Abstract
Auxin response factors (ARFs) play central roles in conferring auxin-mediated responses through selection of target genes in plants. Despite their physiological importance, systematic analysis of ARF genes in potato have not been investigated yet. Our genome-wide analysis identified 20 StARF (Solanum tuberosum ARF) genes from potato and found that they are unevenly distributed in all the potato chromosomes except chromosome X. Sequence alignment and conserved motif analysis suggested the presence of all typical domains in all but StARF18c that lacks B3 DNA-binding domain. Phylogenetic analysis indicated that potato ARF could be clustered into 3 distinct subgroups, a result supported by exon-intron structure, consensus motifs, and domain architecture. In silico expression analysis and quantitative real-time PCR experiments revealed that several StARFs were expressed in tissue-specific, biotic/abiotic stress-responsive or hormone-inducible manners, which reflected their potential roles in plant growth, development or under various stress adaptions. Strikingly, most StARFs were identified as highly abiotic stress responsive, indicating that auxin signaling might be implicated in mediating environmental stress-adaptation responses. Taken together, this analysis provides molecular insights into StARF gene family, which paves the way to functional analysis of StARF members and will facilitate potato breeding programs.
Highlights
Auxin response factors (ARFs) play central roles in conferring auxin-mediated responses through selection of target genes in plants
The ARF proteins are a set of plant-specific transcription factors, whose typical architecture consists of a conserved amino-terminal DNA binding domain (DBD), a highly conserved carboxyl-terminal domain (CTD) and a variable middle region (MR)[11]
After removing the non-representative splicing forms of same gene locus, sequences of non-redundant ARF candidates were further verified by a Hidden Markov Model (HMM)-based for the presence of both B3 DNA binding and Auxin_Resp motifs, and a total of 20 ARF members were identified in the genome of Solanum tuberosum
Summary
Auxin response factors (ARFs) play central roles in conferring auxin-mediated responses through selection of target genes in plants Despite their physiological importance, systematic analysis of ARF genes in potato have not been investigated yet. Most StARFs were identified as highly abiotic stress responsive, indicating that auxin signaling might be implicated in mediating environmental stress-adaptation responses Taken together, this analysis provides molecular insights into StARF gene family, which paves the way to functional analysis of StARF members and will facilitate potato breeding programs. The phytohormone auxin provoke almost every aspect of plant growth, development, stress responses, including apical dominance, defense responses against pathogens, leaf morphology, flower/fruit development, root elongation, vascular differentiation and embryogenesis[1,2,3] Some phytopathogens, such as Agrobacterium, Pseudomonas, Streptomyces, and so on, can produce indole-3-acetic acid (IAA) and/or its analogs to modulate or manipulate plant responsive behaviors through auxin-induced signaling cascades and gene expressions[4,5]. Given that multiple members in ARF family, there might be significant functional diversification between individual members
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