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Ntawuhiganayo, E. B., Uwizeye, F. K., Zibera, E., Dusenge, M. E., Ziegler, C., Ntirugulirwa, B., et al. (2020). Traits controlling shade tolerance in tropical montane trees. Tree Physiol., 40(2), 183–197.
Abstract: Tropical canopies are complex, with multiple canopy layers and pronounced gap dynamics contributing to their high species diversity and productivity. An important reason for this complexity is the large variation in shade tolerance among different tree species. At present, we lack a clear understanding of which plant traits control this variation, e.g., regarding the relative contributions of whole-plant versus leaf traits or structural versus physiological traits. We investigated a broad range of traits in six tropical montane rainforest tree species with different degrees of shade tolerance, grown under three different radiation regimes (under the open sky or beneath sparse or dense canopies). The two distinct shade-tolerant species had higher fractional biomass in leaves and branches while shade-intolerant species invested more into stems, and these differences were greater under low radiation. Leaf respiration and photosynthetic light compensation point did not vary with species shade tolerance, regardless of radiation regime. Leaf temperatures in open plots were markedly higher in shade-tolerant species due to their low transpiration rates and large leaf sizes. Our results suggest that interspecific variation in shade tolerance of tropical montane trees is controlled by species differences in whole-plant biomass allocation strategy rather than by difference in physiological leaf traits determining leaf carbon balance at low radiation. © The Author(s) 2019. Published by Oxford University Press.
Keywords: biomass allocation; leaf temperature; plant traits; Rwanda; shade intolerance; shade tolerance; tropical montane forest; article; biomass allocation; breathing; canopy; carbon balance; compensation; photosynthesis; plant leaf; plant stem; rain forest; Rwanda; shade tolerance; species difference; sweating
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Lalague, H., Csilléry, K., Oddou-Muratorio, S., Safrana, J., de Quattro, C., Fady, B., et al. (2014). Nucleotide diversity and linkage disequilibrium at 58 stress response and phenology candidate genes in a European beech (Fagus sylvatica L.) population from southeastern France. Tree Genetics and Genomes, 10(1), 15–26.
Abstract: European beech (Fagus sylvatica L.) is one of the most economically and ecologically important deciduous trees in Europe, yet little is known about its genomic diversity and its adaptive potential. Here, we detail the discovery and analysis of 573 single nucleotide polymorphisms (SNPs) from 58 candidate gene fragments that are potentially involved in abiotic stress response and budburst phenology using a panel of 96 individuals from southeastern France. The mean nucleotide diversity was low (θ π = 2.2 × 10-3) but extremely variable among gene fragments (range from 0.02 to 10), with genes carrying insertion/deletion mutations exhibiting significantly higher diversity. The decay of linkage disequilibrium (LD) measured at gene fragments >800 base pairs was moderate (the half distance of r 2 was 154 bp), consistent with the low average population-scaled recombination rate (ρ = 5.4 × 10-3). Overall, the population-scaled recombination rate estimated in F. sylvatica was lower than for other angiosperm tree genera (such as Quercus or Populus) and similar to conifers. As a methodological perspective, we explored the effect of minimum allele frequency (MAF) on LD and showed that higher MAF resulted in slower decay of LD. It is thus essential that the same MAF is used when comparing the decay of LD among different studies and species. Our results suggest that genome-wide association mapping can be a potentially efficient approach in F. sylvatica, which has a relatively small genome size. © 2013 Springer-Verlag Berlin Heidelberg.
Keywords: Climate adaptation; Effective population size; Forest tree; Genomic diversity; Minor allele frequency (MAF); Recombination rate; Single nucleotide polymorphism (SNP)
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Scotti, I., Calvo-Vialettes, L., Scotti-Saintagne, C., Citterio, M., Degen, B., & Bonal, D. (2010). Genetic variation for growth, morphological, and physiological traits in a wild population of the Neotropical shade tolerant rainforest tree Sextonia rubra (Mez) van der Werff (Lauraceae). Tree Genet. Genomes, 6(2), 319–329.
Abstract: Quantitative genetic diversity is a fundamental component of the interaction between natural populations and their environment. In breeding programmes, quantitative genetic studies on tropical trees have so far focused on fast-growing, light-demanding species, but no information exists on shade-tolerant, slow-growing species. For this study, 27 3-year-old open-pollinated families of the Neotropical shade-tolerant rainforest tree Sextonia rubra were measured in semicontrolled conditions for 20 morphological, growth, and photosynthesis traits; the effect of genetic relatedness, habitat of provenance, and mother tree status on seedling traits was analysed. Nine traits displayed significant genetic effects, while mother tree status and habitat effects were not significant (P > 0.05) for an y trait. Estimated heritability varied between 0.14 and 0.28, with growth-related traits having the highest values. Additive genetic variation correlated positively with nonheritable variation, suggesting that ecological-evolutionary factors increasing or decreasing additive genetic variance may also affect nonheritable variation in the same direction. Our results suggest that quantitative genetic variability should be taken into account in ecological studies on, and in the management of, natural tropical rainforests; further research is needed to investigate genetic x environment interactions, in particular from the point of view of the genetic response of shade-tolerant plant species to variations in light availability.
