Regions of the genome affecting physical and chemical wood properties (quantitative trait loci (QTL)), as well as growth, were identified using a clonally replicated, outbred F 2 family (112 genotypes, each with two ramets) of Eucalyptus globulus, planted in a field trial in north-west Tasmania. Traits studied were growth (assessed by stem diameter), wood density, cellulose content, pulp yield and lignin content. These traits are important in breeding for pulpwood, and will be important in breeding for carbon sequestration and biofuel production. Between one and four QTL were located for each trait, with each QTL explaining between 4% and 12% of the phenotypic variation. Several QTL for chemical wood properties were co-located, consistent with their high phenotypic correlations, and may reflect pleiotropic effects of the same genes. In contrast, QTL for density and lignin content with overlapping confidence intervals were considered to be due to independent genes, since the QTL effects were inherited from different parents. The inclusion of fully informative microsatellites on the linkage map allowed the determination of homology at the linkage group level between QTL and candidate genes in different pedigrees of E. globulus and different eucalypt species. None of the candidate genes mapped in comparable studies co-located with our major QTL for wood chemical properties, arguing that there are important candidate genes yet to be discovered.

The economics of short-rotation pulpwood plantations of Eucalyptus globulus as a coppice crop are influenced by stump survival and subsequent coppice growth rates. This study revealed significant genetic diversity in coppicing traits, both within and between subraces, following felling in a progeny trial after 9 years of growth. A total of 67% of trees coppiced after 14 months, but subraces varied from 43 to 73%. Heritabilities for coppice success (0.07) and subsequent growth (0.16–0.17) were low but statistically significant. Strong genetic correlation between presence/absence of coppice, the number of stems coppicing from the stump and modal coppice height, indicate that selection is possible by using the binary trait. The ability of a tree to coppice was genetically correlated with tree growth prior to felling (rg = 0.61) and with nursery-grown seedling traits, where large genetic differences were observed in the development of lignotubers. Coppicing was genetically correlated with the number of nodes with lignotubers (rg = 0.66) and seedling stem diameter at the cotyledonary node (rg = 0.91). These traits were uncorrelated with later age growth and with each other. The results suggest that coppicing is influenced by three independent mechanisms—lignotuber development, enlargement of the seedling stem at the cotyledonary node and vigorous growth—which enhance ability to survive catastrophic damage, and indicate that both lignotuber and coppice development can be altered by both natural and artificial selection.

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.

BackgroundHop (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.ResultsQTL 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.ConclusionsPleiotropy 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.