Molecular atlas of soybean flowers identifies candidate abscission and reproductive pathways associated with flower...

Soybean exhibits great variance of flower abortion, with 20-80% of flowers aborting before pod set, posing a major constraint to yield improvement. Although physiological factors contributing to flower drop are well recognized, the underlying genetic and molecular mechanisms governing abscission and floral retention remain poorly understood. To elucidate the molecular determinants of flower abortion, we performed a comparative transcriptomic analysis of high and low abortion soybean genotypes across four reproductive stages-bud, closed flower, open flower, dry flower, and the leaf as vegetative tissue for reference.

Differential expression and functional enrichment analyses revealed distinct transcriptional landscapes between high and low abortion plants, particularly in genes associated with hormonal signaling, abscission regulation, cell wall remodelling, and reproductive failure. The high abortion plants showed an elevated expression of ethylene responsive and abscission-associated genes, including Inflorescence Deficient in Abscission (IDA), Inflorescence Deficient in Abscission-Like (IDL), Homeobox Protein Knotted-1-Like 6 (KNAT6) and Arabidopsis thaliana Homeobox Gene 1 (ATH1/BEL-1), along with increased activity of pectin-degrading proteins. In contrast, low abortion plants exhibited upregulation of Mitogen-Activated Protein Kinase Phosphatase 1 (MKP1) and KNAT1, consistent with repression of MAPK activity and maintenance of boundary integrity.

Our findings identify distinct transcriptional programs associated with contrasting flower abortion phenotype and highlight coordinated changes in hormone signaling, cell wall remodeling, and boundary specification pathways.