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Diversity arrays technology (DArT) markers in apple for genetic linkage maps |
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| Authors: | Henk J. Schouten W. Eric van de Weg Jason Carling Sabaz Ali Khan Steven J. McKay Martijn P. W. van Kaauwen Alexander H. J. Wittenberg Herma J. J. Koehorst-van Putten Yolanda Noordijk Zhongshan Gao D. Jasper G. Rees Maria M. Van Dyk Damian Jaccoud Michael J. Considine Andrzej Kilian |
| Affiliation: | 1. Wageningen University and Research Centre, P.O. Box 16, 6700 AA, Wageningen, The Netherlands 2. Diversity Arrays Technology, PO Box 7141, Yarralumla, ACT, 2600, Australia 3. Department of Horticultural Science, University of Minnesota, Alderman Hall, 1970 Folwell Ave, St. Paul, MN, 55108, USA 7. KeyGene bv, P.O. Box 216, 6700 AE, Wageningen, The Netherlands 4. Department of Horticulture, Zhejiang University, Hangzhou, 310029, China 8. ARC: Biotechnology Platform, Agricultural Research Council, Private Bag X5, Onderstepoort, Pretoria, 0110, South Africa 9. Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Hatfield, Pretoria, 0028, South Africa 5. School of Plant Biology, and the Institute of Agriculture, University of Western Australia, M084, Crawley, WA, 6009, Australia 6. Department of Agriculture and Food Western Australia, South Perth, WA, 6151, Australia |
| Abstract: | 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 PstI 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11032-011-9579-5) contains supplementary material, which is available to authorized users. |
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