Genome-Wide Identification and Expression Analysis of the Aux/IAA and Auxin Response Factor Gene Family in Medicago truncatula

Abstract

Aux/IAA and auxin response transcription factor (ARF) genes are key regulators of auxin responses in plants. A total of 25 MtIAA and 40 MtARF genes were identified based on the latest updated Medicago truncatula reference genome sequence. They were clustered into 10 and 8 major groups, respectively. The homologs among M. truncatula, soybean, and Arabidopsis thaliana shared close relationships based on phylogenetic analysis. Gene structure analysis revealed that MtIAA and MtARF genes contained one to four concern motifs and they are localized to eight chromosomes, except chromosome 6 without MtARFs. In addition, some MtIAA and MtARF genes were expressed in all tissues, while others were specifically expressed in specific tissues. Analysis of cis-acting elements in promoter region and expression profiles revealed the potential response of MtIAA and MtARF genes to hormones and abiotic stresses. The prediction protein–protein interaction network showed that some ARF proteins could interact with multiple Aux/IAA proteins, and the reverse is also true. The investigation provides valuable, basic information for further studies on the biological functions of MtIAA and MtARF genes in the regulation of auxin-related pathways in M. truncatula.

Genome-Wide Identification and Expression Analysis of the Aux/IAA Gene Family of the Drumstick Tree (Moringa oleifera Lam.) Reveals Regulatory Effects on Shoot Regeneration

“…Several studies have indicated that promoters influence the temporal and spatial expression of genes, and cis-elements within promoters are key to regulating gene function through interplay with trans-acting factors [ 33 ]. Multiple Aux/IAA genes with promoter elements associated with abiotic stress and hormones have been found to participate in these abiotic stress responses [ 34 ]. For example, OsIAA20 and most of the MtIAA genes exhibited wide-ranging responses to salt stress, and more than half of the FveIAA genes responded to IAA treatment [ 35 ].…”

“…Generally, the interaction between MoIAAs and MoARFs was complex; some MoIAA proteins may interact with several MoARFs and vice versa, representing functional redundancy within the Aux/IAA proteins [ 38 ]. For example, MtIAA12 and MtIAA21 interacted with MtARF29, which also interacts with most of the MtARFs [ 34 ]. Notably, MoIAA3 and MoIAA13 proteins were at the center of the network, suggesting that they interact strongly with other proteins, while MoARF2.1 and MoARF17 exhibit the least interaction with others.…”

Identification of potential Auxin Response Candidate genes for soybean rapid canopy coverage through comparative evolution and expression analysis

“…To our knowledge, phylogenetic analysis of these TIR1/AFB auxin receptors found in the G. max genome have not yet been explored. We identified 61 Aux/IAA genes in G. max , which largely followed the clade structure of previous analyses (Remington et al ., 2004; Liu et al ., 2021; Ali et al ., 2022). Similarly, we identified 55 ARFs in the G. max genome which fell into orthology groups largely as expected based on previous analyses (Le et al ., 2016).…”

“…AtARF8 and AtARF6 also play an essential role in cambium establishment and maintenance (Ben-Targem et al, 2021). In M. truncatula , the ARF8 ortholog exhibits slightly elevated expression in the petiole and stem, but not the leaf (Liu et al, 2021). Similarly, our analysis found a slight association of GmARF8_C.1 with hypocotyl, leaf and cotyledon tissues.…”

“…GmARF9, here GmARF9_C.1 variant, is associated with promoting first pod height (Jiang et al ., 2018). In M. truncatula , MtARF9 has elevated expression levels in the leaves, shoots, and petioles among other tissues in the roots and seeds (Liu et al, 2021). There is otherwise a notable lack of literature that draws any meaningful connection between ARF9 and shoot architecture.…”