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Background  Rice ( Oryza sativa  L.) is one of the most important crops that serves as staple food for ~ 50% of the human population worldwide. Some important agronomic traits that allow rice to cope with numerous abiotic and biotic stresses have been selected and fixed during domestication. Knowledge on how expression divergence of genes gradually contributes to phenotypic differentiation in response to biotic stress and their contribution to rice population speciation is still limited.    Results  Here, we explored gene expression divergence between a  japonica  rice cultivar Nipponbare and an  indica  rice cultivar 93–11 in response to invasion by the filamentous ascomycete fungus  Magnaporthe oryzae  ( Pyricularia oryzae ), a plant pathogen that causes significant loss to rice production worldwide. We investigated differentially expressed genes in the two cultivars and observed that evolutionarily conserved orthologous genes showed highly variable expression patterns under rice blast infection. Analysis of promoter region of these differentially expressed orthologous genes revealed the existence of  cis -regulatory elements associated with the differentiated expression pattern of these genes in the two rice cultivars. Further comparison of these regions in global rice population indicated their fixation and close relationship with rice population divergence.    Conclusion  We proposed that variation in the expression patterns of these orthologous genes mediated by  cis -regulatory elements in the two rice cultivars, may constitute an alternative evolutionary mechanism that distinguishes these two genetically and ecologically divergent rice cultivars in response to  M. oryzae  infection.    Electronic supplementary material  The online version of this article (10.1186/s12284-019-0270-5) contains supplementary material, which is available to authorized users.

Expression Divergence as an Evolutionary Alternative Mechanism Adopted by Two Rice Subspecies Against Rice Blast Infection