Identification and cloning of SVN7 controlling small vascular bundle number in the rice flag leaf

Leaf vascular bundles play a crucial role in the transport of photosynthates, and their number, size, and capacity directly affect transport efficiency. Here, we performed a genome-wide association study (GWAS) of small vascular bundle number (SVN) in the flag leaf using 307 rice cultivars and identified SVN7, an allele of OsBZR1. A SVN7 knockout mutant was generated using CRISPR/Cas9. The flag-leaf SVN of svn7 mutants was significantly higher than that of the wild-type Zhonghua 11 (ZH11), indicating that SVN7 negatively regulates small vascular bundle number. Compared with ZH11, svn7 mutants also showed significantly increased numbers of large and small vascular bundles in the panicle neck, increased flag-leaf width, and increased grain number per panicle, whereas plant height and grain weight were significantly reduced. These results indicate that SVN7 has pleiotropic effects and coordinately regulates source-, sink-, and flow-related traits. Among the 307 accessions, the superior haplotype Hap1 was associated with higher flag-leaf SVN, wider flag leaves, more grains per panicle, and higher yield per plant. This haplotype may be useful for molecular design breeding to develop new high-yield rice varieties.