CRISPR/Cas9-engineered mutation to identify the roles of phytochromes in regulating photomorphogenesis and flowering time in soybean

Soybean ( Glycine max ) responds to ambient light variation by undergoing multiform morphological alterations, influencing its yield potential and stability in the field. Phytochromes (PHYs) are plant-specific red (R) and far-red (FR) light photoreceptors mediating photomorphogenesis and photoperiodic flowering. As an ancient tetraploid, soybean harbors four PHYA , two PHYB , and two PHYE paralogs. Except for GmPHYA2/E4 and GmPHYA3/E3, which have been identified as photoperiod-dependent flowering repressors, the functions of GmPHYs are still largely unclear. We generated a series of individual or combined mutations targeting the GmPHYA or GmPHYB genes using CRISPR/Cas9 technology. Phenotypic analysis revealed that GmPHYB1 mediates predominantly R-light induced photomorphogenesis, whereas GmPHYA2/E4 and GmPHYA3/E3, followed by GmPHYA1 and GmPHYB2, function redundantly and additively in mediating FR light responses in seedling stage. GmPHYA2/E4 and GmPHYA3/E3, with weak influence from GmPHYA1 and GmPHYA4, delay flowering time under natural long-day conditions. This study has demonstrated the diversified functions of GmPHYAs and GmPHYBs in regulating light response, and provides a core set of phytochrome mutant alleles for characterization of their functional mechanisms in regulating agronomic traits of soybean.