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Keymessage <p>A novel <i>semi-dwarf</i> cucumber mutant (<i>sd</i>), identified from an EMS mutagenesis screen, was characterized as being caused by a single-nucleotide mutation in <i>CsBRP1</i>—a gene encoding a PHD-type domain-containing protein—a function in regulating plant architecture that was further verified by VIGS.</p> Abstract <p>Plant height is a key agronomic trait influencing biomass and yield in crops. Semi-dwarf varieties can improve planting density and light use efficiency, thereby increasing yield. In this study, we identified a <i>semi-dwarf</i> mutant (<i>sd</i>) from an EMS-mutagenized cucumber population, which displayed compact growth, smaller dark green leaves, and normal fertility. Genetic analysis revealed the trait is controlled by a single recessive nuclear gene. Microscopic observation showed the dwarfism was mainly due to shortened internode cell length. Using BSA-seq and fine mapping in an F₂ population from a cross between <i>sd</i> and the wild type (CCMC), the candidate region was initially located within a 4.27&#xa0;Mb interval on chromosome 3 and further narrowed to 183.7&#xa0;kb between markers SNP6-1 and SNP6-3. Sequencing identified <i>CsBRP1</i> as the causal gene, encoding a PHD-type domain-containing protein. A G → A point mutation in the first exon introduced a premature stop codon, resulting in a truncated protein lacking the PHD domain. qRT-PCR showed <i>CsBRP1</i> was expressed in multiple tissues, with significantly lower expression in <i>sd</i>. Virus-induced gene silencing (VIGS) of <i>CsBRP1</i> recapitulated the semi-dwarf phenotype, confirming its role in regulating plant architecture. RNA-seq analysis indicated that the <i>sd</i> mutant had upregulated ribosome and histone modification-related genes and downregulated hormone signaling genes, especially auxin-related genes. These results suggest <i>CsBRP1</i> regulates semi-dwarfism through hormonal and epigenetic pathways. This study reveals the role of <i>CsBRP1</i> in cucumber plant architecture and provides a basis for further dissection of crop development mechanisms.</p>

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A mutation in CsBRP1, encoding a PHD-type domain-containing protein, causes semi-dwarfism in cucumber (Cucumis sativus L.)

  • 期刊论文

  • 发表日期：

    2026年3月17日

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  • Xiaoxu Han,
  • Juan Yin,
  • Xueying Jiao,
  • Ruolin Hu,
  • Yingjie Zhang,
  • Fahang Chen,
  • Biao Dong,
  • Chunyan Cheng,
  • Yuhui Wang,
  • Chunhua Wang,
  • Ji Li,
  • Tao Wu,
  • Jinfeng Chen,
  • Qunfeng Lou

摘要

Keymessage

A novel semi-dwarf cucumber mutant (sd), identified from an EMS mutagenesis screen, was characterized as being caused by a single-nucleotide mutation in CsBRP1—a gene encoding a PHD-type domain-containing protein—a function in regulating plant architecture that was further verified by VIGS.

Abstract

Plant height is a key agronomic trait influencing biomass and yield in crops. Semi-dwarf varieties can improve planting density and light use efficiency, thereby increasing yield. In this study, we identified a semi-dwarf mutant (sd) from an EMS-mutagenized cucumber population, which displayed compact growth, smaller dark green leaves, and normal fertility. Genetic analysis revealed the trait is controlled by a single recessive nuclear gene. Microscopic observation showed the dwarfism was mainly due to shortened internode cell length. Using BSA-seq and fine mapping in an F₂ population from a cross between sd and the wild type (CCMC), the candidate region was initially located within a 4.27 Mb interval on chromosome 3 and further narrowed to 183.7 kb between markers SNP6-1 and SNP6-3. Sequencing identified CsBRP1 as the causal gene, encoding a PHD-type domain-containing protein. A G → A point mutation in the first exon introduced a premature stop codon, resulting in a truncated protein lacking the PHD domain. qRT-PCR showed CsBRP1 was expressed in multiple tissues, with significantly lower expression in sd. Virus-induced gene silencing (VIGS) of CsBRP1 recapitulated the semi-dwarf phenotype, confirming its role in regulating plant architecture. RNA-seq analysis indicated that the sd mutant had upregulated ribosome and histone modification-related genes and downregulated hormone signaling genes, especially auxin-related genes. These results suggest CsBRP1 regulates semi-dwarfism through hormonal and epigenetic pathways. This study reveals the role of CsBRP1 in cucumber plant architecture and provides a basis for further dissection of crop development mechanisms.