Geographical genetics and the conservation of forest trees

Trees are key ecosystem engineers. Many analyses of the genetic diversity of forest trees over substantial parts of their distributional ranges are appearing. These studies are of relevance for forest and landscape management, the inventory of botanical genetic resources and the conservation biology of rare, endemic, relictual, and endangered tree species. This review focuses on (i) recent investigations of the influence of human disturbances, (ii) comparative analyses of closely related and hybridizing species, (iii) reconstructions of refugia and of the spread of tree populations during the postglacial, (iv) studies of both range-wide and range-edge genetic patterns, and (v) assessments of the role of tree genetic diversity in the face of future climate warming. There is a need to include more tropical and austral trees in genetic analyses, as most studies have dealt with the relatively species-poor Palaearctic and Nearctic regions. Further studies are also needed on the role of tree genetic diversity in variations in phenology, resistance to insect defoliators and fungal pathogens, reactions to increased CO₂ and ozone concentrations, growth, mortality rates and other traits. Most macroecological and scaling patterns of species richness still need to be studied for genetic diversity. Open research questions in this rapidly evolving field involve invasion biology, island biogeography, and urban ecology. There is a need for more knowledge transfer from the many studies of tree genetic diversity to the day-to-day management of trees and forests.     

Genetic variation of Marchalina hellenica (Hemiptera: Margarodidae) sampled from different hosts and localities in Greece

Random amplified polymorphic DNA (RAPD) analysis was applied to 120 individuals of Marchalina hellenica (Gennadius) representing six populations collected in northern, central and southern mainland Greece. One population was sampled on one species of fir tree and the others on two species of pine trees. Four random decamer primers were used to evaluate genetic variation among the populations examined. The results revealed intra- and interpopulation polymorphism both related to host type and region of origin. Phylogenetic analysis based on genetic distances estimated by the RAPD frequencies revealed an important genetic differentiation in samples collected on fir trees in southern Greece and to a lesser extent in samples from pine trees in central and northern Greece. Furthermore, considerable subdivision and restricted gene flow among the populations examined were observed. The results are discussed in relation to the biology and geographical distribution of M. hellenica in Greece.     

柳树遗传学研究现状与前景

柳树种类繁多, 分布广泛, 是重要的阔叶树种, 其遗传学研究也较早受到重视。该文从柳树性状遗传变异、群体遗传、遗传鉴定、遗传图谱构建和QTL定位几个角度介绍了柳树遗传学的研究进展, 并结合木本植物的特点和柳树的生物学特性进行分析, 认为柳树是理想的林木遗传学研究材料, 可作为模式树种, 应受到特别关注。     

Metabolite profiling of Douglas-fir (Pseudotsuga menziesii) field trials reveals strong environmental and weak genetic variation

The primary objective of this study was to assess metabolomics for its capacity to discern biological variation among 10 full-sib families of a Douglas-fir tree breeding population, replicated on two sites. The differential accumulation of small metabolites in developing xylem was examined through metabolite profiles (139 metabolites common to 181 individual trees) generated by gas chromatography mass spectrometry and a series of statistical analyses that incorporated family, site, and tree growth and quantitative phenotypic wood traits (wood density, microfibril angle, wood chemistry and fiber morphology). Multivariate discriminant, canonical discriminant and factor analyses and broad-sense heritabilities revealed that metabolic and phenotypic traits alike were strongly related to site, while similar associations relating to genetic (family) structure were weak in comparison. Canonical correlation analysis subsequently identified correlations between specific phenotypic traits (i.e. tree growth, fibre morphology and wood chemistry) and metabolic traits (i.e. carbohydrate and lignin biosynthetic metabolites), demonstrating a coherent relationship between genetics, metabolism, environmental and phenotypic expression in wood-forming tissue. The association between cambial metabolites and tree phenotype, as revealed by metabolite profiling, demonstrates the value of metabolomics for systems biology approaches to understanding tree growth and secondary cell wall biosynthesis in plants.     

Upper bounds on maximum likelihood for phylogenetic trees

We introduce a mechanism for analytically deriving upper bounds on the maximum likelihood for genetic sequence data on sets of phylogenies. A simple 'partition' bound is introduced for general models. Tighter bounds are developed for the simplest model of evolution, the two state symmetric model of nucleotide substitution under the molecular clock. This follows earlier theoretical work which has been restricted to this model by analytic complexity. A weakness of current numerical computation is that reported 'maximum likelihood' results cannot be guaranteed, both for a specified tree (because of the possibility of multiple maxima) or over the full tree space (as the computation is intractable for large sets of trees). The bounds we develop here can be used to conclusively eliminate large proportions of tree space in the search for the maximum likelihood tree. This is vital in the development of a branch and bound search strategy for identifying the maximum likelihood tree. We report the results from a simulation study of approximately 10(6) data sets generated on clock-like trees of five leaves. In each trial a likelihood value of one specific instance of a parameterised tree is compared to the bound determined for each of the 105 possible rooted binary trees. The proportion of trees that are eliminated from the search for the maximum likelihood tree ranged from 92% to almost 98%, indicating a computational speed-up factor of between 12 and 44.     

