Genome-wide analysis of the WOX gene family and function exploration of RhWOX331 in rose (R. ‘The Fairy’)

<i>WOXs</i> are a class of plant-specific transcription factors that play key roles in plant growth and stress responses. However, the mechanism by which <i>WOXs</i> influence adventitious root development in <i>Rosa hybrida</i> remains unclear. In this study, <i>RcWOX</i> gene family in rose was identified and phylogenetically analyzed using bioinformatics analysis. A total of 381 <i>RcWOX</i> gene members were localized on seven chromosomes except of nine members. The main <i>cis</i>-acting elements involved in hormonal, light, developmental, and abiotic stress responses were identified in the promoters of <i>RcWOX</i> genes, suggesting their regulation by these signals. Nine <i>RhWOX</i> genes had significant different expression during rooting process of rose. <i>RhWOX331</i>, <i>RhWOX308</i>, <i>RhWOX318</i> were positive with the formation of rose roots. RhWOX331 was positively involved in the formation of adventitious root primordia, which gene coding a transcription factor localized in the nucleus. The HOX conserved domain in the protein contributed to the self-activating activity of RhWOX331. We obtained genetically modified Arabidopsis to validate the function of <i>RhWOX331</i>. Overexpression of <i>RhWOX331</i> gene alleviated the inhibition of root length of <i>A. thaliana</i> primary roots by high concentration of IBA and NPA, and significantly increased the number of lateral roots on the primary roots, as well as the height of <i>A. thaliana</i> plants. Additionally, <i>RhWOX331</i> promoted adventitious root formation in A. thaliana and mitigated hormonal inhibition by exogenous 6-BA, NPA, and GA₃. The <i>RhWOX331</i> promoter contained cis-acting elements such as ABRE, Box 4 and CGTCA-motif et.al. GUS activity analysis showed that the gene acted at the cotyledon attachment site. Taken together, these studies identified a significant expansion of the <i>RcWOX</i> gene family, inferred roles of certain branch members in adventitious root formation, elucidated the function of <i>RhWOX331</i> in adventitious root initiation, and laid the foundation for further research on the function of <i>WOX</i> gene family in roses.