Hypocotyl length is a critical determinant in establishing high quality seedlings for successful cucumber production, but knowledge on the molecular regulation of hypocotyl growth in cucumber is very limited. Here we reported identi cation and characterization of a cucumber elongated hypocotyl 1 (elh1) mutant. We found that the longer hypocotyl in elh1 was due to longitudinal growth of hypocotyl cells. With ne mapping, the elh1 locus was delimited to a 20.9-kb region containing three annotated genes; only one polymorphism was identi ed in this region between two parental lines, which was a non-synonymous SNP (G28153633A) in the third exon of CsHY2 (CsGy1G030000) that encodes a phytochromobilin (PΦB) synthase. Uniqueness of the mutant allele at CsHY2 was veri ed in 515 cucumber lines. Ectopic expression of CsHY2 in Arabidopsis hy2-1 mutant led to reduced hypocotyl length. The PΦB protein was targeted to chloroplasts. The expression levels of CsHY2 and ve phytochrome genes, CsPHYA1, CsPHYA2, CsPHYB, CsPHYC and CsPHYE were all signi cantly down-regulated while several cell elongation related genes were up-regulated in elh1 mutant compared to wild type cucumber, which are correlated with dynamic hypocotyl elongation in the mutant. RNA-seq analysis in the WT and mutant revealed differentially expressed genes involved in porphyrin and chlorophyll metabolisms, cell elongation, and plant hormone signal transduction pathways. This is the rst report to characterize and clone the CsHY2 gene in cucumber. This work reveals the important of CsHY2 in regulating hypocotyl length and extends our understanding of the roles of CsHY2 in cucumber.

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Hypocotyl length is a critical determinant in establishing high quality seedlings for successful cucumber production, but knowledge on the molecular regulation of hypocotyl growth in cucumber is very limited. Here we reported identification and characterization of a cucumber elongated hypocotyl 1 (elh1) mutant. We found that the longer hypocotyl in elh1 was due to longitudinal growth of hypocotyl cells. With fine mapping, the elh1 locus was delimited to a 20.9-kb region containing three annotated genes; only one polymorphism was identified in this region between two parental lines, which was a non-synonymous SNP (G28153633A) in the third exon of CsHY2 (CsGy1G030000) that encodes a phytochromobilin (PΦB) synthase. Uniqueness of the mutant allele at CsHY2 was verified in 515 cucumber lines. Ectopic expression of CsHY2 in Arabidopsis hy2-1 mutant led to reduced hypocotyl length. The PΦB protein was targeted to chloroplasts. The expression levels of CsHY2 and five phytochrome genes, CsPHYA1, CsPHYA2, CsPHYB, CsPHYC and CsPHYE were all significantly down-regulated while several cell elongation related genes were up-regulated in elh1 mutant compared to wild type cucumber, which are correlated with dynamic hypocotyl elongation in the mutant. RNA-seq analysis in the WT and mutant revealed differentially expressed genes involved in porphyrin and chlorophyll metabolisms, cell elongation, and plant hormone signal transduction pathways. This is the first report to characterize and clone the CsHY2 gene in cucumber. This work reveals the important of CsHY2 in regulating hypocotyl length and extends our understanding of the roles of CsHY2 in cucumber.