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

Genetic and Epigenetic Diversity of Pinus pinea L.: Conservation Implications for Priority Populations in Greece

BACKGROUND/OBJECTIVES

The stone pine (Pinus pinea L.) is an evergreen coniferous species valued for its edible seeds, which provide significant economic benefits to local populations. Remarkable phenotypic plasticity but low genetic variation characterizes the species. In Greece, natural populations of P. pinea are part of the Natura 2000 network and are protected under Annex I Priority Habitat type 2270. These populations, located across six Natura 2000 sites (including two islands), face increasing threats from tourism and climate change, leading to ecosystem degradation. Genetic and epigenetic studies are critical for the conservation of forest species because they provide insights into the genetic diversity, adaptive potential, and resilience of species, helping to inform effective management strategies and protect biodiversity in changing environments. This study aims to assess the genetic and epigenetic diversity of P. pinea in four Natura 2000 sites using molecular markers and to propose conservation strategies to ensure the species' long-term sustainability. Additionally, a preliminary investigation of water potential under maximum daily water demand was conducted to evaluate the species' adaptive response.

METHODS

Genetic analysis was performed using Amplified Fragment Length Polymorphism (AFLP) markers, while epigenetic analysis was conducted using Methylation-Susceptible Amplified Polymorphism (MSAP) markers. Sampling was carried out in four Natura 2000 areas, where genetic and epigenetic diversity patterns were examined. Furthermore, a preliminary study on water potential under peak daily water demand conditions was conducted to assess the species' physiological adaptation to environmental stress.

RESULTS

The results of this study provide valuable insights into conservation strategies by highlighting the potential role of epigenetic variation in the adaptability of P. pinea, despite its low genetic variability. Understanding the species' epigenetic flexibility can inform conservation efforts aimed at enhancing its resilience to environmental stressors, such as climate change. Additionally, the preliminary water potential analysis contributes to identifying physiological traits that may help predict the species' survival under varying environmental conditions, guiding the development of more targeted conservation practices and management plans. Further research could refine these findings and strengthen their application in conservation efforts.

CONCLUSIONS

The conclusions emphasize the critical importance of this research in informing conservation efforts for P. pinea in Greece, particularly considering climate change and human pressures. The results highlight the need for both in-situ and ex-situ conservation strategies to ensure the long-term sustainability of the species. The key recommendations include the protection of natural habitats, the implementation of controlled seed collection practices, and further research into the epigenetic mechanisms that may enhance the species' resilience to environmental stress. Future studies should focus on deepening our understanding of these epigenetic factors and their role in the adaptability of P. pinea, which will be essential for developing more effective conservation measures.

Epigenetic responses of trees to environmental stress in the context of climate change

In long-lived tree populations, when environmental change outpaces rates of evolutionary adaptation, plasticity in traits related to stress tolerance, dormancy, and dispersal may be vital for preventing extinction. While a population's genetic background partly determines its ability to adapt to a changing environment, so too do the many types of epigenetic modifications that occur within and among populations, which vary on timescales orders of magnitude faster than the emergence of new beneficial alleles. Consequently, phenotypic plasticity driven by epigenetic modification may be especially critical for sessile, long-lived organisms such as trees that must rely on this plasticity to keep pace with rapid anthropogenic environmental change. While studies have reported large effects of DNA methylation, histone modification, and non-coding RNAs on the expression of stress-tolerance genes and resulting phenotypic responses, little is known about the role of these effects in non-model plants and particularly in trees. Here, we review new findings in plant epigenetics with particular relevance to the ability of trees to adapt to or escape stressors associated with rapid climate change. Such findings include specific epigenetic influences over drought, heat, and salinity tolerance, as well as dormancy and dispersal traits. We also highlight promising findings concerning transgenerational inheritance of an epigenetic 'stress memory' in plants. As epigenetic information is becoming increasingly easy to obtain, we close by outlining ways in which ecologists can use epigenetic information better to inform population management and forecasting efforts. Understanding the molecular mechanisms behind phenotypic plasticity and stress memory in tree species offers a promising path towards a mechanistic understanding of trees' responses to climate change.

