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Special Issue "Genetics and Genomics of Forest Trees"

A special issue of Forests (ISSN 1999-4907). This special issue belongs to the section "Forest Ecophysiology and Biology".

Deadline for manuscript submissions: closed (28 February 2018)

Printed Edition Available!
A printed edition of this Special Issue is available here.

Special Issue Editor

Guest Editor
Prof. Dr. Filippos A. (Phil) Aravanopoulos

Faculty of Agriculture, Forestry & Natural Environment, Aristotle University of Thessaloniki, P.O. Box 278, University Campus, Thessaloniki, 54124, Greece
Website | E-Mail

Special Issue Information

Dear Colleagues,

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 unravel the genotype-phenotype relationship and to 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 that future adaptation may be questionable. Moreover, the pace of contemporary environmental change put a great challenge on forest tree populations and their ability to adapt taking into account 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 epigenetics/epigenomics to phenotype and genotype, and the use of genetics/genomics as well as genetic monitoring to advance conservation priorities. We encourage manuscript submission to this Special Issue from all relevant fields, both regarding experimental studies and modelling approaches, in order to promote knowledge in the areas of genetics and genomics of forest trees including the management and conservation of forest genetic resources.

Prof. Dr. Filippos A. (Phil) Aravanopoulos
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Forests is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1400 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Population/Landscape Genetics/Genomics

  • Conservation Genetics/Genomics

  • Functional Genomics

  • Epigenetics/Epigenomics

  • Adaptation

  • QTL/Association Mapping

  • Molecular Evolution

  • Proteomics

  • Phylogeography

  • Management of Forest Genetic Resources

Published Papers (20 papers)

