De novo transcriptome analysis in radish (Raphanus sativus L.) and identification of critical genes involved in bolting and flowering

BMC Genomics

Research Article

Danqiong Huang¹  Everlyne M. Muleke²  Liwang Liu²  Shanshan Nie²  Chao Li²  Xiaochuan Sun²  Yan Wang²  Yang Xie²  Liang Xu² 

[1] Department of Plant Sciences, North Dakota State University, 58108, Fargo, ND, USA;National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, 210095, Nanjing, People’s Republic of China;Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China) of the Ministry of Agriculture of P.R. China, 210095, Nanjing, People’s Republic of China;

关键词: Radish;    De novo;    Bolting and flowering;    Transcriptome;    Flowering regulatory network;   

DOI  :  10.1186/s12864-016-2633-2

 received in 2015-08-26, accepted in 2016-04-21,  发布年份 2016

来源: Springer

【 摘 要 】

BackgroundThe appropriate timing of bolting and flowering is pivotal for reproductive success in Brassicaceae crops including radish (Raphanus sativus L.). Although several flowering regulatory pathways had been described in some plant species, no study on genetic networks of bolting and flowering regulation was performed in radish. In this study, to generate dataset of radish unigene sequences for large-scale gene discovery and functional pathway identification, a cDNA library from mixed radish leaves at different developmental stages was subjected to high-throughput RNA sequencing (RNA-seq).ResultsA total of 54.64 million clean reads and 111,167 contigs representing 53,642 unigenes were obtained from the radish leaf transcriptome. Among these, 50,385 unigenes were successfully annotated by BLAST searching against the public protein databases. Functional classification and annotation indicated that 42,903 and 15,382 unique sequences were assigned to 55 GO terms and 25 COG categories, respectively. KEGG pathway analysis revealed that 25,973 unigenes were classified into 128 functional pathways, among which 24 candidate genes related to plant circadian rhythm were identified. Moreover, 142 potential bolting and flowering-related genes involved in various flowering pathways were identified. In addition, seven critical bolting and flowering-related genes were isolated and profiled by T-A cloning and RT-qPCR analysis. Finally, a schematic network model of bolting and flowering regulation and pathways was put forward in radish.ConclusionsThis study is the first report on systematic identification of bolting and flowering-related genes based on transcriptome sequencing and assembly in radish. These results could provide a foundation for further investigating bolting and flowering regulatory networks in radish, and facilitate dissecting molecular genetic mechanisms underlying bolting and flowering in Brassicaceae vegetable crops.

【 授权许可】

CC BY   
© Nie et al. 2016