Shading in combination with extended photoperiods can cause exaggerated stem elongation (ESE) in soybean, leading to lodging and reduced yields when planted at high-density in high-latitude regions. However, the genetic basis of plant height in adaptation to these regions remains unclear. Here, through a genome-wide association study, we identify a plant height regulating gene on chromosome 13 (PH13) encoding a WD40 protein with three main haplotypes in natural populations. We find that an insertion of a Ty1/Copia-like retrotransposon in the haplotype 3 leads to a truncated PH13^H3 with reduced interaction with GmCOP1s, resulting in accumulation of STF1/2, and reduced plant height. In addition, PH13^H3 allele has been strongly selected for genetic improvement at high latitudes. Deletion of both PH13 and its paralogue PHP can prevent shade-induced ESE and allow high-density planting. This study provides insights into the mechanism of shade-resistance and offers potential solutions for breeding high-yielding soybean cultivar for high-latitude regions.

Major cereal crops have benefitted from Green Revolution traits such as shorter and more compact plants that permit high-density planting, but soybean has remained relatively overlooked. To balance ideal soybean yield with plant height under dense planting, shortening of internodes without reducing the number of nodes and pods is desired. Here, we characterized a short-internode soybean mutant, reduced internode 1 (rin1). Partial loss of SUPPRESSOR OF PHYA 105 3a (SPA3a) underlies rin1. RIN1 physically interacts with two homologs of ELONGATED HYPOCOTYL 5 (HY5), STF1 and STF2, to promote their degradation. RIN1 regulates gibberellin metabolism to control internode development through a STF1/STF2–GA2ox7 regulatory module. In field trials, rin1 significantly enhances grain yield under high-density planting conditions comparing to its wild type of elite cultivar. rin1 mutants therefore could serve as valuable resources for improving grain yield under high-density cultivation and in soybean–maize intercropping systems.

Soybean is a photoperiod-sensitive staple crop. Its photoperiodic flowering has major consequences for latitudinal adaptation and grain yield. Here, we identify and characterise a flowering locus named Time of flower 4b (Tof4b), which encodes E1-Like b (E1Lb), a homologue of the key soybean floral repressor E1. Tof4b protein physically associates with the promoters of two FLOWERING LOCUS T (FT) genes to repress their transcription and delay flowering to impart soybean adaptation to high latitudes. Three E1 homologues undergo subfunctionalisation and show differential subcellular localisation. Moreover, they all possess self-repression capability and each suppresses the two homologous counterparts. Subfunctionalisation and the transcriptional regulation of E1 genes collectively finetune flowering time and high-latitude adaptation in soybean. We propose a model for the functional fate of the three E1 genes after the soybean whole-genome duplication events, refine the molecular mechanisms underlying high-latitude adaption, and provide a potential molecular-breeding resource.

The development of soybean (Glycine max) is regulated by the photoperiod, with genes related to photoperiod sensitivity primarily focused on the flowering time. However, their roles in post-flowering reproductive development and the mechanisms by which the photoperiod affects them are not yet determined. In this study, we found that pod formation is sensitive to the photoperiod. Long-day conditions tended to extend the time from flowering to pod formation, and the first wave of flowers tended to fall off. Additionally, the photoperiod affected the pistil morphology; under short-day conditions, the stigma had a curved hook-like structure that facilitated better interaction with the filaments when pollen was released, ultimately influencing the timing of pod formation. Photoperiod-insensitive mutants, lacking E1 family and Evening Complex (EC) genes, showed no difference in the pod formation time under long-day or short-day conditions. Hormone content analysis and transcriptome data analysis indicated that various hormones, reactive oxygen species (ROS) burst pathway signals, and the application of sucrose solution in vitro might influence floral organ abscission.

The development of soybean ( Glycine max ) is regulated by photoperiod, with genes related to photoperiod sensitivity primarily focused on flowering time. However, their roles in post-flowering reproductive development and the mechanisms by which photoperiod affects them are not yet determined. In this study, we found that pod formation is sensitive to photoperiod. Long-day (LD) conditions tend to extend the time from flowering to pod formation (R1 to R3 stage), and the first wave of flowers tends to fall off. Additionally, photoperiod affects pistil morphology; under short-day (SD) conditions, the stigma has a curved hook-like structure that facilitates better interaction with the filaments when pollen is released, ultimately influencing the timing of pod formation. Photoperiod-insensitive mutants, lacking E1 family and Evening Complex genes, showed no difference in pod formation time under LD or SD conditions. Hormone content analysis and transcriptome data analysis indicated that various hormones, ROS signals, and the application of sucrose solution in vitro might influence floral organ abscission. Highlight: Photoperiod sensitivity after flowering affects the pod-setting time in soybean.