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

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. 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.