title: SHORT HYPOCOTYL1 Encodes a SMARCA3-Like Chromatin Remodeling Factor Regulating Elongation.
abstract: 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-elongation-related 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.
authors: Horticulture Department, University of Wisconsin, Madison, Wisconsin 53706 (K.B., Y.P., Y.Wa., P.W.S., Y.We.); Horticulture College, Nanjing Agricultural University, Nanjing 210095, China (K.B., J.C.);Horticulture College, Northwest A&F University, Yangling 712100, China (H.W., Y.P., Y.L.);Division of Vegetable Science, Indian Agricultural Research Institute, New Delhi 10012, India (T.K.B.);Division of Crop Improvement, Indian Council of Agricultural Research-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh 221305, India (S.P.);Beijing Vegetable Research Center and National Engineering Research Center for Vegetables, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China (C.W.); andVegetable Crops Research Unit, United States Department of Agriculture Agricultural Research Service, Madison, Wisconsin 53706 (P.W.S., Y.We.).
authors: Kailiang
authors: K
authors: Bo
authors: Horticulture Department, University of Wisconsin, Madison, Wisconsin 53706 (K.B., Y.P., Y.Wa., P.W.S., Y.We.); Horticulture College, Nanjing Agricultural University, Nanjing 210095, China (K.B., J.C.);Horticulture College, Northwest A&F University, Yangling 712100, China (H.W., Y.P., Y.L.);Division of Vegetable Science, Indian Agricultural Research Institute, New Delhi 10012, India (T.K.B.);Division of Crop Improvement, Indian Council of Agricultural Research-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh 221305, India (S.P.);Beijing Vegetable Research Center and National Engineering Research Center for Vegetables, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China (C.W.); andVegetable Crops Research Unit, United States Department of Agriculture Agricultural Research Service, Madison, Wisconsin 53706 (P.W.S., Y.We.).
authors: Hui
authors: 0000-0002-6053-443X
authors: H
authors: Wang
authors: Horticulture Department, University of Wisconsin, Madison, Wisconsin 53706 (K.B., Y.P., Y.Wa., P.W.S., Y.We.); Horticulture College, Nanjing Agricultural University, Nanjing 210095, China (K.B., J.C.);Horticulture College, Northwest A&F University, Yangling 712100, China (H.W., Y.P., Y.L.);Division of Vegetable Science, Indian Agricultural Research Institute, New Delhi 10012, India (T.K.B.);Division of Crop Improvement, Indian Council of Agricultural Research-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh 221305, India (S.P.);Beijing Vegetable Research Center and National Engineering Research Center for Vegetables, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China (C.W.); andVegetable Crops Research Unit, United States Department of Agriculture Agricultural Research Service, Madison, Wisconsin 53706 (P.W.S., Y.We.).
authors: Yupeng
authors: 0000-0003-4662-601X
authors: Y
authors: Pan
authors: Horticulture Department, University of Wisconsin, Madison, Wisconsin 53706 (K.B., Y.P., Y.Wa., P.W.S., Y.We.); Horticulture College, Nanjing Agricultural University, Nanjing 210095, China (K.B., J.C.);Horticulture College, Northwest A&F University, Yangling 712100, China (H.W., Y.P., Y.L.);Division of Vegetable Science, Indian Agricultural Research Institute, New Delhi 10012, India (T.K.B.);Division of Crop Improvement, Indian Council of Agricultural Research-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh 221305, India (S.P.);Beijing Vegetable Research Center and National Engineering Research Center for Vegetables, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China (C.W.); andVegetable Crops Research Unit, United States Department of Agriculture Agricultural Research Service, Madison, Wisconsin 53706 (P.W.S., Y.We.).
authors: Tusar K
authors: TK
authors: Behera
authors: Horticulture Department, University of Wisconsin, Madison, Wisconsin 53706 (K.B., Y.P., Y.Wa., P.W.S., Y.We.); Horticulture College, Nanjing Agricultural University, Nanjing 210095, China (K.B., J.C.);Horticulture College, Northwest A&F University, Yangling 712100, China (H.W., Y.P., Y.L.);Division of Vegetable Science, Indian Agricultural Research Institute, New Delhi 10012, India (T.K.B.);Division of Crop Improvement, Indian Council of Agricultural Research-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh 221305, India (S.P.);Beijing Vegetable Research Center and National Engineering Research Center for Vegetables, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China (C.W.); andVegetable Crops Research Unit, United States Department of Agriculture Agricultural Research Service, Madison, Wisconsin 53706 (P.W.S., Y.We.).
authors: Sudhakar
authors: S
authors: Pandey
authors: Horticulture Department, University of Wisconsin, Madison, Wisconsin 53706 (K.B., Y.P., Y.Wa., P.W.S., Y.We.); Horticulture College, Nanjing Agricultural University, Nanjing 210095, China (K.B., J.C.);Horticulture College, Northwest A&F University, Yangling 712100, China (H.W., Y.P., Y.L.);Division of Vegetable Science, Indian Agricultural Research Institute, New Delhi 10012, India (T.K.B.);Division of Crop Improvement, Indian Council of Agricultural Research-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh 221305, India (S.P.);Beijing Vegetable Research Center and National Engineering Research Center for Vegetables, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China (C.W.); andVegetable Crops Research Unit, United States Department of Agriculture Agricultural Research Service, Madison, Wisconsin 53706 (P.W.S., Y.We.).
