Bm Potts

The genome of Eucalyptus grandis

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.

PLANT HYBRID ZONES AFFECT BIODIVERSITY: TOOLS FOR A GENETIC‐BASED UNDERSTANDING OF COMMUNITY STRUCTURE

Plant hybrid zones are dynamic centers of ecological and evolutionary processes for plants and their associated communities. Studies in the wild and in gardens with synthetic crosses showed that hybrid eucalypts supported the greatest species richness and abundances of insect and fungal taxa. In an updated review of 152 case studies of taxa associated with diverse hybridizing systems, there were 43 (28%) cases of hybrids being more susceptible than their parent species, 7 (5%) resistant, 35 (23%) additive, 35 (23%) dominant, and 32 (21%) showed no response to hybridization. Thus, most taxa respond to hybrids in ways that result in equal or greater abundance, and hybrids tend to accumulate the taxa of their parent species. These studies suggest that genetic-based plant traits affect the distribution of many species and that the variation in hybrids can be used as tools to examine the genetic components of community structure and biodiversity. Several patterns have emerged thus far. (1) Genetic variation between classes of hybrids (e.g., F1’s vs. backcrosses) may equal or even exceed that found between species. (2) As a reflection of this genetic variation, herbivores are more likely to differentiate between hybrid classes than they are to differentiate between pure plant species. (3) The communities associated with different hybrid classes can differ from one another as well as from their parental species. (4) Generalist and specialist herbivores predictably vary in their responses to hybrids. (5) Plant hybrid zones may represent essential habitat for some arthropod species. (6) Even nesting birds respond to hybridizing plants. (7) Including multiple trophic levels and taxa from microbes to vertebrates, susceptible hybrid genotypes support greater biodiversity than resistant genotypes. (8) The effects of hybridization on common or keystone species can either positively or negatively affect biodiversity. The indirect impacts of hybridization on biodiversity may exceed the direct impacts and may result in “apparent” herbivore resistance or susceptibility at the community level. (9) Although hybrids are often maligned, exotic or problem hybrids generally result from human disturbances, whereas native hybrids are part of natural ecosystems and should be conserved. Three predictions are made: (1) Intermediate genetic differences between the parental species will result in the greatest genetic variation in the hybrid zone, which in turn will have a positive effect on biodiversity. (2) Bidirectional introgression enhances species richness on hybrids, whereas F1 sterility and unidirectional introgression limit the accumulation of species on hybrids. (3) Although susceptible hybrids are likely to support the greatest biodiversity, the impacts of hybridization on keystone species will be crucial in determining the overall effect.

PLANT GENETICS AFFECTS ARTHROPOD COMMUNITY RICHNESS AND COMPOSITION: EVIDENCE FROM A SYNTHETIC EUCALYPT HYBRID POPULATION

To examine how genetic variation in a plant population affects arthropod community richness and composition, we quantified the arthropod communities on a synthetic population of Eucalyptus amygdalina, E. risdonii, and their F1 and advanced‐generation hybrids. Five major patterns emerged. First, the pure species and hybrid populations supported significantly different communities. Second, species richness was significantly greatest on hybrids (F1 > F2 > E. amygdalina > E. risdonii). These results are similar to those from a wild population of the same species and represent the first case in which both synthetic and wild population studies confirm a genetic component to community structure. Hybrids also acted as centers of biodiversity by accumulating both the common and specialist taxa of both parental species (100% in the wild and 80% in the synthetic population). Third, species richness was significantly greater on F1s than the single F2 family, suggesting that the increased insect abundance on hybrids may not be caused by the breakup of coadapted gene complexes. Fourth, specialist arthropod taxa were most likely to show a dominance response to F1 hybrids, whereas generalist taxa exhibited a susceptible response. Fifth, in an analysis of 31 leaf terpenoids that are thought to play a role in plant defense, hybrids were generally intermediate to the parental chemotypes. Within the single F2 family, we found significant associations between the communities of individual trees and five individual oil components, including oil yield, demonstrating that there is a genetic effect on plant defensive chemistry that, in turn, may affect community structure. These studies argue that hybridization has important community‐level consequences and that the genetic variation present in hybrid zones can be used to explore the genetic‐based mechanisms that structure communities.

