Identification and Transcriptome Analysis of C1 Nullisomic in Allotetraploid Brassica napus L

The purposes of this study are to compare euploid B. napus cv. “Oro” and the C1 nullisomics transcriptome profiling (RNA-seq) and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis. Methods: Leaves mRNA profiles of 30-day-old euploid B. napus cv. “Oro” and the C1 nullisomics were generated by deep sequencing, in triplicate, using Illumina. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods. qRT–PCR validation was performed. Results: After the high-throughput sequencing, each sample generated 7.2G Clean data on average and the 44.6-53.8 million clean reads were generated. Our study represents detailed analysis of leaves transcriptomes in euploid B. napus and nullisomic, with biologic replicates, generated by RNA-seq technology for comparative investigations of expression profiles. Our results show that Dose complementary effect exists between highly homologous genes, and partial loss of C subgenomic chromosome will lead to increased expression of A genome. Overall design: The mRNA profiles of 30-day-old wild euploid Brassica napus cv. “Oro” and aneuploidy Brassica napus cv. "null".