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Research

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Open AccessArticle Mediterranean Islands Hosting Marginal and Peripheral Forest Tree Populations: The Case of Pinus brutia Ten. in Cyprus
Forests 2018, 9(9), 514; https://doi.org/10.3390/f9090514
Received: 20 July 2018 / Revised: 15 August 2018 / Accepted: 21 August 2018 / Published: 24 August 2018
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Abstract
Mediterranean islands have served as important Tertiary and glacial refuges, hosting important peripheral and ecologically marginal forest tree populations. These populations, presumably harboring unique gene complexes, are particularly interesting in the context of climate change. Pinus brutia Ten. is widespread in the eastern
[...] Read more.
Mediterranean islands have served as important Tertiary and glacial refuges, hosting important peripheral and ecologically marginal forest tree populations. These populations, presumably harboring unique gene complexes, are particularly interesting in the context of climate change. Pinus brutia Ten. is widespread in the eastern Mediterranean Basin and in Cyprus in particular it is the most common tree species. This study evaluated genetic patterns and morphoanatomical local adaptation along the species geographical distribution and altitudinal range in Cyprus. Analysis showed that the Cyprus population of P. brutia is a peripheral population with high genetic diversity, comprised of different subpopulations. Evidence suggests the presence of ongoing dynamic evolutionary processes among the different subpopulations, while the most relic and isolated subpopulations exhibited a decreased genetic diversity compared to the most compact subpopulations in the central area of the island. These results could be the consequence of the small size and prolonged isolation of the former. Comparing populations along an altitude gradient, higher genetic diversity was detected at the middle level. The phenotypic plasticity observed is particularly important for the adaptive potential of P. brutia in an island environment, since it allows rapid change in local environmental conditions. Full article
(This article belongs to the Special Issue Genetics and Genomics of Forest Trees) Printed Edition available
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Open AccessArticle The Transcriptomic Responses of Pinus massoniana to Drought Stress
Forests 2018, 9(6), 326; https://doi.org/10.3390/f9060326
Received: 29 April 2018 / Revised: 30 May 2018 / Accepted: 31 May 2018 / Published: 4 June 2018
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Abstract
Masson pine (Pinus massoniana) is a major fast-growing timber species planted in southern China, a region of seasonal drought. Using a drought-tolerance genotype of Masson pine, we conducted large-scale transcriptome sequencing using Illumina technology. This work aimed to evaluate the transcriptomic
[...] Read more.
Masson pine (Pinus massoniana) is a major fast-growing timber species planted in southern China, a region of seasonal drought. Using a drought-tolerance genotype of Masson pine, we conducted large-scale transcriptome sequencing using Illumina technology. This work aimed to evaluate the transcriptomic responses of Masson pine to different levels of drought stress. First, 3397, 1695 and 1550 unigenes with differential expression were identified by comparing plants subjected to light, moderate or severe drought with control plants. Second, several gene ontology (GO) categories (oxidation-reduction and metabolism) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways (plant hormone signal transduction and metabolic pathways) were enriched, indicating that the expression levels of some genes in these enriched GO terms and pathways were altered under drought stress. Third, several transcription factors (TFs) associated with circadian rhythms (HY5 and LHY), signal transduction (ERF), and defense responses (WRKY) were identified, and these TFs may play key roles in adapting to drought stress. Drought also caused significant changes in the expression of certain functional genes linked to osmotic adjustment (P5CS), abscisic acid (ABA) responses (NCED, PYL, PP2C and SnRK), and reactive oxygen species (ROS) scavenging (GPX, GST and GSR). These transcriptomic results provide insight into the molecular mechanisms of drought stress adaptation in Masson pine. Full article
(This article belongs to the Special Issue Genetics and Genomics of Forest Trees) Printed Edition available
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Open AccessArticle Tamarix microRNA Profiling Reveals New Insight into Salt Tolerance
Forests 2018, 9(4), 180; https://doi.org/10.3390/f9040180
Received: 27 February 2018 / Revised: 26 March 2018 / Accepted: 27 March 2018 / Published: 3 April 2018
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Abstract
The halophyte tamarisk (Tamarix) is extremely salt tolerant, making it an ideal material for salt tolerance-related studies. Although many salt-responsive genes of Tamarix were identified in previous studies, there are no reports on the role of post-transcriptional regulation in its salt
[...] Read more.
The halophyte tamarisk (Tamarix) is extremely salt tolerant, making it an ideal material for salt tolerance-related studies. Although many salt-responsive genes of Tamarix were identified in previous studies, there are no reports on the role of post-transcriptional regulation in its salt tolerance. We constructed six small RNA libraries of Tamarix chinensis roots with NaCl treatments. High-throughput sequencing of the six libraries was performed and microRNA expression profiles were constructed. We investigated salt-responsive microRNAs to uncover the microRNA-mediated genes regulation. From these analyses, 251 conserved and 18 novel microRNA were identified from all small RNAs. From 191 differentially expressed microRNAs, 74 co-expressed microRNAs were identified as salt-responsive candidate microRNAs. The most enriched GO (gene ontology) terms for the 157 genes targeted by differentially expressed microRNAs suggested that transcriptions factors were highly active. Two hub microRNAs (miR414, miR5658), which connected by several target genes into an organic microRNA regulatory network, appeared to be the key regulators of post-transcriptional salt-stress responses. As the first survey on the tamarisk small RNAome, this study improves the understanding of tamarisk salt-tolerance mechanisms and will contribute to the molecular-assisted resistance breeding. Full article
(This article belongs to the Special Issue Genetics and Genomics of Forest Trees) Printed Edition available
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Open AccessArticle De Novo Sequencing and Assembly Analysis of Transcriptome in Pinus bungeana Zucc. ex Endl.
Forests 2018, 9(3), 156; https://doi.org/10.3390/f9030156
Received: 24 January 2018 / Revised: 14 March 2018 / Accepted: 19 March 2018 / Published: 20 March 2018
Cited by 1 | PDF Full-text (6179 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
