Comparative transcriptome analyses of drought-resistant and - susceptible Brassica napus L. and development of EST-SSR markers by RNA-Seq
- 453 Downloads
Brassica napus is a dicotyledonous plant in the family Brassicaceae. It is an important oil crop which has been widely cultivated over the world. However, drought stress is a very important threatening to B. napus production. In this study, two B. napus strains with different resistance to drought stress were treated with 200 g/L PEG-6000 as drought simulation agent (marked as S, R)and two controls were treated with 1/2 Hoagland medium(marked as ST, RT). With the help of Illumina paired-end RNA-seq technology and de novo assembly by Trinity, we obtained 107,294 Unigenes (integrated four sample results) with an average length of 834 bp and N50 1245. Of these Unigenes, 84,768, 92,545, 54,857, 28,129, 75,278 were assigned to NR, NT, Swiss-Prot, COG and GO database respectively. A total of 46,861 were mapped to 128 pathways by BLAST comparison against the KEGG database. In order to have an overall understanding of the unique genes’ expression difference among four samples, we utilized RPKM to calculate Unigene expression, and to identify differentially expressed genes. Besides, 22,414 SSRs were developed in this study.
KeywordsBrassica napus L. Drought stress RNA-seq Transcriptome analysis
Unable to display preview. Download preview PDF.
- Andersen MN, Heidmann T, Plauborg F. (1996) The effects of drought and nitrogen on light interception, growth and yield of winter oilseed rape. Acta Agr Scand, Sect B, 46:55–67Google Scholar
- Conesa A, Götz S, García-Gómez JM, Terol J, Talón M, Robles M. (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21:3674–3676Google Scholar
- Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, Palma FD, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A. (2011) Full length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29:644–652PubMedCentralPubMedCrossRefGoogle Scholar
- Hall AE. (1992) Breeding for heat tolerance. Plant Breed Rev 10:129–168Google Scholar
- Iseli C, Jongeneel CV, Bucher P. (1999) ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. Proc Int Conf Intell Syst Mol Biol 138–148Google Scholar
- Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, Katayama T, Kawashima S, Okuda S, Tokimatsu T, Yamanishi Y. (2008) KEGG for linking genomes to life and the environment. Nucleic Acids Res 36(Database issue):D480–4Google Scholar
- Mendham NJ, Salisbury PA. (1995) Physiology, crop development, growth and yield. In: Kimber, D.S. and D.I. McGregor. Brassica Oilseeds: Production and utilization. CAB International, London:11–64Google Scholar
- Stoker R, Carter KE. (1984) Effect of irrigation and nitrogen on yield and quality of oilseed rape. N Z J Exp Agr 12:219–224Google Scholar
- Wang D, Yang C, Gui Y, Zhang S, Zhu J, Wang J. (2011) Drought resistance and identification method and evaluation index in Brassica napus. Acta Agriculturae Boreali-occidentalis Sinica 20:77–82Google Scholar
- Ye J, Fang L, Zheng H, Zhang Y, Chen J, Zhang Z, Wang J, Li S, Li R, Bolund L, Wang J. (2006) WEGO: a web tool for plotting GO annotations. Nucleic Acids Res 34(Web Server issue):W293–W297Google Scholar