A phylogenomic approach reveals a low somatic mutation rate in a long-lived plant.

Somatic mutations can have important effects on the life history, ecology, and evolution of plants, but the rate at which they accumulate is poorly understood and difficult to measure directly. Here, we develop a method to measure somatic mutations in individual plants and use it to estimate the somatic mutation rate in a large, long-lived, phenotypically mosaic Eucalyptus melliodora tree. Despite being 100 times larger than Arabidopsis, this tree has a per-generation mutation rate only ten times greater, which suggests that this species may have evolved mechanisms to reduce the mutation rate per unit of growth. This adds to a growing body of evidence that illuminates the correlated evolutionary shifts in mutation rate and life history in plants.

Overexpression of a developing xylem cDNA library in transgenic poplar generates high mutation rate specific to wood formation.

We investigated feasibility of the Full-length complementary DNA OvereXpression (FOX) system as a mutagenesis approach in poplar, using developing xylem tissue. The main goal was to assess the overall mutation rate and if the system will increase instances of mutants affected in traits linked to the xylem tissue. Indeed, we found a high mutation rate of 17.7%, whereas 80% of all mutants were significantly affected in cellulose, lignin and/or hemicellulose. Cell wall biosynthesis is a major process occurring during xylem development. Enrichment of mutants affected in cell wall composition suggests that the tissue source for the FOX library influenced the occurrence of mutants affected in a trait linked to this tissue. Additionally, we found that FLcDNAs from mutants affected in cell wall composition were homologous to genes known to be involved in cell wall biosynthesis and most recovered FLcDNAs corresponded to genes whose native expression was highest in xylem. We characterized in detail a mutant line with increased diameter. The phenotype was caused by a poplar homolog of LONELY GUY 1 (LOG1), which encodes an enzyme in cytokinin biosynthesis and significantly increased xylem proliferation. The causative role of LOG1 in the observed phenotype was further reaffirmed by elevated cytokinin concentration in the mutant and recapitulation overexpression experiment wherein multiple independent lines phenocopied the original FOX mutant. Our experiments show that the FOX approach can be efficiently used for gene discovery and molecular interrogation of traits specific to woody perennial growth and development.

New approaches to tannin analysis of leaves can be used to explain in vitro biological activities associated with herbivore defence.

Although tannins have been an important focus of studies of plant-animal interactions, traditional tannin analyses cannot differentiate between the diversity of structures present in plants. This has limited our understanding of how different mixtures of these widespread secondary metabolites contribute to variation in biological activity. We used UPLC-MS/MS to determine the concentration and broad composition of tannins and polyphenols in 628 eucalypt (Eucalyptus, Corymbia and Angophora) samples, and related these to three in vitro functional measures believed to influence herbivore defence: protein precipitation capacity, oxidative activity at high pH and capacity to reduce in vitro nitrogen (N) digestibility. Protein precipitation capacity was most strongly correlated with concentrations of procyanidin subunits in proanthocyanidins (PAs), and late-eluting ellagitannins. Capacity to reduce in vitro N digestibility was affected most by the subunit composition and mean degree of polymerisation (mDP) of PAs. Finally, concentrations of ellagitannins and prodelphinidin subunits of PAs were the strongest determinants of oxidative activity. The results illustrate why measures of total tannins rarely correlate with animal feeding responses. However, they also confirm that the analytical techniques utilised here could allow researchers to understand how variation in tannins influence the ecology of individuals and populations of herbivores, and, ultimately, other ecosystem processes.

High marker density GWAS provides novel insights into the genomic architecture of terpene oil yield in Eucalyptus.

Terpenoid-based essential oils are economically important commodities, yet beyond their biosynthetic pathways, little is known about the genetic architecture of terpene oil yield from plants. Transport, storage, evaporative loss, transcriptional regulation and precursor competition may be important contributors to this complex trait. Here, we associate 2.39 million single nucleotide polymorphisms derived from shallow whole-genome sequencing of 468 Eucalyptus polybractea individuals with 12 traits related to the overall terpene yield, eight direct measures of terpene concentration and four biomass-related traits. Our results show that in addition to terpene biosynthesis, development of secretory cavities, where terpenes are both synthesized and stored, and transport of terpenes were important components of terpene yield. For sesquiterpene concentrations, the availability of precursors in the cytosol was important. Candidate terpene synthase genes for the production of 1,8-cineole and α-pinene, and ß-pinene (which comprised > 80% of the total terpenes) were functionally characterized as a 1,8-cineole synthase and a ß/α-pinene synthase. Our results provide novel insights into the genomic architecture of terpene yield and we provide candidate genes for breeding or engineering of crops for biofuels or the production of industrially valuable terpenes.