To enrich the molecular data of Pinus bungeana Zucc. ex Endl. and study the regulating factors of different morphology controled by apical dominance. In this study, de novo assembly of transcriptome annotation was performed for two varieties of Pinus bungeana Zucc. ex Endl.
[...] Read more.
To enrich the molecular data of Pinus bungeana Zucc. ex Endl. and study the regulating factors of different morphology controled by apical dominance. In this study, de novo assembly of transcriptome annotation was performed for two varieties of Pinus bungeana Zucc. ex Endl. that are obviously different in morphology. More than 147 million reads were produced, which were assembled into 88,092 unigenes. Based on a similarity search, 11,692 unigenes showed significant similarity to proteins from Picea sitchensis (Bong.) Carr. From this collection of unigenes, a large number of molecular markers were identified, including 2829 simple sequence repeats (SSRs). A total of 158 unigenes expressed differently between two varieties, including 98 up-regulated and 60 down-regulated unigenes. Furthermore, among the differently expressed genes (DEGs), five genes which may impact the plant morphology were further validated by reverse transcription quantitative polymerase chain reaction (RT-qPCR). The five genes related to cytokinin oxidase/dehydrogenase (CKX), two-component response regulator ARR-A family (ARR-A), plant hormone signal transduction (AHP), and MADS-box transcription factors have a close relationship with apical dominance. This new dataset will be a useful resource for future genetic and genomic studies in Pinus bungeana Zucc. ex Endl. Full article
(This article belongs to the Special Issue Genetics and Genomics of Forest Trees) Printed Edition available
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Open AccessArticle Use of Nuclear Microsatellite Loci for Evaluating Genetic Diversity of Selected Populations of Picea abies (L.) Karsten in the Czech Republic
Forests 2018, 9(2), 92; https://doi.org/10.3390/f9020092
Received: 8 December 2017 / Revised: 13 February 2018 / Accepted: 13 February 2018 / Published: 15 February 2018
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Abstract
DNA polymorphism at nine nuclear microsatellites of nine selected naturally-regenerated Norway spruce populations growing mainly within gene conservation units in different parts of the Czech Republic was studied. To verify the genetic quality of the selected gene conservation unit, we analyzed nine Norway
[...] Read more.
DNA polymorphism at nine nuclear microsatellites of nine selected naturally-regenerated Norway spruce populations growing mainly within gene conservation units in different parts of the Czech Republic was studied. To verify the genetic quality of the selected gene conservation unit, we analyzed nine Norway spruce subpopulations from gene conservation unit GZ 102–Orlické hory. Genetic parameters can be used in state administrative decision making on including stands into gene conservation units. The level of genetic diversity within 17 investigated Czech Norway spruce units was relatively high. Mean values for the number of different alleles ranged from 12.2 (population SM 08) to 16.2 (subpopulation SM T4). The values of observed heterozygosity (Ho) ranged from 0.65 to 0.80 and expected heterozygosity (He) from 0.74 to 0.81. Pairwise population FST values ranging from 0.006 to 0.027 indicated low genetic differentiation between units, and values of Nei’s genetic distance among Norway spruce units ranged from 0.046 to 0.168, thus structuring of the investigated Norway spruce units was confirmed. Closer genetic similarity was seen in subpopulations from the gene conservation unit in Orlické hory than in the studied populations from other genetic conservation units. Additionally, the populations SM 01 and SM 05, both of Hurst ecotypes, were the closest to one another and the populations of mountain and alpine ecotypes were assembled into another group. Full article
(This article belongs to the Special Issue Genetics and Genomics of Forest Trees) Printed Edition available
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Open AccessArticle Genome-Wide Analysis of Gene and microRNA Expression in Diploid and Autotetraploid Paulownia fortunei (Seem) Hemsl. under Drought Stress by Transcriptome, microRNA, and Degradome Sequencing
Forests 2018, 9(2), 88; https://doi.org/10.3390/f9020088
Received: 14 January 2018 / Revised: 7 February 2018 / Accepted: 9 February 2018 / Published: 13 February 2018
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Abstract
Drought is a common and recurring climatic condition in many parts of the world, and it can have disastrous impacts on plant growth and development. Many genes involved in the drought response of plants have been identified. Transcriptome, microRNA (miRNA), and degradome analyses
[...] Read more.
Drought is a common and recurring climatic condition in many parts of the world, and it can have disastrous impacts on plant growth and development. Many genes involved in the drought response of plants have been identified. Transcriptome, microRNA (miRNA), and degradome analyses are rapid ways of identifying drought-responsive genes. The reference genome sequence of Paulownia fortunei (Seem) Hemsl. is now available, which makes it easier to explore gene expression, transcriptional regulation, and post-transcriptional in this species. In this study, four transcriptome, small RNA, and degradome libraries were sequenced by Illumina sequencing, respectively. A total of 258 genes and 11 miRNAs were identified for drought-responsive genes and miRNAs in P. fortunei. Degradome sequencing detected 28 miRNA target genes that were cleaved by members of nine conserved miRNA families and 12 novel miRNAs. The results here will contribute toward enriching our understanding of the response of Paulownia fortunei trees to drought stress and may provide new direction for further experimental studies related the development of molecular markers, the genetic map construction, and other genomic research projects in Paulownia. Full article
(This article belongs to the Special Issue Genetics and Genomics of Forest Trees) Printed Edition available
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Open AccessArticle Intraspecific Variation in Pines from the Trans-Mexican Volcanic Belt Grown under Two Watering Regimes: Implications for Management of Genetic Resources
Forests 2018, 9(2), 71; https://doi.org/10.3390/f9020071
Received: 19 October 2017 / Revised: 22 January 2018 / Accepted: 26 January 2018 / Published: 30 January 2018
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Abstract
Management of forest genetic resources requires experimental data related to the genetic variation of the species and populations under different climatic conditions. Foresters also demand to know how the main selective drivers will influence the adaptability of the genetic resources. To assess the
[...] Read more.
