Genome-wide identification and expression analysis of peach auxin response factor gene families

Plant auxin response factors (ARFs) are involved in plant growth, development and multiple other processes. In this study, the ARF gene family in the peach genome was identified by bioinformatics software and RT-PCR. In total, 18 PpARF candidate genes were found in the peach genome. The DNA-binding and ARF domains, as well as motif III and IV of the PpARF gene family were highly conserved. The phylogenetic analysis revealed that PpARF gene family was divided into five classes: Class I (three members), Class II (four members), Class III (five members), Class IV (three members) and Class V (three members). The results of an intron-exon structure analysis indicated that PpARF gene family members were composed of 2–15 exons. A chromosome mapping analysis revealed that PpARF genes were distributed with different densities over eight chromosomes, with the largest number of PpARF genes on chromosome 1 (four genes), followed by chromosome 4 and 6 (three genes each). Only one gene was located on each of chromosome 3, 7 and 8. A conserved motif analysis revealed that the DNA-binding and ARF domains were observed in all PpARF proteins (except for PpARF18). Class I contained no motifs III or IV (except for PpARF7). RT-PCR results indicated that all of the PpARF genes, with the exception of PpARF15 and PpARF17, were expressed in at least one of the tissues (roots, stems, leaves, flowers and five stages of fruit development). These results suggested that the PpARF gene family members are highly and structurally conserved, and are involved in various aspects of peach growth and development, especially in fruit development.