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Advances in molecular genetics and biotechnology have improved the efficiency and reduced the cost of applying marker assisted selection in plant breeding. Several molecular marker systems are available and have been employed in a variety of crops. Recently, Diversity Array Technology (DArT) was developed to score polymorphic DNA markers in a microarray format. This approach was employed to generate genotypic information that could be used to construct genetic maps and perform quantitative trait loci (QTL) mapping of important noodle quality characters and rust resistance in wheat doubled haploid populations.