Transcriptome‐Wide Association Uncovers LncRNAs Controlling Seed Weight in Soybean

Abstract Long non‐coding RNAs (lncRNAs) are emerging as key regulators of various biological processes in plants, yet their role in seed weight regulation remains underexplored. To systematically investigate lncRNAs associated with seed weight variation, transcriptome‐wide association studies (TWAS) are performed across a diversity panel of 238 soybean accessions. The analysis identifies 175 and 50 TWAS‐significant lncRNAs at 14 and 21 days after flowering, respectively. Functional validation reveals that two candidate lncRNAs positively regulate seed weight through transcriptional modulation of key genes in seed development pathways. Additionally, an lncRNA‐lncRNA co‐expression module is identified as significantly correlated with seed weight. The eQTL analysis reveals dynamic and static eQTLs that coordinately modulate lncRNA expression across seed developmental stages. Notably, integration of major‐effect proximal and minor‐effect distal eQTLs enhances phenotype prediction of seed weight, underscoring the significant impact of distal eQTLs on phenotypic variation. These findings elucidate the intricate mechanisms by which lncRNAs contribute to seed weight regulation, offering novel insights for enhancing crop yield.