SHORT HYPOCOTYL 1 Encodes a SMARCA3-like Chromatin Remodeling Factor Regulating Elongation

Abstract

(Y.We.).In Arabidopsis (Arabidopsis thaliana), the UVR8-mediated signaling pathway is employed to attain UVB protection and acclimation to deal with low-dosage UVB (LDUVB)-induced stresses. Here, we identified SHORT HYPOCOTYL1 (SH1) in cucumber (Cucumis sativus), which regulates LDUVB-dependent hypocotyl elongation by modulating the UVR8 signaling pathway. We showed that hypocotyl elongation in cucumbers carrying the recessive sh1 allele was LDUVB insensitive and that Sh1 encoded a human SMARCA3-like chromatin remodeling 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 semiwild Xishuangbanna cucumber, and the wild cucumber population is largely at Hardy-Weinberg equilibrium for the two alleles. The SH1 protein sequence was highly conserved among eukaryotic organisms, but its regulation of hypocotyl elongation in cucumber seems to be a novel function. While Sh1 expression was inhibited by LDUVB, its transcript abundance was highly correlated with hypocotyl elongation rate and the expression level of cell-elongationrelated genes. Expression profiling of key regulators in the UVR8 signaling pathway revealed significant differential expression of CsHY5 between two near isogenic lines of Sh1. Sh1 and CsHY5 acted antagonistically at transcriptional level. A working model was proposed in which Sh1 regulates LDUVB-dependent hypocotyl elongation in cucumber through changing the chromatin states and thus the accessibility of CsHY5 in the UVR8 signaling pathway to promoters of LDUVB-responsive genes for hypocotyl elongation.The hypocotyl of dicotyledonous plants is the embryonic stem connecting the two embryonic leaves (cotyledons) and the primary root (radicle). The hypocotyl, which has a relatively simple architecture (Scheres et al., 1994), is a very plastic organ, strongly influenced by both external and internal cues known to regulate cell elongation, such as light, gravity, temperature, and hormones. In Arabidopsis (Arabidopsis thaliana), after germination, hypocotyl growth relies mainly on longitudinal cell elongation rather than cell divisions; its length can increase by more than 10-fold (Gendreau et al., 1997). The morphological simplicity, growth behavior, availability of mutants, and ease of phenotyping of mutants of this organ makes it a model for understanding the mechanism of cell elongation and various biological events that participate in its control (Gendreau et al., 1997;Vandenbussche et al., 2005;Boron and Vissenberg, 2014).In nature, the development of germinated seeds starts under soil cover; the seedling undergoing skotomorphogenic growth has a very long hypocotyl, which allows quick attaining of light and de-etiolation after

LITTLELEAF (LL) encodes a WD40 repeat domain‐containing protein associated with organ size variation in cucumber

“…Nucleotide diversity at the ll locus was investigated among 108 resequenced cucumber lines (Qi et al ., ) following Bo et al . (). The DNA‐binding residues in the LL protein were predicted with the DP‐Bind program (http://lcg.rit.albany.edu/dp-bind/).…”

“…We genotyped 12 cucumber lines with the ll-dCAPS2 marker inside the ll gene ( Figure S2) and found that all ll lines shared the ll allele at this marker locus. We examined the nucleotide variation at the LL locus among 108 resequenced lines, of which 11, 17 and 80 belonged to the wild, semi-wild and cultivated groups, respectively (Bo et al, 2016). Eleven single-nucleotide polymorphisms (SNPs) were identified within the CDSs; their positions and resulting amino acid substitutions among the three botanical varieties are presented in Table S2 and Figure S3, respectively.…”

“…To validate the ll candidate gene, 12 cucumber lines with or without the ll allele were genotyped with the co-segregated marker ll-dCAPS2. Nucleotide diversity at the ll locus was investigated among 108 resequenced cucumber lines (Qi et al, 2013) following Bo et al (2016). The DNA-binding residues in the LL protein were predicted with the DP-Bind program (http://lcg.…”

Transcriptome analysis reveals new microRNAs-mediated pathway involved in anther development in male sterile wheat

“…Little is known about the roles of the SWI/SNF chromatin-remodeling complex and CAF1 gene in plants. In Arabidopsis , a SMARCA3 -Like chromatin remodeling factor regulates low-dosage UVB-dependent hypocotyl elongation [ 11 ]. Loss-function of both AtCAF1a and AtCAF1b reduced expression of pathogenesis-related genes and was more susceptible to pathogen infection [ 12 ].…”

A valid name for the Xishuangbanna gourd, a cucumber with carotene-rich fruits

“…Flowering time and fruit size variation in the Xishuangbanna cucumber have also been studied, and a QTL analysis implicated 11 QTLs on two chromosomes in determining photoperiod-dependent flowering time and the round fruit shape ( Qu et al 2014 ; Pan et al 2017 ). The short hypocotyl is controlled by a recessive allele ( Bo et al 2016 ), and the carpel number of usually 5, not three carpels as in var. hardwickii and var.…”