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The TRANSPORT INHIBITOR RESPONSE 1/AUXIN SIGNALING F-BOX (TIR1/AFB) protein serves as auxin receptor and links with Aux/IAA repressor protein leading to its degradation via SKP-Cullin-F box (SCFTIR1/AFB) complex in the auxin signaling pathway. Present study revealed 11 TIR1/AFB genes in wheat by genome-wide search using AFB HMM profile. Phylogenetic analysis clustered these genes in two classes. Several phytohormone, abiotic, and biotic stress responsive cis-elements were detected in promoter regions of TIR1/AFB genes. These genes were localized on homoeologous chromosome groups 2, 3, and 5 showing orthologous relation with other monocot plants. Most genes were interrupted by introns and the gene products were localized in cytoplasm, nucleus, and cell organelles. TaAFB3, TaAFB5, and TaAFB8 had nuclear localization signals. The evolutionary constraint suggested paralogous sister pairs and orthologous genes went through strong purifying selection process and are slowly evolving at protein level. Functional annotation revealed all TaAFB genes participated in auxin activated signaling pathway and SCF-mediated ubiquitination process. Furthermore, in silico expression study revealed their diverse expression profiles during various developmental stages in different tissues and organs as well as during biotic and abiotic stress. QRT-PCR based studies suggested distinct expression pattern of TIR1-1, TIR1-3, TaAFB1, TaAFB2, TaAFB3, TaAFB4, TaAFB5, TaAFB7, and TaAFB8 displaying maximum expression at 24 and 48 h post inoculation in both susceptible and resistant near isogenic wheat lines infected with leaf rust pathogen. Importantly, this also reflects coordinated responses in expression patterns of wheat TIR1/AFB genes during progression stages of leaf rust infection. [ABSTRACT FROM AUTHOR]

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. [Display omitted] [ABSTRACT FROM AUTHOR]

WRKY, a plant-specific transcription factor family, has important roles in pathogen defense, abiotic cues and phytohormone signaling, yet little is known about their roles and molecular mechanism of function in response to rust diseases in wheat. We identified 100 TaWRKY sequences using wheat Expressed Sequence Tag database of which 22 WRKY sequences were novel. Identified proteins were characterized based on their zinc finger motifs and phylogenetic analysis clustered them into six clades consisting of class IIc and class III WRKY proteins. Functional annotation revealed major functions in metabolic and cellular processes in control plants; whereas response to stimuli, signaling and defense in pathogen inoculated plants, their major molecular function being binding to DNA. Tag-based expression analysis of the identified genes revealed differential expression between mock and Puccinia triticina inoculated wheat near isogenic lines. Gene expression was also performed with six rust-related microarray experiments at Gene Expression Omnibus database. TaWRKY10, 15, 17 and 56 were common in both tag-based and microarray-based differential expression analysis and could be representing rust specific WRKY genes. The obtained results will bestow insight into the functional characterization of WRKY transcription factors responsive to leaf rust pathogenesis that can be used as candidate genes in molecular breeding programs to improve biotic stress tolerance in wheat. [ABSTRACT FROM AUTHOR]