Challenges and Perspectives in the Epigenetics of Climate Change-Induced Forests Decline

Forest tree species are highly vulnerable to the effects of climate change. As sessile organisms with long generation times, their adaptation to a local changing environment may rely on epigenetic modifications when allele frequencies are not able to shift fast enough. However, the current lack of knowledge on this field is remarkable, due to many challenges that researchers face when studying this issue. Huge genome sizes, absence of reference genomes and annotation, and having to analyze huge amounts of data are among these difficulties, which limit the current ability to understand how climate change drives tree species epigenetic modifications. In spite of this challenging framework, some insights on the relationships among climate change-induced stress and epigenomics are coming. Advances in DNA sequencing technologies and an increasing number of studies dealing with this topic must boost our knowledge on tree adaptive capacity to changing environmental conditions. Here, we discuss challenges and perspectives in the epigenetics of climate change-induced forests decline, aiming to provide a general overview of the state of the art.

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Dendroecology as a Research Tool to Investigate Climate Change Resilience on Magnolia vovidesii, a Threatened Mexican Cloud Forest Tree Species of Eastern Mexico

Latin American Dendroecology ◽

10.1007/978-3-030-36930-9_1 ◽

2020 ◽

pp. 3-20

Author(s):

Ernesto Chanes Rodríguez-Ramírez ◽

Isolda Luna-Vega

Keyword(s):

Climate Change ◽

Tree Species ◽

Cloud Forest ◽

Forest Tree ◽

Research Tool ◽

Forest Tree Species ◽

Climate Change Resilience

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Dendroecological assessment of climate resilience of the rare and scattered forest tree species Tilia cordata Mill. in northwestern Europe

Forestry An International Journal of Forest Research ◽

10.1093/forestry/cpaa011 ◽

2020 ◽

Vol 93 (5) ◽

pp. 675-684

Author(s):

Nicolas Latte ◽

Philippe Taverniers ◽

Tanguy de Jaegere ◽

Hugues Claessens

Keyword(s):

Climate Change ◽

Climatic Change ◽

Tree Ring ◽

Tree Species ◽

Forest Tree ◽

Tilia Cordata ◽

The Past ◽

Lime Tree ◽

Over Time ◽

Forest Managers

Abstract To increase forest resilience to global change, forest managers are often directing forest stands towards a broader diversity of tree species. The small-leaved lime (Tilia cordata Mill.), a rare and scattered species in northwestern Europe, is a promising candidate for this purpose. Its life traits suggest a high resilience to climate change and a favourable impact on forest ecosystem services. This study used a dendroecological approach to assess how lime tree radial growth had responded to the past climatic change. First, 120 lime trees from nine sites were selected in southern Belgium based on criteria adapted to the rareness of the species. Chronology quality was assessed and resulting tree-ring series were validated at site and region levels. Second, a range of dendrochronological methods was used to analyze the changes over time in the variability and long-term trends of lime tree growth and their relation to climate during the period 1955–2016. Last, behaviour of lime trees was compared with that of beech from the same region and time period. For this purpose, the same methodology was applied to an additional beech tree-ring dataset (149 trees from 13 sites). Beech is the climax tree species of the region, but is known to be drought-sensitive and has shown weaknesses in the current climate. The quality of our tree-ring series attests that dendroecological investigation using rare and scattered species is possible, opening the way to further analysis on other such lesser-known forest tree species. The analysis showed that the small-leaved lime had been resilient to the past climatic change in multiple ways. Lime growth increased during the preceding decades despite an increased frequency and intensity of stressful climatic events. Lime growth quickly recovered in the years following the stresses. The growth–climate relationships were either stable over time or had a positive evolution. The behaviour of lime contrasted strongly with that of beech. Lime performed better than beech in every analysis. Small-leaved lime is thus a serious candidate for addressing climate change challenges in the region. It should be considered by forest managers planning to improve the sustainability and resilience of their forests, in particular in vulnerable beech stands.

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Maladaptation, migration and extirpation fuel climate change risk in a forest tree species

Nature Climate Change ◽

10.1038/s41558-020-00968-6 ◽

2021 ◽

Vol 11 (2) ◽

pp. 166-171 ◽

Cited By ~ 1

Author(s):

Andrew V. Gougherty ◽

Stephen R. Keller ◽

Matthew C. Fitzpatrick

Keyword(s):

Climate Change ◽

Tree Species ◽

Forest Tree ◽

Climate Change Risk ◽

Forest Tree Species

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Fate of forest tree biotechnology facing climate change

Silvae Genetica ◽

10.2478/sg-2021-0010 ◽

2021 ◽

Vol 70 (1) ◽

pp. 117-136

Author(s):

M. R. Ahuja

Keyword(s):

