Functional–structural plant models: a growing paradigm for plant studies

A number of research groups in various areas of plant biology as well as computer science and applied mathematics have addressed modelling the spatiotemporal dynamics of growth and development of plants. This has resulted in development of functional–structural plant models (FSPMs). In FSPMs, the plant structure is always explicitly represented in terms of a network of elementary units. In this respect, FSPMs are different from more abstract models in which a simplified representation of the plant structure is frequently used (e.g. spatial density of leaves, total biomass, etc.). This key feature makes it possible to build modular models and creates avenues for efficient exchange of model components and experimental data. They are being used to deal with the complex 3-D structure of plants and to simulate growth and development occurring at spatial scales from cells to forest areas, and temporal scales from seconds to decades and many plant generations. The plant types studied also cover a broad spectrum, from algae to trees. This special issue of Annals of Botany features selected papers on FSPM topics such as models of morphological development, models of physical and biological processes, integrated models predicting dynamics of plants and plant communities, modelling platforms, methods for acquiring the 3-D structures of plants using automated measurements, and practical applications for agronomic purposes.     

Experimentally reduced root–microbe interactions reveal limited plasticity in functional root traits in Acer and Quercus

Background and Aims

Interactions between roots and soil microbes are critical components of below-ground ecology. It is essential to quantify the magnitude of root trait variation both among and within species, including variation due to plasticity. In addition to contextualizing the magnitude of plasticity relative to differences between species, studies of plasticity can ascertain if plasticity is predictable and whether an environmental factor elicits changes in traits that are functionally advantageous.

Methods

To compare functional traits and trait plasticities in fine root tissues with natural and reduced levels of colonization by microbial symbionts, trimmed and surface-sterilized root segments of 2-year-old Acer rubrum and Quercus rubra seedlings were manipulated. Segments were then replanted into satellite pots filled with control or heat-treated soil, both originally derived from a natural forest. Mycorrhizal colonization was near zero in roots grown in heat-treated soil; roots grown in control soil matched the higher colonization levels observed in unmanipulated root samples collected from field locations.

Key Results

Between-treatment comparisons revealed negligible plasticity for root diameter, branching intensity and nitrogen concentration across both species. Roots from treated soils had decreased tissue density (approx. 10–20 %) and increased specific root length (approx. 10–30 %). In contrast, species differences were significant and greater than treatment effects in traits other than tissue density. Interspecific trait differences were also significant in field samples, which generally resembled greenhouse samples.

Conclusions

The combination of experimental and field approaches was useful for contextualizing trait plasticity in comparison with inter- and intra-specific trait variation. Findings that root traits are largely species dependent, with the exception of root tissue density, are discussed in the context of current literature on root trait variation, interactions with symbionts and recent progress in standardization of methods for quantifying root traits.     

Chemical and enzymatic fractionation of cell walls from Fucales: insights into the structure of the extracellular matrix of brown algae

Background and Aims

Brown algae are photosynthetic multicellular marine organisms evolutionarily distant from land plants, with a distinctive cell wall. They feature carbohydrates shared with plants (cellulose), animals (fucose-containing sulfated polysaccharides, FCSPs) or bacteria (alginates). How these components are organized into a three-dimensional extracellular matrix (ECM) still remains unclear. Recent molecular analysis of the corresponding biosynthetic routes points toward a complex evolutionary history that shaped the ECM structure in brown algae.

Methods

Exhaustive sequential extractions and composition analyses of cell wall material from various brown algae of the order Fucales were performed. Dedicated enzymatic degradations were used to release and identify cell wall partners. This approach was complemented by systematic chromatographic analysis to study polymer interlinks further. An additional structural assessment of the sulfated fucan extracted from Himanthalia elongata was made.

Key Results

The data indicate that FCSPs are tightly associated with proteins and cellulose within the walls. Alginates are associated with most phenolic compounds. The sulfated fucans from H. elongata were shown to have a regular α-(1→3) backbone structure, while an alternating α-(1→3), (1→4) structure has been described in some brown algae from the order Fucales.

Conclusions

The data provide a global snapshot of the cell wall architecture in brown algae, and contribute to the understanding of the structure–function relationships of the main cell wall components. Enzymatic cross-linking of alginates by phenols may regulate the strengthening of the wall, and sulfated polysaccharides may play a key role in the adaptation to osmotic stress. The emergence and evolution of ECM components is further discussed in relation to the evolution of multicellularity in brown algae.     

