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Background  The most sustainable approach to control rice blast disease is to develop durably resistant cultivars. In molecular breeding for rice blast resistance, markers developed based on polymorphisms between functional and non-functional alleles of resistance genes, can provide precise and accurate selection of resistant genotypes without the need for difficult, laborious and time-consuming phenotyping. The  Pi2  and  Pi9  genes confer broad-spectrum resistance against diverse blast isolates. Development of allele-specific markers for  Pi2  and  Pi9  would facilitate breeding of blast resistant rice by using the two blast resistance genes.    Result  In this work, we developed two new markers, named Pi9-Pro and Pi2-LRR respectively, targeting the unique polymorphisms of the resistant and susceptible alleles of  Pi2  and of  Pi9 . The InDel marker Pi9-Pro differentiates three different genotypes corresponding to the  Pi2/Piz-t ,  Pi9  and non- Pi2/Piz-t/Pi9  alleles, and the CAPS marker Pi2-LRR differentiates the  Pi2  allele from the non- Pi2  allele. Based on the two newly developed markers and two available markers Pi2SNP and Pi9SNP, the presence of  Pi2  and  Pi9  was assessed in a set of 434 rice accessions consisting of 377 Chinese  indica  cultivars/breeding materials and 57 Chinese  japonica  cultivars/breeding materials. Of the 434 accessions tested, while one  indica  restorer line Huazhan was identified harboring the  Pi2  resistance allele, no other rice line was identified harboring the  Pi2  or  Pi9  resistance alleles.    Conclusions  Allele-specific marker-based assessment revealed that  Pi2  and  Pi9  have not been widely incorporated into diverse Chinese  indica  rice cultivars. Thus, the two blast resistance genes can be new gene sources for developing blast resistant rice, especially  indica  rice, in China. The two newly developed markers should be highly useful for using  Pi2  and  Pi9  in marker-assisted selection (MAS) breeding programs.    Electronic supplementary material  The online version of this article (doi:10.1186/s12284-016-0091-8) contains supplementary material, which is available to authorized users.

rice

Allele-specific marker-based assessment revealed that the rice blast resistance genes Pi2 and Pi9 have not been widely deployed in Chinese indica rice cultivars