Laiyuan Zhai, Zhiyuan Zhang, Kuitian Shao, Yijun Tang , Shumila Ishfaq ,Yun Wang,Kai Chen, Jianlong Xu

Journal of Advanced Research; 2026; IF: 13

DOI: 10.1016/j.jare.2026.05.019

Abstract

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 yieldquality 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 3K 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.