Comparative transcriptome analyses of drought-resistant and - susceptible Brassica napus L. and development of EST-SSR markers by RNA-Seq

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.