Keywords: Ecophysiological traits; Heritability; Guiana shield; Amazon; Ecological genetics
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Brendel, O., Le Thiec, D., Scotti-Saintagne, C., Bodenes, C., Kremer, A., & Guehl, J. M. (2008). Quantitative trait loci controlling water use efficiency and related traits in Quercus robur L. Tree Genet. Genomes, 4(2), 263–278.
Abstract: Genetic variation for intrinsic water use efficiency (W-i) and related traits was estimated in a full-sib family of Quercus robur L. over 3 years. The genetic linkage map available for this F1 family was used to locate quantitative trait loci (QTL) for W-i, as estimated by leaf carbon stable isotope composition (delta C-13) or the ratio of net CO2 assimilation rate (A) to stomatal conductance to water vapour (g(w)) and related leaf traits. Gas exchange measurements were used to standardize estimates of A and g(w) and to model the sensitivity of gw to leaf-to-air vapour pressure deficit (sg(VPD)). delta C-13 varied by more than 3% among the siblings, which is equivalent to 40% variation of W-i. Most of the studied traits exhibited high clonal mean repeat-abilities (> 50%; proportion of clonal mean variability in global variance). Repeatabilities for delta C-13, leaf mass per area (LMA) and leaf nitrogen content were higher than 70%. For delta C-13, ten QTLs were detected, one of which was detected repeatedly for all 3 years and consistently explained more than 20% of measured variance. Four genomic regions were found in which co-localizing traits linked variation in W-i to variations in leaf chlorophyll and nitrogen content, LMA and sg(VPD). A positive correlation using clonal means between delta C-13 and A/g(w), as well as a co-localisation of QTL detected for both traits, can be seen as validation of the theoretical model linking the genetic architecture of these two traits.
Keywords: Quercus robur; carbon isotope composition; delta C-13; water use efficiency; QTL
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Scotti, I., Burelli, A., Cattonaro, F., Chagne, D., Fuller, J., Hedley, P. E., et al. (2005). Analysis of the distribution of marker classes in a genetic linkage map: a case study in Norway spruce (Picea abies karst). Tree Genet. Genomes, 1(3), 93–102.
Abstract: In order to analyze the large-scale structure of the genome of Norway spruce (Picea abies Karst.), a pseudo-testcross genetic linkage map was built using markers of six different types, belonging to the low (amplified fragment length polymorphisms, simple sequence repeats) or high (sequence-specific amplified polymorphisms, inter-retrotransposon amplified polymorphisms) copy-number fraction of the genome, and including expressed region-derived markers (expressed sequence tag polymorphisms). Twenty seven and 23 linkage groups of at least four markers were obtained for the female and the male parent maps, respectively. A subset of these linkage groups coalesced into 13 bi-parental linkage groups through markers shared between the two maps. This map was used to investigate the frequency of each marker type over chromosomes and the distribution of marker types relative to each other, using autocorrelation techniques. Our results show that, while the composition of chromosomes is homogeneous, low- and high-copy-number markers tend to occupy separate regions of the linkage groups, and that expressed sequences are preferentially associated with microsatellites and separated from retrotranspo sons. These results indicate that the spatial structure of Norway spruce chromosomes is not homogeneous.
Keywords: Picea abies; conifers; linkage map; genome structure; molecular markers; autocorrelation
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Chevolot, M., Louisanna, E., Azri, W., Leblanc-Fournier, N., Roeckel-Drevet, P., Scotti-Saintagne, C., et al. (2011). Isolation of primers for candidate genes for mechano-sensing in five Neotropical tree species. Tree Genet. Genomes, 7(3), 655–661.
Abstract: Mechanical signals have an impact on plant development. Tropical rainforest trees display large variability for life-history traits related to biomechanics and therefore are a unique study system to better understand biomechanical trait variability from an evolutionary perspective. From sequences and gene expression data available in model species, we developed specific primers for six candidate genes for mechano-sensing in five tropical species. Most of the gene sequences were polymorphic in most species.
Keywords: Population genomics; Functional gene; Mechanical signals; Fabaceae
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Porth, I., Scotti-Saintagne, C., Barreneche, T., Kremer, A., & Burg, K. (2005). Linkage mapping of osmotic stress induced genes of oak. Tree Genet. Genomes, 1(1), 31–40.
