Genome-wide analysis of the auxin response factors (ARF) gene family in rice (Oryza sativa)

Auxin response factors (ARFs) are transcription factors that bind with specificity to TGTCTC-containing auxin response elements (AuxREs) found in promoters of primary/early auxin response genes and mediate responses to the plant hormone auxin. The ARF genes are represented by a large multigene family in plants. A comprehensive genome-wide analysis was carried out in this study to find all ARFs in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa subsp. japonica), 23 and 25 ARF genes, named as AtARFs and OsARFs, were identified, respectively. Chromosomal locations of all OsARFs were presented and it was found that the duplication of OsARFs was associated with only the chromosomal block duplications but not local tandem duplications. A phylogenetic tree was generated from alignments of the full-length protein sequences of 25 OsARFs and 23 AtARFs to examine the phylogenetic relationships of rice and Arabidopsis ARF proteins. All 48 members of ARF gene families fell into three major classes, a total of 13 sister pairs, including 9 OsARF–OsARF, 2 AtARF–AtARF and 2 AtARF–OsARF sister pairs were formed, showing different orthologous relationships between AtARFs and OsARFs. EST analysis and RT-PCR assays demonstrated that 24 of all 25 OsARF genes were active and the transcript abundance of some OsARF genes was affected by auxin treatment or light- and dark-grown conditions. The outcome of the present study provides basic genomic information for the rice ARF gene family and will pave the way for elucidating the precise role of OsARFs in plant growth and development in the future.