authors: Changlong
authors: C
authors: Wen
authors: Horticulture Department, University of Wisconsin, Madison, Wisconsin 53706 (K.B., Y.P., Y.Wa., P.W.S., Y.We.); Horticulture College, Nanjing Agricultural University, Nanjing 210095, China (K.B., J.C.);Horticulture College, Northwest A&F University, Yangling 712100, China (H.W., Y.P., Y.L.);Division of Vegetable Science, Indian Agricultural Research Institute, New Delhi 10012, India (T.K.B.);Division of Crop Improvement, Indian Council of Agricultural Research-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh 221305, India (S.P.);Beijing Vegetable Research Center and National Engineering Research Center for Vegetables, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China (C.W.); andVegetable Crops Research Unit, United States Department of Agriculture Agricultural Research Service, Madison, Wisconsin 53706 (P.W.S., Y.We.).
authors: Yuhui
authors: Y
authors: Wang
authors: Horticulture Department, University of Wisconsin, Madison, Wisconsin 53706 (K.B., Y.P., Y.Wa., P.W.S., Y.We.); Horticulture College, Nanjing Agricultural University, Nanjing 210095, China (K.B., J.C.);Horticulture College, Northwest A&F University, Yangling 712100, China (H.W., Y.P., Y.L.);Division of Vegetable Science, Indian Agricultural Research Institute, New Delhi 10012, India (T.K.B.);Division of Crop Improvement, Indian Council of Agricultural Research-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh 221305, India (S.P.);Beijing Vegetable Research Center and National Engineering Research Center for Vegetables, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China (C.W.); andVegetable Crops Research Unit, United States Department of Agriculture Agricultural Research Service, Madison, Wisconsin 53706 (P.W.S., Y.We.).
authors: Philipp W
authors: PW
authors: Simon
authors: Horticulture Department, University of Wisconsin, Madison, Wisconsin 53706 (K.B., Y.P., Y.Wa., P.W.S., Y.We.); Horticulture College, Nanjing Agricultural University, Nanjing 210095, China (K.B., J.C.);Horticulture College, Northwest A&F University, Yangling 712100, China (H.W., Y.P., Y.L.);Division of Vegetable Science, Indian Agricultural Research Institute, New Delhi 10012, India (T.K.B.);Division of Crop Improvement, Indian Council of Agricultural Research-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh 221305, India (S.P.);Beijing Vegetable Research Center and National Engineering Research Center for Vegetables, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China (C.W.); andVegetable Crops Research Unit, United States Department of Agriculture Agricultural Research Service, Madison, Wisconsin 53706 (P.W.S., Y.We.).
authors: Yuhong
authors: Y
authors: Li
authors: Horticulture Department, University of Wisconsin, Madison, Wisconsin 53706 (K.B., Y.P., Y.Wa., P.W.S., Y.We.); Horticulture College, Nanjing Agricultural University, Nanjing 210095, China (K.B., J.C.);Horticulture College, Northwest A&F University, Yangling 712100, China (H.W., Y.P., Y.L.);Division of Vegetable Science, Indian Agricultural Research Institute, New Delhi 10012, India (T.K.B.);Division of Crop Improvement, Indian Council of Agricultural Research-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh 221305, India (S.P.);Beijing Vegetable Research Center and National Engineering Research Center for Vegetables, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China (C.W.); andVegetable Crops Research Unit, United States Department of Agriculture Agricultural Research Service, Madison, Wisconsin 53706 (P.W.S., Y.We.) yiqun.weng@wisc.edu jfchen@njau.edu.cn.
authors: Jinfeng
authors: 0000-0002-4690-6778
authors: J
authors: Chen
authors: Horticulture Department, University of Wisconsin, Madison, Wisconsin 53706 (K.B., Y.P., Y.Wa., P.W.S., Y.We.); Horticulture College, Nanjing Agricultural University, Nanjing 210095, China (K.B., J.C.);Horticulture College, Northwest A&F University, Yangling 712100, China (H.W., Y.P., Y.L.);Division of Vegetable Science, Indian Agricultural Research Institute, New Delhi 10012, India (T.K.B.);Division of Crop Improvement, Indian Council of Agricultural Research-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh 221305, India (S.P.);Beijing Vegetable Research Center and National Engineering Research Center for Vegetables, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China (C.W.); andVegetable Crops Research Unit, United States Department of Agriculture Agricultural Research Service, Madison, Wisconsin 53706 (P.W.S., Y.We.) yiqun.weng@wisc.edu jfchen@njau.edu.cn.
authors: Yiqun
authors: 0000-0001-9457-2234
authors: Y
authors: Weng
mesh_terms: D001483:Base Sequence; D042002:Chromatin Assembly and Disassembly; D002874:Chromosome Mapping / Q000379:methods; D032461:Chromosomes, Plant / Q000235:genetics; D003001:Cloning, Molecular; D018553:Cucumis sativus / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism; D020869:Gene Expression Profiling / Q000379:methods; D018507:Gene Expression Regulation, Developmental / Q000528:radiation effects*; D018506:Gene Expression Regulation, Plant / Q000528:radiation effects*; D005787:Gene Frequency; D005838:Genotype; D018546:Hypocotyl / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D015810:Linkage Disequilibrium; D010802:Phylogeny; D010940:Plant Proteins / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D017422:Sequence Analysis, DNA; D012689:Sequence Homology, Nucleic Acid; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism; D014466:Ultraviolet Rays
chemical_list: D004268:DNA-Binding Proteins; C100023:HLTF protein, human; D010940:Plant Proteins; D014157:Transcription Factors