PthXo2B Orthologue Tal7 of Xanthomonas oryzae pv. oryzae Strain IX-221 Acts as a Major Virulence Factor in Indica Rice Without Activating a Clade III SWEET Gene.

In rice bacterial blight, Xanthomonas oryzae pv. oryzae deploys transcription activator-like effectors (TALEs) that upregulate host susceptibility genes. Thirty-four amino acid repeats in TALEs each specify a base in the DNA target, via a repeat-variable diresidue (RVD; positions 12 and 13). Some aberrant-length repeats can disengage to accommodate single base deletions. Clade III SWEET genes SWEET11, -13 and -14 are major susceptibility targets of different TALEs. xa13 is a SWEET11 allele lacking the TALE binding site and thus confers resistance to some strains. It has been deployed widely in India. We report that an xa13-breaking Indian isolate, IX-221, harbours one SWEET14- and two SWEET13-activating TALEs, with one or two disengageable repeats. One, Tal7, orthologous to PthXo2B of Philippines strain PXO61 but with minor, non-RVD sequence differences, like PthXo2B upregulates SWEET13 in a japonica variety and no clade III SWEET in an indica, yet unlike PthXo2B renders both varieties susceptible. A designer TALE with distinct, minor differences also failed to render the indica susceptible. The results suggest that Tal7 activates an alternative susceptibility gene and that non-RVD polymorphism can affect TALE targeting. Moreover, IX-221 provides evidence that the deployment of xa13 in India resulted in strains super-equipped with TALEs that break it.