Sugarcane - whole genome genotyping & GWAS

[gen_novice]

Hi all,
Planning to do whole genome genotyping and association studies in Sugarcane.
Presently reference genome is not available.
Kindly suggest which method I should go for whole genome SNP genotyping. I am thinking about the ddRAD.
Whether its advisable to go with that?.
Kindly suggest

Thanks
Parameswari B

[SNPsaurus]

If your population is not highly diverse genetically then ddRAD should not have too many locus dropouts from SNPs in the two cut sites or creation of new cut sites in the fragment, so should work fine.

I think one potential trouble would be if you want to assay a small number of loci it will be difficult to amplify with such a large genome. The other possible problem is if you have high ploidy levels and duplicated regions it will be difficult to determine if reads should collapse into one stack at a locus or if reads are paralogs and should be considered two different loci.

[gen_novice]

Thank you very much for your response.
Planning to go with ddRAD.