The Identification and Characterization of WOX Family Genes in Coffea arabica Reveals Their Potential Roles in Somatic Embryogenesis and the Cold-Stress Response

<i>WUSCHEL-related homeobox</i> (<i>WOX</i>) genes play significant roles in plant development and stress responses. Difficulties in somatic embryogenesis are a significant constraint on the uniform seedling production and genetic modification of <i>Coffea arabica</i>, hindering efforts to improve coffee production in Yunnan, China. This study comprehensively analyzed <i>WOX</i> genes in three <i>Coffea</i> species. A total of 23 <i>CaWOXs</i>, 12 <i>CcWOXs</i>, and 10 <i>CeWOXs</i> were identified. Transcriptomic profile analysis indicated that about half of the <i>CaWOX</i> genes were actively expressed during somatic embryogenesis. The most represented <i>CaWOXs</i> were <i>CaWOX2a</i>, <i>CaWOX2b</i>, <i>CaWOX8a</i>, and <i>CaWOX8b</i>, which are suggested to promote the induction and development of the embryogenic callus, whereas <i>CaWOX13a</i> and <i>CaWOX13b</i> are suggested to negatively impact these processes. Co-expression analysis revealed that somatic embryogenesis-related <i>CaWOXs</i> were co-expressed with genes involved in embryo development, post-embryonic development, DNA repair, DNA metabolism, phenylpropanoid metabolism, secondary metabolite biosynthesis, and several epigenetic pathways. In addition, qRT-PCR showed that four <i>WOX</i> genes responded to cold stress. Overall, this study offers valuable insights into the functions of <i>CaWOX</i> genes during somatic embryogenesis and under cold stress. The results suggest that certain <i>WOX</i> genes play distinct regulatory roles during somatic embryogenesis, meriting further functional investigation. Moreover, the cold-responsive genes identified here are promising candidates for further molecular analysis to assess their potential to enhance cold tolerance.