Open Access Research article

Quantitative trait loci in hop (Humulus lupulus L.) reveal complex genetic architecture underlying variation in sex, yield and cone chemistry

Erin L McAdam1*, Jules S Freeman12, Simon P Whittock13, Emily J Buck4, Jernej Jakse5, Andreja Cerenak6, Branka Javornik5, Andrzej Kilian7, Cai-Hong Wang8, Dave Andersen9, René E Vaillancourt1, Jason Carling7, Ron Beatson9, Lawrence Graham9, Donna Graham9, Peter Darby10 and Anthony Koutoulis1

Author Affiliations

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

2 Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Locked Bag 4, Maroochydore 4558 QLD, Australia

3 Hop Products Australia, 26 Cambridge Road, Bellerive 7018 TAS, Australia

4 The New Zealand Institute for Plant & Food Research Limited, Private Bag 11 600, Palmerston North 4442, New Zealand

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

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

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

8 Department of Horticulture, Qingdao Agricultural University, Qingdao 266109, China

9 The New Zealand Institute for Plant & Food Research Limited, Old Mill Road, Motueka 7120, New Zealand

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

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BMC Genomics 2013, 14:360  doi:10.1186/1471-2164-14-360

Published: 30 May 2013



Hop (Humulus lupulus L.) is cultivated for its cones, the secondary metabolites of which contribute bitterness, flavour and aroma to beer. Molecular breeding methods, such as marker assisted selection (MAS), have great potential for improving the efficiency of hop breeding. The success of MAS is reliant on the identification of reliable marker-trait associations. This study used quantitative trait loci (QTL) analysis to identify marker-trait associations for hop, focusing on traits related to expediting plant sex identification, increasing yield capacity and improving bittering, flavour and aroma chemistry.


QTL analysis was performed on two new linkage maps incorporating transferable Diversity Arrays Technology (DArT) markers. Sixty-three QTL were identified, influencing 36 of the 50 traits examined. A putative sex-linked marker was validated in a different pedigree, confirming the potential of this marker as a screening tool in hop breeding programs. An ontogenetically stable QTL was identified for the yield trait dry cone weight; and a QTL was identified for essential oil content, which verified the genetic basis for variation in secondary metabolite accumulation in hop cones. A total of 60 QTL were identified for 33 secondary metabolite traits. Of these, 51 were pleiotropic/linked, affecting a substantial number of secondary metabolites; nine were specific to individual secondary metabolites.


Pleiotropy and linkage, found for the first time to influence multiple hop secondary metabolites, have important implications for molecular selection methods. The selection of particular secondary metabolite profiles using pleiotropic/linked QTL will be challenging because of the difficulty of selecting for specific traits without adversely changing others. QTL specific to individual secondary metabolites, however, offer unequalled value to selection programs. In addition to their potential for selection, the QTL identified in this study advance our understanding of the genetic control of traits of current economic and breeding significance in hop and demonstrate the complex genetic architecture underlying variation in these traits. The linkage information obtained in this study, based on transferable markers, can be used to facilitate the validation of QTL, crucial to the success of MAS.

Linkage map; Transferable marker; Diversity arrays technology DArT; Pleiotropy; Sex-linked marker; Dry cone weight; Plant secondary metabolite; Hop acid; Essential oil