Thanks to advances in next generation sequencing it is now straightforward to develop tens or even hundreds of thousands of SNP markers. Advances in genotyping technology have made it feasible to genotype progenies of crosses, panels of genotypes, or even a complete breeding program, by using arrays with tens of thousands of SNPs, or by random or targeted sequencing technologies. Recently software has been developed for dosage scoring and linkage mapping in polyploid crops. This means that advanced genetic analyses can now also be performed in many polyploid ornamentals. A DNA marker, such as a single nucleotide polymorphism (SNP), linked to a trait enables following a gene or allele during crosses and in a breeding program. Association of a SNP marker to a trait or a component of a trait may be done through QTL analysis in segregating populations, by genome-wide association analysis (GWAS) in a set of accessions, or through an analysis across a pedigree. In these analyses, a dense linkage map is a very important tool, to delineate and possibly narrow down the QTL interval and to filter away false positive SNPs. New developments in linkage mapping include paying attention to even marker coverage, and new ways to use markers to infer haplotypes. The latter is especially important in polyploids, in populations with multiple parents, or in wide panels used for association studies. In such cases multiple functional alleles may segregate simultaneously, that cannot all be tagged uniquely by single biallelic SNP markers.