A change in the timing or rate of developmental events throughout ontogeny is referred to as heterochrony, and it is a major evolutionary process in plants and animals. We investigated the genetic basis for natural variation in the timing of vegetative phase change in the tree Eucalyptus globulus, which undergoes a dramatic change in vegetative morphology during the juvenile-to-adult transition. Quantitative trait loci analysis in an outcross F2 family derived from crosses between individuals from a coastal population of E. globulus with precocious vegetative phase change and individuals from populations in which vegetative phase change occurs several years later implicated the microRNA EglMIR156.5 as a potential contributor to this heterochronic difference. Additional evidence for the involvement of EglMIR156.5 was provided by its differential expression in trees with early and late phase change. Our findings suggest that changes in the expression of miR156 underlie natural variation in vegetative phase change in E. globulus, and may also explain interspecific differences in the timing of this developmental transition.
Eucalypts are the world's most widely planted hardwood trees. Their outstanding diversity, adaptability and growth have made them a global renewable resource of fibre and energy. We sequenced and assembled >94% of the 640-megabase genome of Eucalyptus grandis. Of 36,376 predicted protein-coding genes, 34% occur in tandem duplications, the largest proportion thus far in plant genomes. Eucalyptus also shows the highest diversity of genes for specialized metabolites such as terpenes that act as chemical defence and provide unique pharmaceutical oils. Genome sequencing of the E. grandis sister species E. globulus and a set of inbred E. grandis tree genomes reveals dynamic genome evolution and hotspots of inbreeding depression. The E. grandis genome is the first reference for the eudicot order Myrtales and is placed here sister to the eurosids. This resource expands our understanding of the unique biology of large woody perennials and provides a powerful tool to accelerate comparative biology, breeding and biotechnology.
Patterns of adaptive variation within plant species are best studied through common garden experiments, but these are costly and time-consuming, especially for trees that have long generation times. We explored whether genome-wide scanning technology combined with outlier marker detection could be used to detect adaptation to climate and provide an alternative to common garden experiments. As a case study, we sampled nine provenances of the widespread forest tree species, Eucalyptus tricarpa, across an aridity gradient in southeastern Australia. Using a Bayesian analysis, we identified a suite of 94 putatively adaptive (outlying) sequence-tagged markers across the genome. Population-level allele frequencies of these outlier markers were strongly correlated with temperature and moisture availability at the site of origin, and with population differences in functional traits measured in two common gardens. Using the output from a canonical analysis of principal coordinates, we devised a metric that provides a holistic measure of genomic adaptation to aridity that could be used to guide assisted migration or genetic augmentation.
Species ranges have been shifting since the Pleistocene, whereby fragmentation, isolation, and the subsequent reduction in gene flow have resulted in local adaptation of novel genotypes and the repeated evolution of endemic species. While there is a wide body of literature focused on understanding endemic species, very few studies empirically test whether or not the evolution of endemics results in unique function or ecological differences relative to their widespread congeners; in particular while controlling for environmental variation. Using a common garden composed of 15 Eucalyptus species within the subgenus Symphyomyrtus (9 endemic to Tasmania, 6 non-endemic), here we hypothesize and show that endemic species are functionally and ecologically different from non-endemics. Compared to non-endemics, endemic Eucalyptus species have a unique suite of functional plant traits that have extended effects on herbivores. We found that while endemics occupy many diverse habitats, they share similar functional traits potentially resulting in an endemic syndrome of traits. This study provides one of the first empirical datasets analyzing the functional differences between endemics and non-endemics in a common garden setting, and establishes a foundation for additional studies of endemic/non-endemic dynamics that will be essential for understanding global biodiversity in the midst of rapid species extinctions and range shifts as a consequence of global change.
