Methodology article

Coupling amplified DNA from flow-sorted chromosomes to high-density SNP mapping in barley

Hana Šimková^1,2 , Jan T Svensson^3,4 , Pascal Condamine³ , Eva Hřibová¹ , Pavla Suchánková¹ , Prasanna R Bhat³ , Jan Bartoš¹ , Jan Šafář¹ , Timothy J Close³ and Jaroslav Doležel^1,2

¹Laboratory of Molecular Cytogenetics and Cytometry, Institute of Experimental Botany, Sokolovská 6, CZ-77200 Olomouc, Czech Republic

²Department of Cell Biology and Genetics, Palacký University, Šlechtitelů 11, CZ-78371 Olomouc, Czech Republic

³Department of Botany and Plant Sciences, University of California, Riverside, CA-92521-0124, USA

⁴VKR Center of Excellence Pro-Active Plants, Department of Plant Biology and Biotechnology, University of Copenhagen, DK-1871 Frederiksberg C, Denmark

author email corresponding author email

BMC Genomics 2008, 9:294doi:10.1186/1471-2164-9-294

Published:	19 June 2008

Abstract

Background

Flow cytometry facilitates sorting of single chromosomes and chromosome arms which can be used for targeted genome analysis. However, the recovery of microgram amounts of DNA needed for some assays requires sorting of millions of chromosomes which is laborious and time consuming. Yet, many genomic applications such as development of genetic maps or physical mapping do not require large DNA fragments. In such cases time-consuming de novo sorting can be minimized by utilizing whole-genome amplification.

Results

Here we report a protocol optimized in barley including amplification of DNA from only ten thousand chromosomes, which can be isolated in less than one hour. Flow-sorted chromosomes were treated with proteinase K and amplified using Phi29 multiple displacement amplification (MDA). Overnight amplification in a 20-microlitre reaction produced 3.7 – 5.7 micrograms DNA with a majority of products between 5 and 30 kb. To determine the purity of sorted fractions and potential amplification bias we used quantitative PCR for specific genes on each chromosome. To extend the analysis to a whole genome level we performed an oligonucleotide pool assay (OPA) for interrogation of 1524 loci, of which 1153 loci had known genetic map positions. Analysis of unamplified genomic DNA of barley cv. Akcent using this OPA resulted in 1426 markers with present calls. Comparison with three replicates of amplified genomic DNA revealed >99% concordance. DNA samples from amplified chromosome 1H and a fraction containing chromosomes 2H – 7H were examined. In addition to loci with known map positions, 349 loci with unknown map positions were included. Based on this analysis 40 new loci were mapped to 1H.

Conclusion

The results indicate a significant potential of using this approach for physical mapping. Moreover, the study showed that multiple displacement amplification of flow-sorted chromosomes is highly efficient and representative which considerably expands the potential of chromosome flow sorting in plant genomics.