A single nucleotide deletion in CsSCP4 disrupts brassinosteroid biosynthesis and confers a super compact phenotype in cucumber

Abstract

Dwarf mutants in higher plants serve as ideal models for studying the mechanisms underlying stem elongation and plant development. Moreover, the compact stature of dwarf plants renders them advantageous for high-density planting and mechanized harvesting. In this study, we identified a naturally occurring super-compact cucumber mutant, designated scp159. Due to reduced cell elongation, scp159 exhibits an extremely compact plant morphology. Using bulk segregant analysis coupled with whole-genome sequencing and fine genetic mapping, we narrowed down the scp-4 locus to a 67.6 kb region on chromosome 6. Through resequencing and molecular cloning, CsSCP4 was identified as a candidate gene underlying the scp-4 locus, which encodes 3-epi-6-deoxocathasterone 23-monooxygenase CYP90C1, a key enzyme involved in brassinosteroid (BR) biosynthesis. Compared to the wild-type YZ205A, the scp159 mutant harbors a single-base deletion (adenine) within the fourth exon region of the CsSCP4. Measurements of endogenous hormone levels confirmed a significant reduction in BR levels in scp159 mutants. Exogenous application of brassinolide at a concentration of 0.2 mg/L effectively alleviated the super-compact phenotype. Silencing of the CsSCP4 gene in cucumber plants resulted in reduced plant height. Comparative transcriptomic analysis further revealed significant downregulation of positive regulators of the BR signaling pathway, such as BAK1 and BSK, and marked upregulation of the negative regulator BKI1 in the scp159 mutant. Furthermore, differential expression was observed in genes associated with auxin and gibberellin biosynthesis and signaling pathways. Collectively, our findings demonstrate that the CsSCP4 gene plays a crucial role in BR biosynthesis, thus significantly influencing cucumber plant growth and development.