We analysed DNA and complementary DNA (cDNA) from two inbred lines (CMS-ARIT121 and CMS-ARIT2) along with their respective maintainer lines with eight known genes (atpa, atp6, atp9, coxI, coxII, orfB, orf222 and orf224) reported in other cytoplasmic male sterility (CMS) systems. DNA analyses indicated that only orf224 was different in the maintainer and CMS in ARIT121. Sequencing analysis indicated that CMS-ARIT121 has a similar sequence to that of polima CMS. However, CMS-ARIT2 was quite unique, with no sequence difference at DNA or cDNA level in all eight candidate genes, with the exception of a two-base substitution in the atp6 gene between the CMS and maintainer lines. The similar amplification pattern with all primers, especially orf224, indicates that CMS-ARIT2 is unique and does not correspond to polima, ogura or nap. However, further research is required to establish the causes of sterility in this cms, since we could not find any significant difference at transcript level between CMS-ARIT2 and its corresponding maintainer line. However, the same restorer PR121 as for CMS-ARIT121 was able to restore CMS-ARIT2, and as such can be used for hybrid seed production in Brassica napus L. Overall, this study provides important information for breeders selecting new cytoplasmic male sterility (CMS) in B. napus L. and use of molecular markers to identify CMS lines at early seedling stage that will enhance the B. napus L. breeding program
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