Using native trees from near the northern and southern extremities of the relatively continuous eastern distribution of Eucalyptus globulus in Tasmania, we compared the progenies derived from natural open-pollination (OP) with those generated from within-region and long-distance outcrossing. Controlled outcrossing amongst eight parents - with four parents from each of the northern and southern regions - was undertaken using a diallel mating scheme. The progeny were planted in two field trials located within the species native range in southern Tasmania, and their survival and diameter growth were monitored over a 13-year-period. The survival and growth performances of all controlled cross types exceeded those of the OP progenies, consistent with inbreeding depression due to a combination of selfing and bi-parental inbreeding. The poorer survival of the northern regional (?N?N) outcrosses compared with the local southern regional outcrosses (?S?S) indicated differential selection against the former. Despite this mal-adaptation of the non-local ?N?N crosses at both southern sites, the survival of the inter-regional hybrids (?N?S and ?S?N) was never significantly different from that of the local ?S?S crosses. Significant site-dependent heterosis was detected for the growth of the surviving long-distance hybrids. This was expressed as mid-parent heterosis, particularly at the more northern planting site. Heterosis increased with age, while the difference between the regional ?N?N and ?S?S crosses remained insignificant at any age at either site. Nevertheless, the results for growth suggest that the fitness of individuals derived from long-distance crossing may be better at the more northern of the planting sites. Our results demonstrate the potential for early-age assessments of pollen dispersal to underestimate realised gene flow, with local inbreeding under natural open-pollination resulting in selection favouring the products of longer-distance pollinations. Indeed, heterosis derived from long-distance pollinations may be sufficient to counter local mal-adaptation, at least in the first generation.
· Eucalypts are one of the most planted tree genera worldwide, and there is increasing interest in marker-assisted selection for tree improvement. Implementation of marker-assisted selection requires a knowledge of the stability of quantitative trait loci (QTLs). This study aims to investigate the stability of QTLs for wood properties and growth across contrasting sites and multiple pedigrees of Eucalyptus globulus. · Saturated linkage maps were constructed using 663 genotypes from four separate families, grown at three widely separated sites, and were employed to construct a consensus map. This map was used for QTL analysis of growth, wood density and wood chemical traits, including pulp yield. · Ninety-eight QTLs were identified across families and sites: 87 for wood properties and 11 for growth. These QTLs mapped to 38 discrete regions, some of which co-located with candidate genes. Although 16% of QTLs were verified across different families, 24% of wood property QTLs and 38% of growth QTLs exhibited significant genotype-by-environment interaction. · This study provides the most detailed assessment of the effect of environment and pedigree on QTL detection in the genus. Despite markedly different environments and pedigrees, many QTLs were stable, providing promising targets for the application of marker-assisted selection.
Understanding among and within population genetic variation of ecologically important plant traits provides insight into the potential evolutionary processes affecting those traits. The strength and consistency of selection driving variability in traits would be affected by plasticity in differences among genotypes across environments (G×E). We investigated population divergence, selection and environmental plasticity of foliar plant secondary metabolites (PSMs) in a dominant tree species, Eucalyptus globulus. Using two common garden trials we examined variation in PSMs at multiple genetic scales; among 12 populations covering the full geographic range of the species and among up to 60 families within populations. Significant genetic variation in the expression of many PSMs resides both among and within populations of E. globulus with moderate (e.g., sideroxylonal A h(2)op?=?0.24) to high (e.g., macrocarpal G h(2)op?=?0.48) narrow sense heritabilities and high coefficients of additive genetic variation estimated for some compounds. A comparison of Qst and Fst estimates suggest that variability in some of these traits may be due to selection. Importantly, there was no genetic by environment interaction in the expression of any of the quantitative chemical traits despite often significant site effects. These results provide evidence that natural selection has contributed to population divergence in PSMs in E. globulus, and identifies the formylated phloroglucinol compounds (particularly sideroxylonal) and a dominant oil, 1,8-cineole, as candidates for traits whose genetic architecture has been shaped by divergent selection. Additionally, as the genetic differences in these PSMs that influence community phenotypes is stable across environments, the role of plant genotype in structuring communities is strengthened and these genotypic differences may be relatively stable under global environmental changes.
