DNA sequences of fatty acid elongase 1 genes FAE1.1 (EA) and FAE1.2 (EC) were isolated and characterized for 30 commercialized low erucic acid rapeseed (LEAR) cultivars in China. Four types of independent mutation leading to low erucic acid trait were found, i.e., a single-base transition (eA1), a two-base deletion (eC2) and four-base deletion (eC4) as well as single-base transition with a four-base deletion (eA*). Three genotypes, i.e., eA1eA1eC2eC2, eA1eA1eC4eC4 and eA*eA*eC4eC4 were responsible for LEA content in storage lipids of different rapeseed cultivars. Most of the LEAR cultivars had a genotype of eA1eA1eC2eC2, which were descended from the first LEAR cultivar, Oro. Yeast expression analysis revealed that two-base-pair (AA) deletion (eC2) at the base sites of 1422–1423 in the C genome FAE1 gene resulted in the absence of the condensing enzyme and led to the failure to produce erucic acid. Coexpression of FAE1 and ketoacyl-CoA reductase (KCR) or enoyl-CoA reductase (ECR) was found in high erucic acid rapeseed (HEAR) but not in LEAR (eA1eA1eC2eC2 or eA1eA1eC4eC4). Moreover, KCR and ECR were still coordinately regulated in eA1eA1eC2eC2 or eA1eA1eC4eC4 genotypes, suggesting that the expression of two genes was tightly linked. In addition, specific detection methods were developed by high-resolution melting curve analysis in order to detect eA1 and eC4 .

To characterize the DNA rearrangement of both the T-DNA region and the genomic insertion site during T-DNA insertion, the Genomewalker strategy was used to isolate the junctions between the inserted DNA and the plant genomic DNA in six rapeseed events as well as the genomic DNA at the sites before integration. During transformation in each of the six events, portions of both the right border (RB) and left border (LB) regions of the T-DNA were deleted, ranging from a 7 nucleotide deletion of the LB repeats in event RF1 to a 207 bp deletion of the LB region in event RF2. For the six events, T-DNA integration resulted in a deletion at the target site spanning less than 100 bp. Sequence analysis indicated that the T-DNA was integrated into the coding region of various native rapeseed genes in events RF1 and RF2. Duplications of the genomic DNA target site were observed in events RF2, RF3 and Topas 19/2. And multimerization of transgenes was found in event Topas 19/2, in which, the T-DNA was integrated as a head-to-head (RB-to-RB) concatemer into the recipient genome. In event MS1, chromosomal translocation or a large target-site deletion may have occurred during T-DNA integration, which was identified due to a failure to amplify the presumptive insertion site based on the flanking rapeseed DNA sequences. Our results provide comprehensive data concerning transgene organization and the genomic context of the T-DNA in six rapeseed events, which can aid in the developing of insert fingerprinting and the monitoring of long-term genetic stability and potential unintended effects of transgenic events.