The RNA-seq approach to discriminate gene expression profiles in response to melatonin on cucumber lateral root formation

Na Zhang, Hai Jun Zhang, Bing Zhao, Qian Qian Sun, Yun Yun Cao, Ren Li, Xin Xin Wu, Sarah Weeda, Li Li, Shuxin Ren, Russel J Reiter, Yang Dong Guo

Research output: Contribution to journalArticle

128 Citations (Scopus)

Abstract

Cucumber is a model cucurbitaceous plant with a known genome sequence which is important for studying molecular mechanisms of root development. In this study, RNA sequencing was employed to explore the mechanism of melatonin-induced lateral root formation in cucumber under salt stress. Three groups of seeds were examined, that is, seeds primed without melatonin (CK), seeds primed in a solution containing 10 or 500 μmol/L melatonin (M10 and M500, respectively). These seeds were then germinated in NaCl solution. The RNA-seq analysis generated 16,866,670 sequence reads aligned with 17,920 genes, which provided abundant data for the analysis of lateral root formation. A total of 17,552, 17,450, and 17,393 genes were identified from roots of the three treatments (CK, M10 and M500, respectively). The expression of 121 genes was significantly up-regulated, and 196 genes were significantly down-regulated in M500 which showed an obvious increase on the number of lateral roots. These genes were significantly enriched in 57 KEGG pathways and 16 GO terms (M500 versus CK). Based on their expression pattern, peroxidase-related genes were selected as the candidates to be involved in the melatonin response. Several transcription factor families might play important roles in lateral root formation processes. A number of genes related to cell wall formation, carbohydrate metabolic processes, oxidation/reduction processes, and catalytic activity also showed different expression patterns as a result of melatonin treatments. This RNA-sequencing study will enable the scientific community to better define the molecular processes that affect lateral root formation in response to melatonin treatment.

Original languageEnglish (US)
Pages (from-to)39-50
Number of pages12
JournalJournal of Pineal Research
Volume56
Issue number1
DOIs
StatePublished - Jan 2014

Fingerprint

Cucumis sativus
Melatonin
Transcriptome
RNA
Seeds
Genes
RNA Sequence Analysis
Cell Wall
Peroxidase
Oxidation-Reduction
Transcription Factors
Salts
Carbohydrates
Genome
Gene Expression

Keywords

  • cucumber
  • gene expression
  • lateral root formation
  • melatonin
  • RNA sequencing

ASJC Scopus subject areas

  • Endocrinology

Cite this

The RNA-seq approach to discriminate gene expression profiles in response to melatonin on cucumber lateral root formation. / Zhang, Na; Zhang, Hai Jun; Zhao, Bing; Sun, Qian Qian; Cao, Yun Yun; Li, Ren; Wu, Xin Xin; Weeda, Sarah; Li, Li; Ren, Shuxin; Reiter, Russel J; Guo, Yang Dong.

In: Journal of Pineal Research, Vol. 56, No. 1, 01.2014, p. 39-50.

Research output: Contribution to journalArticle

Zhang, N, Zhang, HJ, Zhao, B, Sun, QQ, Cao, YY, Li, R, Wu, XX, Weeda, S, Li, L, Ren, S, Reiter, RJ & Guo, YD 2014, 'The RNA-seq approach to discriminate gene expression profiles in response to melatonin on cucumber lateral root formation', Journal of Pineal Research, vol. 56, no. 1, pp. 39-50. https://doi.org/10.1111/jpi.12095
Zhang, Na ; Zhang, Hai Jun ; Zhao, Bing ; Sun, Qian Qian ; Cao, Yun Yun ; Li, Ren ; Wu, Xin Xin ; Weeda, Sarah ; Li, Li ; Ren, Shuxin ; Reiter, Russel J ; Guo, Yang Dong. / The RNA-seq approach to discriminate gene expression profiles in response to melatonin on cucumber lateral root formation. In: Journal of Pineal Research. 2014 ; Vol. 56, No. 1. pp. 39-50.
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