Two Paralogous Seed Protein Trait-Associated Genes Influence Light and Phytohormone Signaling, Maturity, and Seed Storage in Soybean

The soybean gene Glyma.20G085100 (Gm20P), contributing to the cqSeed protein-003 QTL, and its paralog Glyma.10G134400 (Gm10P), were edited using the CRISPR/Cas9-based genome editing reagents. Two mutants, a gm20p single mutant and a gm10p gm20p double mutant devoid of editing reagents, were identified. Additional gm10p and gm20p single mutants were isolated from F2 population of the cross between the gm10p gm20p double mutant and the wild-type Thorne. The above mutants were characterized in different growing conditions. Seed protein content of the gm10p single and the gm10p gm20p double mutant were significantly reduced relative to the gm20p single mutant and Thorne, with a concomitant increase in oil and starch content. A delayed maturity phenotype was observed in the gm20p single, the gm10p single, and gm10p gm20p double mutants under field conditions across multiple environments. Under controlled conditions in a growth chamber, prominent delayed maturity was only observed under short-day conditions, while long-day conditions induced phenotypic changes in growth in the gm10p gm20p double mutant, but slight delay in maturity. Transcriptomic analysis revealed that the gm10p gm20p double mutant exhibited repression of genes involved in light signaling, enhanced expression of JAZs in JA signaling, suppression of ABA-responsive and senescence-related genes, and elevation of genes that inhibit IAA signaling. Furthermore, the gm10p gm20p double mutant displayed higher sensitivity to salt and ABA during germination. Collectively, these results suggest that both Gm10P and Gm20P modulate light signaling and impact soybean development, maturity and seed reserve content.