Genome-wide identification and expression profiling of 4-coumarate:coenzyme A ligase genes influencing soybean isoflavones at the seedling stage

Context The 4-coumarate:coenzyme A ligase (4CL) genes are involved in the phenylalanine pathway of the plant flavonoid biosynthesis pathway, controlling the synthesis of flavonoid secondary metabolites. Isoflavone is an important quality component of soybean (Glycine max). Aims The purpose of this study was to investigate the effects of different 4CL gene family members on isoflavone synthesis in soybean seedlings, and to identify those with a positive effect on soybean isoflavone content. Methods Genome identification and bioinformatics analyses of Gm4CL gene family members were conducted based on soybean genome annotation and Bio-Analytic Resource online data. Quantitative real-time PCR was used to detect the expression of Gm4CL genes, and genes related to the isoflavone synthesis pathway. Ultra-high-performance liquid chromatography was used to detect the contents of various isoflavones. Key results The study revealed 20 members of the Gm4CL gene family distributed on 13 chromosomes, with expression mainly distributed in cytoplasmic peroxisomes, and showing homology to the 4CL genes of peanut (Arachis hypogaea) and Arabidopsis. Gene structure analysis showed that Gm4CL genes had between two and seven exons. Gm4CL promoter sequences were shown to contain abundant cis-acting elements, with Gm4CL4 and Glyma.11G1945001 containing MBSI cis-acting elements. Notably, the expression of Gm4CL genes varied with the synthesis of isoflavones at seedling stage. Conclusions At seedling stage, Gm4CL4 activated enzymes related to the isoflavone synthesis pathway, catalysing isoflavone synthesis, whereas Glyma.17G06440.1 and Glyma.17G0645001 tended to serve the lignin synthesis pathway and inhibit isoflavone synthesis. These results suggest that isoflavone synthesis in seedling leaves may be regulated by other mechanisms. Implications The study provides a basis for further research into the synthesis and accumulation mechanism of isoflavones.