Tree species and drought: Two mysterious long-standing counterparts

Around 252 million years ago (Late Permian), Earth experienced one of its most significant drought periods, coinciding with a global climate crisis, resulting in a devastating loss of forest trees with no hope of recovery. In the current epoch (Anthropocene), the worsening of drought stress is expected to significantly affect forest communities. Despite extensive efforts, there is significantly less research at the molecular level on forest trees than on annual crop species. Would it not be wise to allocate equal efforts to woody species, regardless of their importance in providing essential furniture and sustaining most terrestrial ecosystems? For instance, the poplar genome is roughly quadruple the size of the Arabidopsis genome and has 1.6 times the number of genes. Thus, a massive effort in genomic studies focusing on forest trees has become inevitable to understand their adaptation to harsh conditions. Nevertheless, with the emerging role and development of high-throughput DNA sequencing systems, there is a growing body of literature about the responses of trees under drought at the molecular and eco-physiological levels. Therefore, synthesizing these findings through contextualizing drought history and concepts is essential to understanding how woody species adapt to water-limited conditions. Comprehensive genomic research on trees is critical for preserving biodiversity and ecosystem function. Integrating molecular insights with eco-physiological analysis will enhance forest management under climate change.

Can DNA methylation shape climate response in trees?

Woody plants create the ecosystems they occupy and shape their biodiversity. Today's rapidly warming climate threatens these long-lived species by creating new environments in which existing populations become maladapted. Plants show enormous phenotypic diversity in response to environmental change, which can be caused by genotype or epigenetic mechanisms that influence the expression of the underlying DNA sequence. Whether epigenetics can affect ecologically important traits in trees is an important and controversial question. We explore the evidence that DNA methylation can affect gene expression, both directly and indirectly via its interaction with transposable elements (TEs), and subsequently shapes phenotypic variation in natural tree populations. Furthermore, we consider the potential of epigenetic approaches to assist in their conservation management strategies.

Epigenetics Regulation in Responses to Abiotic Factors in Plant Species: A Systematic Review

Plants have several mechanisms to adapt or acclimate to environmental stress. Morphological, physiological, or genetic changes are examples of complex plant responses. In recent years, our understanding of the role of epigenetic regulation, which encompasses changes that do not alter the DNA sequence, as an adaptive mechanism in response to stressful conditions has advanced significantly. Some studies elucidated and synthesized epigenetic mechanisms and their relationships with environmental change, while others explored the interplay between epigenetic modifications and environmental shifts, aiming to deepen our understanding of these complex processes. In this study, we performed a systematic review of the literature to analyze the progression of epigenetics studies on plant species' responses to abiotic factors. We also aimed to identify the most studied species, the type of abiotic factor studied, and the epigenetic technique most used in the scientific literature. For this, a search for articles in databases was carried out, and after analyzing them using pre-established inclusion criteria, a total of 401 studies were found. The most studied species were Arabidopsis thaliana and Oryza sativa, highlighting the gap in studies of non-economic and tropical plant species. Methylome DNA sequencing is the main technique used for the detection of epigenetic interactions in published studies. Furthermore, most studies sought to understand the plant responses to abiotic changes in temperature, water, and salinity. It is worth emphasizing further research is necessary to establish a correlation between epigenetic responses and abiotic factors, such as extreme temperatures and light, associated with climate change.

Epigenetic stress memory in gymnosperms

Gymnosperms are long-lived, cone-bearing seed plants that include some of the most ancient extant plant species. These relict land plants have evolved to survive in habitats marked by chronic or episodic stress. Their ability to thrive in these environments is partly due to their phenotypic flexibility, and epigenetic regulation likely plays a crucial part in this plasticity. We review the current knowledge on abiotic and biotic stress memory in gymnosperms and the possible epigenetic mechanisms underlying long-term phenotypic adaptations. We also discuss recent technological improvements and new experimental possibilities that likely will advance our understanding of epigenetic regulation in these ancient and hard-to-study plants.

