Identification and classification of the WRKY transcription factors family in Japonica rice

WRKY gene family encodes a large group of transcription factors regulating biotic and abiotic stress-responsive genes. In order to identify the WRKY gene family members in rice (Oryza sativa ssp. japonica), multiple searches were done in the related databases. Rice WRKY-conserved sequences were used as the templates for tBLASTN searches in datasets for finding new members. An HMM profile of WRKY domain was also used to find WRKY gene family. Multiple sequence alignment was done using clustalW software, and phylogenetic trees were drawn using MEGA10 software based on a neighbour-joining method with a 1000 repeats bootstrap index. According to the results, 165 members of the WRKY gene family were found in rice, of which 63 were new members. Sequences were divided into three main groups based on the number of WRKY domains and the structure of zinc-finger motifs. Conclusively, there were 21 proteins with two WRKY conserved domains in group I, 53 proteins with one WRKY conserved domain and Cx7Cx23HxC zinc-finger motif in group III and 82 proteins with one WRKY conserved domain and Cx4-5Cx22-23HxH zinc-finger motif in group II. The chromosomal location of OsWRKYs was detected on the rice genome. The different groups were distributed on various chromosomes. The greatest number of OsWRKY genes (32 members) were located on chromosome 1. Following complementary research and identification of promising candidate genes involved in tolerance to each stress, they can be used to increase tolerance to the desired stresses and provide food security using genetic engineering or molecular breeding approaches.