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Diversity Arrays Technology effectively reveals DNA polymorphism in a large and complex genome of sugarcane

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Abstract

Diversity Arrays Technology (DArT) provides whole genome profiling for hundreds to thousands of polymorphic markers in a single assay using a high-throughput microarray platform. The presented work aimed to establish DArT genotyping for the genetically challenging genome of sugarcane. Due to the genome complexity of this sugar-producing crop of high economic importance, an application of DArT genotyping to this species required extensive testing and optimization. As the method of genome complexity reduction determines the efficiency of polymorphism identification in DArT, various approaches and several methods were tested, in order to establish the most optimal. The sugarcane DArT markers generated with these established methods identified high genetic differentiation of sugarcane ancestral species from modern cultivars, in agreement with the data available for other types of molecular markers for this crop. The majority of sugarcane DArT markers segregated in a Mendelian fashion and were readily incorporated into the framework genetic map. As the DArT markers are sequence-ready genomic clones, we sequenced 384 clones and found that one-third of sequenced markers came from the transcribed portion of the sugarcane genome. The presented results further validate the potential of DArT technology in providing cost-effective genetic profiles for plants, irrespective of their genome complexity, for effective applications in molecular-assisted breeding, diversity analysis or genetic identity testing.

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Acknowledgments

We would like to thank colleagues from Diversity Arrays Technology for technical assistance and continuous help, Damian Jaccoud for performing the redundancy analysis and Aurélie Bonin for critical reading and valuable comments on the manuscript. This project was supported by a grant from the Cooperative Research Center for Sugar Industry Innovation through Biotechnology, Australia and by International Consortium for Sugarcane Biotechnology (ICSB).

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Authors and Affiliations

  1. Diversity Arrays Technology Pty. Ltd, Canberra, ACT, 2600, Australia

    Katarzyna Heller-Uszynska, Grzegorz Uszynski, Eric Huttner, Margaret Evers, Jason Carlig, Vanessa Caig & Andrzej Kilian

  2. CSIRO Plant Industry, St. Lucia, QLD, 4067, Australia

    Karen Aitken & Phillip Jackson

  3. BSES Limited, Brisbane, QLD, 4068, Australia

    George Piperidis, Mike Cox & Ross Gilmour

  4. CIRAD, UMR 1096 DAP, Montpellier, France

    Angelique D’Hont & Jean-Christophe Glaszmann

  5. SASRI, Mt Edgecombe, South Africa

    Mike Butterfield

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  1. Katarzyna Heller-Uszynska
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  2. Grzegorz Uszynski
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  4. Margaret Evers
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Correspondence to Andrzej Kilian.

Electronic supplementary material

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11032_2010_9460_MOESM1_ESM.pdf

Online Resource 1 Title: Summary of the methods used to reduce complexity of sugarcane genome. Description: The table shows primary and secondary Restriction Enzymes deployed in testing of the genome complexity reduction methods, sequences of ligated adaptors, and sequences of primers and amplification regimes used to amplify genomic representations. (PDF 111 kb)

11032_2010_9460_MOESM2_ESM.pdf

Online Resource 2 Title: Components of the array used to assess the segregation patterns of DArT markers in sugarcane. Description: The table summarizes the details of the library/array used for genotyping experiment of the IJ76-514 × Q165 mapping population: methods of genome complexity reduction, the sugarcane genotypes used to generate library/array and number of clones per each method. (PDF 103 kb)

11032_2010_9460_MOESM3_ESM.pdf

Online Resource 3 Title: Correlation values between the technical replicates of the PstI/TaqI genomic representations of two sugarcane genotypes. Description: The table displays the correlation matrix for the relative signal intensity calculated for 12 arrays per genotype for two sugarcane accessions (Q813 and F172). Each correlation value was calculated using the relative signal intensity (log2 of ratio derived from fluorescence signal of genomic representation divided by reference signal) of all clones on the array (1,536 clones printed in triplicate). The method of preparation of genomic representations used in this analysis is described in details in Methods and briefly in the legend of the table. Supplementary material 3 (PDF 107 kb)

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Heller-Uszynska, K., Uszynski, G., Huttner, E. et al. Diversity Arrays Technology effectively reveals DNA polymorphism in a large and complex genome of sugarcane. Mol Breeding 28, 37–55 (2011). https://doi.org/10.1007/s11032-010-9460-y

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