The pleiotropic gene LVN3 increases rice grain yield by modulating GA signaling to increase sink strength, source supply, and vascular flow

In rice ( Oryza sativa L.), the vascular bundle tissue in the panicle neck plays a critical role in transporting photosynthetic products, nutrients, and water from the roots and leaves to the panicles, and is positively associated with grain yield. However, the genetic mechanisms regulating vascular bundle number in the panicle neck remain poorly understood. Here, we report the map-based cloning and functional characterization of LVN3 , a quantitative trait locus controlling the number of large vascular bundles in rice ( Oryza sativa L.) panicle neck. LVN3 encodes OsGA20ox1, an enzyme in gibberellin (GA) biosynthesis. It is expressed in developing panicles and vascular bundles, and positively regulates both the number and cross-sectional area of vascular bundles in the panicle neck and the second internode, as well as flag leaf size and grain number per panicle. Compared with the near-isogenic line NIL- LVN3 LT , NIL- LVN3 TQ showed significantly increased vascular bundle number and area, enlarged flag leaves, and improved panicle morphology, ultimately leading to a 6.6% increase in grain yield. RNA-seq analysis revealed that LVN3 affects the expression of auxin-related genes in the shoot apex, suggesting that LVN3 -mediated vascular development is partly driven by crosstalk between GA and auxin signaling. Cultivars carrying the LVN3 -2 haplotype exhibited moderate effective panicle number per plant, grain number, and grain weight, yet achieved the highest grain yield among six haplotypes, identifying LVN3 -2 as a superior haplotype for optimizing grain yield components. Moreover, natural variation at position rs3:36150392 in the LVN3 promoter may represent a functional site associated with vascular bundle development and grain number per panicle in the japonic a ( Geng ) subpopulation. Together, these findings demonstrate that LVN3 regulates source capacity, sink size, and transport efficiency, showing potential for application in rice breeding programs aimed at increasing grain yield.