Management of forest genetic resources requires experimental data related to the genetic variation of the species and populations under different climatic conditions. Foresters also demand to know how the main selective drivers will influence the adaptability of the genetic resources. To assess the inter- and intraspecific variation and plasticity in seedling drought tolerance at a relevant genetic resource management scale, we tested the changes in growth and biomass allocation of seedlings of Pinus oocarpa, P. patula and P. pseudostrobus under two contrasting watering regimes. We found general significant intraspecific variation and intraspecific differences in plasticity, since both population and watering by population interaction were significant for all three species. All the species and populations share a common general avoidance mechanism (allometric adjustment of shoot/root biomass). However, the intraspecific variation and differences in phenotypic plasticity among populations modify the adaptation strategies of the species to drought. Some of the differences are related to the climatic conditions of the location of origin. We confirmed that even at reduced geographical scales, Mexican pines present differences in the response to water stress. The differences among species and populations are relevant in afforestation programs as well as in genetic conservation activities. Full article
(This article belongs to the Special Issue Genetics and Genomics of Forest Trees) Printed Edition available
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Open AccessArticle Genetic Parameters of Growth Traits and Stem Quality of Silver Birch in a Low-Density Clonal Plantation
Forests 2018, 9(2), 52; https://doi.org/10.3390/f9020052
Received: 4 December 2017 / Revised: 19 January 2018 / Accepted: 22 January 2018 / Published: 23 January 2018
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Abstract
Silver birch (Betula pendula Roth) is productive on abandoned agriculture land, and thus might be considered as an option for profitable plantation forestry. Application of the most productive genotypes is essential. However, information about genetic gains in low-density plantations is still lacking.
[...] Read more.
Silver birch (Betula pendula Roth) is productive on abandoned agriculture land, and thus might be considered as an option for profitable plantation forestry. Application of the most productive genotypes is essential. However, information about genetic gains in low-density plantations is still lacking. A 40-year-old low-density (400 trees ha−1) plantation of 22 grafted silver birch plus-tree clones growing on former agricultural land in the central Latvia was studied. Although grafted plantations are not common in commercial forestry, the trial provided an opportunity to assess genetic parameters of middle-aged birch. The plantation that had reached the target diameter for final harvest (DBH (diameter at breast height) = 27.7 ± 5.5 cm) had an 85% survival rate, and stemwood productivity was 5.25 m3 ha−1year−1. Still, rootstock × scion interaction and cyclophysis might have caused some biases. Broad-sense heritability (H2) ranged from 0.02 for probability of spike knots to 0.40 for branch angle. Estimated H2 for monetary value of stemwood was 0.16. In general, the correlations between growth and stem quality traits were weak, implying independent genetic control, though branchiness strongly correlated with diameter at breast height. The monetary value of stemwood strongly correlated with productivity traits. The observed correlations suggested that productivity and stem quality of birch might be improved simultaneously by genetic selection. Full article
(This article belongs to the Special Issue Genetics and Genomics of Forest Trees) Printed Edition available
Open AccessArticle Genetic Diversity and Structure of Natural Quercus variabilis Population in China as Revealed by Microsatellites Markers
Forests 2017, 8(12), 495; https://doi.org/10.3390/f8120495
Received: 3 November 2017 / Revised: 6 December 2017 / Accepted: 7 December 2017 / Published: 11 December 2017
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Abstract
Quercus variabilis is a tree species of ecological and economic value that is widely distributed in China. To effectively evaluate, use, and conserve resources, we applied 25 pairs of simple sequence repeat (SSR) primers to study its genetic diversity and genetic structure in
[...] Read more.
Quercus variabilis is a tree species of ecological and economic value that is widely distributed in China. To effectively evaluate, use, and conserve resources, we applied 25 pairs of simple sequence repeat (SSR) primers to study its genetic diversity and genetic structure in 19 natural forest or natural secondary forest populations of Q. variabilis (a total of 879 samples). A total of 277 alleles were detected. Overall, the average expected heterozygosity (He) was 0.707 and average allelic richness (AR) was 7.79. Q. variabilis manifested a loss of heterozygosity, and the mean of inbreeding coefficient (FIS) was 0.044. Less differentiation among populations was observed, and the genetic differentiation coefficient (FST) was 0.063. Bayesian clustering analysis indicated that the 19 studied populations could be divided into three groups based on their genetic makeup, namely, the Southwest group, Central group, and Northeastern group. The Central group, compared to the populations of the Southwest and Northeast group, showed higher genetic diversities and lower genetic differentiations. As a widely distributed species, the historical migration of Q. variabilis contributed to its genetic differentiation. Full article
(This article belongs to the Special Issue Genetics and Genomics of Forest Trees) Printed Edition available
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Open AccessArticle Comprehensive Analysis of the Cork Oak (Quercus suber) Transcriptome Involved in the Regulation of Bud Sprouting
Forests 2017, 8(12), 486; https://doi.org/10.3390/f8120486
Received: 7 October 2017 / Revised: 20 November 2017 / Accepted: 29 November 2017 / Published: 6 December 2017
Cited by 1 | PDF Full-text (3701 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Cork oaks show a high capacity of bud sprouting as a response to injury, which is important for species survival when dealing with external factors, such as drought or fires. The characterization of the cork oak transcriptome involved in the different stages of
[...] Read more.
Cork oaks show a high capacity of bud sprouting as a response to injury, which is important for species survival when dealing with external factors, such as drought or fires. The characterization of the cork oak transcriptome involved in the different stages of bud sprouting is essential to understanding the mechanisms involved in these processes. In this study, the transcriptional profile of different stages of bud sprouting, namely (1) dormant bud and (2) bud swollen, vs. (3) red bud and (4) open bud, was analyzed in trees growing under natural conditions. The transcriptome analysis indicated the involvement of genes related with energy production (linking the TCA (tricarboxylic acid) cycle and the electron transport system), hormonal regulation, water status, and synthesis of polysaccharides. These results pinpoint the different mechanisms involved in the early and later stages of bud sprouting. Furthermore, some genes, which are involved in bud development and conserved between species, were also identified at the transcriptional level. This study provides the first set of results that will be useful for the discovery of genes related with the mechanisms regulating bud sprouting in cork oak. Full article
