Many types of genetic reference populations can be employed. In the NABGMP we have based many of our QTL detection efforts on populations of homozygous doubled haploid genotypes. Genetic reference populations are characterized in terms of markers. In general, DNA-based markers are used, as they are abundant and provide complete chromosomes coverage. However, morphological and biochemical markers provide important reference points. A linkage map is constructed based on the marker data. This map is useful for comparison with other maps within the species and for making inter-specific and inter-generic comparisons. At the same time, the reference populations are characterized for target traits, which range from resistance to biotic and abiotic stresses to quality and agronomic performance parameters. Finally, the phenotype and genotype data sets are integrated for QTL analysis. QTL are located to regions of the genome at specified levels of statistical probability. QTL information can then be used as a basis for germplasm characterization, conservation, and improvement. For example, molecular marker-assisted selection can be used to transfer QTL from one genotype to another, to improve populations, or as a basis for cloning and characterizing genes.

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