Genome-wide identification and expression analysis of auxin response factor gene family in Medicago truncatula

Abstract

Auxin response factors (ARFs) bind specifically to auxin response elements (AuxREs) in the promoters of down-stream target genes and play roles in plant responses to diverse environmental factors. Using the latest updated Medicago truncatula reference genome sequence, a comprehensive characterization and analysis of 24 MtARF (M. truncatula ARF) genes were performed. To uncover the basic information and functions of MtARF genes during symbiosis, we analyzed the expression patterns of MtARF genes during the early phase of Sinorhizobium meliloti infection. The systematic analysis indicated that changes in MtARF gene expression occur during these early stages of infection, suggesting a functional role in symbiosis. Furthermore, the roles of MtARF-mediated auxin signaling in symbiosis were tested in the infection resistant mutant (dmi3). The expression responses of MtARFs to S. meliloti infection were attenuated in the mutant compared to wild-type A17. In summary, our results show that changes in MtARF gene expression occur during the response to S. meliloti infection, suggesting that members of this family may have important roles in the symbiotic interaction.

The MicroRNA390/TAS3 Pathway Mediates Symbiotic Nodulation and Lateral Root Growth

“…ARFs belong to a large gene family with 12 to 39 members, depending on the species (Finet et al, 2013). In M. truncatula, this gene family is composed of 24 members (Shen et al, 2015).…”

Identification and Network-Enabled Characterization of Auxin Response Factor Genes in Medicago truncatula

“…A total of 22 MtARF genes, with signature conserved domains and significant transcriptional activities, were thus identified and given temporary names based on their chromosomal locations. Of these MtARFs, 14 were previously identified in a similar study conducted in 2015 (Shen et al, 2015), and the remaining 8 are our novel discoveries. In Table 1 we provide information about each of the 22 MtARF genes, including chromosomal location, ORF length, intron count, polypeptide length, molecular weight, and isoelectric point.…”

“…Central to this symbiosis is auxin, whose polar transport and interplay with cytokinin are believed to be indispensable in proper nodule formation and development (Liu et al, 2015; Shen et al, 2015). Prior to nodule initiation in indeterminate legumes such as M. truncatula , acropetal auxin transport is inhibited at the initiation site, and auxin-responsive reporter gene expression localizes in the dividing inner and outer cortical cells (Mathesius et al, 1998; van Noorden et al, 2007).…”

“…As an integral component of auxin-regulation, the ARF gene family encodes proteins that regulate nodule formation and development in M. truncatula (Breakspear et al, 2014; Shen et al, 2015). More specifically, the role of ARFs in the regulation of symbiosis has been confirmed through functional characterization, with orthologous mutant arf16a resisting Sinorhizobium meliloti ( S. meliloti ) infection (Breakspear et al, 2014), and thus further exemplifying auxin's role in the initiation of nodules.…”

“…Computational approaches have been utilized to identify putative ARF genes in rice ( Oryza sativa ), field mustard ( Brassica rapa ), poplar ( Populus trichocarpa ), and tomato ( Solanum lycopersicon ) based on A. thaliana ARF (AtARF) gene family members discovered through both functional and in silico genomic analysis (Hagen and Guilfoyle, 2002; Kalluri et al, 2007; Wang et al, 2007; Zhang et al, 2012; Zouine et al, 2014). Specifically, in M. truncatula , genome analysis has helped identify several putative members of MtARF gene family, and their associated expression patterns following infection by S. meliloti (Shen et al, 2015). Yet a comprehensive study of the currently available genome and transcriptome data is clearly needed to catalog putative members of the MtARF gene family and understand their significance through a systems-level analysis.…”