title: RNA-Seq-based transcriptome profiling of early nitrogen deficiency response in cucumber seedlings provides new insight into the putative nitrogen regulatory network.
abstract: Nitrogen (N) is both an important macronutrient and a signal for plant growth and development. However, the early regulatory mechanism of plants in response to N starvation is not well understood, especially in cucumber, an economically important crop that normally consumes excessive N during production. In this study, the early time-course transcriptome response of cucumber leaves under N deficiency was monitored using RNA sequencing (RNA-Seq). More than 23,000 transcripts were examined in cucumber leaves, of which 364 genes were differentially expressed in response to N deficiency. Based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database, gene ontology (GO) and protein-protein interaction analysis, 64 signaling-related N-deficiency-responsive genes were identified. Furthermore, the potential regulatory mechanisms of anthocyanin accumulation, Chl decline and cell wall remodeling were assessed at the transcription level. Increased ascorbic acid synthesis was identified in cucumber seedlings and fruit under N-deficient conditions, and a new corresponding regulatory hypothesis has been proposed. A data cross-comparison between model plants and cucumber was made, and some common and specific N-deficient response mechanisms were found in the present study. Our study provides novel insights into the responses of cucumber to nitrogen starvation at the global transcriptome level, which are expected to be highly useful for dissecting the N response pathways in this major vegetable and for improving N fertilization practices.
authors.affiliation: Key Laboratory of Horticultural Crops Genetic Improvement (Ministry of Agriculture), Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun S. St., Beijing 100081, China Beijing Key Laboratory for Agriculture Application and New Technology, Plant Science and Technology College, Beijing University of Agriculture, Beijing 102206, China These authors contributed equally to this work.
authors.forename: Wenchao
authors.initials: W
authors.lastname: Zhao
authors.affiliation: Key Laboratory of Horticultural Crops Genetic Improvement (Ministry of Agriculture), Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun S. St., Beijing 100081, China These authors contributed equally to this work.
authors.forename: Xueyong
authors.initials: X
authors.lastname: Yang
authors.affiliation: Key Laboratory of Horticultural Crops Genetic Improvement (Ministry of Agriculture), Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun S. St., Beijing 100081, China These authors contributed equally to this work.
authors.forename: Hongjun
authors.initials: H
authors.lastname: Yu
authors.affiliation: Key Laboratory of Horticultural Crops Genetic Improvement (Ministry of Agriculture), Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun S. St., Beijing 100081, China jiang8797@sina.com.
authors.forename: Weijie
authors.initials: W
authors.lastname: Jiang
authors.affiliation: Key Laboratory of Horticultural Crops Genetic Improvement (Ministry of Agriculture), Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun S. St., Beijing 100081, China.
authors.forename: Na
authors.initials: N
authors.lastname: Sun
authors.affiliation: Key Laboratory of Horticultural Crops Genetic Improvement (Ministry of Agriculture), Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun S. St., Beijing 100081, China.
authors.forename: Xiaoran
authors.initials: X
authors.lastname: Liu
authors.affiliation: Key Laboratory of Horticultural Crops Genetic Improvement (Ministry of Agriculture), Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun S. St., Beijing 100081, China.
authors.forename: Xiaolin
authors.initials: X
authors.lastname: Liu
authors.affiliation: Key Laboratory of Horticultural Crops Genetic Improvement (Ministry of Agriculture), Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun S. St., Beijing 100081, China.
authors.forename: Xiaomeng
authors.initials: X
authors.lastname: Zhang
authors.affiliation: Key Laboratory of Horticultural Crops Genetic Improvement (Ministry of Agriculture), Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun S. St., Beijing 100081, China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Key Laboratory of Horticultural Crops Genetic Improvement (Ministry of Agriculture), Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun S. St., Beijing 100081, China.
authors.forename: Xingfang
authors.initials: X
authors.lastname: Gu
mesh_terms: D000872:Anthocyanins / Q000096:biosynthesis; D001205:Ascorbic Acid / Q000378:metabolism; D053898:Biosynthetic Pathways / Q000187:drug effects / Q000235:genetics; D002473:Cell Wall / Q000187:drug effects / Q000235:genetics; D016000:Cluster Analysis; D018553:Cucumis sativus / Q000187:drug effects / Q000235:genetics*; D005638:Fruit / Q000187:drug effects / Q000235:genetics; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000187:drug effects; D063990:Gene Ontology; D053263:Gene Regulatory Networks / Q000187:drug effects; D017343:Genes, Plant; D009584:Nitrogen / Q000172:deficiency* / Q000494:pharmacology; D020411:Oligonucleotide Array Sequence Analysis; D010788:Photosynthesis / Q000187:drug effects / Q000235:genetics; D018515:Plant Leaves / Q000187:drug effects / Q000235:genetics; D036226:Seedlings / Q000187:drug effects / Q000235:genetics*; D017423:Sequence Analysis, RNA; D013997:Time Factors
chemical_list: D000872:Anthocyanins; D009584:Nitrogen; D001205:Ascorbic Acid
keywords: Ascorbic acid; Cell wall; Cucumber; Nitrogen deficiency; RNA-Seq; Regulatory network