Dynamic Insertion of Pot3 in <i>AvrPib</i> Prevailing in a Field Rice Blast Population in the Philippines Led to the High Virulence Frequency Against the Resistance Gene <i>Pib</i> in Rice

Abstract

The <i>Magnaporthe oryzae</i> avirulence gene <i>AvrPib</i> is required for the resistance mediated by its cognate resistance gene <i>Pib</i>, which has been intensively used in <i>indica</i> rice breeding programs in many Asian countries. However, the sequence diversity of <i>AvrPib</i> among geographically distinct <i>M. oryzae</i> populations was recently shown to be increasing. Here, we selected a field population consisting of 248 rice blast isolates collected from a disease hotspot in Philippine for the analysis of <i>AvrPib</i> haplotypes and their pathogenicity against <i>Pib</i>. We found that all of the isolates were virulent to <i>Pib</i> and each of them contained an insertion of Pot3 transposon in <i>AvrPib</i>. Moreover, Pot3 insertion was detected in different genomic positions, resulting in three different <i>AvrPib</i> haplotypes, designated avrPib-H1 to H3. We further conducted a genome-wide Pot2 fingerprinting analysis by repetitive element palindromic polymerase chain reaction (PCR) and identified seven different lineages out of 47 representative isolates. The isolates belonging to the same lineage often had the same <i>AvrPib</i> haplotype. In contrast, the isolates having the same <i>AvrPib</i> haplotypes did not always belong to the same lineages. Both mating types MAT1-1 and MAT1-2 were identified in the population in Bohol and the latter appeared dominant. On the host side, we found that 32 of 52 released rice varieties in the Philippines contained <i>Pib</i> diagnosed by PCR gene-specific primers and DNA sequencing of gene amplicons, suggesting that it was widely incorporated in different rice varieties. Our study highlights the genetic dynamics of rice blast population at both the <i>AvrPib</i> locus and the genome-wide levels, providing insight into the mechanisms of the mutations in <i>AvrPib</i> leading to the breakdown of <i>Pib</i>-mediated resistance in rice.