The auxin response factor gene family in wheat (Triticum aestivum L.): Genome-wide identification, characterization and expression analyses in response to leaf rust

Abstract

Auxin response factors (ARFs) are plant-specific transcription factors that bind explicitly to Auxin Response Elements and mediate downstream expression of auxin responsive genes involved at various stages of plant growth and development. This study identified 52 ARF genes located within the wheat genome. Based on phylogenetic analysis, the identified ARF proteins of wheat were classified into four classes (class I, II, III and IV). Synteny analysis revealed the orthologous relation with other monocots. The maximum numbers of predicted ARF genes were mapped on wheat chromosome 3B Ten conserved motifs of ARF was determined on all the identified sequences. Based on amino acid composition of the middle region of the ARF proteins, nine ARF proteins were transcription activators and the remaining were transcription repressors. The ARF genes of wheat contained 1–17 introns and deduced proteins of the genes having similar pattern of intron-exon distribution clustered within the same clade in the phylogenetic tree. TaARF1, TaARF4, TaARF7, TaARF34, TaARF39 were predicted to be targeted by the stress responsive miRNA Tae-miRNA160. The identified proteins were mostly localized within the nucleus and had sequence specific DNA binding activity. They were annotated in regulation of expression of early auxin responsive genes in auxin signaling pathway. Thirty-one TaARF proteins interacted and exhibited co-expressed regulation with other TaARF and Aux/IAA proteins. Increased expression of TaARF1 and TaARF23 at 120 h post inoculation (hpi) and 72 hpi in resistant and susceptible isolines respectively, specifies their roles in providing better resistance to the plant during leaf-rust infection.