Plasticity of maritime pine (Pinus pinaster) wood-forming tissues during a growing season

The seasonal effect is the most significant external source of variation affecting vascular cambial activity and the development of newly divided cells, and hence wood properties. Here, the effect of edapho-climatic conditions on the phenotypic and molecular plasticity of differentiating secondary xylem during a growing season was investigated. Wood-forming tissues of maritime pine (Pinus pinaster) were collected from the beginning to the end of the growing season in 2003. Data from examination of fibre morphology, Fourier-transform infrared spectroscopy (FTIR), analytical pyrolysis, and gas chromatography/mass spectrometry (GC/MS) were combined to characterize the samples. Strong variation was observed in response to changes in edapho-climatic conditions. A genomic approach was used to identify genes differentially expressed during this growing season. Out of 3512 studied genes, 19% showed a significant seasonal effect. These genes were clustered into five distinct groups, the largest two representing genes over-expressed in the early- or late-wood-forming tissues, respectively. The other three clusters were characterized by responses to specific edapho-climatic conditions. This work provides new insights into the plasticity of the molecular machinery involved in wood formation, and reveals candidate genes potentially responsible for the phenotypic differences found between early- and late-wood.     

QTL influencing growth and wood properties in Eucalyptus globulus

Regions of the genome affecting physical and chemical wood properties (quantitative trait loci (QTL)), as well as growth, were identified using a clonally replicated, outbred F₂ family (112 genotypes, each with two ramets) of Eucalyptus globulus, planted in a field trial in north-west Tasmania. Traits studied were growth (assessed by stem diameter), wood density, cellulose content, pulp yield and lignin content. These traits are important in breeding for pulpwood, and will be important in breeding for carbon sequestration and biofuel production. Between one and four QTL were located for each trait, with each QTL explaining between 4% and 12% of the phenotypic variation. Several QTL for chemical wood properties were co-located, consistent with their high phenotypic correlations, and may reflect pleiotropic effects of the same genes. In contrast, QTL for density and lignin content with overlapping confidence intervals were considered to be due to independent genes, since the QTL effects were inherited from different parents. The inclusion of fully informative microsatellites on the linkage map allowed the determination of homology at the linkage group level between QTL and candidate genes in different pedigrees of E. globulus and different eucalypt species. None of the candidate genes mapped in comparable studies co-located with our major QTL for wood chemical properties, arguing that there are important candidate genes yet to be discovered.     

Association genetics in Corymbia citriodora subsp. variegata identifies single nucleotide polymorphisms affecting wood growth and cellulosic pulp yield

Wood is an important biological resource which contributes to nutrient and hydrology cycles through ecosystems, and provides structural support at the plant level. Thousands of genes are involved in wood development, yet their effects on phenotype are not well understood. We have exploited the low genomic linkage disequilibrium (LD) and abundant phenotypic variation of forest trees to explore allelic diversity underlying wood traits in an association study. Candidate gene allelic diversity was modelled against quantitative variation to identify SNPs influencing wood properties, growth and disease resistance across three populations of Corymbia citriodora subsp. variegata, a forest tree of eastern Australia. Nine single nucleotide polymorphism (SNP) associations from six genes were identified in a discovery population (833 individuals). Associations were subsequently tested in two smaller populations (130-160 individuals), 'validating' our findings in three cases for actin 7 (ACT7) and COP1 interacting protein 7 (CIP7). The results imply a functional role for these genes in mediating wood chemical composition and growth, respectively. A flip in the effect of ACT7 on pulp yield between populations suggests gene by environment interactions are at play. Existing evidence of gene function lends strength to the observed associations, and in the case of CIP7 supports a role in cortical photosynthesis.     

Integrating genomics into Eucalyptus breeding

The advent of high throughput genomic technologies has opened new perspectives in the speed, scale and detail with which one can investigate genes, genomes and complex traits in Eucalyptus species. A genomic approach to a more detailed understanding of important metabolic and physiological processes, which affect tree growth and stress resistance, and the identification of genes and their allelic variants, which determine the major chemical and physical features of wood properties, should eventually lead to new opportunities for directed genetic modifications of far-reaching economic impact in forest industry. It should be kept in mind, however, that basic breeding strategies, coupled with sophisticated quantitative methods, breeder's experience and breeder's intuition, will continue to generate significant genetic gains and have a clear measurable impact on production forestry. Even with a much more global view of genetic processes, genomics will only succeed in contributing to the development of improved industrial forests if it is strongly interconnected with intensive fieldwork and creative breeding. Integrated genomic projects involving multi-species expressed sequence tag sequencing and quantitative trait locus detection, single nucleotide polymorphism discovery for association mapping, and the development of a gene-rich physical map for the Eucalyptus genome will quickly move toward linking phenotypes to genes that control the wood formation processes that define industrial-level traits. Exploiting the full power of the superior natural phenotypic variation in wood properties found in Eucalyptus genetic resources will undoubtedly be a key factor to reach this goal.     

Measuring and modelling stem growth and wood formation: An overview

The immediate environment of a cambial initial (weather and nutritional factors, growth regulators, physical stresses) varies continuously over time. Consequently local conditions in the cambium influencing wood formation at any given instant are unique. The distribution of these conditions can be influenced by longitudinal gradients (stem base to apex), circumferentially or by local factors, such as proximity to branches. Not surprisingly, therefore, the variation in wood properties within a stem is large and in seasonal climates, the greatest variation is typically found within an annual ring.A great advantage for the study of wood is that the net product of seasonal processes is recorded in the wood structure across the stem radius. Thus by studying the pattern of wood property variation, within the context of its growth history, we can gain insight into cause and effect relationships between the drivers of wood variability. Combining this with temporal, high-resolution measurements of stem growth, weather, and process modelling enables us to better understand and test hypotheses of wood formation and the causes of variability in wood properties.Over recent years and in partnership with industry and other research providers, we have been attempting to model tree growth (Cabala) and cambial activity (TreeRing and CAMBIUM) at a daily time step to explain radial variability in wood properties. CAMBIUM is the latest development of this effort, modelling a population of eucalypt cambial cells, accounting for fibre and vessel formation using physiologically meaningful relationships.     

