Genetics and Genomics of Forest Trees

Forest tree genetics and genomics are advancing at an accelerated rate, thanks to recent developments in high-throughput, next-generation sequencing capabilities, and novel biostatistical tools. Population and landscape genetics and genomics have seen the rise of new approaches implemented in large-scale studies that employ the use of genome-wide sampling. Such studies have started to discern the dynamics of neutral and adaptive variation in nature and the processes that underlie spatially explicit patterns of genetic and genomic variation in nature. The continuous development of genetic maps in forest trees and the expansion of QTL and association mapping approaches contribute to the unravelling of the genotype-phenotype relationship and lead to marker-assisted and genome-wide selection. However, major challenges lie ahead. Recent literature suggests that species demography and genetic diversity have been affected both by climatic oscillations and anthropogenically induced stresses in a way calls into question the possibility of future adaptation. Moreover, the pace of contemporary environmental change presents a great challenge to forest tree populations and their ability to adapt, taking into consideration their life history characteristics. Several questions emerge that include, but are not limited to, the interpretation of forest tree genome surveillance and their structural/functional properties, the adaptive and neutral processes that have shaped forest tree genomes, the analysis of phenotypic traits relevant to adaptation (especially adaptation under contemporary climate change), the link between epigenetics/epigenomics and phenotype/genotype, and the use of genetics/genomics as well as genetic monitoring to advance conservation priorities

Genetics and epigenetics of Pinus nigra populations with differential exposure to air pollution

Forest species in the course of their evolution have experienced several environmental challenges, which since historic times include anthropogenic pollution. The effects of pollution on the genetic and epigenetic diversity in black pine (Pinus nigra) forests were investigated in the Amyntaio – Ptolemais – Kozani Basin, which has been for decades the largest lignite mining and burning center of Greece, with a total installed generating capacity of about 4.5 GW, operating for more than 70 years and resulting in large amounts of primary air pollutant emissions, mainly SO2, NOx and PM10. P. nigra, a biomarker for air pollution and a keystone species of affected natural ecosystems, was examined in terms of phenology (cone and seed parameters), genetics (283 AFLP loci) and epigenetics (606 MSAP epiloci), using two populations (exposed to pollution and control) of the current (mature trees) and future (embryos) stand. It was found that cone, seed, as well as genetic diversity parameters, did not show statistically significant differences between the exposed population and the control. Nevertheless, statistically significant differences were detected at the population epigenetic level. Moreover, there was a further differentiation regarding the intergenerational comparison: while the epigenetic diversity does not substantially change in the two generations assessed in the control population, epigenetic diversity is significantly higher in the embryo population compared to the parental stand in the exposed population. This study sheds a light to genome dynamics in a forest tree population exposed to long term atmospheric pollution burden and stresses the importance of assessing both genetics and epigenetics in biomonitoring applications

Resilient forests for the future

Forest ecosystems are of global importance, ecologically, economically and culturally. However, despite their fundamental role in mitigating the worst effects of climate change, to date there have been surprisingly few resources devoted to defining, conserving and planning resilient forests for the future. Progress in this field of research, which requires international and interdisciplinary cooperation, collaboration and communication, was presented and discussed at the second biannual conference of the European Research Group, Evoltree (https://www.evoltree.eu). Over four days more than 140 scientists met to share developments and to discuss forest ecology, genetics, genomics and evolution with a focus on realising “Resilient Forests for the Future”. From examining evolutionary dynamics and using the past to understand future responses, to evaluating breeding approaches and the sustainable use of forest genetic resources, the conference addressed critical themes with relevance to this topic. The role of genomics in conservation, investigation of biotic interactions and identifying climate resilient forests were also explored. Finally, innovative methods and approaches which promise to increase the scale and speed with which forest evolutionary research can progress were introduced and evaluated. The Evoltree network and conference series provides invaluable opportunities to share knowledge and increase collaboration on forest genetic research, the need for which has never been greater or more urgent

Whole genome scanning of a Mediterranean basin hotspot collection provide new insights into olive tree biodiversity and biology