Warming appears as the main risk of non-adaptedness for western Mediterranean relict fir forests under expected climate change scenarios

Circum-Mediterranean firs are considered among the most drought-sensitive species to climate change. Understanding the genetic basis of trees' adaptive capacity and intra-specific variability to drought avoidance is mandatory to define conservation measures, thus potentially preventing their extinction. We focus here on Abies pinsapo and Abies marocana, both relict tree species, endemic from south Spain and north Morocco, respectively. A total of 607 samples were collected from eight nuclei: six from Spanish fir and two from Moroccan fir. A genotyping by sequencing technique called double digestion restriction site-associated DNA sequencing (ddRAD-seq) was performed to obtain a genetic matrix based on single-nucleotide polymorphisms (SNPs). This matrix was utilized to study the genetic structure of A. pinsapo populations and to carry out selection signature studies. In order to understand how Spanish fir and Moroccan fir cope with climate change, genotype-environment associations (GEAs) were identified. Further, the vulnerability of these species to climate variations was estimated by the risk of non-adaptedness (RONA). The filtering of the de novo assembly of A. pinsapo provided 3,982 SNPs from 504 out of 509 trees sequenced. Principal component analysis (PCA) genetically separated Grazalema from the rest of the Spanish populations. However, FST values showed significant differences among the sampling points. We found 51 loci potentially under selection. Homolog sequences were found for some proteins related to abiotic stress response, such as dehydration-responsive element binding transcription factor, regulation of abscisic acid signaling, and methylation pathway. A total of 15 associations with 11 different loci were observed in the GEA studies, with the maximum temperature of the warmest month being the variable with the highest number of associated loci. This temperature sensitivity was also supported by the risk of non-adaptedness, which yielded a higher risk for both A. pinsapo and A. marocana under the high emission scenario (Representative Concentration Pathway (RCP) 8.5). This study sheds light on the response to climate change of these two endemic species.

Climate and Soil Microsite Conditions Determine Local Adaptation in Declining Silver Fir Forests

Ongoing climatic change is threatening the survival of drought-sensitive tree species, such as silver fir (Abies alba). Drought-induced dieback had been previously explored in this conifer, although the role played by tree-level genetic diversity and its relationship with growth patterns and soil microsite conditions remained elusive. We used double digest restriction-site-associated DNA sequencing (ddRADseq) to describe different genetic characteristics of five silver fir forests in the Spanish Pyrenees, including declining and non-declining trees. Single nucleotide polymorphisms (SNPs) were used to investigate the relationships between genetics, dieback, intraspecific trait variation (functional dendrophenotypic traits and leaf traits), local bioclimatic conditions, and rhizosphere soil properties. While there were no noticeable genetic differences between declining and non-declining trees, genome-environment associations with selection signatures were abundant, suggesting a strong influence of climate, soil physicochemical properties, and soil microbial diversity on local adaptation. These results provide novel insights into how genetics and diverse environmental factors are interrelated and highlight the need to incorporate genetic data into silver fir forest dieback studies to gain a better understanding of local adaptation.

Comparative analysis of epigenetic variability in two pine species exposed to chronic radiation in the chernobyl and fukushima affected zones

Comparative analysis of epigenetic variability in two pine species affected as a result of the Chernobyl and Fukushima accidents is presented. The absorbed dose rate within the affected Chernobyl sites varies over a wider range (1.5-24.6 μGy/h) than within the Fukushima sites (3.5-6.5 μGy/h). It was shown that chronic irradiation can change the level of whole genome methylation in pine populations, but in different ways. The genomes of Japanese red pines are hypomethylated, and the degree of methylation and hydroxymethylation decreases with an increase in the level of radiation exposure. In contrast, the percentages of genome methylation and hydroxymethylation in Scots pine populations exceed the reference levels. The observed discrepancy in the patterns of genome-wide DNA methylation can be attributed partly to the design of the study (differences in the climate, radiation dose, age and species of the pines) which could affect the results. In the frame of IRAP analysis, a larger number of different bands was observed in the Chernobyl populations compared to the Japanese populations. Both the Japanese and Chernobyl populations are characterized by significant genetic variability. However, the main part of this variability is observed within populations. The dendrograms, based on presence/absence of IRAP fragments and Nei's genetic distances, revealed subdivisions of the Chernobyl and Japanese populations according to the level of radioactive contamination. Analysis of the results presented will improve our understanding of the mechanisms underlying the responses of pine trees to chronic radiation exposure.