Terpenes associated with resistance against the gall wasp, Leptocybe invasa, in Eucalyptus grandis.

Leptocybe invasa is an insect pest causing gall formation on oviposited shoot tips and leaves of Eucalyptus trees leading to leaf deformation, stunting, and death in severe cases. We previously observed different constitutive and induced terpenes, plant specialized metabolites that may act as attractants or repellents to insects, in a resistant and susceptible clone of Eucalyptus challenged with L. invasa. We tested the hypothesis that specific terpenes are associated with pest resistance in a Eucalyptus grandis half-sib population. Insect damage was scored over 2 infestation cycles, and leaves were harvested for near-infrared reflectance (NIR) and terpene measurements. We used Bayesian model averaging for terpene selection and obtained partial least squares NIR models to predict terpene content and L. invasa infestation damage. In our optimal model, 29% of the phenotypic variation could be explained by 7 terpenes, and the monoterpene combination, limonene, α-terpineol, and 1,8-cineole, could be predicted with an NIR prediction ability of  .67. Bayesian model averaging supported α-pinene, γ-terpinene, and iso-pinocarveol as important for predicting L. invasa infestation. Susceptibility was associated with increased γ-terpinene and α-pinene, which may act as a pest attractant, whereas reduced susceptibility was associated with iso-pinocarveol, which may act to recruit parasitoids or have direct toxic effects.

De Novo Transcriptome Study Identifies Candidate Genes Involved in Resistance to Austropuccinia psidii (Myrtle Rust) in Syzygium luehmannii (Riberry).

Austropuccinia psidii, causal agent of myrtle rust, was discovered in Australia in 2010 and has since become established on a wide range of species within the family Myrtaceae. Syzygium luehmannii, endemic to Australia, is an increasingly valuable berry crop. Plants were screened for responses to A. psidii inoculation, and specific resistance, in the form of localized necrosis, was determined in 29% of individuals. To understand the molecular basis underlying this response, mRNA was sequenced from leaf samples taken preinoculation, and at 24 and 48 h postinoculation, from four resistant and four susceptible plants. Analyses, based on de novo transcriptome assemblies for all plants, identified significant expression changes in resistant plants (438 transcripts) 48 h after pathogen exposure compared with susceptible plants (three transcripts). Most significantly up-regulated in resistant plants were gene homologs for transcription factors, receptor-like kinases, and enzymes involved in secondary metabolite pathways. A putative G-type lectin receptor-like kinase was exclusively expressed in resistant individuals and two transcripts incorporating toll/interleukin-1, nucleotide binding site, and leucine-rich repeat domains were up-regulated in resistant plants. The results of this study provide the first early gene expression profiles for a plant of the family Myrtaceae in response to the myrtle rust pathogen.

Transcriptome Profiling of Melaleuca quinquenervia Challenged by Myrtle Rust Reveals Differences in Defense Responses Among Resistant Individuals.

Plants have developed complex defense mechanisms to protect themselves against pathogens. A wide-host-range fungus, Austropuccinia psidii, which has caused severe damage to ecosystems and plantations worldwide, is a major threat to Australian ecosystems dominated by members of the family Myrtaceae. In particular, the east coast wetland foundation tree species Melaleuca quinquenervia, appears to be variably susceptible to this pathogen. Understanding the molecular basis of host resistance would enable better management of this rust disease. We identified resistant and susceptible individuals of M. quinquenervia and explored their differential gene expression in order to discover the molecular basis of resistance against A. psidii. Rust screening of germplasm showed a varying degree of response, with fully resistant to highly susceptible individuals. We used transcriptome profiling in samples collected before and at 5 days postinoculation (dpi). Differential gene expression analysis showed that numerous defense-related genes were induced in susceptible plants at 5 dpi. Mapping reads against the A. psidii genome showed that only susceptible plants contained fungal-derived transcripts. Resistant plants exhibited an overexpression of candidate A. psidii resistance-related genes such as receptor-like kinases, nucleotide-binding site leucine-rich repeat proteins, glutathione S-transferases, WRKY transcriptional regulators, and pathogenesis-related proteins. We identified large differences in the expression of defense-related genes among resistant individuals.

Temporal regulation of terpene synthase gene expression in Eucalyptus globulus leaves upon ozone and wounding stresses: relationships with stomatal ozone uptake and emission responses.