Karelian birch (Betula pendula Roth. var. carelica Merkl.) as a model for studying genetic and epigenetic variation related to the formation of patterned wood

The results of long-term pioneering studies on in vitro micropropagation of Karelian birch patterned forms and simultaneous cytological analysis of plants multiplied using different periods of in vitro culturing are published for the first time. The patterned wood character has been shown to be correlated with the degree of mixoploidy of its somatic tissue, which is higher in the plants obtained from callus cultures during the first years of culturing. Subsequent intracellular selection leads to a decrease in mixoploidy and, hence, in a later expression and lower expressivity of the patterned wood character in regenerant plants. It is also known that extreme growth conditions stimulate the formation of patterned wood. Thus, Karelian birch may serve as a model object for studying the forms of variability (both genetic and epigenetic) that result in patterned wood. The genetic variability is expressed in the variation of the degree of mixoploidy of somatic tissue as a result of various mitotic aberrations. The epigenetic variability is not related to changes in the DNA structure; it is caused by different phenotypic effects of genes located in cells with different ploidy/aneuploidy levels, the ratio between which varies depending on the environmental conditions. The expression of genes, in particular, rRNA genes, is affected by extreme conditions. The appearance of a residual nucleolus at the mitotic metaphase-telophase stages is a cytological expression of this phenomenon.     

Karelian birch (<Emphasis Type="Italic">Betula pendula</Emphasis> Roth. var. <Emphasis Type="Italic">carelica</Emphasis> Merkl.) as a model for studying genetic and epigenetic variation related to the formation of patterned wood

The results of long-term pioneering studies on in vitro micropropagation of Karelian birch patterned forms and simultaneous cytological analysis of plants multiplied using different periods of in vitro culturing are published for the first time. The patterned wood character has been shown to be correlated with the degree of mixoploidy of its somatic tissue, which is higher in the plants obtained from callus cultures during the first years of culturing. Subsequent intracellular selection leads to a decrease in mixoploidy and, hence, in a later expression and lower expressivity of the patterned wood character in regenerant plants. It is also known that extreme growth conditions stimulate the formation of patterned wood. Thus, Karelian birch may serve as a model object for studying the forms of variability (both genetic and epigenetic) that result in patterned wood. The genetic variability is expressed in the variation of the degree of mixoploidy of somatic tissue as a result of various mitotic aberrations. The epigenetic variability is not related to changes in the DNA structure; it is caused by different phenotypic effects of genes located in cells with different ploidy/aneuploidy levels, the ratio between which varies depending on the environmental conditions. The expression of genes, in particular, rRNA genes, is affected by extreme conditions. The appearance of a residual nucleolus at the mitotic metaphase-telophase stages is a cytological expression of this phenomenon.     

Regeneration of the secondary vascular system in poplar as a novel system to investigate gene expression by a proteomic approach

Wood formation is a complex process composing many biological events. To access its key developmental stages, we have established a regeneration system that can mimic the initiation and differentiation of cambium cells for Chinese white poplar. Anatomical studies showed that new cambium and xylem re-appeared in sequence within a few weeks after being debarked. This provides the opportunity to follow key stages of wood formation by sampling clonal trees at different regeneration times. We used this system in combination with a proteomic approach to analyze proteins expressed in different regeneration stages. PMFs for 244 proteins differentially displayed were obtained and queried against public databases. Putative functions of 199 of these proteins were assigned and classified. Regulatory genes for cell cycle progression, differentiation and cell fate were expressed in the formation of cambial tissue, while 27 genes involved in secondary wall formation were predominantly found in the xylem developing stage. This indicates that the change of gene expression pattern is corresponding to the progression of second vascular system regeneration when and where the key events of wood development occur. Further exploration of these interesting genes may provide insight into the molecular mechanisms of wood formation.     

Contrasting gene expression programs correspond with predator‐induced phenotypic plasticity within and across generations in Daphnia

Research has shown that a change in environmental conditions can alter the expression of traits during development (i.e., “within‐generation phenotypic plasticity”) as well as induce heritable phenotypic responses that persist for multiple generations (i.e., “transgenerational plasticity”, TGP). It has long been assumed that shifts in gene expression are tightly linked to observed trait responses at the phenotypic level. Yet, the manner in which organisms couple within‐ and TGP at the molecular level is unclear. Here we tested the influence of fish predator chemical cues on patterns of gene expression within‐ and across generations using a clone of Daphnia ambigua that is known to exhibit strong TGP but weak within‐generation plasticity. Daphnia were reared in the presence of predator cues in generation 1, and shifts in gene expression were tracked across two additional asexual experimental generations that lacked exposure to predator cues. Initial exposure to predator cues in generation 1 was linked to ~50 responsive genes, but such shifts were 3–4× larger in later generations. Differentially expressed genes included those involved in reproduction, exoskeleton structure and digestion; major shifts in expression of genes encoding ribosomal proteins were also identified. Furthermore, shifts within the first‐generation and transgenerational shifts in gene expression were largely distinct in terms of the genes that were differentially expressed. Such results argue that the gene expression programmes involved in within‐ vs. transgeneration plasticity are fundamentally different. Our study provides new key insights into the plasticity of gene expression and how it relates to phenotypic plasticity in nature.