The Prospects of gene introgression from crop wild relatives into cultivated lentil for climate change mitigation

Crop wild relatives (CWRs), landraces and exotic germplasm are important sources of genetic variability, alien alleles, and useful crop traits that can help mitigate a plethora of abiotic and biotic stresses and crop yield reduction arising due to global climatic changes. In the pulse crop genus Lens, the cultivated varieties have a narrow genetic base due to recurrent selections, genetic bottleneck and linkage drag. The collection and characterization of wild Lens germplasm resources have offered new avenues for the genetic improvement and development of stress-tolerant, climate-resilient lentil varieties with sustainable yield gains to meet future food and nutritional requirements. Most of the lentil breeding traits such as high-yield, adaptation to abiotic stresses and resistance to diseases are quantitative and require the identification of quantitative trait loci (QTLs) for marker assisted selection and breeding. Advances in genetic diversity studies, genome mapping and advanced high-throughput sequencing technologies have helped identify many stress-responsive adaptive genes, quantitative trait loci (QTLs) and other useful crop traits in the CWRs. The recent integration of genomics technologies with plant breeding has resulted in the generation of dense genomic linkage maps, massive global genotyping, large transcriptomic datasets, single nucleotide polymorphisms (SNPs), expressed sequence tags (ESTs) that have advanced lentil genomic research substantially and allowed for the identification of QTLs for marker-assisted selection (MAS) and breeding. Assembly of lentil and its wild species genomes (~4Gbp) opens up newer possibilities for understanding genomic architecture and evolution of this important legume crop. This review highlights the recent strides in the characterization of wild genetic resources for useful alleles, development of high-density genetic maps, high-resolution QTL mapping, genome-wide studies, MAS, genomic selections, new databases and genome assemblies in traditionally bred genus Lens for future crop improvement amidst the impending global climate change.

Tree-Level Growth Patterns and Genetic Associations Depict Drought Legacies in the Relict Forests of Abies marocana

The frequency and intensity of drought events are increasing worldwide, challenging the adaptive capacity of several tree species. Here, we evaluate tree growth patterns and climate sensitivity to precipitation, temperature, and drought in the relict Moroccan fir Abies marocana. We selected two study sites, formerly stated as harboring contrasting A. marocana taxa (A. marocana and A. tazaotana, respectively). For each tree, dendrochronological methods were applied to quantify growth patterns and climate-growth sensitivity. Further, ddRAD-seq was performed on the same trees and close saplings to obtain single nucleotide polymorphisms (SNPs) and related genotype-phenotype associations. Genetic differentiation between the two studied remnant populations of A. marocana was weak. Growth patterns and climate-growth relationships were almost similar at the two sites studied, supporting a negative effect of warming. Growth trends and tree size showed associations with SNPs, although there were no relationships with phenotypes related to climatic sensitivity. We found significant differences in the SNPs subjected to selection in the saplings compared to the old trees, suggesting that relict tree populations might be subjected to genetic differentiation and local adaptation to climate dryness. Our results illustrate the potential of tree rings and genome-wide analysis to improve our understanding of the adaptive capacity of drought-sensitive forests to cope with ongoing climate change.

Weak genetic differentiation but strong climate-induced selective pressure toward the rear edge of mountain pine in north-eastern Spain