Ozone and wounding are key abiotic factors but, their interactive effects on temporal changes in terpene synthase gene expression and emission responses are poorly understood. Here, we applied combined acute ozone and wounding stresses to the constitutive isoprenoid-emitter Eucalyptus globulus and studied how isoprene, 1,8-cineole, and isoledene synthase genes were regulated, and how the gene expression was associated with temporal changes in photosynthetic characteristics, product emission rates, and stomatal ozone uptake through recovery phase. Photosynthetic characteristics and emission rate of isoprene, 1,8-cineole, and isoledene were synergistically altered, while three TPS gene expressions were antagonistically altered by combined stress applications. A time-delay analysis indicated that the best correspondences between gene expression and product emission rates were observed for 0 h time-shift for wounding and 0-2 h time-shifts for separate ozone, and combined ozone and wounding treatments. The best correspondence between ozone uptake and gene expression was observed for 0-4 h time-shifts for separate ozone and combined ozone and wounding treatments. Overall, this study demonstrated that expression profiles of isoprene, the monoterpene 1,8-cineole, and the sesquiterpene isoledene synthase genes differentially influenced their corresponding product emissions for separate and combined ozone and wounding treatments through recovery.

Four terpene synthases contribute to the generation of chemotypes in tea tree (Melaleuca alternifolia).

BACKGROUND: Terpene rich leaves are a characteristic of Myrtaceae. There is significant qualitative variation in the terpene profile of plants within a single species, which is observable as "chemotypes". Understanding the molecular basis of chemotypic variation will help explain how such variation is maintained in natural populations as well as allowing focussed breeding for those terpenes sought by industry. The leaves of the medicinal tea tree, Melaleuca alternifolia, are used to produce terpinen-4-ol rich tea tree oil, but there are six naturally occurring chemotypes; three cardinal chemotypes (dominated by terpinen-4-ol, terpinolene and 1,8-cineole, respectively) and three intermediates. It has been predicted that three distinct terpene synthases could be responsible for the maintenance of chemotypic variation in this species. RESULTS: We isolated and characterised the most abundant terpene synthases (TPSs) from the three cardinal chemotypes of M. alternifolia. Functional characterisation of these enzymes shows that they produce the dominant compounds in the foliar terpene profile of all six chemotypes. Using RNA-Seq, we investigated the expression of these and 24 additional putative terpene synthases in young leaves of all six chemotypes of M. alternifolia. CONCLUSIONS: Despite contributing to the variation patterns observed, variation in gene expression of the three TPS genes is not enough to explain all variation for the maintenance of chemotypes. Other candidate terpene synthases as well as other levels of regulation must also be involved. The results of this study provide novel insights into the complexity of terpene biosynthesis in natural populations of a non-model organism.

Transcriptome analysis of terpene chemotypes of Melaleuca alternifolia across different tissues.

Plant chemotypes or chemical polymorphisms are defined by discrete variation in secondary metabolites within a species. This variation can have consequences for ecological interactions or the human use of plants. Understanding the molecular basis of chemotypic variation can help to explain how variation of plant secondary metabolites is controlled. We explored the transcriptomes of the 3 cardinal terpene chemotypes of Melaleuca alternifolia in young leaves, mature leaves, and stem and compared transcript abundance to variation in the constitutive profile of terpenes. Leaves from chemotype 1 plants (dominated by terpinen-4-ol) show a similar pattern of gene expression when compared to chemotype 5 plants (dominated by 1,8-cineole). Only terpene synthases in young leaves were differentially expressed between these chemotypes, supporting the idea that terpenes are mainly synthetized in young tissue. Chemotype 2 plants (dominated by terpinolene) show a greater degree of differential gene expression compared to the other chemotypes, which might be related to the isolation of plant populations that exhibit this chemotype and the possibility that the terpinolene synthase gene in M. alternifolia was derived by introgression from a closely related species, Melaleuca trichostachya. By using multivariate analyses, we were able to associate terpenes with candidate terpene synthases.

The Eucalyptus terpene synthase gene family.