Abstract: Water stress affecting long-lived trees is an important challenge in forestry. Due to global climate change, forest trees will be threatened by extreme conditions like flooding or drought. It is necessary to understand differences in stress tolerance within certain species and to investigate putative relations on genomic level. In this study, osmotic stress induced genes of Quercus ssp. were positioned on two genetic linkage maps of oak. An intra-specific cross 3P*A4 of Quercus robur consisting of 88 offspring and an inter-specific cross 11P*QS29 of Q. robur and Q. petraea comprising 72 full-sibs were analyzed for the inheritance of 14 loci represented by 34 individual single nucleotide polymorphisms. Seven genes in the intra-cross, as well as other six genes in the inter-cross could be mapped and one gene could not be localised due to the severe distortion of the segregation. The collection of expressed sequences involved ribosomal proteins, members of the oxylase/oxygenase gene family, betaine aldehyde dehydrogenase, Dc3 promoter-binding factor, a putative member of the nodulin family, glutathione-S-transferase and proteins with unknown functions. In the inter-cross, two linked markers exhibited 89% deficiency of heterozygosity. Thirteen genes were positioned on ten different oak chromosomes and can serve as orthologous markers in comparative mapping studies within Fagaceae. © Springer-Verlag 2005.
Keywords: Est; Linkage map; Oak; Osmotic stress; Quercus ssp.; Fagaceae; Quercus; Quercus petraea; Quercus robur
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Do, N. A., Dias, D., Zhang, Z., Huang, X., Nguyen, T. T., Pham, V. V., et al. (2020). Study on the behavior of squared and sub-rectangular tunnels using the Hyperstatic Reaction Method. Transp. Geotech., 22(100321).
Keywords: Finite element method; Lining; Squared shape; Sub-rectangular shape; Tunnel; efficiency measurement; finite element method; numerical model; transportation development; transportation planning; tunnel design; tunnel lining
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Touchard, A., Aili, S. R., Fox, E. G. P., Escoubas, P., Orivel, J., Nicholson, G. M., et al. (2016). The biochemical toxin arsenal from ant venoms. Toxins, 8(1), 30.
Abstract: Ants (Formicidae) represent a taxonomically diverse group of hymenopterans with over 13,000 extant species, the majority of which inject or spray secretions from a venom gland. The evolutionary success of ants is mostly due to their unique eusociality that has permitted them to develop complex collaborative strategies, partly involving their venom secretions, to defend their nest against predators, microbial pathogens, ant competitors, and to hunt prey. Activities of ant venom include paralytic, cytolytic, haemolytic, allergenic, pro-inflammatory, insecticidal, antimicrobial, and pain-producing pharmacologic activities, while non-toxic functions include roles in chemical communication involving trail and sex pheromones, deterrents, and aggregators. While these diverse activities in ant venoms have until now been largely understudied due to the small venom yield from ants, modern analytical and venomic techniques are beginning to reveal the diversity of toxin structure and function. As such, ant venoms are distinct from other venomous animals, not only rich in linear, dimeric and disulfide-bonded peptides and bioactive proteins, but also other volatile and non-volatile compounds such as alkaloids and hydrocarbons. The present review details the unique structures and pharmacologies of known ant venom proteinaceous and alkaloidal toxins and their potential as a source of novel bioinsecticides and therapeutic agents. © 2016 by the authors; licensee MDPI, Basel, Switzerland.
Keywords: Alkaloids; Ant venom; Enzymes; Formic acid; Peptides; Toxins; Venom biochemistry
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Barassé, V., Touchard, A., Téné, N., Tindo, M., Kenne, M., Klopp, C., et al. (2019). The peptide venom composition of the fierce stinging ant tetraponera aethiops (formicidae: Pseudomyrmecinae). Toxins, 11(12), 732.
Abstract: In the mutualisms involving certain pseudomyrmicine ants and different myrmecophytes (i.e., plants sheltering colonies of specialized “plant-ant” species in hollow structures), the ant venom contributes to the host plant biotic defenses by inducing the rapid paralysis of defoliating insects and causing intense pain to browsing mammals. Using integrated transcriptomic and proteomic approaches, we identified the venom peptidome of the plant-ant Tetraponera aethiops (Pseudomyrmecinae). The transcriptomic analysis of its venom glands revealed that 40% of the expressed contigs encoded only seven peptide precursors related to the ant venom peptides from the A-superfamily. Among the 12 peptide masses detected by liquid chromatography-mass spectrometry (LC-MS), nine mature peptide sequences were characterized and confirmed through proteomic analysis. These venom peptides, called pseudomyrmecitoxins (PSDTX), share amino acid sequence identities with myrmeciitoxins known for their dual offensive and defensive functions on both insects and mammals. Furthermore, we demonstrated through reduction/alkylation of the crude venom that four PSDTXs were homo- and heterodimeric. Thus, we provide the first insights into the defensive venom composition of the ant genus Tetraponera indicative of a streamlined peptidome.
Keywords: Defensive venom; Dimeric peptides; Peptidome; Tetraponera aethiops
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