Landscape of Sequence Variations in Homologous Copies of FAD2 and FAD3 in Rapeseed (Brassica napus L.) Germplasm with High/Low Linolenic Acid Trait

Genetic manipulation (either restraint or enhancement) of the biosynthesis pathway of α-linolenic acid (ALA) in seed oil is an important goal in Brassica napus breeding. B. napus is a tetraploid plant whose genome often harbors four and six homologous copies, respectively, of the two fatty acid desaturases FAD2 and FAD3, which control the last two steps of ALA biosynthesis during seed oil accumulation. In this study, we compared their promoters, coding sequences, and expression levels in three high-ALA inbred lines 2006L, R8Q10, and YH25005, a low-ALA line A28, a low-ALA/high-oleic-acid accession SW, and the wildtype ZS11. The expression levels of most FAD2 and FAD3 homologs in the three high-ALA accessions were higher than those in ZS11 and much higher than those in A28 and SW. The three high-ALA accessions shared similar sequences with the promoters and CDSs of BnFAD3.C4 and BnFAD3.A3. In A28 and SW, substitution of three amino acid residues in BnFAD2.A5 and BnFAD2.C5, an absence of BnFAD2.C1 locus, and a 549 bp long deletion on the BnFAD3.A3 promoter were detected. The profile of BnFAD2 mutation in the two low-ALA accessions A28 and SW is different from that reported in previous studies. The mutations in BnFAD3 in the high-ALA accessions are reported for the first time. In identifying the sites of these mutations, we provide detailed information to aid the design of molecular markers for accelerated breeding schemes.