BACKGROUND: Terpenoids are abundant in the foliage of Eucalyptus, providing the characteristic smell as well as being valuable economically and influencing ecological interactions. Quantitative and qualitative inter- and intra- specific variation of terpenes is common in eucalypts. RESULTS: The genome sequences of Eucalyptus grandis and E. globulus were mined for terpene synthase genes (TPS) and compared to other plant species. We investigated the relative expression of TPS in seven plant tissues and functionally characterized five TPS genes from E. grandis. Compared to other sequenced plant genomes, Eucalyptus grandis has the largest number of putative functional TPS genes of any sequenced plant. We discovered 113 and 106 putative functional TPS genes in E. grandis and E. globulus, respectively. All but one TPS from E. grandis were expressed in at least one of seven plant tissues examined. Genomic clusters of up to 20 genes were identified. Many TPS are expressed in tissues other than leaves which invites a re-evaluation of the function of terpenes in Eucalyptus. CONCLUSIONS: Our data indicate that terpenes in Eucalyptus may play a wider role in biotic and abiotic interactions than previously thought. Tissue specific expression is common and the possibility of stress induction needs further investigation. Phylogenetic comparison of the two investigated Eucalyptus species gives insight about recent evolution of different clades within the TPS gene family. While the majority of TPS genes occur in orthologous pairs some clades show evidence of recent gene duplication, as well as loss of function.

The Transcriptome and Terpene Profile of Eucalyptus grandis Reveals Mechanisms of Defense Against the Insect Pest, Leptocybe invasa.

Plants have evolved complex defenses that allow them to protect themselves against pests and pathogens. However, there is relatively little information regarding the Eucalyptus defensome. Leptocybe invasa is one of the most damaging pests in global Eucalyptus forestry, and essentially nothing is known regarding the molecular mechanisms governing the interaction between the pest and host. The aim of the study was to investigate changes in the transcriptional landscape and terpene profile of a resistant and susceptible Eucalyptus genotype in an effort to improve our understanding of this interaction. We used RNA-seqencing to investigate transcriptional changes following L. invasa oviposition. Expression levels were validated using real-time quantitative PCR. Terpene profiles were investigated using gas chromatography coupled to mass spectometry on uninfested and oviposited leaves. We found 698 and 1,115 significantly differentially expressed genes from the resistant and susceptible interactions, respectively. Gene Ontology enrichment and Mapman analyses identified putative defense mechanisms including cell wall reinforcement, protease inhibitors, cell cycle suppression and regulatory hormone signaling pathways. There were significant differences in the mono- and sesquiterpene profiles between genotypes and between control and infested material. A model of the interaction between Eucalyptus and L. invasa was proposed from the transcriptomic and chemical data.

Interpreting the modern distribution of Myrtaceae using a dated molecular phylogeny.

The angiosperm family Myrtaceae has extant and fossil taxa from all southern continents and is assumed to be of Gondwanan origin. Many modern groups contain sister taxa that have disjunct transoceanic distributions, which can be interpreted as a result of either vicariance or long-distance dispersal and establishment (LDDE). Further, some Myrtaceae groups occur on Pacific islands with enigmatic geological histories. We tested hypotheses of vicariance and LDDE by estimating divergence times using a relaxed molecular clock calibrated with 12 fossils. In total, 88 genera and 202 species were sampled, representing both subfamilies and all tribes of Myrtaceae. We reconstructed the family as Gondwanan in origin. Of the 22 geographically disjunct sister groups in our study, up to six are potentially explained as the product of vicariance, three resulting from overland dispersal via new land connections, and 13 due to LDDE events. Nine of the 13 hypothesized LDDE events occurred in fleshy-fruited taxa. Our results indicate that most of the transoceanic distribution patterns in Myrtaceae have occurred since the Miocene due to LDDE, whereas inferred vicariance events all occurred before the Late Eocene. There are many instances of sister relationships between species-poor and species-rich groups in Myrtaceae, and at least three occurrences of geographically isolated taxa on long branches of the phylogeny (Arillastrum, Myrtus, and Tepualia), whose modern-day distributions are difficult to explain without additional fossil or geological evidence.

Genomic approaches to selection in outcrossing perennials: focus on essential oil crops.

The yield of essential oil in commercially harvested perennial species (e.g. 'Oil Mallee' eucalypts, Tea Trees and Hop) is dependent on complex quantitative traits such as foliar oil concentration, biomass and adaptability. These often show large natural variation and some are highly heritable, which has enabled significant gains in oil yield via traditional phenotypic recurrent selection. Analysis of transcript abundance and allelic diversity has revealed that essential oil yield is likely to be controlled by large numbers of quantitative trait loci that range from a few of medium/large effect to many of small effect. Molecular breeding techniques that exploit this information could increase gains per unit time and address complications of traditional breeding such as genetic correlations between key traits and the lower heritability of biomass. Genomic selection (GS) is a technique that uses the information from markers genotyped across the whole genome in order to predict the phenotype of progeny well before they reach maturity, allowing selection at an earlier age. In this review, we investigate the feasibility of genomic selection (GS) for the improvement of essential oil yield. We explore the challenges facing breeders selecting for oil yield, and how GS might deal with them. We then assess the factors that affect the accuracy of genomic estimated breeding values, such as linkage disequilibrium (LD), heritability, relatedness and the genetic architecture of desirable traits. We conclude that GS has the potential to significantly improve the efficiency of selection for essential oil yield.

