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Key Message <p>This study demonstrates that CRISPR-mediated cis-regulatory element editing (CRE editing) of the <i>SD1</i> promoter effectively reduces plant height in Kam sweet rice, without compromising yield or grain quality, offering a precise strategy for crop improvement.</p> Abstract <p>Kam sweet rice, a unique aromatic variety, faces challenges with excessive plant height and suboptimal yield. This study explores a precision breeding approach by strengthening an endogenous TCP19–<i>SD1</i> repression module through CRISPR-Cas9-mediated CRE editing to modulate the expression of the <i>SD1</i> gene, a key regulator of gibberellin biosynthesis and stem elongation. By introducing an adenine insertion in the GGCCCCCC cis-regulatory element in the <i>SD1</i> promoter, we enhanced the binding affinity of the transcription factor TCP19, resulting in down-regulated <i>SD1</i> expression. This led to a reduction in gibberellin levels, shortening internodes, and reducing plant height. Phenotypic evaluations revealed that the edited lines exhibited significantly shorter plant height while maintaining grain yield and nitrogen utilization efficiency compared to wild-type plants. Microscopic analysis of the internodes confirmed that the reduced plant height correlated with decreased cell length. Transcriptomic studies indicated that CRE editing modulated a network of genes involved in both gibberellin and auxin signaling pathways, critical for plant growth. Importantly, the genetic modification did not adversely affect grain quality. This study demonstrates the potential of strengthening endogenous transcriptional repression via CRE editing as a precise alternative to conventional gene knockout techniques, offering a powerful strategy for optimizing complex agronomic traits in rice, with applications in modern crop breeding strategies.</p>

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Cis-regulatory editing of SD1 promoter enhances TCP19-mediated repression to optimize plant height in Kam sweet rice

  • 期刊论文

  • 发表日期：

    2026年5月20日

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  • Bowen Wu,
  • Hangfei Luo,
  • Hui Xie,
  • Chufeng Zhao,
  • Pengfei Xie,
  • Xiaochuan Yang,
  • Jian Shi,
  • Weiting Huang,
  • Zhongming Fang

摘要

Key Message

This study demonstrates that CRISPR-mediated cis-regulatory element editing (CRE editing) of the SD1 promoter effectively reduces plant height in Kam sweet rice, without compromising yield or grain quality, offering a precise strategy for crop improvement.

Abstract

Kam sweet rice, a unique aromatic variety, faces challenges with excessive plant height and suboptimal yield. This study explores a precision breeding approach by strengthening an endogenous TCP19–SD1 repression module through CRISPR-Cas9-mediated CRE editing to modulate the expression of the SD1 gene, a key regulator of gibberellin biosynthesis and stem elongation. By introducing an adenine insertion in the GGCCCCCC cis-regulatory element in the SD1 promoter, we enhanced the binding affinity of the transcription factor TCP19, resulting in down-regulated SD1 expression. This led to a reduction in gibberellin levels, shortening internodes, and reducing plant height. Phenotypic evaluations revealed that the edited lines exhibited significantly shorter plant height while maintaining grain yield and nitrogen utilization efficiency compared to wild-type plants. Microscopic analysis of the internodes confirmed that the reduced plant height correlated with decreased cell length. Transcriptomic studies indicated that CRE editing modulated a network of genes involved in both gibberellin and auxin signaling pathways, critical for plant growth. Importantly, the genetic modification did not adversely affect grain quality. This study demonstrates the potential of strengthening endogenous transcriptional repression via CRE editing as a precise alternative to conventional gene knockout techniques, offering a powerful strategy for optimizing complex agronomic traits in rice, with applications in modern crop breeding strategies.