Flow-centered molecular design of vascular system breaks the trade-off between yield and appearance quality in rice

Achieving both high yield and superior grain quality remains a major challenge in rice breeding due to the long-standing trade-off between these traits. Enhancing vascular transport efficiency may provide a strategy to overcome this constraint, yet the genetic basis linking peduncle vascular architecture with yield-quality coordination remains poorly understood.

This study aimed to develop a flow-centered molecular design framework targeting vascular transport capacity to reconcile yield and quality in Oryza sativa.

Using 248 accessions from the 3 K Rice Genomes panel, 14 traits related to peduncle vascular bundles, yield, and quality were phenotyped, and 31 cloned genes were haplotyped. Haplotype validity was confirmed by functional verification using near-isogenic or transgenic lines. Trait correlations, genetic effects, and pyramiding interactions of key genes were assessed. Superior haplotypes were converted into KASP markers and tested across 221 released cultivars. A breeding strategy was proposed and validated using introgression lines.

The peduncle vascular bundles play a crucial role in simultaneously enhancing single-panicle weight and grain appearance quality in japonica/geng rice. Five key genes (GL3.1, GW5, FLO2, LVPA4, and RST1) were identified as synergistic regulators enhancing vascular development, panicle weight, and grain quality without compromising yield. A pyramiding-effect network of genes to guide the simultaneous improvement of yield and quality were constructed. Based on the uneven distribution of superior alleles among modern cultivars, a flow-centered molecular design breeding strategy was subsequently proposed and validated through the development of introgression lines, confirming that optimizing vascular systems can simultaneously improve yield and quality.

This study establishes a flow-centered genetic and conceptual framework linking vascular bundle architecture to yield-quality coordination and provides practical molecular tools for next-generation high-yield, high-quality rice breeding, while also offering a strategic reference for similar improvements in other crops such as wheat and maize.