Effects of Terpene Chemotypes of Melaleuca alternifolia on Two Specialist Leaf Beetles and Susceptibility to Myrtle Rust.

Plant chemical polymorphisms, or plant chemotypes, are characterized by intraspecific discrete differences of plant secondary metabolites in the same plant tissue. Chemotypes that differ in foliar terpene composition are found commonly in Myrtaceae. In this study, we focused on terpene chemotypes of medicinal tea tree, Melalecua alternifolia, to explore whether this variation affects two specialist herbivores Paropsisterna tigrina and Faex sp. (Coleoptera: Chrysomelidae), and if this could explain the maintenance of this variation. We tested whether insect performance, oviposition preference, and plant damage were associated with different chemotypes. We found that larval growth rate of Faex sp. was higher in chemotypes with high concentrations of 1,8-cineole, and that oviposition preference depended on the chemotype of the larval diet. Although performance traits and preference for oviposition of P. tigrina did not vary among chemotypes, adults inflicted less damage on plants with a high concentration of terpinolene. Additionally, we tested whether different chemotypes showed different levels of susceptibility by myrtle rust (Puccinia psidii). We found that plants with a high concentration of 1,8-cineole were more likely to be infected under controlled conditions. Although there is evidence that terpene chemotypes are a mediator of the interaction with natural enemies, the most detrimental pest of this plant, P. tigrina, does not seem to be affected by variation in plant terpenes.

Explaining intraspecific diversity in plant secondary metabolites in an ecological context.

Plant secondary metabolites (PSMs) are ubiquitous in plants and play many ecological roles. Each compound can vary in presence and/or quantity, and the composition of the mixture of chemicals can vary, such that chemodiversity can be partitioned within and among individuals. Plant ontogeny and environmental and genetic variation are recognized as sources of chemical variation, but recent advances in understanding the molecular basis of variation may allow the future deployment of isogenic mutants to test the specific adaptive function of variation in PSMs. An important consequence of high intraspecific variation is the capacity to evolve rapidly. It is becoming increasingly clear that trait variance linked to both macro- and micro-environmental variation can also evolve and may respond more strongly to selection than mean trait values. This research, which is in its infancy in plants, highlights what could be a missing piece of the picture of PSM evolution. PSM polymorphisms are probably maintained by multiple selective forces acting across many spatial and temporal scales, but convincing examples that recognize the diversity of plant population structures are rare. We describe how diversity can be inherently beneficial for plants and suggest fruitful avenues for future research to untangle the causes and consequences of intraspecific variation.

Differences in gene expression within a striking phenotypic mosaic Eucalyptus tree that varies in susceptibility to herbivory.

BACKGROUND: Long-lived trees can accumulate mutations throughout their lifetimes that may influence biotic and abiotic interactions. For example, some Eucalyptus trees display marked variation in herbivore defence within a single canopy. These "mosaic" trees support foliage with distinct chemotypes which are differentially favoured by insect and vertebrate herbivores, resulting in susceptible and resistant branches within a single canopy. These mosaic trees provide a unique opportunity to explore the biosynthesis and genetic regulation of chemical defences in the foliage. The biosynthesis of the principal defence compounds, terpenoid-dominated essential oils, is well understood. However, the regulation of the genes involved and thus the control of phenotypic variation within a single tree canopy remains a mystery. RESULTS: We sequenced the transcriptomes of the leaves of the two different chemotypes of a chemically mosaic Eucalyptus melliodora tree using 454 pyrosequencing technology. We used gene set enrichment analysis to identify differentially expressed transcripts and found the proportion of differentially expressed genes in the resistant and susceptible foliage similar to the transcript difference between functionally distinct tissues of the same organism, for example roots and leaves. We also investigated sequence differences in the form of single nucleotide polymorphisms and found 10 nucleotides that were different between the two branches. These are likely true SNPs and several occur in regulatory genes. CONCLUSION: We found three lines of evidence that suggest changes to a 'master switch' can result in large scale phenotypic changes: 1. We found differential expression of terpene biosynthetic genes between the two chemotypes that could contribute to chemical variation within this plant. 2. We identified many genes that are differentially expressed between the two chemotypes, including some unique genes in each branch. These genes are involved in a variety of processes within the plant and many could contribute to the regulation of secondary metabolism, thus contributing to the chemical variation. 3. We identified 10 SNPs, some of which occur in regulatory genes that could influence secondary metabolism and thus contribute to chemical variation. Whilst this research is inherently limited by sample size, the patterns we describe could be indicative of other plant genetic mosaics.