(This article belongs to the Special Issue Genetics and Genomics of Forest Trees) Printed Edition available
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Open AccessArticle Genetic Structure and Population Demographic History of a Widespread Mangrove Plant Xylocarpus granatum J. Koenig across the Indo-West Pacific Region
Forests 2017, 8(12), 480; https://doi.org/10.3390/f8120480
Received: 29 August 2017 / Revised: 27 November 2017 / Accepted: 29 November 2017 / Published: 5 December 2017
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Abstract
Xylocarpus granatum J. Koenig is one of the most widespread core component species of mangrove forests in the Indo-West Pacific (IWP) region, and as such is suitable for examining how genetic structure is generated across spatiotemporal scales. We evaluated the genetic structure of
[...] Read more.
Xylocarpus granatum J. Koenig is one of the most widespread core component species of mangrove forests in the Indo-West Pacific (IWP) region, and as such is suitable for examining how genetic structure is generated across spatiotemporal scales. We evaluated the genetic structure of this species using maternally inherited chloroplast (cp) and bi-parentally inherited nuclear DNA markers, with samples collected across the species range. Both cp and nuclear DNA showed generally similar patterns, revealing three genetic groups in the Indian Ocean, South China Sea (with Palau), and Oceania, respectively. The genetic diversity of the Oceania group was significantly lower, and the level of population differentiation within the Oceania group was significantly higher, than in the South China Sea group. These results revealed that in addition to the Malay Peninsula—a common land barrier for mangroves—there is a genetic barrier in an oceanic region of the West Pacific that prevents gene flow among populations. Moreover, demographic inference suggested that these patterns were generated in relation to sea level changes during the last glacial period and the emergence of Sahul Shelf which lied northwest of Australia. We propose that the three genetic groups should be considered independent conservation units, and that the Oceania group has a higher conservation priority. Full article
(This article belongs to the Special Issue Genetics and Genomics of Forest Trees) Printed Edition available
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Open AccessArticle Genetic Variation in Quercus acutissima Carruth., in Traditional Japanese Rural Forests and Agricultural Landscapes, Revealed by Chloroplast Microsatellite Markers
Forests 2017, 8(11), 451; https://doi.org/10.3390/f8110451
Received: 23 August 2017 / Revised: 1 November 2017 / Accepted: 13 November 2017 / Published: 17 November 2017
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Abstract
Quercus acutissima Carruth. is an economically important species that has long been cultivated in Japan, so is a valuable subject for investigating the impact of human activities on genetic variation in trees. In total, 2152 samples from 18 naturally regenerated populations and 28
[...] Read more.
Quercus acutissima Carruth. is an economically important species that has long been cultivated in Japan, so is a valuable subject for investigating the impact of human activities on genetic variation in trees. In total, 2152 samples from 18 naturally regenerated populations and 28 planted populations in Japan and 13 populations from the northeastern part of Eurasia, near Japan, were analyzed using six maternally inherited chloroplast (cpDNA) simple sequence repeat (SSR) markers. Although 23 haplotypes were detected in total, both the Japanese natural and artificial populations exhibited much lower genetic diversity than the continental populations. The level of genetic differentiation among natural populations in Japan was also much lower (GST = 0.261) than that on the continent (GST = 0.856). These results suggest that human activities, such as historical seed transfer, have reduced genetic diversity within and among populations and resulted in a homogeneous genetic structure in Japan. The genetic characteristics of natural and artificial populations of Quercus acutissima in Japan are almost the same and it is likely that most of the natural populations are thought to have originated from individuals that escaped from plantations. Full article
(This article belongs to the Special Issue Genetics and Genomics of Forest Trees) Printed Edition available
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Open AccessArticle De Novo Transcriptome Sequencing in Passiflora edulis Sims to Identify Genes and Signaling Pathways Involved in Cold Tolerance
Forests 2017, 8(11), 435; https://doi.org/10.3390/f8110435
Received: 22 September 2017 / Revised: 31 October 2017 / Accepted: 6 November 2017 / Published: 12 November 2017
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Abstract
The passion fruit (Passiflora edulis Sims), also known as the purple granadilla, is widely cultivated as the new darling of the fruit market throughout southern China. This exotic and perennial climber is adapted to warm and humid climates, and thus is generally
[...] Read more.
The passion fruit (Passiflora edulis Sims), also known as the purple granadilla, is widely cultivated as the new darling of the fruit market throughout southern China. This exotic and perennial climber is adapted to warm and humid climates, and thus is generally intolerant of cold. There is limited information about gene regulation and signaling pathways related to the cold stress response in this species. In this study, two transcriptome libraries (KEDU_AP vs. GX_AP) were constructed from the aerial parts of cold-tolerant and cold-susceptible varieties of P. edulis, respectively. Overall, 126,284,018 clean reads were obtained, and 86,880 unigenes with a mean size of 1449 bp were assembled. Of these, there were 64,067 (73.74%) unigenes with significant similarity to publicly available plant protein sequences. Expression profiles were generated, and 3045 genes were found to be significantly differentially expressed between the KEDU_AP and GX_AP libraries, including 1075 (35.3%) up-regulated and 1970 (64.7%) down-regulated. These included 36 genes in enriched pathways of plant hormone signal transduction, and 56 genes encoding putative transcription factors. Six genes involved in the ICE1–CBF–COR pathway were induced in the cold-tolerant variety, and their expression levels were further verified using quantitative real-time PCR. This report is the first to identify genes and signaling pathways involved in cold tolerance using high-throughput transcriptome sequencing in P. edulis. These findings may provide useful insights into the molecular mechanisms regulating cold tolerance and genetic breeding in Passiflora spp. Full article
