In silico analysis for gene content in rice genomic regions mapped for the gall midge resistance genes

Abstract

So far, 11 gall midge resistance genes (Gm1 through Gm11) have been identified in rice though classical inheritance studies and several of these have been mapped through linked markers. Nevertheless, the exact identity of these genes is still eluding. Hence, the present study aimed to identify the potential candidate genes involved in rice-gall midge interactions by in silico analysis for gene content of 4.02 Mb genomic regions containing the gall midge R genes. The candidate genes were identified in terms of common genes among the different gall midge resistance regions, transcriptomics data analysis from earlier studies and, reported genes widely implicated in defense against plant-pathogen interactions. Results revealed, of the 375 annotated genes, five genes with one or more copy number were common among these regions such as the genes encoding NBS-LRR class proteins, no apical meristem protein, Fbox family protein, pentatricopeptide repeat containing protein and SET domain containing protein. Further, 15 genes from these regions have been reported in earlier transcriptomics studies covering in incompatible (9 genes) and compatible (6 genes) rice-gall midge interactions and 22 genes are known to be implicated in different plant-pathogen interactions. From the present study, we have shortlisted 24 genes and developed 33 primer pairs. These primers are ready to use for conducting real time PCR validation.