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 <italic>SVN7</italic>, an allele of <italic>OsBZR1</italic>. A <italic>SVN7</italic> knockout mutant was generated using CRISPR/Cas9. The flag-leaf SVN of <italic>svn7</italic> mutants was significantly higher than that of the wild-type Zhonghua 11 (ZH11), indicating that <italic>SVN7</italic> negatively regulates small vascular bundle number. Compared with ZH11, <italic>svn7</italic> 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 <italic>SVN7</italic> 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.