Genetic pollution of native eucalypt gene pools—identifying the risks

The contamination of native-eucalypt gene pools via exotic pollen is of concern as (i) pollen dispersal is believed to be much more widespread than seed dispersal, (ii) reproductive barriers are often weak between closely related species, (iii) European settlement has already had a major impact on Australias eucalypt woodlands and mallee, (iv) there has been a rapid expansion of eucalypt plantations and restoration plantings in Australia and (v) Australia is the custodian of an internationally important genetic resource. Pollen flow between plantation and native eucalypt species has already been reported and implementation of strategies to minimise the risk and consequences of genetic pollution is important if Australian forestry is to be considered sustainable. The risks associated with the introduction of non-native species, provenances and hybrids include direct effects on the gene pool through genetic pollution as well as indirect effects on dependent biodiversity. In many cases, the risk of genetic pollution will be small due to strong barriers to hybridisation between distantly related species, differences in flowering time or poor fitness of hybrids. There is no risk of hybridisation between species from the different major eucalypt genera and/or subgenera (e.g. symphyomyrts, monocalypts, eudesmids, bloodwoods and angophora). The main plantation species are symphyomyrts and within this subgenus, the probability of successful hybridisation generally decreases with increasing taxonomic distance between species. The planting of non-local provenances or improved material within the range of native populations has the potential to have an impact on local gene pools to varying degrees, indicating the requirement for the adoption of management strategies to reduce this risk. Naturally small or remnant populations are at particular risk. A framework for assessment of the risk of genetic pollution is developed herein.

Interspecific hybridization of Eucalyptus: key issues for breeders and geneticists

Eucalypt hybrids are significant in forestry, particularly in sub-tropic and tropical regions, where cost efficient, clonal propagation is the key to their exploitation. However, the outstanding success of selected hybrid clones has given a biased impression of the vigor of eucalypt hybrids and the strength of reproductive barriers in the genus. When full account is made of losses through the life cycle, a picture of high incompatibility and inviability often emerges. Hybrid inviability tends to increase with increasing taxonomic distance between parents, but there are exceptions. Hybrids also seem more susceptible to pests than their pure species. Intense selection may still result in elite hybrid clones, but such inviability and susceptibility adds a significant cost to their development. Breeders must carefully evaluate the costs of hybrid development and deployment compared with pure species options. A key to hybrid selection is the rapid development and testing of large populations and application of high selection intensities. However, eventually this approach must be linked with more formal breeding strategies. As most traits are intermediate in F1 hybrids there is increasing interest in advanced generation hybrids to provide desirable trait combinations. In such cases, there is a clear role for marker assisted selection to speed introgression.

Plant hybrid zones as centers of biodiversity: the herbivore community of two endemic Tasmanian eucalypts

We found the hybrid zone between Eucalyptus amygdalina and Eucalyptus risdonii to be a center of insect and fungal species richness and abundance. Of 40 taxa examined, 73% were significantly more abundant in the hybrid zone than in pure zones, 25% showed on significant differences, and 2% were most abundant on a pure host species. The average hybrid tree supported 53% more insect and fungal species, and relative abundances were, on average, 4 times greater on hybrids than on either eucalypt species growing in pure stands. Hybrids may act as refugia for rare species: 5 of 40 species were largely restricted to the hybrid zone. Also, 50% of the species coexisted only in the hybrid zone, making for mique species assemblages. Although hybrids support more species and greater abundances, all hybrids are not equal: 68% of the 40 taxa examined were significantly more abundant on one hybrid phenotype than another. While herbivore concentrations on F1 type intermediates were rare, concentrations were common on phenotypes resembling backcrosses either to E. amygdalina or E. risdonii. For specialist herbivores, the hybrid phenotype most heavily utilized appears to be determined by its phenotypic affinity to its host species. Generalists exhibit an overall greater abundance on hybrids, but are less likely to utilize one hybrid phenotype over another. Mechanistic explanations for these distributions are numerous and probably species specific, but are likely to include: increased genetic susceptibility of hybrids due to hybrid breakdown; increased stress in the hybrid zone resulting in greater plant susceptibility; and a greater diversity of resources in the hybrid zone which could support more species. Seed capsule production by hybrids and their parental species is negatively correlated with herbivory. However, it is difficult to determine whether herbivores cause this pattern as hybrids may have inherently lower sexual reproduction. Laws enacted to protect rare and endangered species do not include hybrids. We argue that a re-examination of our current “hybrid policy” is warranted. Plant hybrid zones are centers of plant evolution and speciation, sources of economically important plants and potential biocontrol agents, and, as our study suggests, also provide essential habitats for phytophagous communities.

Partitioning and distribution of RAPD variation in a forest tree species, Eucalyptus globulus(Myrtaceae).