Despite the ecological and economic importance of lignin and other wood chemical components, there are few studies of the natural genetic variation that exists within plant species and its adaptive significance. We used models developed from near infra-red spectroscopy to study natural genetic variation in lignin content and monomer composition (syringyl-to-guaiacyl ratio [S/G]) as well as cellulose and extractives content, using a 16-year-old field trial of an Australian tree species, Eucalyptus globulus. We sampled 2163 progenies of 467 native trees from throughout the native geographic range of the species. The narrow-sense heritability of wood chemical traits (0.25-0.44) was higher than that of growth (0.15), but less than wood density (0.51). All wood chemical traits exhibited significant broad-scale genetic differentiation (Q(ST) = 0.34-0.43) across the species range. This differentiation exceeded that detected with putatively neutral microsatellite markers (F(ST) = 0.09), arguing that diversifying selection has shaped population differentiation in wood chemistry. There were significant genetic correlations among these wood chemical traits at the population and additive genetic levels. However, population differentiation in the S/G ratio of lignin in particular was positively correlated with latitude (R(2) = 76%), which may be driven by either adaptation to climate or associated biotic factors.
One of the major factors affecting the outcrossing rate in Eucalyptus globulus is thought to be the inherent self-incompatibility (SI) level of the female tree. SI in this species is mainly due to late-acting pre- and post-zygotic mechanisms operating in the ovary, and not S alleles. This study aimed to assess the phenotypic variation in SI levels within E. globulus and determine its genetic control and stability across pollination techniques, sites and seasons.
While habitat fragmentation is a central issue in forest conservation studies in the face of broad-scale anthropogenic changes to the environment, its effects on contemporary mating patterns remain controversial. This is partly because of the inherent variation in mating patterns which may exist within species and the fact that few studies have replication at the landscape level. To study the effect of forest fragmentation on contemporary mating patterns, including effective pollen dispersal, we compared four native populations of the Australian forest tree, Eucalyptus globulus. We used six microsatellite markers to genotype 1289 open-pollinated offspring from paired fragmented and continuous populations on the island of Tasmania and in Victoria on mainland Australia. The mating patterns in the two continuous populations were similar, despite large differences in population density. In contrast, the two fragmented populations were variable and idiosyncratic in their mating patterns, particularly in their pollen dispersal kernels. The continuous populations showed relatively high outcrossing rates (86-89%) and low correlated paternity (0.03-0.06) compared with the fragmented populations (65-79% and 0.12-0.20 respectively). A greater proportion of trees contributed to reproduction in the fragmented (de/d>or= 0.5) compared with the continuous populations (de/d = 0.03-0.04). Despite significant inbreeding in the offspring of the fragmented populations, there was little evidence of loss of genetic diversity. It is argued that enhanced medium- and long-distance dispersal in fragmented landscapes may act to partly buffer the remnant populations from the negative effects of inbreeding and drift.
Forest trees frequently form species complexes, complicating taxonomic classification and gene pool management. This is certainly the case in Eucalyptus, and well exemplified by the Eucalyptus globulus complex. This ecologically and economically significant complex comprises four taxa (sspp. bicostata, globulus, maidenii, pseudoglobulus) that are geographically and morphologically distinct, but linked by extensive "intergrade" populations. To resolve their genetic affinities, nine microsatellites were used to genotype 1200 trees from throughout the natural range of the complex in Australia, representing 33 morphological core and intergrade populations. There was significant spatial genetic structure (F(ST) = 0.10), but variation was continuous. High genetic diversity in southern ssp. maidenii indicates that this region is the center of origin. Genetic diversity decreases and population differentiation increases with distance from this area, suggesting that drift is a major evolutionary process. Many of the intergrade populations, along with other populations morphologically classified as ssp. pseudoglobulus or ssp. globulus, belong to a "cryptic genetic entity" that is genetically and geographically intermediate between core ssp. bicostata, ssp. maidenii, and ssp. globulus. Geography, rather than morphology, therefore, is the best predictor of overall genetic affinities within the complex and should be used to classify germplasm into management units for conservation and breeding purposes.
