SNP markers
Single Nucleotide Polymorphisms (SNPs) are increasingly used as the basis for generating genetic markers, and have the potential to be of particular value in the analysis of Brassica genomes, where multiple homeologous and/or paralogous copies of individual genes may exist. There are opportunities for collating information relating to SNP discovery (screening range of germplasm), as well as integrating efforts to establish community-wide SNP screening platforms. If you are involved in such a project or consortium please provide information to include in the table below.
| Species | Platform | Consortium | Source | Amplicon targets | More information | Contact |
|---|---|---|---|---|---|---|
| Brassica | Illumina | Infinium - will be continued to at least 2016 | multi | 60,000 | Illumina Consortium | |
| B. napus | Illumina; 'digital transcriptome' | JIC | RNA | ~20,000 | download SNP list (Excel) or as text file; and |
M. Trick |
| B. napus | Pyrosequencing, multiplexing | Trait Genetics, Gaterslaben | ESTs | >2,000 | Trait Genetics website | |
| B. napus | Re-sequencing | NAM, Germany | DNA | 4,300,000 SNPs | Resequencing of 52 B. napus genomes - Scientific Data/Nature) |
- SNP discovery in Brassica napus using Solexa transcriptome sequencing (Trick et al., 2009)
- autoSNPdb for Brassica at ACPFG