Estimating quantitative genetic parameters in wild populations: a comparison of pedigree and genomic approaches

The estimation of quantitative genetic parameters in wild populations is generally limited by the accuracy and completeness of the available pedigree information. Using relatedness at genomewide markers can potentially remove this limitation and lead to less biased and more precise estimates. We estimated heritability, maternal genetic effects and genetic correlations for body size traits in an unmanaged long‐term study population of Soay sheep on St Kilda using three increasingly complete and accurate estimates of relatedness: (i) Pedigree 1, using observation‐derived maternal links and microsatellite‐derived paternal links; (ii) Pedigree 2, using SNP‐derived assignment of both maternity and paternity; and (iii) whole‐genome relatedness at 37 037 autosomal SNPs. In initial analyses, heritability estimates were strikingly similar for all three methods, while standard errors were systematically lower in analyses based on Pedigree 2 and genomic relatedness. Genetic correlations were generally strong, differed little between the three estimates of relatedness and the standard errors declined only very slightly with improved relatedness information. When partitioning maternal effects into separate genetic and environmental components, maternal genetic effects found in juvenile traits increased substantially across the three relatedness estimates. Heritability declined compared to parallel models where only a maternal environment effect was fitted, suggesting that maternal genetic effects are confounded with direct genetic effects and that more accurate estimates of relatedness were better able to separate maternal genetic effects from direct genetic effects. We found that the heritability captured by SNP markers asymptoted at about half the SNPs available, suggesting that denser marker panels are not necessarily required for precise and unbiased heritability estimates. Finally, we present guidelines for the use of genomic relatedness in future quantitative genetics studies in natural populations.     

Virtualisation of stress distribution in heart valve tissue

This study presents an image-based finite element analysis incorporating histological photomicrographs of heart valve tissues. We report stress fields inside heart valve tissues, where heterogeneously distributed collagen fibres are responsible for transmitting forces into cells. Linear isotropic and anisotropic tissue material property models are incorporated to quantify the overall stress distributions in heart valve tissues. By establishing an effective predictive method with new computational tools and by performing virtual experiments on the heart valve tissue photomicrographs, we clarify how stresses are transferred from matrix to cell. The results clearly reveal the roles of heterogeneously distributed collagen fibres in mitigating stress developments inside heart valve tissues. Moreover, most local peak stresses occur around cell nuclei, suggesting that higher stress may be mediated by cells for biomechanical regulations.     

The evolutionary ecology of testicular function: size isn't everything

Larger testes are considered the quintessential adaptation to sperm competition. However, the strong focus on testis size in evolutionary research risks ignoring other potentially adaptive features of testicular function, many of which will also be shaped by post‐mating sexual selection. Here we advocate a more integrated research programme that simultaneously takes into account the developmental machinery of spermatogenesis and the various selection pressures that act on this machinery and its products. The testis is a complex organ, and so we begin by outlining how we can think about the evolution of testicular function both in terms of the composition and spatial organisation of the testis (‘testicular histology’), as well as in terms of the logical organisation of cell division during spermatogenesis (‘testicular architecture’). We then apply these concepts to ask which aspects of testicular function we can expect to be shaped by post‐mating sexual selection. We first assess the impact of selection on those traits most strongly associated with sperm competition, namely the number and kind of sperm produced. A broad range of studies now support our contention that post‐mating sexual selection affects many aspects of testicular function besides gross testis size, for example, to maximise spermatogenic efficiency or to enable the production of particular sperm morphologies. We then broaden our focus to ask how testicular function is affected by fluctuation in sperm demand. Such fluctuation can occur over an individual's lifetime (for example due to seasonality in reproduction) and may select for particular types of testicular histology and architecture depending on the particular reproductive ecology of the species in question. Fluctuation in sperm demand also occurs over evolutionary time, due to shifts in the mating system, and this may have various consequences for testicular function, for example on rates of proliferation‐induced mutation and for dealing with intragenomic conflict. We end by suggesting additional approaches that could be applied to study testicular function, and conclude that simultaneously considering the machinery, products and scheduling of spermatogenesis will be crucial as we seek to understand more fully the evolution of this most fundamental of male reproductive traits.