Engineering the NAT-ULT module increases seed number per pod in soybean

In a breakthrough study, researchers have identified and validated a soybean NAT-ULT regulatory module that significantly increases ovule and seed number per pod. By subjecting a Glycine max cv. Williams 82 population to fast-neutron irradiation, scientists pinpointed MO27, a variant that boosted four-seeded pod frequency from 2-4% in wild-type plants to a remarkable 27-30%. Remarkably, this genetic tweak did not alter plant architecture, total pod count, or seed morphology.

Further investigation revealed that MO27 originates from a 46.7-kb chromosome 2 deletion containing the genes GmNAT1 and chromosome 6 deletions encompassing GmULT-B1 and GmULT-B3. Ovule-clearing analysis demonstrated that the enhanced seed number occurs prior to fertilization through the formation of four-ovule ovaries.

Utilizing CRISPR/Cas9 gene-editing technology, researchers were able to replicate the MO27 effect by mutating GmNAT1, GmULT-B1, and GmULT-B3, which consistently increased four-seeded pod frequency without any negative impact on seed weight, total pod number, or plant height. Notably, similar genetic modifications in tomato plants with SlULT triple mutations also showed increased floral organ and locule numbers, suggesting a conserved ULT-like function in reproductive organ patterning across species.

Genomic and transcriptomic analyses provided evidence of a chromosome 6-dominant transcriptional state, accompanied by selective non-additive reprogramming of hormone/ovule-number and cell-wall-remodeling modules. The researchers propose a hierarchical model in which NAT-ULT perturbation enhances meristematic competence and reprograms reproductive developmental programs, while additional background-induced changes from the fast-neutron irradiation may further modulate the phenotype.

Ultimately, these findings establish the NAT-ULT module as a promising molecular target for engineering soybean seed number per pod, potentially leading to increased crop yields.