Butler_whole_thesis.pdf (4.36 MB)
Studies of eucalypt genetic and genomic architecture
thesisposted on 2023-05-27, 09:30 authored by Jakob ButlerJakob Butler
The utility of genomics for theoretical and practical outcomes has been greatly enhanced by the advent of high throughput molecular technologies. This thesis reports the application of linkage mapping, quantitative trait loci analysis, gene family annotation and comparative genomics to study various aspects of the genetic and genomic architecture of eucalypts, a group of Myrtaceous flora that are of significant economic and ecological value worldwide. Linkage mapping was employed to compare the genomic architecture of Corymbia and Eucalyptus. Three independent high density linkage maps for two Corymbia species (Corymbia citriodora subsp. variegata and C. torelliana) were constructed from two hybrid pedigrees of C. torelliana individuals crossed with a common C. citriodora subsp. variegata parent. Subsequent analysis provided evidence for large (from 1 - 13 MB) intra-chromosomal rearrangements between Corymbia and Eucalyptus on seven of their 11 chromosomes. Most rearrangements were supported through comparisons of the three Corymbia maps to the E. grandis reference genome, and to other Eucalyptus linkage maps. These are the first large-scale chromosomal rearrangements discovered between eucalypts. However, in the context of a divergence approximately 52 million years ago, the genomic structure of the two genera was remarkably conserved; adding to growing evidence for conservation of genome structure within lineages of woody angiosperms. These maps informed the collaborative assembly of the Corymbia reference genome (not itself part of this thesis), which formed the basis of further research reported below. The genetic basis of variation in resistance to myrtle rust, caused by Austropuccinia psidii (formerly Puccinia psidii), was examined using an E. globulus linkage map. Quantitative trait loci (QTL) analysis was undertaken using 218 genotypes of an outcross E. globulus F2 mapping family, phenotyped by controlled inoculation of their open pollinated progeny (11 per genotype on average) with A. psidii. To examine possible independent control of different aspects of plant resistance, QTL analyses were conducted by classifying individuals as symptomless versus those exhibiting symptoms, and those exhibiting a hypersensitive reaction versus more severe symptoms. Four QTL were identified; two influencing the symptomless response, and two influencing the hypersensitive response. The potential resistance mechanisms underlying these different QTL are discussed. Together with past findings, this study suggests that A. psidii resistance in eucalypts is quantitative in nature and influenced by the complex interaction of multiple loci of variable effect. To examine differences in genetic architecture underlying disease resistance in Corymbia and Eucalyptus and explore differences in resistance to exotic and co-evolved pathogens, the Corymbia linkage maps were used to perform the first QTL study for disease resistance in this genus. Resistance was examined to the pandemic strain of A. psidii and two strains of the native pathogen Quambalaria pitereka (QSB1 and QSB2). These analyses were undertaken using 360 genotypes from the two C. citriodora subsp. variegata x C. torelliana F1 hybrid mapping crosses, phenotyped in separate controlled inoculations. Twenty QTL were identified; six for rust, nine for QSB1 and five for QSB2. Positioning these QTL on the Corymbia reference genome revealed only one case of QTL co-location (peak location within ¬¨¬± 2 MB) between rust and QSB, while no QTL for either of the QSB strains were co-located. Resistance to A. psidii and Q. pitereka in Corymbia appears to be controlled by multiple independent loci, with a larger percentage of variation explained by both the mean effect of individual QTL and the total combined effect within pedigree in the response to QSB compared to rust. Notable co-locations with E. globulus resistance QTL for rust and other pathogens were detected, and the implications of this conservation explored. Variation in genome architecture between Corymbia and Eucalyptus was further examined through comparison of the number, phylogenetic relatedness and physical distribution of the terpene synthase (TPS) gene family. Terpenes are important foliar chemicals for both primary and secondary metabolism, and Eucalyptus is notable for its expansive TPS gene family. This gene family was manually annotated in the Corymbia reference genome, revealing a similar overall number and subfamily representation of TPS genes relative to Eucalyptus, suggesting these features are characteristic of eucalypts. Physical arrangement of TPS genes involved in the synthesis of secondary metabolites differed significantly between Eucalyptus and Corymbia with translocation, expansion/contraction and loss of TPS gene clusters. In contrast, those involved in primary metabolism were often highly conserved, likely reflecting different selective constraints. The mechanisms underlying the fine-scale variability in TPS genes despite the broad conservation observed between the eucalypts are explored. Combined, these results reveal a common theme of broad conservation in genomic and genetic architecture between different eucalypt genera, with greater variation in fine-scale features such as chromosomal structure, genetic architecture underlying variation in disease resistance and gene family arrangement. This work adds to a fundamental understanding of what differentiates Eucalyptus and Corymbia, and serves to highlight the potential differences one can expect between tree genera.
Rights statementCopyright 2018 the author Chapter 2 appears to be the equivalent of a post-print version of an article published as: Butler, J. B., Vaillancourt, R. E., Potts, B. M., Lee, D. J., King, G. J., Baten, A., Shepherd, M., Freeman, J. S., 2017. Comparative genomics of Eucalyptus and Corymbia reveals low rates of genome structural rearrangement. BMC genomics, 18:397. The article is Copyright the author(s). 2017 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated Chapter 3 appears to be the equivalent of a post-peer-review, pre-copyedit version of an article published in Tree genetics and genomes. The final authenticated version is available online at: https://doi.org/10.1007/s11295-016-0987-x Chapter 5 appears to be the equivalent of a post-print version of an article published as: Butler, J. B., Freeman, J. S., Potts, B. M., Vaillancourt, R. E., Grattapaglia, D., Silva-Junior, O. B., Simmons, B. A., Healey, A. L., Schmutz, J., Barry, K. W., Lee, D. J., Henry, R. J., King, G. J., Baten, A., Shepherd, M., 2018. Annotation of the Corymbia terpene synthase gene family shows broad conservation but dynamic evolution of physical clusters relative to Eucalyptus, Heredity, 121, 87-104. The chapter is subject to Springer Nature re-use terms. https://www.nature.com/authors/policies/license.html#AAMtermsV1