If you are keen to genotype the population only with SNPs then there are many assay formats like Taqman; Simple Probe; HRM; KASp; Golden Gate Assay; Fluidigm; MASS-Array; Microarray for the same, only with the availability of SNP marker information. But your datapoint size (sample*marker) plays a key role in selecting the assay type as the cost of SNP genotyping is proportional to your datapoint size when you depend on these assays.
One more good alternative is Genotyping by Sequencing (GBS), a technique that performs simultaneous development and genotyping of SNPs. This helps to identify SNPs from your own lines.
Thus developed genotyping data can be used to study the genetic diversity.
As Padmakar suggested you can try those tests, but you also need to use a good multiple sequence alignments (MSA) programs that can interpret your data. Take a look at the attached article it may help in this regard.
Article Assessment of molecular (dis)similarity: The role of multipl...