林木蛋白质组学研究进展

近年来,应用新的基因组学技术来研究林木生长发育以及林木对生物与非生物胁迫的反应已使得人们对林木生物学有了相当大的了解。蛋白质组学是林木生物学的重要内容。本文综述了林木蛋白质组学在群体遗传、遗传作图、逆境生理、组织器官以及木材形成等方面的研究进展,并简要介绍了林木蛋白质组数据库。最后展望了林木蛋白质组学的发展前景。     

Characterization of rubber tree microRNA in phytohormone response using large genomic DNA libraries,promoter sequence and gene expression analysis

The para rubber tree is the most widely cultivated tree species for producing natural rubber (NR) latex. Unfortunately, rubber tree characteristics such as a long life cycle, heterozygous genetic backgrounds, and poorly understood genetic profiles are the obstacles to breeding new rubber tree varieties, such as those with improved NR yields. Recent evidence has revealed the potential importance of controlling microRNA (miRNA) decay in some aspects of NR regulation. To gain a better understanding of miRNAs and their relationship with rubber tree gene regulation networks, large genomic DNA insert-containing libraries were generated to complement the incomplete draft genome sequence and applied as a new powerful tool to predict a function of interested genes. Bacterial artificial chromosome and fosmid libraries, containing a total of 120,576 clones with an average insert size of 43.35 kb, provided approximately 2.42 haploid genome equivalents of coverage based on the estimated 2.15 gb rubber tree genome. Based on these library sequences, the precursors of 1 member of rubber tree-specific miRNAs and 12 members of conserved miRNAs were successfully identified. A panel of miRNAs was characterized for phytohormone response by precisely identifying phytohormone-responsive motifs in their promoter sequences. Furthermore, the quantitative real-time PCR on ethylene stimulation of rubber trees was performed to demonstrate that the miR2118, miR159, miR164 and miR166 are responsive to ethylene, thus confirmed the prediction by genomic DNA analysis. The cis-regulatory elements identified in the promoter regions of these miRNA genes help augment our understanding of miRNA gene regulation and provide a foundation for further investigation of the regulation of rubber tree miRNAs.     

Genetic transformation of fruit trees: current status and remaining challenges

Genetic transformation has emerged as a powerful tool for genetic improvement of fruit trees hindered by their reproductive biology and their high levels of heterozygosity. For years, genetic engineering of fruit trees has focussed principally on enhancing disease resistance (against viruses, fungi, and bacteria), although there are few examples of field cultivation and commercial application of these transgenic plants. In addition, over the years much work has been performed to enhance abiotic stress tolerance, to induce modifications of plant growth and habit, to produce marker-free transgenic plants and to improve fruit quality by modification of genes that are crucially important in the production of specific plant components. Recently, with the release of several genome sequences, studies of functional genomics are becoming increasingly important: by modification (overexpression or silencing) of genes involved in the production of specific plant components is possible to uncover regulatory mechanisms associated with the biosynthesis and catabolism of metabolites in plants. This review focuses on the main advances, in recent years, in genetic transformation of the most important species of fruit trees, devoting particular attention to functional genomics approaches and possible future challenges of genetic engineering for these species in the post-genomic era.     

Recent advances in the genetic transformation of trees

As the commercial production of transgenic annual crops becomes a reality in many parts of the world, many people wonder if the genetic engineering of perennial trees will allow their eventual commercialization. Not long ago, trees were considered to be recalcitrant material for most molecular biology techniques, including genetic transformation. However, transgenes for shortening the juvenile phase or for phytoremediation purposes have now been incorporated, and the alteration of lignin biosynthesis and increased cellulose accumulation in forest trees have also been accomplished. For long-lived tree species, new questions arise regarding the stability of integration and expression of foreign genes. Biosafety considerations, including transgene dispersion through the pollen and advances in strategies to avoid this, are also important.     

