Xa1 Allelic R Genes Activate Rice Blight Resistance Suppressed by Interfering TAL Effectors

Abstract

<i>Xanthomonas oryzae</i> pathovar <i>oryzae</i> (<i>Xoo</i>) uses transcription activator-like effectors (TALEs) to cause bacterial blight (BB) in rice. In turn, rice has evolved several mechanisms to resist BB by targeting TALEs. One mechanism involves the nucleotide-binding leucine-rich repeat (NLR) resistance gene <i>Xa1</i> and TALEs. Reciprocally, <i>Xoo</i> has evolved TALE variants, C-terminally truncated versions (interfering TALEs or iTALEs), to overcome <i>Xa1</i> resistance. However, it remains unknown to what extent the two co-adaptive mechanisms mediate <i>Xoo</i>-rice interactions. In this study, we cloned and characterized five additional <i>Xa1</i> allelic <i>R</i> genes, <i>Xa2</i>, <i>Xa31(t)</i>, <i>Xa14</i>, <i>CGS-Xo1</i>_<i>11</i> , and <i>Xa45(t)</i> from a collection of rice accessions. Sequence analysis revealed that <i>Xa2</i> and <i>Xa31(t)</i> from different rice cultivars are identical. These genes and their predicted proteins were found to be highly conserved, forming a group of <i>Xa1</i> alleles. The XA1 alleles could be distinguished by the number of C-terminal tandem repeats consisting of 93 amino acid residues and ranged from four in XA14 to seven in XA45(t). <i>Xa1</i> allelic genes were identified in the 3000 rice genomes surveyed. On the other hand, iTALEs could suppress the resistance mediated by <i>Xa1</i> allelic <i>R</i> genes, and iTALE genes were prevalent (∼95%) in Asian, but not in African <i>Xoo</i> strains. Our findings demonstrate the prominence of a defense mechanism in which rice depends on <i>Xa1</i> alleles and a counteracting mechanism in which <i>Xoo</i> relies on iTALEs for BB.