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Acta Agronomica Sinica ›› 2026, Vol. 52 ›› Issue (5): 1364-1372.doi: 10.3724/SP.J.1006.2026.52045

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

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

Yan An1,2(), Jiang Kun-Wei1,4(), Wang Rong-Yuan1, Tian Lin1, Zhang Lu1,2, Wang Yun1,*(), Xu Jian-Long2,3,*()   

  1. 1 Agronomy College of Shenyang Agricultural University, Shenyang 110866, Liaoning, China
    2 State Key Laboratory of Crop Gene Resources and Breeding / Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
    3 Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture / Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, Guangdong, China
    4 Tieling Academy of Agricultural Sciences, Tieling 112616, Liaoning, China
  • Received:2025-12-31 Accepted:2026-02-27 Online:2026-05-12 Published:2026-03-05
  • Contact: *Wang Yun, E-mail: wangyun1981@syau.edu.cn; Xu Jian-Long, E-mail: xujianlong@caas.cn
  • About author:First author contact:**Contributed equally to this work
  • Supported by:
    National Key Research and Development Program of China(2023YFF1000400);Basic Research Project of the Department of Education of Liaoning Province(LJ212410157119);National Natural Science Foundation of China(32072035)

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Abstract:

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.

Key words: rice, small vascular bundle in flag leaf, genome-wide association analysis, SVN7 gene, yield

Fig. 1

Identification of a candidate gene for small vascular bundle number (SVN) in the rice flag leaf on chromosome 7 by GWAS A: box plot of SVN in flag leaf; B: correlation analysis of SVN in flag leaf and leaf shape related traits; C: manhattan plot of GWAS for the SVN in flag leaf of 307 accessions; D: local Manhattan plot (upper) and linkage disequilibrium (LD) heatmap (lower) surrounding the peak on chromosome 7, the blue dotted line interval indicates the interval of qSVN7; E: structure of LOC_Os07g39220 gene; F: violin plot for SVN based on the haplotypes (Hap) for LOC_Os07g39220. SVN: small vascular bundle number; FLL: flag leaf length; FLW: flag leaf width; FLA: flag leaf area; xian: indica; geng: japonica. Asterisks indicate significant differences by Student’s t-test (***: P < 0.001; **: P < 0.01). Different letters in box plots indicate significant differences by Duncan’s multiple range test (P < 0.05)."

Fig. 2

Vascular bundle number-related traits in CRISPR/Cas9-mediated svn7 mutants A: target sites and mutation sequences of SVN7 gene; B: plant morphology of Zhonghua 11 (ZH11) and svn7 mutants (scale bar = 10 cm); C: cross-sections of flag leaf in ZH11 and svn7 mutants (scale bar = 200 μm); D: vascular bundle number in flag leaf of ZH11 and svn7 mutant; E: cross-sections of panicle neck in ZH11 and svn7 mutants (scale bar = 50 μm); F: vascular bundle number in panicle neck of ZH11 and svn7 mutants. SVN: small vascular bundle number; LVN: large vascular bundle number; ZH11: Zhonghua 11. Asterisks indicate significant differences by Student’s t-test (***: P < 0.001); ns, no significant difference."

Fig. 3

Yield and yield-related phenotypes of Zhonghua 11 and svn7 mutants A: leaf shape of Zhonghua 11 (ZH11) and svn7 mutants (scale bar = 5 cm); B: phenotypes of flag leaf-related traits of ZH11 and svn7 mutants; C: panicle shape of ZH11 and svn7 mutants (scale bar = 1 cm); D: phenotypes of yield and yield-related traits of ZH11 and svn7 mutants. Asterisks indicate significant differences by Student’s t-test (***: P < 0.001, **: P < 0.01, *: P < 0.05); ns, no significant difference."

Fig. 4

Haplotype analysis of SVN7 A: haplotype of SVN7; B: yield and yield-related traits are compared among accessions (more than 20 accessions) carrying Hap1, Hap2 and Hap3. Different letters in violin plots indicate significant differences by Duncan’s multiple range test (P < 0.05)."

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