Olive tree (Olea europaea L. subsp. europaea var. europaea) is one of the most important species of the Mediterranean region and one of the most ancient species domesticated. The availability of whole genome assemblies and annotations of olive tree cultivars and oleaster (O. europaea subsp. europaea var. sylvestris) has contributed to a better understanding of genetic and genomic differences between olive tree cultivars. However, compared to other plant species there is still a lack of genomic resources for olive tree popula-tions that span the entire Mediterranean region. In the present study we developed the most complete genomic variation map and the most comprehensive catalog/resource of molecular variation to date for 89 olive tree genotypes originating from the entire Mediterranean basin, revealing the genetic diversity of this commercially significant crop tree and explaining the divergence/similarity among different variants. Addi-tionally, the monumental ancient tree ‘Throuba Naxos’ was studied to characterize the potential origin or routes of olive tree domestication. Several candidate genes known to be associated with key agronomic traits, including olive oil quality and fruit yield, were uncovered by a selective sweep scan to be under selection pressure on all olive tree chromosomes. To further exploit the genomic and phenotypic resources obtained from the current work, genome-wide association analyses were performed for 23 morphological and two agronomic traits. Significant associations were detected for eight traits that provide valuable candidates for fruit tree breeding and for deeper understanding of olive tree biology.info:eu-repo/semantics/publishedVersio

Marginality indices for biodiversity conservation in forest trees

Marginal and peripheral populations are important for biodiversity conservation. Their original situation in a species’ geographic and ecological space often confers them genetic diversity and traits of high adaptive value. Yet theoretical hypotheses related to marginality are difficult to test because of confounding factors that influence marginality, namely environment, geography, and history. There is an urgent need to develop metrics to disentangle these confounding factors. We designed nine quantitative indices of marginality and peripherality that define where margins lie within species distributions, from a geographical, an environmental and a historical perspective. Using the distribution maps of eight European forest tree species, we assessed whether these indices were idiosyncratic or whether they conveyed redundant information. Using a database on marginal and peripheral populations based on expert knowledge, we assessed the capacity of the indices to predict the marginality status of a population. There was no consistent pattern of correlation between indices across species, confirming that the indices conveyed different information related to the specific geometry of the species distributions. Contrasting with this heterogeneity of correlation patterns across species, the relative importance of the indices to predict the marginality status of populations was consistent across species. However, there was still a significant country effect in the marginality status, showing a variation in expert opinion of marginality vis-á-vis the species distribution. The marginality indices that we developed are entirely based on distribution maps and can be used for any species. They pave the way for testing hypotheses related to marginality and peripherality, with important implications in quantitative ecology, genetics, and biodiversity conservation

Whole genome scanning of a Mediterranean basin hotspot collection provides new insights into olive tree biodiversity and biology

Olive tree (Olea europaea L. subsp. europaea var. europaea) is one of the most important species of the Mediterranean region and one of the most ancient species domesticated. The availability of whole genome assemblies and annotations of olive tree cultivars and oleaster (O. europaea subsp. europaea var. sylvestris) has contributed to a better understanding of genetic and genomic differences between olive tree cultivars. However, compared to other plant species there is still a lack of genomic resources for olive tree populations that span the entire Mediterranean region. In the present study we developed the most complete genomic variation map and the most comprehensive catalog/resource of molecular variation to date for 89 olive tree genotypes originating from the entire Mediterranean basin, revealing the genetic diversity of this commercially significant crop tree and explaining the divergence/similarity among different variants. Additionally, the monumental ancient tree ‘Throuba Naxos’ was studied to characterize the potential origin or routes of olive tree domestication. Several candidate genes known to be associated with key agronomic traits, including olive oil quality and fruit yield, were uncovered by a selective sweep scan to be under selection pressure on all olive tree chromosomes. To further exploit the genomic and phenotypic resources obtained from the current work, genome-wide association analyses were performed for 23 morphological and two agronomic traits. Significant associations were detected for eight traits that provide valuable candidates for fruit tree breeding and for deeper understanding of olive tree biology.This research was financed by Greek Public Investments Program (PIP) of General Secretariat for Research & Technology (GSRT), under the Emblematic Action ‘The Olive Road’ (project code:2018ΣE01300000). Sebastián Ramos-Onsins is supported by the grant PID2020-119255GB-I00 (MICINN, Spain) and the CERCA Programme/Generalitat de Catalunya and acknowledges financial support from the Spanish Ministry of Economy and Competitiveness, through the Severo Ochoa Programme for Centres of Excellence in R&D 2016–2019 and 2020–2023 (SEV-2015-0533, CEX2019-000917) and the European Regional Development Fund (ERDF).The publication of the article in OA mode was financially supported by HEAL-Link.With funding from the Spanish government through the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000917).Peer reviewe