Diversity arrays technology (DArT) markers in apple for genetic linkage maps

• Published in: Molecular breeding Vol. 29; no. 3; pp. 645 - 660
• Main Authors: Schouten, Henk J., van de Weg, W. Eric, Carling, Jason, Khan, Sabaz Ali, McKay, Steven J., van Kaauwen, Martijn P. W., Wittenberg, Alexander H. J., Koehorst-van Putten, Herma J. J., Noordijk, Yolanda, Gao, Zhongshan, Rees, D. Jasper G., Van Dyk, Maria M., Jaccoud, Damian, Considine, Michael J., Kilian, Andrzej
• Format: Journal Article
• Language: English
• Published: Dordrecht Springer Netherlands 01.03.2012; Springer Nature B.V
• Subjects: Apples; Arrays; assisted selection; Biomedical and Life Sciences; Biotechnology; Complexity; consensus map; Data points; fire-blight resistance; Gene mapping; Genetic diversity; Genomes; Genotyping; Life Sciences; Low cost; malus-pumila mill; Mapping; Markers; Methylation; Molecular biology; Plant biology; Plant Genetics and Genomics; Plant Pathology; Plant Physiology; Plant Sciences; Populations; quantitative trait loci; Reduction; Redundancy; scab resistance; ssr markers; venturia-inaequalis; wild relatives; x-domestica borkh; DArT; Genetic mapping; Molecular markers; Apple; Diversity
• ISSN: 1380-3743; 1572-9788
• DOI: 10.1007/s11032-011-9579-5

Diversity Arrays Technology (DArT) provides a high-throughput whole-genome genotyping platform for the detection and scoring of hundreds of polymorphic loci without any need for prior sequence information. The work presented here details the development and performance of a DArT genotyping array for apple. This is the first paper on DArT in horticultural trees. Genetic mapping of DArT markers in two mapping populations and their integration with other marker types showed that DArT is a powerful high-throughput method for obtaining accurate and reproducible marker data, despite the low cost per data point. This method appears to be suitable for aligning the genetic maps of different segregating populations. The standard complexity reduction method, based on the methylation-sensitive Pst I restriction enzyme, resulted in a high frequency of markers, although there was 52–54% redundancy due to the repeated sampling of highly similar sequences. Sequencing of the marker clones showed that they are significantly enriched for low-copy, genic regions. The genome coverage using the standard method was 55–76%. For improved genome coverage, an alternative complexity reduction method was examined, which resulted in less redundancy and additional segregating markers. The DArT markers proved to be of high quality and were very suitable for genetic mapping at low cost for the apple, providing moderate genome coverage.