Any suggestions for cultivar identification using SSR (simple sequence repeat) markers
Use Fst (migration statistic) such as the Fstat program to generate a distance matrix and solve it via clustering, such as UPGMA or neighbor-joining. This analysis is particularly useful for diploids. I presume you have heterozygotes in your analysis. You can switch Fis (inbreeding) if you have excessive homozygosity.
The other way in is a haplotype network. When I get a minute I'll post the link to the programs. Machine learning isn't needed in this instance, although you could do a PCA style analysis, i.e. unsupervised learning. Unsupervised learning doesn't need a large sample size.

The other solution is a stepwise mutation phylogeny, but this is for microsatellites (one to four repeats). This is called Delta Mu squared and describes the method of repeat unit mutation. It is a distance method.
Again when I have a moment I will supply weblinks.