Comparative Analysis of the Structure, Organization, Evolution and Expression Profiles of Genes Encoding ADP-Ribosylation Factors in the C3 Model, Rice and a C4 Model, Foxtail Millet

ADP-ribosylation factors (ARFs) function in diverse physiological and molecular activities. Recent studies also demonstrate the role of ARFs in biotic and abiotic stress responses of plants. Through a whole genome scan, we identified 23 and 25 candidate ARF protein-encoding genes in the C₃ model, rice and a C₄ model, foxtail millet, respectively. Phylogenetic analysis classified these proteins into four classes (I-IV) with ARFs in class I to III and ARF-like (ARL) proteins in class IV. Sequence and domain composition analyses showed the presence of several domains in addition to the conserved ARF motif, which could be attributed to the functional divergence of ARF/ARL proteins. Involvement of ARFs/ARLs in stress response mechanisms was suggested by the presence of several cis-elements related to stress and hormone response in their promoter region. Furthermore, physical and comparative genome mapping of the genes among the Poaceae family members elucidated their duplication and divergence patterns. Analysis of transcript abundance of rice ARF/ARL genes in different tissues, abiotic stresses and hormones showed their spatio-temporal differential expression profiles with higher expression of a few genes in at least one stress (salt, dehydration, cold and desiccation). Comparative analysis of the ARF/ARL locus from five rice cultivars revealed the presence of putative allelic polymorphisms specific to stress-tolerant cultivars. Taken together, this study provides comprehensive insights on ARF/ARL gene family in rice and foxtail millet, which could be utilized to identify candidates for further functional analysis to define their precise roles in abiotic stress responses of the two model plants.