Comprehensive in silico characterization of soybean (Glycine max L.) isoflavone reductase genes and their expressions in response to spermidine and ultrasonication

Abstract

Soybean (Glycine max L.) is a globally important industrial legume crop that provides several important dietary components but faces growth challenges under various stresses, that cause production and economic losses. Isoflavone reductase (IFR) is a key gene involved in isoflavonoid biosynthesis and response to plant growth and stresses. However, IFR genes remain unexplored in the soybean genome. In this study, 37 IFR genes were identified and comprehensively characterized for the first time in the soybean genome. All GmIFR proteins contained NmrA conserved domains with diverse physicochemical properties including 1 to 9 motifs, and 1 to 10 exons. Chromosomal distribution revealed 11 GmIFR genes located on chromosomes 1 and 11. Cis-element analysis unveiled GmIFR genes role in phytohormones and stress responses. Synteny analysis identified 13 segmental and 2 tandem GmIFR duplicates under purifying selection. Additionally, 118 gma-miRNAs from 76 families were identified to be targeting all 37 GmIFR genes. Potential transcription factors including ERF, MYB, Dof, BBR-BPC, and bHLHs were predicted and visualized in a network interacting with GmIFR genes. The annotation results exhibit that GmIFR genes were highly related to the biosynthesis of metabolites, phenylpropanoid pathway, and response to stresses. FPKM expression data highlighted the significant upregulation of GmIFR genes in soybean tissues under different stress conditions. qRT-PCR results exhibited that most GmIFR genes, mainly GmIFR9/17 and GmIFR36 were highly upregulated in soybean cotyledon followed by hypocotyl and root tissues under spermidine and ultrasonication treatments than control, suggesting their key role in growth and developmental processes in soybean. These findings laid the foundation for further functional studies of GmIFR genes to elucidate their contributions to soybean improvement under adverse conditions.