Genome-Wide Analysis of the RAV Transcription Factor Genes in Rice Reveals Their Response Patterns to Hormones and Virus Infection

The RAV family is part of the B3 superfamily and is one of the most abundant transcription factor families in plants. Members have highly conserved B3 or AP2 DNA binding domains. Although the family genes of several species have been systematically identified from genome-wide studies, there has been no comprehensive study to identify rice family genes. Here, we identified 15 genes of the RAV family in the rice genome and analyzed their phylogenetic relationships, gene structure, conserved domains, and chromosomal distribution. Based on domain similarity and phylogenetic topology, rice RAV transcription factors were phylogenetically clustered into four groups. qRT-PCR analyses showed that expression of these genes was significantly up-regulated or down-regulated by plant hormone treatments, including BL, NAA, IAA, MeJA, and SA. Most of the rice genes were dramatically down-regulated in response to rice stripe virus (RSV) and mostly up-regulated in response to Southern rice black-streaked dwarf virus (SRBSDV). These results suggest that the rice genes are involved in diverse signaling pathways and in varied responses to virus infection.