(This article belongs to the Special Issue Genetics and Genomics of Forest Trees) Printed Edition available
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Open AccessArticle Genetic Variation, Heritability and Genotype × Environment Interactions of Resin Yield, Growth Traits and Morphologic Traits for Pinus elliottii at Three Progeny Trials
Forests 2017, 8(11), 409; https://doi.org/10.3390/f8110409
Received: 26 July 2017 / Revised: 25 October 2017 / Accepted: 25 October 2017 / Published: 30 October 2017
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Abstract
To better understand the genetic control of resin yield, growth traits and morphologic traits for Pinus elliottii families, genetic relationships among these traits were examined in three 27-year-old progeny trials located in Jingdezhen, Jian and Ganzhou, Jiangxi Province, China. In total, 3695 trees
[...] Read more.
To better understand the genetic control of resin yield, growth traits and morphologic traits for Pinus elliottii families, genetic relationships among these traits were examined in three 27-year-old progeny trials located in Jingdezhen, Jian and Ganzhou, Jiangxi Province, China. In total, 3695 trees from 112 families were assessed at the three sites. Significant site, family and family × site effects were found for resin yield, growth traits and morphologic traits. Resin yield and growth traits were found to be under moderate genetic control for the three sites combined, with family heritability and individual narrow-sense heritability ranging from 0.41 to 0.55 and 0.11 to 0.27, respectively. The coefficient of genotypic variation (CVG) of stem volume (SV) and crown surface area (CSA) were higher than those of other traits at each site. Genetic correlation estimates indicated that selection for growth traits might lead to a large increment in resin yield (RY), and most morphologic traits had moderate to strong correlations with growth traits at each individual site. One possible strategy in tree breeding would be to maximize resin production through selection for growth traits. Full article
(This article belongs to the Special Issue Genetics and Genomics of Forest Trees) Printed Edition available
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Open AccessArticle Transcriptome Sequencing and Comparative Analysis of Piptoporus betulinus in Response to Birch Sawdust Induction
Forests 2017, 8(10), 374; https://doi.org/10.3390/f8100374
Received: 18 August 2017 / Revised: 25 September 2017 / Accepted: 27 September 2017 / Published: 7 October 2017
Cited by 1 | PDF Full-text (1307 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Piptoporus betulinus, a brown-rot parasitic fungus of birch trees (Betula species), has been used as a common anti-parasitic and antibacterial agent. The lack of genetic resource data for P. betulinus has limited the exploration of this species. In this present study,
[...] Read more.
Piptoporus betulinus, a brown-rot parasitic fungus of birch trees (Betula species), has been used as a common anti-parasitic and antibacterial agent. The lack of genetic resource data for P. betulinus has limited the exploration of this species. In this present study, we used Illumina Hiseq 2500 technology to examine the transcriptome assembly of P. betulinus in response to birch sawdust induction. By de novo assembly, 21,882 non-redundant unigenes were yielded, and 21,255 (97.1%) were annotated with known gene sequences. A total of 340 responsive unigenes were highly homologous with putative lignocellulose-degrading enzyme candidates. Additionally, 86 unigenes might be involved in the chemical reaction in xenobiotics biodegradation and metabolism, which suggests that this fungus could convert xenobiotic materials and has the potential ability to clean up environmental pollutants. To our knowledge, this was the first study on transcriptome sequencing and comparative analysis of P. betulinus, which provided a better understanding of molecular mechanisms underlying birch sawdust induction and identified lignocelluloses degrading enzymes. Full article
(This article belongs to the Special Issue Genetics and Genomics of Forest Trees) Printed Edition available
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Open AccessArticle Long Non-Coding RNAs Responsive to Witches’ Broom Disease in Paulownia tomentosa
Forests 2017, 8(9), 348; https://doi.org/10.3390/f8090348
Received: 16 August 2017 / Revised: 12 September 2017 / Accepted: 12 September 2017 / Published: 15 September 2017
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Abstract
Paulownia witches’ broom (PaWB) disease caused by phytoplasmas is a fatal disease that leads to considerable economic losses. Long non-coding RNAs (lncRNAs) have been demonstrated to play critical regulatory roles in posttranscriptional and transcriptional regulation. However, lncRNAs and their functional roles remain poorly
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Paulownia witches’ broom (PaWB) disease caused by phytoplasmas is a fatal disease that leads to considerable economic losses. Long non-coding RNAs (lncRNAs) have been demonstrated to play critical regulatory roles in posttranscriptional and transcriptional regulation. However, lncRNAs and their functional roles remain poorly characterized in Paulownia. To identify lncRNAs and investigate their roles in the response to PaWB phytoplasmas, RNA sequencing was performed for healthy Paulownia tomentosa, PaWB-infected P. tomentosa, and for healthy and PaWB-infected P. tomentosa treated with 100 mg L−1 rifampicin. A total of 28,614 unique mRNAs and 3693 potential lncRNAs were identified. Comparisons between lncRNAs and coding genes indicated that lncRNAs tended to have shorter transcripts and fewer exon numbers, and displayed significant expression specificity. Based on our comparison scheme, 1063 PaWB-related mRNAs and 110 PaWB-related lncRNAs were identified; among them, 12 PaWB-related candidate target genes that were regulated by nine PaWB-related lncRNAs were characterized. This study provides the first catalog of lncRNAs expressed in Paulownia and gives a revealing insight into the molecular mechanism responsible for PaWB. Full article
(This article belongs to the Special Issue Genetics and Genomics of Forest Trees) Printed Edition available
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Open AccessArticle Effective Seed Dispersal and Fecundity Variation in a Small and Marginal Population of Pinus pinaster Ait. Growing in a Harsh Environment: Implications for Conservation of Forest Genetic Resources
Forests 2017, 8(9), 312; https://doi.org/10.3390/f8090312
Received: 3 July 2017 / Revised: 4 August 2017 / Accepted: 23 August 2017 / Published: 26 August 2017
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Abstract
Small-size, relict and marginal tree-species populations are a priority for conservation of forest genetic resources. In-situ conservation of these populations relies on adequate forest management planning based on knowledge and understanding of both ecological (i.e., recruitment or dispersal dynamics) and population-genetic processes (i.e.,
