StCYP90C1 modulates plant architecture via regulating brassinosteroid biosynthesis in potato

Brassinosteroid (BR) exert a crucial regulatory role in shaping plant architecture. However, the BR biosynthesis and underlying genetic variations governing potato plant architecture remain poorly understood. Here, we identified a single recessive locus, ap, which controls the abnormal architectural plant (AP) with dark-green curled leaves, shortened internodes, and delayed flowering, using a BC₄S₁ population. The functional gene, StCYP90C1, encoding 3-epi-6-deoxocathasterone 23-monooxygenase, was identified at this locus. StCYP90C1 expression was significantly lower in the leaves of APs than in normal architectural plants (NPs), and this reduced expression was identified to be associated with two key variations in the promoter region of APs. CRISPR/Cas9-mediated knockout of StCYP90C1 resulted in typical BR-deficient traits, including dark-green curled leaves, shortened internodes, and dwarfism. Quantification of BR intermediates revealed that the levels of 6-deoxocathasterone (6-dexoCS) and cathasterone (CS) were significantly lower in stcyp90c1-ko mutants compared to the wild type. Transcriptome analysis revealed some candidate genes associated with plant morphogenesis in the knockout mutant. This study elucidates the important role of StCYP90C1 in modulating plant architecture via BR biosynthesis and identifies a deleterious mutation locus that should be excluded from inbred line development in potato breeding.