Academic Editor: Jen-Tsung Chen
Background: The plant hormones auxin affects most aspects of plant growth and development. The auxin transport and signaling are regulated by different factors that modulate plant morphogenesis and respond to external environments. The modulation of gene expression by Auxin Response Factors (ARFs) and inhibiting Auxin/Indole-3-Acetic Acid (Aux/IAA) proteins are involved in auxin signaling pathways. These components are encoded by gene families with numerous members in most flowering plants. Methods: However, there is no genome-wide analysis of the expression profile and the structural and functional properties of the ARF and Aux/IAA gene families in soybean. Using various online tools to acquire of genomic and expression data, and analyzing them to differentiate the selected gene family’s expression, interaction, and responses in plant growth and development. Results: Here, we discovered 63 GmIAAs and 51 GmARFs in a genome-wide search for soybean and analyzed the genomic, sequential and structural properties of GmARFs and GmIAAs. All of the GmARFs found have the signature B3 DNA-binding (B3) and ARF (Aux rep) domains, with only 23 possessing the C-terminal PB1 (Phox and Bem1) domain (Aux/IAA), according to domain analysis. The number of exons in GmARFs and GmIAAs genes varies from two to sixteen, indicating that the gene structure of GmARFs and GmIAAs is highly variable. Based on phylogenetic analysis, the 51 GmARFs and 63 GmIAAs were classified into I–V and I–VII groups. The expression pattern of GmARFs and GmIAAs revealed that the GmARF expression is more specific to a particular part of the plant; for example, ARF 2, 7, and 11 are highly expressed in the root. In contrast, GmIAAs expression has occurred in various parts of the plants. The interaction of ARF with functional genes showed extensive interactions with genes involved in auxin transport which helps to control plant growth and development. Furthermore, we also elaborate on the DNA-protein interaction of ARFs by identifying the residues involved in DNA recognition. Conclusions: This study will improve our understanding of the auxin signaling system and its regulatory role in plant growth and development.