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Small-size, relict and marginal tree-species populations are a priority for conservation of forest genetic resources. In-situ conservation of these populations relies on adequate forest management planning based on knowledge and understanding of both ecological (i.e., recruitment or dispersal dynamics) and population-genetic processes (i.e., female reproductive success, gene flow or inbreeding). Here, we estimate the fecundity (or female reproductive success) of adult trees (i.e., the number of successfully established offspring/adult tree) and the effective dispersal distance distribution in the pine forest of Fuencaliente (southern Spain), a small-sized, marginal and relict population of maritime pine growing on a steep, craggy hill with just 312 reproductively active individuals. Previous studies have shown the population to present reduced allelic richness and suffer from genetic introgression from nearby exotic plantations of unknown origin. Between 2003 and 2004, we surveyed all adults and recruits and we measured several adult-specific covariates, including the number of cones of all adults. The population was found to be distributed into two nuclei with 268 (Stand 1) and 44 adults (Stand 2). We used inverse modeling to adjust several dispersal-and-fecundity models including a model with random variation in fecundity among adults (Unrestricted Fecundity or UF model). Results show that: (i) the average fecundity is 2.5–3.2 recruits/adult; (ii) the mean effective dispersal distance is restricted to 13–24 m and (iii) fecundity is most likely controlled by the spatial location of adult trees in Stand ,1 but it should be considered randomly distributed in Stand 2 (in this stand five adults mothered 80% of recruits). We conclude that the low fecundity in Stand 1 and the unequal fecundity in Stand 2 may decrease the population genetic diversity and lead to lower effective population size while the low average dispersal distance may reduce the probability of this population expanding to adjacent areas. In light of the results, we define the management priorities for in-situ conservation of this population. Full article
(This article belongs to the Special Issue Genetics and Genomics of Forest Trees) Printed Edition available
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Open AccessArticle Expression Profiling in Pinus pinaster in Response to Infection with the Pine Wood Nematode Bursaphelenchus xylophilus
Forests 2017, 8(8), 279; https://doi.org/10.3390/f8080279
Received: 22 June 2017 / Revised: 20 July 2017 / Accepted: 31 July 2017 / Published: 3 August 2017
Cited by 1 | PDF Full-text (2211 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Forests are essential resources on a global scale, not only for the ecological benefits, but also for economical and landscape purposes. However, in recent years, a large number of forest species have suffered a serious decline, with maritime pine being one of the
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Forests are essential resources on a global scale, not only for the ecological benefits, but also for economical and landscape purposes. However, in recent years, a large number of forest species have suffered a serious decline, with maritime pine being one of the most affected. In Portugal, the maritime pine forest has been devastated by the pine wood nematode (PWN), the causal agent of pine wilt disease. In this study, RNA-Seq data was used to characterize the maritime pine response to infection with PWN, by determining the differentially expressed genes and identifying the regulatory networks and pathways associated. The analyses showed clear differences between an early response that occurs immediately after inoculation and a late response that is observed seven days after inoculation. Moreover, differentially expressed genes related to secondary metabolism, oxidative stress and defense against pathogen infection were identified over different time points. These results provide new insights about the molecular mechanisms and metabolic pathways involved in the response of Pinus pinaster against PWN infection, which will be a useful resource in follow-up studies and for future breeding programs to select plants with lower susceptibility to this disease. Full article
(This article belongs to the Special Issue Genetics and Genomics of Forest Trees) Printed Edition available
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Open AccessArticle In Vitro Tetraploid Induction from Leaf and Petiole Explants of Hybrid Sweetgum (Liquidambar styraciflua × Liquidambar formosana)
Forests 2017, 8(8), 264; https://doi.org/10.3390/f8080264
Received: 4 June 2017 / Revised: 15 July 2017 / Accepted: 20 July 2017 / Published: 28 July 2017
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Abstract
Liquidambar is an important forestry species used to generate many commercial wood products, such as plywood. Inducing artificial polyploidy is an effective method to encourage genetic enhancements in forestry breeding. This report presents the first in vitro protocol for the induction of genus
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Liquidambar is an important forestry species used to generate many commercial wood products, such as plywood. Inducing artificial polyploidy is an effective method to encourage genetic enhancements in forestry breeding. This report presents the first in vitro protocol for the induction of genus Liquidambar tetraploids based on the established in vitro regeneration system of hybrid sweetgum (Liquidambar styraciflua × Liquidambar formosana). The leaves and petioles from three genotypes were pre-cultured in woody plant medium (WPM) supplemented with 0.1 mg/L thidiazuron (TDZ), 0.8 mg/L benzyladenine (BA), and 0.1 mg/L α-naphthalene acetic acid (NAA) for a variable number of days (4, 6 or 8 days), and exposed to varying concentrations of colchicine (120, 160, 200 mg/L) for 3, 4 or 5 days; the four factors were investigated using an orthogonal experimental design. Adventitious shoots were rooted in 1/2 WPM medium supplemented with 2.0 mg/L indole butyric acid (IBA) and 0.1 mg/L NAA. The ploidy level was assessed using flow cytometry and chromosome counting. Four tetraploids and nine mixoploids were obtained from the leaves. Pre-treatment of the leaves for 8 days and exposure to 200 mg/L colchicine for 3 days led to the most efficient tetraploid induction. Producing 11 tetraploids and five mixoploids from petioles, the best tetraploid induction treatment for petioles was almost the same as that with the leaves, except that pre-culturing was required for only 6 days. In total, 15 tetraploids were obtained with these treatments. This study described a technique for the induction of tetraploid sweetgum from the leaves or petioles of parental material. Based on the success of polyploid breeding in other tree species, the production of hybrid sweetgum allotetraploids constitutes a promising strategy for the promotion of future forestry breeding. Full article
(This article belongs to the Special Issue Genetics and Genomics of Forest Trees) Printed Edition available
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Review

