A nanopore-based cucumber genome assembly reveals structural variations at two QTLs controlling hypocotyl elongation.

This article focuses on the assembly of a high-quality genome of the semiwild Xishuangbanna (XIS) cucumber variety XIS49 using Oxford Nanopore long-read sequencing, enabling the identification of structural variations (SVs) compared to the cultivated Chinese Long (CL) cucumber. Two quantitative trait loci (QTLs), SH3.1 and SH6.1, controlling hypocotyl elongation under low light were fine-mapped; SH3.1 corresponds to the red-light receptor gene Phytochrome B (PhyB) with promoter deletions in XIS49 affecting its expression, while SH6.1 encodes a CCCH-type zinc finger protein named FRIGIDA-ESSENTIAL LIKE (FEL), whose function is disrupted in CL cucumber by a retrotransposon insertion. FEL negatively regulates hypocotyl elongation by binding to the promoter of CONSTITUTIVE PHOTOMORPHOGENIC 1a (COP1a), a central repressor of photomorphogenesis, thus elucidating a genetic mechanism underlying cucumber hypocotyl growth responses to low light. The study provides insights into cucumber domestication and adaptation through genome structural variation and gene regulation.