Transcription Activator-Like (TAL) effectors are type III-delivered transcription factors that enhance virulence of plant pathogenic Xanthomonas species through the activation of host susceptibility (S) genes. TAL effectors recognize their DNA target(s) via a partially degenerate code whereby modular repeats in the TAL effector bind to nucleotide sequences in the host promoter. While this knowledge has greatly facilitated our power to identify new S genes, it can also be easily used to screen plant genomes for variations in TAL effectors target sequences and predict for loss-of-function gene candidates in silico. In a proof-of-principle experiment, we screened a germplasm of 169 rice accessions for polymorphism in the promoter of the major bacterial blight susceptibility S gene OsSWEET14 which encodes a sugar transporter targeted by numerous strains of X. oryzae pv. oryzae. We identified a single allele with a deletion of 18-bp overlapping with the binding sites targeted by several TAL effectors known to activate the gene. We show that this allele, which we call xa41(t), confers resistance against half of the tested Xoo strains representative of various geographic origins and genetic lineages, highlighting the selective pressure for the pathogen to accommodate with OsSWEET14 polymorphism and reciprocally the apparent limited possibilities for the host to create variability at this particular S gene. Analysis of xa41(t) conservation across the Oryza genus enabled to raise scenarios as to its evolutionary history prior and during domestication. Our findings demonstrate that resistance through TAL effector-dependent loss of S genes expression can be greatly fostered upon knowledge-based molecular screening of large collection of host plants.
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