Genome-wide identification and expression analysis of auxin response factor (ARF) gene family in pecan indicates its possible roles during graft union formation

Auxin responsive factors (ARFs) are central components of auxin signaling, with critical roles in numerous developmental processes and stress responses. However, systematic analysis of pecan ARF (CiARF) gene family has not been conducted. Here, we performed a genome-wide identification and expression analysis of ARF gene family in pecan. In total, 31 non-redundant CiARF genes were detected and unevenly distributed among 16 chromosomes. Phylogenetic study suggested that the 31 CiARFs could be divided into three groups, in which members of the same group commonly exhibited similar exon-intron structures and motif patterns. Segmental duplication was found to be the main driving force for CiARF gene family expansion. Promoter analysis revealed that CiARFs contained elements associated with environmental stimuli, hormone response, and cellular development. GO enrichment detection showed that the 31 CiARFs were all involved in auxin-activated signaling pathway, among which, CiARF10a and CiARF10b regulated cell division as well. Expression pattern analysis demonstrated that 7 CiARFs including CiARF2e/5/10b/10c/10e/10f/19b were highly up-regulated at specific time points during graft union formation. Among them, the consistently up-regulated CiARF5 and CiARF2e were also persistently induced by drought stress and during embryo development, respectively. Analysis of CiARF gene family provides a valuable information for understanding the molecular mechanisms of auxin signaling during graft union formation.