Multi-Stage Transcriptome Analysis Identifies Key Molecular Pathways for Soybean Under Phosphorus-Limited Conditions

Phosphorus deficiency significantly limits soybean production across 74% of China's arable land. This study investigated the molecular mechanisms enabling soybean to access insoluble phosphorus through transcriptome sequencing of the Heinong 48 variety across four developmental stages (Trefoil, Flower, Podding, and Post-podding). RNA-Seq analysis identified 2755 differentially expressed genes (DEGs), with 2506 up-regulated and 249 down-regulated genes. Notably, early developmental stages showed the most substantial transcriptional reprogramming, with 3825 DEGs in the Trefoil stage and 10,660 DEGs in the Flower stage, compared to only 523 and 393 DEGs in the Podding and Post-podding stages, respectively. Functional enrichment analysis revealed 44 significantly enriched GO terms in the Trefoil stage and 137 in the Flower stage, with 13 GO terms shared between both stages. KEGG pathway analysis identified 8 significantly enriched pathways in the Trefoil stage and 21 in the Flower stage, including key pathways related to isoflavonoid biosynthesis, alpha-linolenic acid metabolism, and photosynthesis. Among 87 differentially expressed transcription factors from 31 families, <i>bHLH</i> (8.08%), <i>bZIP</i> (7.18%), and <i>WRKY</i> (5.94%) were most prevalent. These findings provide genetic targets for developing soybean varieties with improved phosphorus acquisition capacity, potentially reducing fertilizer requirements and supporting more sustainable agricultural practices.