Mutant Population to Identify Candidate Rice Blast Defense Response Genes

Abstract

Rice is the most widely consumed staple food in the world, feeding over half of global population. Thailand has long been an important rice producer and exporter, ranked 6th in the world regarding total milled rice yield. Unfortunately, the major problem of rice production worldwide is rice blast disease which caused by the fungus Magnaporthe oryzae. The most effective method for managing rice blast disease is using resistant rice varieties. One of Thai rice variety that show highly resistance against various rice blast fungus isolates is Jao Hom Nin (JHN) rice, containing broad-spectrum resistance gene, Pi7. However, the identification of resistance genes other than the R gene will confer long-lasting and sustainable resistance to the plant, which lead to identification of genes involved in the plant’s defense against the rice blast fungus in this study. JHN were previously mutagenized with fast-neutron radiation. 2,200 JHN M4 lines were inoculated with mixture of five Thai rice blast fungus isolates. Five susceptible lines lost their resistance due to mutations in the Pi7 gene, while one susceptible line with an intact Pi7 gene could not be characterized as it failed to produce an F1 population. Two moderate resistance lines with intact Pi7 gene were sent for whole-genome resequencing along with JHN wildtype. The sequence comparison between JHN and two mutant lines revealed 491,759 Indel variants. The Indel variants, whose nucleotide sequences differed by less than 10 bp between JHN and mutants, were filtered out. Consequently 33 candidate rice blast defense response genes were predicted to contain high-impact effect Indels, with only 15 of them having predicted functions. Eleven genes were identified as transposons or retrotransposons. Four genes with predicted functions stand out as interesting candidates for future characterization.