Genome-wide comparative analysis of homeobox transcription factors in rice and expression profiles of selected genes reveal potential tissue and developmental stage specificity as well as abiotic stress responsiveness

Introduction Homeobox (HB) transcription factors are essential for plant development and can participate in regulating plant responses to diverse biotic and abiotic stresses. Methods In this study, we performed an in-silico analysis of the different HB gene and protein subfamilies in rice, including Oryza sativa subsp. indica and O. sativa subsp. japonica . Results A total of 112 and 156 sequences annotated as HB transcription factors were retrieved from PlantTFDB for O. sativa subsp. indica and subsp. japonica , respectively, which showed 94% sequence identity. The homeobox–plant homeodomain finger (HB-PHD) subfamily showed 100% identity, whereas the three-amino-acid-loop-extension (TALE), WUSCHEL-related homeobox (WOX), and zinc-finger-homeodomain (ZF-HD) subfamilies displayed values equal to or higher than 95%; in contrast, HB-OTHERS showed the lowest identity (82%). Phylogenetic analysis grouped the proteins into six major subfamilies: HB-PHD, HD-ZIP, TALE, WOX, ZF-HD, and HB-OTHERS. In the promoter regions of HB genes of O. sativa subsp. japonica , 688 cis -regulatory motifs were retrieved as potentially associated with hormonal and stress responses such as drought, salinity, and cold; among the most frequent were ABRE, CGTCA-motif, TGACG-motif, and ARE. In addition, de novo motif analysis retrieved regulatory patterns specific to HB genes with significant similarity to transcription factors reported in specialized databases, suggesting conserved regulatory mechanisms. Selected representative genes from the TALE , WOX , and HD-ZIP subfamilies displayed relatively high expression under salinity or drought conditions. Discussion Overall, our findings expand the understanding of the diversity and potential functions of HB transcription factors in rice, providing a comparative framework and a set of candidate HB genes for subsequent experimental studies addressing their roles in rice development and abiotic-stress responses.