Local differentiation at distribution limits may influence species' adaptive capacity to environmental changes. However, drivers, such gene flow and local selection, are still poorly understood. We focus on the role played by range limits in mountain forests to test the hypothesis that relict tree populations are subjected to genetic differentiation and local adaptation. Two alpine treelines of mountain pine (Pinus uncinata Ram. ex DC) were investigated in the Spanish Pyrenees. Further, an isolated relict population forming the species' southernmost distribution limit in north-eastern Spain was also investigated. Using genotyping by sequencing, a genetic matrix conformed by single nucleotide polymorphisms (SNPs) was obtained. This matrix was used to perform genotype-environment and genotype-phenotype associations, as well as to model risk of non-adaptedness. Increasing climate seasonality appears as an essential element in the interpretation of SNPs subjected to selective pressures. Genetic differentiations were overall weak. The differences in leaf mass area and radial growth rate, as well as the identification of several SNPs subjected to selective pressures, exceeded neutral predictions of differentiation among populations. Despite genetic drift might prevail in the isolated population, the Fst values (0.060 and 0.066) showed a moderate genetic drift and Nm values (3.939 and 3.555) indicate the presence of gene flow between the relict population and both treelines. Nonetheless, the SNPs subjected to selection pressures provide evidences of possible selection in treeline ecotones. Persistence in range boundaries seems to involve several selective pressures in species' traits, which were significantly related to enhanced drought seasonality at the limit of P. uncinata distribution range. We conclude that gene flow is unlikely to constrain adaptation in the P. uncinata rear edge, although this species shows vulnerability to future climate change scenarios involving warmer and drier conditions.

Epigenetic variation: A major player in facilitating plant fitness under changing environmental conditions

Recent research in plant epigenetics has increased our understanding of how epigenetic variability can contribute to adaptive phenotypic plasticity in natural populations. Studies show that environmental changes induce epigenetic switches either independently or in complementation with the genetic variation. Although most of the induced epigenetic variability gets reset between generations and is short-lived, some variation becomes transgenerational and results in heritable phenotypic traits. The short-term epigenetic responses provide the first tier of transient plasticity required for local adaptations while transgenerational epigenetic changes contribute to stress memory and help the plants respond better to recurring or long-term stresses. These transgenerational epigenetic variations translate into an additional tier of diversity which results in stable epialleles. In recent years, studies have been conducted on epigenetic variation in natural populations related to various biological processes, ecological factors, communities, and habitats. With the advent of advanced NGS-based technologies, epigenetic studies targeting plants in diverse environments have increased manifold to enhance our understanding of epigenetic responses to environmental stimuli in facilitating plant fitness. Taking all points together in a frame, the present review is a compilation of present-day knowledge and understanding of the role of epigenetics and its fitness benefits in diverse ecological systems in natural populations.

Multiomics Molecular Research into the Recalcitrant and Orphan Quercus ilex Tree Species: Why, What for, and How

The holm oak (Quercus ilex L.) is the dominant tree species of the Mediterranean forest and the Spanish agrosilvopastoral ecosystem, "dehesa." It has been, since the prehistoric period, an important part of the Iberian population from a social, cultural, and religious point of view, providing an ample variety of goods and services, and forming the basis of the economy in rural areas. Currently, there is renewed interest in its use for dietary diversification and sustainable food production. It is part of cultural richness, both economically (tangible) and environmentally (intangible), and must be preserved for future generations. However, a worrisome degradation of the species and associated ecosystems is occurring, observed in an increase in tree decline and mortality, which requires urgent action. Breeding programs based on the selection of elite genotypes by molecular markers is the only plausible biotechnological approach. To this end, the authors' group started, in 2004, a research line aimed at characterizing the molecular biology of Q. ilex. It has been a challenging task due to its biological characteristics (long life cycle, allogamous, high phenotypic variability) and recalcitrant nature. The biology of this species has been characterized following the central dogma of molecular biology using the omics cascade. Molecular responses to biotic and abiotic stresses, as well as seed maturation and germination, are the two main objectives of our research. The contributions of the group to the knowledge of the species at the level of DNA-based markers, genomics, epigenomics, transcriptomics, proteomics, and metabolomics are discussed here. Moreover, data are compared with those reported for Quercus spp. All omics data generated, and the genome of Q. ilex available, will be integrated with morphological and physiological data in the systems biology direction. Thus, we will propose possible molecular markers related to resilient and productive genotypes to be used in reforestation programs. In addition, possible markers related to the nutritional value of acorn and derivate products, as well as bioactive compounds (peptides and phenolics) and allergens, will be suggested. Subsequently, the selected molecular markers will be validated by both genome-wide association and functional genomic analyses.