Traditionally, mapping of loci that have an effect on a trait e.g. disease resistance, has been performed on a bi-parental population. It is a method with a great power to detect variants segregating in the population, but the disadvantage of only sampling the genetic variation represented in the two founder genomes. Alternatively, mapping can be performed by sampling of distantly related individuals for association mapping of a whole population. This method can capture more genetic diversity, but at the cost of needing very large sample sizes in order to have enough power to reliably detect loci. Multi-parental populations have gained increasing attention over the recent years for genetic mapping studies in plants because they combine the genetic diversity of whole population association studies with the power of bi-parental populations. Several variations of multi-parental populations exist, of which Multi-parent Advanced Generation Intercrosses (MAGIC) and Nested Association Mapping (NAM) populations are most frequently reported. The MAGIC population is an inter-mated population where multiple inbred founders are crossed repeatedly before inbreeding the outbred individuals in the population for several generations resulting in a genetically diverse population consisting of isogenic lines with fine-scale mosaics of genomic diversity from each founder. The NAM population is developed by crossing a single inbred donor line to a successive collection of different inbred and adapted parent lines. NAM populations were developed in order to increase the power and precision of Quantitative Trait Locus (QTL) mapping by combining the advantages of association mapping and bi-parental mapping. In an ongoing study, four NAM populations were developed from two Chinese wheat Landraces and two synthetic hexaploid wheat lines as donors for resistance for different important diseases such as powdery mildew, yellow rust and fusarium head blight. In total, 717 lines were developed. Lines were genotyped using the wheat SNP 15k array and phenotyped in two consecutive years for disease resistances. The initial association mapping results have identified and mapped new QTL for disease resistance. Additionally, four MAGIC populations have been developed using eight genetically distinct founders as donor of resistance to important diseases such as powdery mildew, septoria tritici blotch, yellow rust and fusarium head blight. In total, approximately 800 lines have been developed and genotyped using a wheat SNP 20k array. These lines have been phenotyped in the field and subjected to association studies for a variety of resistance traits.