RiceMetaSysB: a database of blast and bacterial blight responsive genes in rice and its utilization in identifying key blast-resistant WRKY genes

Abstract

Nearly two decades of revolution in the area of genomics serves as the basis of present-day molecular breeding in major food crops such as rice. Here we report an open source database on two major biotic stresses of rice, named RiceMetaSysB, which provides detailed information about rice blast and bacterial blight (BB) responsive genes (RGs). Meta-analysis of microarray data from different blast- and BB-related experiments across 241 and 186 samples identified 15135 unique genes for blast and 7475 for BB. A total of 9365 and 5375 simple sequence repeats (SSRs) in blast and BB RGs were identified for marker development. Retrieval of candidate genes using different search options like genotypes, tissue, developmental stage of the host, strain, hours/days post-inoculation, physical position and SSR marker information is facilitated in the database. Search options like 'common genes among varieties' and 'strains' have been enabled to identify robust candidate genes. A 2D representation of the data can be used to compare expression profiles across genes, genotypes and strains. To demonstrate the utility of this database, we queried for blast-responsive WRKY genes (fold change ≥5) using their gene IDs. The structural variations in the 12 WRKY genes so identified and their promoter regions were explored in two rice genotypes contrasting for their reaction to blast infection. Expression analysis of these genes in panicle tissue infected with a virulent and an avirulent strain of Magnaporthe oryzae could identify WRKY7, WRKY58, WRKY62, WRKY64 and WRKY76 as potential candidate genes for resistance to panicle blast, as they showed higher expression only in the resistant genotype against the virulent strain. Thus, we demonstrated that RiceMetaSysB can play an important role in providing robust candidate genes for rice blast and BB.

Figure 1

Distribution and functional annotation of common 6243 DEGs under rice blast and BB RGs.

Figure 2

Distribution of DEGs in RiceMetaSys (biotic stress). (A–C) Distribution of rice blast RGs across tissues,dpi and strains. (D–F) Distribution of bacterial leaf blight RGs across tissues, hpi and strains.

Figure 3

Distribution of microsatellites in the rice blast and BB RGs.

Figure 4

(A) Hompage of the RiceMetaSysB (biotic stress) database and two separate links for rice blast and BB RGs. (B) Different search options available in the database like genotype, tissue, stage, days, strain, common among varieties/strains, locus, physical position and resistant vs. susceptible genotypes search. (C) Resistant vs. susceptible search input, its output and hyperlink of locus search. (D) Interactive graph results of candidate genes in single and multiple strains.

Figure 5

Phylogenetic analysis of 12 DE WRKY genes in blast experiments using (A) complete genes, (B) proteins and (C) 1 kb promoter regions in three genotypes Tetep, HP2216 and Nipponbare using ClustalX2.1 tool.

Figure 6

Expression analysis of WRKY genes in blast-infected panicle tissues at three-time intervals. T means Tetep; H, HP2216 with virulent and avirulent M. oryzae strains. Asterisks indicate a significant difference compared with untreated at P < 0.05, by Student’s t-test.