Hi all,

I am analyzing 24 genomes of a rare plant species. I have identified SNPs and I have the VCF files. There are 2 groups of phenotypes (12 genomes corresponding to each phenotype), and I am trying to find trait-associated SNPs across the entire genome. I don’t know whether the genetic underpinning is mono- or poly-genic. I have been told that this is a small number of samples to be used in GWAS analysis. In that case, may please anyone recommend an alternative?. Is there any software to undertake this analysis?.

I have found the software assotesteR, from this thread: Snp Cluster Analysis

but I think I need to know the loci I want to test with this program, so I need to undertake first the trait-associated SNPs identification. I understand that today there are a lot of genomes available from many species, but, what happens when it is a rare species or there is no money and you only have a small number of samples?. I am wondering whether an alternative exists.

Thank you very much in advance.