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Open AccessReview Do Silviculture and Forest Management Affect the Genetic Diversity and Structure of Long-Impacted Forest Tree Populations?
Forests 2018, 9(6), 355; https://doi.org/10.3390/f9060355
Received: 20 March 2018 / Revised: 1 May 2018 / Accepted: 26 May 2018 / Published: 14 June 2018
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Abstract
The consequences of silviculture and management on the genetic variation and structure of long-impacted populations of forest tree are reviewed assessed and discussed, using Mediterranean forests as a working paradigm. The review focuses on silviculture and management systems, regeneration schemes, the consequences of
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The consequences of silviculture and management on the genetic variation and structure of long-impacted populations of forest tree are reviewed assessed and discussed, using Mediterranean forests as a working paradigm. The review focuses on silviculture and management systems, regeneration schemes, the consequences of coppicing and coppice conversion to high forest, the effects of fragmentation and exploitation, and the genetic impact of forestry plantations. It emerges that averaging genetic diversity parameters, such as those typically reported in the assessment of forest population genetics, do not generally present significant differences between populations under certain silvicultural systems/forest management methods and “control” populations. Observed differences are usually rather subtler and regard the structure of the genetic variation and the lasting adaptive potential of natural forest tree populations. Therefore, forest management and silvicultural practices have a longer-term impact on the genetic diversity and structure and resilience of long-impacted populations of forest tree; their assessment should be based on parameters that are sensitive to population perturbations and bottlenecks. The nature and extent of genetic effects and impact of silviculture and forest management practices, call for a concerted effort regarding their thorough study using genetic, genomic, as well as monitoring approaches, in order to provide insight and potential solutions for future silviculture and management regimes. Full article
(This article belongs to the Special Issue Genetics and Genomics of Forest Trees) Printed Edition available
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