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High-throughput genotyping of hop (Humulus lupulus L.) utilising diversity arrays technology (DArT)

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Abstract

Implementation of molecular methods in hop (Humulus lupulus L.) breeding is dependent on the availability of sizeable numbers of polymorphic markers and a comprehensive understanding of genetic variation. However, use of molecular marker technology is limited due to expense, time inefficiency, laborious methodology and dependence on DNA sequence information. Diversity arrays technology (DArT) is a high-throughput cost-effective method for the discovery of large numbers of quality polymorphic markers without reliance on DNA sequence information. This study is the first to utilise DArT for hop genotyping, identifying 730 polymorphic markers from 92 hop accessions. The marker quality was high and similar to the quality of DArT markers previously generated for other species; although percentage polymorphism and polymorphism information content (PIC) were lower than in previous studies deploying other marker systems in hop. Genetic relationships in hop illustrated by DArT in this study coincide with knowledge generated using alternate methods. Several statistical analyses separated the hop accessions into genetically differentiated North American and European groupings, with hybrids between the two groups clearly distinguishable. Levels of genetic diversity were similar in the North American and European groups, but higher in the hybrid group. The markers produced from this time and cost-efficient genotyping tool will be a valuable resource for numerous applications in hop breeding and genetics studies, such as mapping, marker-assisted selection, genetic identity testing, guidance in the maintenance of genetic diversity and the directed breeding of superior cultivars.

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Acknowledgments

This work has been conducted with support from Horticulture Australia Limited (project numbers OT04003 and HP08002), Hop Products Australia, S.S. Steiner Inc. and John I. Haas Inc. The authors would like to acknowledge the contribution of Grey Leggett who was the Hop Breeder with Hop Products Australia between 1988 and 2006. Thanks also go to Kim Hummer (NCGR Corvalis) for providing assistance with source accession details.

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Authors and Affiliations

  1. School of Plant Science, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia

    E. L. Howard, S. P. Whittock & A. Koutoulis

  2. Agronomy Department, Centre for Plant Biotechnology and Breeding, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia

    J. Jakše & B. Javornik

  3. Diversity Arrays Technology Pty Ltd, PO Box 7141, Yarralumla, ACT, 2600, Australia

    J. Carling & A. Kilian

  4. S. S. Steiner Inc, 655 Madison Ave, New York, NY, 10065-8043, USA

    P. D. Matthews

  5. John I. Haas Inc, PO Box 1441, Yakima, WA, 98907, USA

    G. Probasco

  6. Hop Genetics and Breeding Program, USDA-ARS, 3450 SW Campus Way, Corvallis, OR, 97331, USA

    J. A. Henning

  7. Wye Hops Ltd., China Farm, Harbledown, Canterbury, Kent, CT2 9AR, UK

    P. Darby

  8. Slovenian Institute of Hop Research and Brewing, Cesta Zalskega Tabora 2, 3310, Zalec, Slovenia

    A. Cerenak

  9. Hop Products Australia, 26 Cambridge Road, Bellerive, TAS, 7001, Australia

    S. P. Whittock

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  1. E. L. Howard
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  3. J. Jakše
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  9. A. Cerenak
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  10. B. Javornik
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  11. A. Kilian
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  12. A. Koutoulis
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Correspondence to A. Koutoulis.

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Communicated by P. Heslop-Harrison.

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Howard, E.L., Whittock, S.P., Jakše, J. et al. High-throughput genotyping of hop (Humulus lupulus L.) utilising diversity arrays technology (DArT). Theor Appl Genet 122, 1265–1280 (2011). https://doi.org/10.1007/s00122-011-1529-4

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