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<p>Abstract</p> <p>Background</p> <p><it>FAE1 </it>(<it>fatty acid elongase1</it>) is the key gene in the control of erucic acid synthesis in seeds of <it>Brassica </it>species. Due to oil with low erucic acid (LEA) content is essential for human health and not enough LEA resource could be available, thus new LEA genetic resources are being sought for <it>Brassica </it>breeding. EcoTILLING, a powerful genotyping method, can readily be used to identify polymorphisms in <it>Brassica.</it></p> <p>Results</p> <p>Seven <it>B. rapa</it>, nine <it>B. oleracea </it>and 101 <it>B. napus </it>accessions were collected for identification of <it>FAE1 </it>polymorphisms. Three polymorphisms were detected in the two <it>FAE1 </it>paralogues of <it>B. napus </it>using EcoTILLING and were found to be strongly associated with differences in the erucic acid contents of seeds. In genomic <it>FAE1 </it>sequences obtained from seven <it>B. rapa </it>accessions, one SNP in the coding region was deduced to cause loss of gene function. Molecular evolution analysis of <it>FAE1 </it>homologues showed that the relationship between the <it>Brassica </it>A and C genomes is closer than that between the A/C genomes and <it>Arabidopsis </it>genome. Alignment of the coding sequences of these <it>FAE1 </it>homologues indicated that 18 <it>SNPs </it>differed between the A and C genomes and could be used as genome-specific markers in <it>Brassica</it>.</p> <p>Conclusion</p> <p>This study showed the applicability of EcoTILLING for detecting gene polymorphisms in <it>Brassica</it>. The association between <it>B. napus FAE1 </it>polymorphisms and the erucic acid contents of seeds may provide useful guidance for LEA breeding. The discovery of the LEA resource in <it>B. rapa </it>can be exploited in <it>Brasscia </it>cultivation.</p>