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Background  The rice ( Oryza sativa ) gene  Xa7  has been hypothesized to be a typical executor resistance gene against  Xanthomonas oryzae  pv.  oryzae  ( Xoo ), and has conferred durable resistance in the field for decades. Its identity and the molecular mechanisms underlying this resistance remain elusive.    Results  Here, we filled in gaps of genome in  Xa7  mapping locus via BAC library construction, revealing the presence of a 100-kb non-collinear sequence in the line IRBB7 compared with Nipponbare reference genomes. Complementary transformation with sequentially overlapping subclones of the BACs demonstrated that  Xa7  is an orphan gene, encoding a small novel protein distinct from any other resistance proteins reported. A 27-bp effector binding element (EBE) in the  Xa7  promoter is essential for AvrXa7-inducing expression model. XA7 is anchored in the endoplasmic reticulum membrane and triggers programmed cell death in rice and tobacco ( Nicotiana benthamiana ). The  Xa7  gene is absent in most cultivars, landraces, and wild rice accessions, but highly homologs of XA7 were identified in  Leersia perrieri , the nearest outgroup of the genus  Oryza .    Conclusions   Xa7  acts as a trap to perceive AvrXa7 via EBE AvrXa7  in its promoter, leading to the initiation of resistant reaction. Since EBE AvrXa7  is ubiquitous in promoter of rice susceptible gene  SWEET14 , the elevated expression of which is conducive to the proliferation of  Xoo , that lends a great benefit for the  Xoo  strains retaining AvrXa7. As a result, varieties harboring  Xa7  would show more durable resistance in the field.  Xa7  alleles analysis suggests that the discovery of new resistance genes could be extended beyond wild rice, to include wild grasses such as  Leersia  species.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12284-021-00490-z.

Xa7, a Small Orphan Gene Harboring Promoter Trap for AvrXa7, Leads to the Durable Resistance to Xanthomonas oryzae Pv. oryzae