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SHORT HYPOCOTYL 1 encodes a SMARCA3-like chromatin remodeling factor regulating elongation

Kailiang Bo, Hui Wang, Yupeng Pan, Tusar K. Behera, Sudhakar Pandey, Changlong Wen, Yuhui Wang, Philipp W. Simon, Yuhong Li, Jinfeng Chen, Yiqun Weng
Plant physiology 2016 v.172 no.2 pp. 1273-1292
Cucumis sativus, alleles, chromatin, cucumbers, domestication, gene frequency, hypocotyls, loci, seedling growth, signal transduction, transcription factors, ultraviolet radiation
Understanding the mechanisms and control of hypocotyl elongation is important for greenhouse vegetable crop production. In this study, we identified SHORT HYPOCOTYL1 (SH1) in cucumber which regulates low-dosage ultraviolet B (LDUVB)-dependent hypocotyl elongation by recruiting the cucumber UVR8 signaling pathway. We showed that hypocotyl elongation in cucumbers carrying the recessive sh1 allele was LDUVB-insensitive. We found that Sh1 encoded a human SMARCA3-like chromatin remodeling transcription factor. The allele frequency and distribution pattern at this locus among natural populations supported the wild cucumber origin of sh1 for local adaptation, which was under selection during domestication. The cultivated cucumber carries predominantly the Sh1 allele; the sh1 allele is nearly fixed in the semi-wild Xishuangbanna cucumber, and the wild cucumber population is largely at HW equilibrium for the alleles. The SH1 protein sequence was highly conserved among eukaryotic organisms, but its function in regulating hypocotyl elongation was unique to cucumber. While Sh1 expression was inhibited by LDUVB, its transcript abundance was highly correlated with hypocotyl elongation rate and the expression level of cell elongation-related genes. We provided evidence to support our hypothesis that the SH1 protein regulates LDUVB-dependent hypocotyl elongation in cucumber by modulating the UVR8 signaling pathway through changing the chromatin states thus the accessibility of CsHY5 to promoters of LDUVB-responsive genes for hypocotyl elongation. We also discussed potential use of this gene in cucumber breeding for production in protected environments.