Indirect genetic effects (IGEs) are heritable effects of individuals on trait values of their conspecifics. IGEs may substantially affect response to selection, but empirical studies on IGEs are sparse and their magnitude and correlation with direct genetic effects are largely unknown in plants. Here we used linear mixed models to estimate genetic (co)variances attributable to direct and indirect effects for growth and foliar disease damage in a large pedigreed population of Eucalyptus globulus. We found significant IGEs for growth and disease damage, which increased with age for growth. The correlation between direct and indirect genetic effects was highly negative for growth, but highly positive for disease damage, consistent with neighbour competition and infection, respectively. IGEs increased heritable variation by 71% for disease damage, but reduced heritable variation by 85% for growth, leaving nonsignificant heritable variation for later age growth. Thus, IGEs are likely to prevent response to selection in growth, despite a considerable ordinary heritability. IGEs change our perspective on the genetic architecture and potential response to selection. Depending on the correlation between direct and indirect genetic effects, IGEs may enhance or diminish the response to natural or artificial selection compared with that predicted from ordinary heritability.
Genetic linkage maps are invaluable resources in plant research. They provide a key tool for many genetic applications including: mapping quantitative trait loci (QTL); comparative mapping; identifying unlinked (i.e. independent) DNA markers for fingerprinting, population genetics and phylogenetics; assisting genome sequence assembly; relating physical and recombination distances along the genome and map-based cloning of genes. Eucalypts are the dominant tree species in most Australian ecosystems and of economic importance globally as plantation trees. The genome sequence of E. grandis has recently been released providing unprecedented opportunities for genetic and genomic research in the genus. A robust reference linkage map containing sequence-based molecular markers is needed to capitalise on this resource. Several high density linkage maps have recently been constructed for the main commercial forestry species in the genus (E. grandis, E. urophylla and E. globulus) using sequenced Diversity Arrays Technology (DArT) and microsatellite markers. To provide a single reference linkage map for eucalypts a composite map was produced through the integration of data from seven independent mapping experiments (1950 individuals) using a marker-merging method.
Plant secondary metabolites (PSMs) mediate a wide range of ecological interactions. Investigating the effect of environment on PSM production is important for our understanding of how plants will adapt to large scale environmental change, and the extended effects on communities and ecosystems. We explored the production of PSMs under elevated atmospheric carbon dioxide ([CO(2)]) in the species rich, ecologically and commercially important genus Eucalyptus. Seedlings from multiple Eucalyptus globulus and E. pauciflora populations were grown in common glasshouse gardens under elevated or ambient [CO(2)]. Variation in primary and secondary chemistry was determined as a function of genotype and treatment. There were clear population differences in PSM expression in each species. Elevated [CO(2)] did not affect concentrations of individual PSMs, total phenolics, condensed tannins or the total oil yield, and there was no population by [CO(2)] treatment interaction for any traits. Multivariate analysis revealed similar results with significant variation in concentrations of E. pauciflora oil components between populations. A [CO(2)] treatment effect was detected within populations but no interactions were found between elevated [CO(2)] and population. These eucalypt seedlings appear to be largely unresponsive to elevated [CO(2)], indicating stronger genetic than environmental (elevated [CO(2)]) control of expression of PSMs.
Widespread species often occur across a range of climatic conditions, through a combination of local genetic adaptations and phenotypic plasticity. Species with greater phenotypic plasticity are likely to be better positioned to cope with rapid anthropogenic climate changes, while those displaying strong local adaptations might benefit from translocations to assist the movement of adaptive genes as the climate changes. Eucalyptus tricarpa occurs across a climatic gradient in south-eastern Australia, a region of increasing aridity, and we hypothesised that this species would display local adaptation to climate. We measured morphological and physiological traits reflecting climate responses in nine provenances from sites of 460-1040 mm annual rainfall, in their natural habitat and in common gardens near each end of the gradient. Local adaptation was evident in functional traits and differential growth rates in the common gardens. Some traits displayed complex combinations of plasticity and genetic divergence among provenances, including clinal variation in plasticity itself. Provenances from drier locations were more plastic in leaf thickness, whereas leaf size was more plastic in provenances from higher rainfall locations. Leaf density and stomatal physiology (as indicated by ?(13) C and ?(18) O) were highly and uniformly plastic. In addition to variation in mean trait values, genetic variation in trait plasticity may play a role in climate adaptation.
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