Multiple alleles encoding atypical NLRs with unique central tandem repeats (CTRs) in rice confer resistance to Xanthomonas oryzae pv. oryzae

Abstract Plants have developed various mechanisms for avoiding the invasion of pathogen, including resistance (R) genes. Most of the R genes encode nucleotide-binding and leucine-rich repeat proteins (NLRs). Here we are reporting the isolation of three new bacterial blight R genes in rice, Xa1-2, Xa14 and Xa31(t), which were allelic to Xa1 and encoded atypical NLRs with unique central tandem repeats (CTRs). We also found that Xa31(t) was the same gene as Xa1-2. Though Xa1-2 and Xa14 conferred different resistance spectrums, their performance could be attenuated by iTALEs, like Xa1. XA1, XA1-2, XA14 and non-resistant RGAF differed mainly in substructure of the LRR domain. They all contained unique central tandem repeats (CTRs) and belonged to CTR-NLRs, which existed only in Gramineae. We also found that interactions existed among these genes and led to different performance in resistance. In conclusion, our results uncover a unique locus in rice consisting of at least three multiple alleles which encode CTR-NLRs and confer resistance to Xanthomonas oryzae pv. oryzae (Xoo).