Allele-specific SNP markers for the new low linolenic mutant genotype of winter oilseed rape

One of the goals in oilseed rape breeding is the identification of genotypes with low linolenic acid content in seed oil. Here, we present new genetic markers for mutant alleles of a chemically induced low linolenic rapeseed line DH219/05. Genomic clones comprising fatty acids desaturase 3 (FAD3) genes from the mutant and wild-type rapeseed lines were sequenced. Two statistically important single nucleotide polymorphisms were detected: (1) a C to T substitution in the third position of the sixth codon of the seventh exon in the BnaA.FAD3 gene and (2) a G to A transition in the 5' splice donor site of the sixth intron in the BnaC.FAD3 gene. Allele-specific SNP markers were designed involving detection of the wild-type and mutant alleles by SNaPshot analysis and locus-specific PCR primers. Strong negative correlation between the presence of mutant alleles in the A and C genomes and linolenic acid content was revealed by analysis of variance. Sequence analysis of transcript variants confirmed predictions on possible negative effects of mutations on FAD3 gene expression.