南京农业大学学报2018，Vol.41Issue(2)：308-320,13.DOI:10.7685/jnau.201703026
基于RNA-Seq的拟南芥不定芽再生过程的基因表达谱分析
Analysis of RNA-Seq-based expression profiles during adventitious shoot regeneration in Arabidopsis thaliana
摘要
Abstract
[Objectives]To study the underlying regulation mechanisms of adventitious shoot regeneration,we analyzed the dynamic transcriptome profiles of two step procedure during Arabidopsis thaliana adventitious shoot regeneration. [Methods]In this study, adventitious shoots were regenerated from root explants through the two-step process which means preincubation on an auxin-rich callus induction medium(CIM)before transferred to a cytokinin-rich shoot induction medium(SIM). We obtained the transcriptome data from three developmental time-points(0,4 d on CIM and 3 d on SIM in vitro culture). [Results]To identify the differentially expressed genes(DEGs)during callus formation,we compared the expression profiles of 4 d CIM to 0 d CIM and detected 4 332 DEGs in total,among which 1 399 genes were upregulated and 2 933 were downregulated. Moreover,we identified DEGs during adventitious shoot regeneration by comparing expression profiles of 3 d SIM to 4 d CIM. Finally,we identified a total of 2 910 DEGs including 2 231 up-regulated and 679 down-regulated genes.We performed the Gene Ontology(GO)enrichment analysis of the DEGs and our results suggested that those genes with highly enriched GO terms were associated with phytohormone biosynthesis and degradation. During callus formation,some genes involved in cytokinin oxidase CKX and indole-3-acetic acid amido synthetase GH3 gene family were highly expressed,while some members of cytokinin synthetase were downregulated. During adventitious shoot regeneration,some genes related to cytokinin synthetase were upregulated,and member genes of CKX family were downregulated. Additionally,we investigated the expression changes of some transcription factor during the two different stages,including AP2/EREBP family members. [Conclusions]Here,we compared and analyzed the transcriptome profiles of two stages during adventitious shoot regeneration of Arabidopsis by RNA sequencing technology. The transcriptome data will provide a valuable reference for future research on regulatory mechanisms underlying plant adventitious shoot regeneration.关键词
拟南芥/不定芽再生/两步培养法/RNA-Seq/基因表达/植物激素Key words
Arabidopsis thaliana/adventitious shoot regeneration/two-step process/RNA-Seq/gene expression/phytohormone分类
生物科学引用本文复制引用
向亚男,黄蕊蕊,顾婷婷,甘立军..基于RNA-Seq的拟南芥不定芽再生过程的基因表达谱分析[J].南京农业大学学报,2018,41(2):308-320,13.基金项目
国家自然科学基金项目(31400269) （31400269）