Climate Change ◽

Somatic Embryogenesis ◽

Loblolly Pine ◽

Tree Species ◽

Forest Tree ◽

Future Climate Change ◽

Forest Trees ◽

Forest Tree Species ◽

Tree Biotechnology

Abstract Woody plants have been cultured in vitro since the 1930s. After that time much progress has been made in the culture of tissues, organs, cells, and protoplasts in tree species. Tree biotechnology has been making strides in clonal propagation by organogenesis and somatic embryogenesis. These regeneration studies have paved the way for gene transfer in forest trees. Transgenics from a number of forest tree species carrying a variety of recombinant genes that code for herbicide tolerance, pest resistance, lignin modification, increased woody bio-mass, and flowering control have been produced by Agrobacterium-mediated and biolistic methods, and some of them are undergoing confined field trials. Although relatively stable transgenic clones have been produced by genetic transformation in trees using organogenesis or somatic embryogenesis, there were also unintended unstable genetic events. In order to overcome the problems of randomness of transgene integration and instability reported in Agrobacterium-mediated or biolistically transformed plants, site-specific transgene insertion strategies involving clustered regularly interspaced short palindromic repeats (CRISPR-Cas9) platform offer prospects for precise genome editing in plants. Nevertheless, it is important to monitor phenotypic and genetic stability of clonal material, not just under greenhouse conditions, but also under natural field conditions. Genetically modified poplars have been commercialized in China, and eucalypts and loblolly pine are expected to be released for commercial deployment in USA. Clonal forestry and transgenic forestry have to cope with rapid global climate changes in the future. Climate change is impacting species distributions and is a significant threat to biodiversity. Therefore, it is important to deploy Strategies that will assist the survival and evolution of forest tree species facing rapid climate change. Assisted migration (managed relocation) and biotechnological approaches offer prospects for adaptation of forest trees to climate change.

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Kmer2SNP: reference-free SNP calling from raw reads based on matching

10.1101/2020.05.17.100305 ◽

2020 ◽

Author(s):

Yanbo Li ◽

Yu Lin

Keyword(s):

Reference Genome ◽

State Of The Art ◽

Fundamental Problem ◽

Disease Diagnosis ◽

Hybrid Assembly ◽

Snp Calling ◽

Sequencing Technologies ◽

Order Of Magnitude ◽

Maximum Weight Matching ◽

Reference Genomes

AbstractThe development of DNA sequencing technologies provides the opportunity to call heterozygous SNPs for each individual. SNP calling is a fundamental problem of genetic analysis and has many applications, such as gene-disease diagnosis, drug design, and ancestry inference. Reference-based SNP calling approaches generate highly accurate results, but they face serious limitations especially when high-quality reference genomes are not available for many species. Although reference-free approaches have the potential to call SNPs without using the reference genome, they have not been widely applied on large and complex genomes because existing approaches suffer from low recall/precision or high runtime.We develop a reference-free algorithm Kmer2SNP to call SNP directly from raw reads. Kmer2SNP first computes the k-mer frequency distribution from reads and identifies potential heterozygous k-mers which only appear in one haplotype. Kmer2SNP then constructs a graph by choosing these heterozygous k-mers as vertices and connecting edges between pairs of heterozygous k-mers that might correspond to SNPs. Kmer2SNP further assigns a weight to each edge using overlapping information between heterozygous k-mers, computes a maximum weight matching and finally outputs SNPs as edges between k-mer pairs in the matching.We benchmark Kmer2SNP against reference-free methods including hybrid (assembly-based) and assembly-free methods on both simulated and real datasets. Experimental results show that Kmer2SNP achieves better SNP calling quality while being an order of magnitude faster than the state-of-the-art methods. Kmer2SNP shows the potential of calling SNPs only using k-mers from raw reads without assembly. The source code is freely available at https://github.com/yanboANU/Kmer2SNP.

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Can Forest Trees Cope with Climate Change?—Effects of DNA Methylation on Gene Expression and Adaptation to Environmental Change

International Journal of Molecular Sciences ◽

10.3390/ijms222413524 ◽

2021 ◽

Vol 22 (24) ◽

pp. 13524

Author(s):

Ewelina A. Klupczyńska ◽

Ewelina Ratajczak

Keyword(s):

Climate Change ◽

Gene Expression ◽

Dna Methylation ◽

Global Climate ◽

Regional Climate ◽

Expression Patterns ◽

Forest Tree ◽

Epigenetic Modifications ◽

Specific Expression ◽

Epigenome Editing

Epigenetic modifications, including chromatin modifications and DNA methylation, play key roles in regulating gene expression in both plants and animals. Transmission of epigenetic markers is important for some genes to maintain specific expression patterns and preserve the status quo of the cell. This article provides a review of existing research and the current state of knowledge about DNA methylation in trees in the context of global climate change, along with references to the potential of epigenome editing tools and the possibility of their use for forest tree research. Epigenetic modifications, including DNA methylation, are involved in evolutionary processes, developmental processes, and environmental interactions. Thus, the implications of epigenetics are important for adaptation and phenotypic plasticity because they provide the potential for tree conservation in forest ecosystems exposed to adverse conditions resulting from global warming and regional climate fluctuations.

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