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Open Access Research article

DArT markers for the rye genome - genetic diversity and mapping

Hanna Bolibok-Brągoszewska1*, Katarzyna Heller-Uszyńska2, Peter Wenzl2, Grzegorz Uszyński2, Andrzej Kilian2 and Monika Rakoczy-Trojanowska1

Author Affiliations

1 Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences (SGGW), 159 Nowoursynowska Str, 02-776 Warsaw, Poland

2 Diversity Arrays Technology P/L, 1 Wilf Crane Crescent, Yarralumla, Canberra, ACT, 2600, Australia

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BMC Genomics 2009, 10:578  doi:10.1186/1471-2164-10-578

Published: 3 December 2009

Abstract

Background

Implementation of molecular breeding in rye (Secale cereale L.) improvement programs depends on the availability of high-density molecular linkage maps. However, the number of sequence-specific PCR-based markers available for the species is limited. Diversity Arrays Technology (DArT) is a microarray-based method allowing for detection of DNA polymorphism at several thousand loci in a single assay without relying on DNA sequence information. The objective of this study was the development and application of Diversity Arrays technology for rye.

Results

Using the PstI/TaqI method of complexity reduction we created a rye diversity panel from DNA of 16 rye varieties and 15 rye inbred lines, including parents of a mapping population consisting of 82 recombinant inbred lines. The usefulness of a wheat diversity panel for identification of DArT markers for rye was also demonstrated. We identified 1022 clones that were polymorphic in the genotyped ILs and varieties and 1965 clones that differentiated the parental lines L318 and L9 and segregated in the mapping population. Hierarchical clustering and ordination analysis were performed based on the 1022 DArT markers to reveal genetic relationships between the rye varieties and inbred lines included in the study. Chromosomal location of 1872 DArT markers was determined using wheat-rye addition lines and 1818 DArT markers (among them 1181 unique, non-cosegregating) were placed on a genetic linkage map of the cross L318 × L9, providing an average density of one unique marker every 2.68 cM. This is the most saturated rye linkage map based solely on transferable markers available at the moment, providing rye breeders and researches with a better choice of markers and a higher probability of finding polymorphic markers in the region of interest.

Conclusion

The Diversity Arrays Technology can be efficiently and effectively used for rye genome analyses - assessment of genetic similarity and linkage mapping. The 11520-clone rye genotyping panel with several thousand markers with determined chromosomal location and accessible through an inexpensive genotyping service is a valuable resource for studies on rye genome organization and in molecular breeding of the species.