Strategies to mitigate shifts in red oak (Quercus sect. Lobatae) distribution under a changing climate.

Red oaks (Quercus sect. Lobatae) are a taxonomic group of hardwood trees, which occur in swamp forests, subtropical chaparral and savannahs from Columbia to Canada. They cover a wide range of ecological niches, and many species are thought to be able to cope with current trends in climate change. Genus Quercus encompasses ca. 500 species, of which ca. 80 make up sect. Lobatae. Species diversity is greatest within the southeastern USA and within the northern and eastern regions of Mexico. This review discusses the weak reproductive barriers between species of red oaks and the effects this has on speciation and niche range. Distribution and diversity have been shaped by drought adaptations common to the species of sect. Lobatae, which enable them to fill various xeric niches across the continent. Drought adaptive traits of this taxonomic group include deciduousness, deep tap roots, ring-porous xylem, regenerative stump sprouting, greater leaf thickness and smaller stomata. The complex interplay between these anatomical and morphological traits has given red oaks features of drought tolerance and avoidance. Here, we discuss physiological and genetic components of these adaptations to address how many species of sect. Lobatae reside within xeric sites and/or sustain normal metabolic function during drought. Although extensive drought adaptation appears to give sect. Lobatae a resilience to climate change, aging tree stands, oak life history traits and the current genetic structures place many red oak species at risk. Furthermore, oak decline, a complex interaction between abiotic and biotic agents, has severe effects on red oaks and is likely to accelerate species decline and fragmentation. We suggest that assisted migration can be used to avoid species fragmentation and increase climate change resilience of sect. Lobatae.

Genome-wide association study identifies SNP markers and putative candidate genes for terpene traits important for Leptocybe invasa resistance in Eucalyptus grandis.

Terpenes are an important group of plant specialized metabolites influencing, amongst other functions, defence mechanisms against pests. We used a genome-wide association study to identify single nucleotide polymorphism (SNP) markers and putative candidate genes for terpene traits. We tested 15,387 informative SNP markers derived from genotyping 416 Eucalyptus grandis individuals for association with 3 terpene traits, 1,8-cineole, γ-terpinene, and p-cymene. A multilocus mixed model analysis identified 21 SNP markers for 1,8-cineole on chromosomes 2, 4, 6, 7, 8, 9, 10, and 11, that individually explained 3.0%-8.4% and jointly 42.7% of the phenotypic variation. Association analysis of γ-terpinene found 32 significant SNP markers on chromosomes 1, 2, 4, 5, 6, 9, and 11, explaining 3.4-15.5% and jointly 54.5% of phenotypic variation. For p-cymene, 28 significant SNP markers were identified on chromosomes 1, 2, 3, 5, 6, 7, 10, and 11, explaining 3.4-16.1% of the phenotypic variation and jointly 46.9%. Our results show that variation underlying the 3 terpene traits is influenced by a few minor loci in combination with a few major effect loci, suggesting an oligogenic nature of the traits.

The molecular basis of quantitative variation in foliar secondary metabolites in Eucalyptus globulus.

Eucalyptus is characterized by high foliar concentrations of plant secondary metabolites with marked qualitative and quantitative variation within a single species. Secondary metabolites in eucalypts are important mediators of a diverse community of herbivores. We used a candidate gene approach to investigate genetic associations between 195 single nucleotide polymorphisms (SNPs) from 24 candidate genes and 33 traits related to secondary metabolites in the Tasmanian Blue Gum (Eucalyptus globulus). We discovered 37 significant associations (false discovery rate (FDR) Q < 0.05) across 11 candidate genes and 19 traits. The effects of SNPs on phenotypic variation were within the expected range (0.018 < r(2) < 0.061) for forest trees. Whereas most marker effects were nonadditive, two alleles from two consecutive genes in the methylerythritol phosphate pathway (MEP) showed additive effects. This study successfully links allelic variants to ecologically important phenotypes which can have a large impact on the entire community. It is one of very few studies to identify the genetic variants of a foundation tree that influences ecosystem function.