Brassica genomic assays
Methods and compositions for detecting, identifying, and quantifying Brassica A genomic DNA are described. The methods are specific to the Brassica A genome and do not cross-react with other Brassica species, crops or weedy relatives that could contribute to contamination of a canola field.
1. An amplicon comprising at least one of the nucleotide sequences of a genomic region selected from the group consisting of SEQ ID NOS: 26, 27, and 28 wherein the amplicon is not larger than 500 base pairs and further comprising a probe, wherein the probe comprises a fluorescent detectable label and wherein the amplicon discriminates the Brassica A genome from the Brassica B and C genomes.
2. A method of determining a trait purity of a Brassica trait, the method comprising:
a) obtaining a DNA sample of a Brassica plant containing a trait; and
b) performing a Brassica A genome specific assay, wherein the Brassica A genome specific assay comprises:
(i) amplifying a genomic DNA fragment of the Brassica A genome with two or more oligonucleotide primer sequences selected from the group consisting of SEQ ID NOS: 19-24, wherein the amplified DNA fragment comprises at least one of the nucleotide sequences of a genomic region selected from the group consisting of SEQ ID NOS: 25, 26, 27 and 28, and wherein SEQ ID NOS: 25, 26, 27 and 28 of the amplified fragment identifies the presence of Brassica A genome in the sample; and
(ii) detecting the amplified DNA fragment and quantifying the Brassica A genome from the amplified DNA fragment of the Brassica A genome
thereby determining trait purity of the Brassica trait.
3. The method of claim 2 , wherein the Brassica trait is selected from the group consisting of RT73, RT200, MON88302, DP-073496, HCN92, T45 (HCN28), 23-18-17, 23-198, OXY-235, MS1, MS3, MS6, MS8, RF1, RF2, RF3, and Topas 19/2.
4. The method of claim 2 , wherein the determination comprises performing a quantitative polymerase chain reaction.