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Molecular and quantitative genetic analyses of hop (Humulus lupulus L.)

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McAdam, EL 2013 , 'Molecular and quantitative genetic analyses of hop (Humulus lupulus L.)', PhD thesis, University of Tasmania.

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Abstract

Beer derives bitterness, flavour and aroma from the secondary metabolites of the hop cone. Breeding programs strive to produce superior hop cultivars with higher yields and desirable brewing characteristics as well as to increase efficiency and reduce input costs. In pursuing these goals, classical breeding approaches rely on morphological and biochemical markers to assess the genetic potential of hop. These methods are, however, hampered by environmental influences and by the complex interactions between hop secondary metabolites and the brewing process. Genetic-based analyses are able to account for these environmental influences to assess quantitative variation at the genetic level. This thesis describes investigations into two of these analyses, using molecular markers for quantitative trait loci (QTL) identification and the estimation of quantitative genetic parameters. These investigations were conducted with the aim of improving our understanding of the genetic control of hop cone chemistry and important agronomic traits as well as to provide some insight as to the potential of these methods to inform hop breeding programs.
Molecular technologies are generally costly, low throughput and reliant on DNA sequence information. Diversity arrays technology (DArT) is a marker system invented specifically to overcome these barriers. This thesis examines the applicability of DArT for high-throughput, cost-effective genotyping of hop. A total of 1241 polymorphic markers were identified from 497 hop accessions. A genetic diversity analysis was conducted on representative hop accessions to validate the robustness of these markers in the hop system. Hop accessions separated into two broad, genetically distinct groups (European and North American origin), with hybrids between them clearly distinguishable. These genetic relationships concur with the current understanding of hop phylogenetics and diversity, demonstrating the accuracy and resolution of DArT markers in a hop system and their potential as an effective marker technology for this species.
The DArT markers, in conjunction with microsatellite, RAPD, STS and AFLP markers, were used to construct genetic linkage maps of two hop mapping populations; these linkage maps were then used for QTL analysis. This study focussed on identifying QTL for traits relating to three key targets in the genetic improvement of hop: expediting plant sex identification, increasing yield capacity and improving the organoleptic properties of hop cones. Sixty-three significant QTL were detected for 36 traits, including two yield traits (dry cone weight and essential oil content) and 33 different secondary metabolite traits. A previously identified sex-linked marker (HLAGA7) was also verified in a third hop pedigree, demonstrating the utility of this marker as a routine screening tool in hop breeding programs. Many of the QTL identified were co-located, providing the first demonstration of pleiotropy/linkage influencing secondary metabolites in hop. Both pleiotropy and linkage have implications for hop breeding, as selection for specific secondary metabolites associated with such loci are likely to instigate adverse changes to other secondary metabolites, impeding the breeding for particular chemical profiles. Specific QTL influencing single secondary metabolites were also identified, demonstrating the potential for selection of particular chemical traits in isolation. The findings of this study significantly advance our understanding of the genetic control of sex, yield and secondary metabolites in hop, and provide important information on incorporating QTL for these complex traits into hop molecular selection programs.
The genetic control of hop traits was also examined through quantitative genetics analysis. Traits related to cone chemistry, yield and plant growth were assessed in a hop progeny trial, consisting of 108 families of diverse genetic backgrounds (European, North American and hybrid origins). The investigation revealed significant genetic diversity between families in emergence of shoots, vegetative morphology and all assessed cone chemical traits, but not in cone yield. Cone chemical traits were generally more heritable (0.15 to 0.29) than growth traits (0.04 to 0.20), reflecting the more intense genetic selection of hop cone chemistry and the greater environmental and agronomical influences on plant growth. Significant genetic correlations existed between cone chemistry and plant growth traits, with more vigorous plants associated with lower levels of α-acid and β-acid. This trend may reflect the underlying binary population structure of founder genotypes having either European or North American origin, or possibly the influence of selection in the Australian environment. This study also showed for the first time that sex has an effect on the phenotype of hop plants as early as emergence. It is currently held that male and female hop plants are indistinguishable until flowering, but this study found that male and female plants display differences in variation from emergence to cone maturity. This study provides valuable information on the potential genetic variation in cone chemistry and growth traits available to hop breeders, the prospective heritability of these traits and the influence that factors other than additive genetic influences have on the hop phenotype. Relationships between cone chemistry and plant growth traits present several growth measures that could be used as proxy selection indicators for particular cone chemical attributes.
This thesis provides a comprehensive investigation of two genetic-based techniques to assess quantitative genetic variation in hop traits. The findings of both molecular and quantitative genetic analyses provide important insights into the underlying genetic architecture of hop and reveal novel information on the biology of this species. The knowledge gained from both techniques demonstrates the value of their incorporation into breeding programs.

Item Type: Thesis - PhD
Authors/Creators:McAdam, EL
Keywords: hop (Humulus lupulus L), Quantitative Trait Loci (QTL), linkage map, Diversity Arrays Technology (DArT), secondary metabolite, dioecy, molecular marker
Copyright Information:

Copyright 2013 the author

Additional Information:

Chapter 2 appears to be the equivalent of a post-peer-review, pre-copyedit version of an article published in TAG theoretical and applied genetics. The final authenticated version is available online at: https://doi.org/10.1007/s00122-011-1529-4
Chapter 3 appears to be a post-print version of an article published as: McAdam, E. L., Freeman, J. S., Whittock, S. P., Buck, E. J., Jakše, J., Cerenak, A., Javornik, B., Kilian, A., Wang, C. H., Andersen, D., Vaillancourt, R. E., Carling, J., Beatson, R., Graham, L., Graham, D., Darby, P., Koutouli,s A., 2013. Quantitative trait loci in hop (Humulus lupulus L.) reveal complex genetic architecture underlying variation in sex, yield and cone chemistry, BMC genomics, 14: 360. Licensed under Creative Commons Attribution 2.0 (CC BY 2.0) https://creativecommons.org/licenses/by/2.0/
Chapter 4 appears to be the equivalent of a post-print version of article published as McAdam, E. l. et al. 2014. Quantitative genetic parameters for yield, plant growth and cone chemical traits in hop (Humulus lupulus L.), BMC genetics, 15:22. Licensed under Creative Commons Attribution CC0 1.0 Universal (CC 1.0) Public Domain Dedication https://creativecommons.org/publicdomain/zero/1.0/

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