SNP annotation and Candidate gene identification using different but closely related species?

Question

[vetriventhan]

Dear all,

I am planning to do GBS of little millet (Panicum sumatrense) but we do not have reference genome to identify SNPs and perform GWAS for candidate gene identification. Is it possible or ok to use the closely related species switchgrass (Panicum virgatum) as reference genome for Panicum sumatrense)?

Thanks and Regards

Vetri

[carlopecoraro2]

It is possible but it depends on the percentage of successfully mapped sequences. Hope this helps.