柳树遗传学研究现状与前景

柳树种类繁多,分布广泛,是重要的阔叶树种,其遗传学研究也较早受到重视。该文从柳树性状遗传变异、群体遗传、遗传鉴定、遗传图谱构建和QTL定位几个角度介绍了柳树遗传学的研究进展,并结合木本植物的特点和柳树的生物学特性进行分析,认为柳树是理想的林木遗传学研究材料,可作为模式树种,应受到特别关注。     

Algorithms for mapping of mRNA targets for microRNA

MicroRNAs (miRNAs) are involved in human health and disease as endogenous suppressors of the translation of coding genes. At this early point of time in miRNA biology, it is important to identify specific cognate mRNA targets for miRNA. Investigation of the significance of miRNAs in disease processes relies on algorithms that hypothetically link specific miRNAs to their putative target genes. The development of such algorithms represents a hot area of research in biomedical informatics. Lack of biological data linking specific miRNAs to their respective mRNA targets represents the most serious limitation at this time. This article presents a concise review addressing the most popular concepts underlying state-of-the-art algorithms and principles aimed at target mapping for specific miRNAs. Strategies for improvement of the current bioinformatics tools and effective approaches for biological validation are discussed.     

Tree thinking,time and topology: comments on the interpretation of tree diagrams in evolutionary/phylogenetic systematics

This paper presents a graph theoretical overview of tree diagrams applied extensively in systematic biology. Simple evolutionary models involving three speciation processes (splitting, budding and anagenesis) are used for evaluating the ability of different rooted trees to demonstrate temporal and ancestor–descendant relationships within or among species. On this basis, they are classified into four types: (i) diachronous trees depict evolutionary history faithfully because the order of nodes along any path agrees with the temporal sequence of respective populations or species, (ii) achronous trees show ancestor–descendant relationships for species or higher taxa such that the time aspect is disregarded, (iii) synchronous trees attempt to reveal evolutionary pathways and/or distributional patterns of apomorphic characters for organisms living at the same point of time, and (iv) asynchronous trees may do the same regardless the time of origin (e.g. when extant and extinct species are evaluated together). Trees of the last two types are cladograms, the synchronous ones emphasizing predominantly—but not exclusively—the evolutionary process within a group, while asynchronous cladograms are usually focused on pattern and infrequently on process. Historical comments and the examples demonstrate that each of these tree types is useful on its own right in evolutionary biology and systematics. In practice, separation among them is not sharp, and their features are often combined into eclectic tree forms whose interpretation is not entirely free from problems.     

Age versus size determination of radial variation in wood specific gravity: lessons from eccentrics

Radial increases in wood specific gravity have been shown to characterize early successional trees from tropical forests. Here, we develop and apply a novel method to test whether radial increases are determined by tree age or tree size. The method compares the slopes of specific gravity changes across a short radius and a long radius of trees with eccentric trunks. If radial changes are determined by size, then the slope of the change should be the same on both radii. If radial changes are determined by age, then the slope should be greater on the short radius. For 30 trees from 12 species with eccentricity of at least 4%, the ratio of the slopes of the linear regressions of specific gravity on radial distance (short radius slope/long radius slope) was regressed on the ratio of radii lengths (long radius/short radius). The regression was highly significant, and the faster increase in specific gravity on the short radius was sufficient to compensate for the difference in radius lengths, so the specific gravity of wood along the short radius was equal to the specific gravity on the long radius at any given proportional distance on the radius. Therefore, trees that are producing xylem faster on one radius than another produce wood of comparable specific gravity on both radii at the same time, so radial increases in specific gravity are dependent on tree age, not tree size.     

Eight variable microsatellite loci for a Neotropical tree, Jacaranda copaia (Aubl.) D.Don (Bignoniaceae)

The Dendrogene Project (Genetic Conservation within Managed Forests in Amazonia) aims to understand the genetic and ecological processes that underpin tree species survival and in particular their response to forest management regimes. As part of the project, we developed eight microsatellite markers for Jacaranda copaia to be used for genetic structure, gene flow and reproductive biology studies. Polymorphism was evaluated using 96 adult trees from the Tapajos National Forest in the Eastern Brazilian Amazon. An average of 22 alleles per locus were detected, with expected heterozygosity ranging from 0.731 to 0.94.     

Genetic variation in a tropical tree species influences the associated epiphytic plant and invertebrate communities in a complex forest ecosystem

Genetic differences among tree species, their hybrids and within tree species are known to influence associated ecological communities and ecosystem processes in areas of limited species diversity. The extent to which this same phenomenon occurs based on genetic variation within a single tree species, in a diverse complex ecosystem such as a tropical forest, is unknown. The level of biodiversity and complexity of the ecosystem may reduce the impact of a single tree species on associated communities. We assessed the influence of within-species genetic variation in the tree Brosimum alicastrum (Moraceae) on associated epiphytic and invertebrate communities in a neotropical rainforest. We found a significant positive association between genetic distance of trees and community difference of the epiphytic plants growing on the tree, the invertebrates living among the leaf litter around the base of the tree, and the invertebrates found on the tree trunk. This means that the more genetically similar trees are host to more similar epiphyte and invertebrate communities. Our work has implications for whole ecosystem conservation management, since maintaining sufficient genetic diversity at the primary producer level will enhance species diversity of other plants and animals.