Loss and Natural Variations of Blast Fungal Avirulence Genes Breakdown Rice Resistance Genes in the Sichuan Basin of China

Abstract

<i>Magnaporthe oryzae</i> is the causative agent of rice blast, a devastating disease in rice worldwide. Based on the gene-for-gene paradigm, resistance (R) proteins can recognize their cognate avirulence (AVR) effectors to activate effector-triggered immunity. <i>AVR</i> genes have been demonstrated to evolve rapidly, leading to breakdown of the cognate resistance genes. Therefore, understanding the variation of <i>AVR</i> genes is essential to the deployment of resistant cultivars harboring the cognate <i>R</i> genes. In this study, we analyzed the nucleotide sequence polymorphisms of eight known <i>AVR</i> genes, namely, <i>AVR-Pita1, AVR-Pii, AVR-Pia, AVR-Pik, AVR-Pizt, AVR-Pi9, AVR-Pib</i>, and <i>AVR-Pi54</i> in a total of 383 isolates from 13 prefectures in the Sichuan Basin. We detected the presence of <i>AVR-Pik, AVR-Pi54, AVR-Pizt, AVR-Pi9</i>, and <i>AVR-Pib</i> in the isolates of all the prefectures, but not <i>AVR-Pita1, AVR-Pii</i>, and <i>AVR-Pia</i> in at least seven prefectures, indicating loss of the three <i>AVR</i>s. We also detected insertions of Pot3, Mg-SINE, and indels in <i>AVR-Pib</i>, solo-LTR of Inago2 in <i>AVR-Pizt</i>, and gene duplications in <i>AVR-Pik</i>. Consistently, the isolates that did not harboring <i>AVR-Pia</i> were virulent to IRBLa-A, the monogenic line containing <i>Pia</i>, and the isolates with variants of <i>AVR-Pib</i> and <i>AVR-Pizt</i> were virulent to IRBLb-B and IRBLzt-t, the monogenic lines harboring <i>Pib</i> and <i>Piz-t</i>, respectively, indicating breakdown of resistance by the loss and variations of the avirulence genes. Therefore, the use of blast resistance genes should be alarmed by the loss and nature variations of avirulence genes in the blast fungal population in the Sichuan Basin.