Genome-wide analysis of the auxin response factors (ARF) gene family in barley (Hordeum vulgare L.)

Auxin response factors (ARFs) is one of common transcription factor (TF) family found in plants. By binding to its specific target in promoters, they regulate key genes related to auxin and mediating plant responses. So far, ARF family TFs have been identified in some plants, but no information is available regarding ARF genes in barley. In this study, we identified 20 ARF genes (HvARF) in the barley genome. Based on the comparative phylogenetic analysis, HvARFs were divided into six major Classes (I–VI). Duplication analysis revealed that four segmental and one tandem duplication contributed to the expansion of HvARF genes which were preferentially distributed at distal parts of the chromosomes. Mining of cis-acting regulatory elements in the promoter resulted that HvARF genes are mainly associated with hormone, stress and light responsiveness. In addition, they involve in miRNA-mediated gene regulation in which seven HvARF members were potentially targeted by five different miRNAs. Among those, hvu-miR160 simultaneously targets Class II ARF members (HvARF14, HvARF15, HvARF16, and HvARF17). Besides, the expression pattern of 20 HvARFs was assessed in different embryonic development and stress-induced (heat, drought, salinity, and excess boron) conditions, which pointed out that HvARFs functionally involve in developmental stages and stress adaptation of barley, by regulating the auxin-mediated genes. The results represented here provide comprehensive infomation on ARF family genes and could provide a framework for further cloning and functional verification of HvARF members for the purposes of crop improvement.