Eucalyptus globulus is an important species for pulpwood production in many countries. The pattern and partitioning of variation is important baseline knowledge for tree breeding. Currently the species is divided into four subspecies: globulus, bicostata, pseudoglobulus and maidenii. Random Amplified Polymorphic DNA (RAPD) markers were used to analyse variation in 173 representatives of 37 natural populations of E. globulus: 31 localities of ssp. globulus (148 individuals), two localities each of ssp. bicostata (nine individuals), ssp. maidenii (ten individuals) and ssp. pseudoglobulus (six individuals). Ten 10-mer primers amplified a total of 162 scorable bands, of which 149 (91.9 per cent) were polymorphic, AMOVA analysis of a Euclidean distance matrix based on presence/absence of polymorphic bands found most variation within localities, but significant differences between localities and regions. Principal components analysis (PCA) identified a major latitudinal cline in RAPD phenotype that differentiated southern Tasmanian localities from other ssp. globulus localities on mainland Australia. Many localities previously identified as intermediate between subspecies globulus and other subspecies in morphology were not intermediate in RAPD phenotype. In some cases regions which showed marked differentiation between localities in capsule and juvenile leaf morphology showed Utile RAPD differentiation between localities. RAPDs also provided new insights into the affinities of outlying localities. Although RAPD technology has not yet been applied to many forest tree species, patterns of variation were similar to those found in other outcrossing species studied using both RAPDs and other molecular markers.

Geographic patterns of genetic variation in Eucalyptus globulus ssp globulus and a revised racial classification

The geographic patterns of genetic variation in a wide variety of quantitative traits were studied in Eucalyptus globulus ssp. globulus and its intergrades, leading to a revised racial classification. The analysis was based on 35 traits assessed in five field trials in northern Tasmania from approximately 500 open-pollinated families, encompassing 49 collection localities in native stands. There were significant differences between the collection localities for most traits. While growth and survival traits exhibited weak spatial structuring, there were clear regional patterns in bark thickness, wood basic density, flowering precocity and some aspects of juvenile leaf morphology. There were a number of significant correlations between trait locality means, but few simple correlations between the regional patterns observed and climate. Multivariate analyses indicated that the localities could be effectively amalgamated into larger, geographically concordant races. A hierarchy of five major groupings of 13 races and 20 subraces is proposed to account for most of the quantitative genetic variation while allowing for outliers and intermediate populations. Some areas of the distribution may need further sampling to more accurately elucidate their racial affinities, especially those with traits of high economic importance.

Progress in Myrtaceae genetics and genomics: Eucalyptus as the pivotal genus

The status of genomics and genetics research in the Myrtaceae, a large family of dicotyledonous woody plants, is reviewed with Eucalyptus as the focal genus. The family contains over 5,650 species in 130 to 150 genera, predominantly of neo-tropical and Southern Hemisphere distribution. Several genera are well known for their economic importance worldwide. Myrtaceae are typically diploids with small to intermediate genome size. Microsatellites have been developed for several genera while higher throughput marker systems such as diversity arrays technology and single nucleotide polymorphism are available for Eucalyptus. Molecular data have been fundamental to current perspectives on the phylogeny, phylogeography and taxonomy of the Myrtaceae, while numerous studies of genetic diversity have been carried out particularly as it relates to endangered, rare, fragmented, overharvested or economically important species. Large expressed sequence tag collections for species of Eucalyptus have recently become public to support the annotation of the Eucalyptus grandis genome. Transcriptomics in Eucalyptus has advanced by microarrays and next-generation sequencing focusing on wood development. Linkage maps for Eucalyptus display high synteny across species and have been extensively used to map quantitative trait loci for a number of traits including growth, wood quality, disease and insect resistance. Candidate gene-based association genetics have successfully found marker–trait associations for wood and fiber traits. Genomic selection experiments have demonstrated clear potential to improve the efficiency of breeding programs while freeze-tolerant transgenic Eucalyptus trials have recently been initiated. The recently released E. grandis genome, sequenced to an average coverage of 8×, will open up exceptional opportunities to advance Myrtaceae genetics and genomics research.

HYBRIDIZATION AS A DISPERSAL MECHANISM

An example from the genus Eucalyptus is used to argue that hybridization may be of evolutionary significance as a means of gene dispersal where seed dispersal is limited. A previous study of regeneration of E. risdonii and E. amygdalina indicated that the current selective regime was favoring E. risaonii. However, the dispersal of E. risdonii by seeds is shown to be limited (s, = 4.6 m). By comparison, the flow of E. risdonii genes into the range of E. amygdalina by pollen dispersal and F1 hybridization is widespread (sp = 82 m). While the actual level of hybridization is low, interspecific hybridization effectively doubles the dispersal of E. risdonii genes into the range of E. amygdalina. This pollen flow can have a significant genetic impact, since isolated hybrids or patches of abnormal phenotypes have been found 200–300 m from the species boundary. Based on lignotuber size, some of these patches appear to have been founded by F1 hybrids. The frequency of E. risdonii types in the patches appears to increase with patch size suggesting that there is selection for this phenotype in subsequent generations. E. risdonii‐like individuals were recovered in the progeny from both intermediate and E. risdonii backcross phenotypes. These results suggest that E. risdonii may invade suitable habitat islands within the E. amygdalina forest, independently of seed migration, by long‐distance pollen migration followed by selection for the gene combinations of the pollen parent.