Special Issue "Genetics and Improvement of Forest Trees"

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

Deadline for manuscript submissions: closed (25 October 2020) | Viewed by 25566

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Special Issue Editor

ret. Prof. Emer. Yuji Ide
E-Mail Website
Guest Editor
Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
Interests: forest tree improvement; phylogeography of trees

Special Issue Information

Dear Colleagues,

Forest tree improvement has mainly been implemented for the purpose of improving the productivity of planted forests. However, in the drastically changing global environment, tree improvements in various traits related to environmental adaptability are also required. Furthermore, since the environmental changes are remarkable, more rapid improvement is required than ever. Advances in plant genome research have revealed the genetic background of various useful traits. Even in trees, abundant genomic or genetic information has been accumulated in several groups that are important as forest resources, such as Pinus, Picea, Cryptomeria, Populus, Eucalyptus, etc. Such information not only enables the rapid improvement of new traits, but also greatly contributes to the verification of the results of forest tree breeding programs that have been carried out and the improvement of the program itself based on them. However, there are not many cases where such genetic information is actually used in forest tree improvement. This Special Issue will focus on genetic information that contributes to tree improvement, including not only the inheritance of traits, but also genetic information related to physiological responses behind such traits. This issue will also focus on the specific application of genetic information to forest tree improvement.

Prof. Dr. Yuji Ide
Guest Editor

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Keywords

  • Environmental adaptability
  • Adaptation measures for environmental change
  • Physiology and gene expression of trees
  • Genetic background of genetic–environment interaction
  • Phenotyping and genomic selection
  • Breeding against pests and diseases
  • Verification of traditional tree improvement

Published Papers (20 papers)

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Editorial

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Editorial
Genetics and Improvement of Forest Trees
Forests 2021, 12(2), 182; https://doi.org/10.3390/f12020182 - 05 Feb 2021
Cited by 1 | Viewed by 704
Abstract
Forest tree improvement has mainly been implemented to enhance the productivity of artificial forests [...] Full article
(This article belongs to the Special Issue Genetics and Improvement of Forest Trees)

Research

Jump to: Editorial, Review

Article
Reforestation or Genetic Disturbance: A Case Study of Pinus thunbergii in the Iki-no-Matsubara Coastal Forest (Japan)
Forests 2021, 12(1), 72; https://doi.org/10.3390/f12010072 - 10 Jan 2021
Cited by 2 | Viewed by 1344
Abstract
In the twentieth century, a substantial decline in Pinus thunbergii populations in Japan occurred due to the outbreak of pine wood nematode (PWN), Burshaphelencus xylophilus. A PWN-P. thunbergii resistant trees-breeding project was developed in the 1980s to provide reforestation materials to [...] Read more.
In the twentieth century, a substantial decline in Pinus thunbergii populations in Japan occurred due to the outbreak of pine wood nematode (PWN), Burshaphelencus xylophilus. A PWN-P. thunbergii resistant trees-breeding project was developed in the 1980s to provide reforestation materials to minimalize the pest damage within the population. Since climate change can also contribute to PWN outbreaks, an intensive reforestation plan instated without much consideration can impact on the genetic diversity of P. thunbergii populations. The usage and deployment of PWN-P. thunbergii resistant trees to a given site without genetic management can lead to a genetic disturbance. The Iki-no-Matsubara population was used as a model to design an approach for the deployment management. This research aimed to preserve local genetic diversity, genetic structure, and relatedness by developing a method for deploying Kyushu PWN-P. thunbergii resistant trees as reforestation-material plants into Iki-no-Matsubara. The local genotypes of the Iki-no-Matsubara population and the Kyushu PWN-P. thunbergii resistant trees were analyzed using six microsatellite markers. Genotype origins, relatedness, diversity, and structure of both were investigated and compared with the genetic results previously obtained for old populations of P. thunbergii throughout Japan. A sufficient number of Kyushu PWN-P. thunbergii resistant trees, as mother trees, within seed orchards and sufficient status number of the seedlings to deploy are needed when deploying the Kyushu PWN-P. thunbergii resistant trees as reforestation material planting into Iki-no-Matsubara population. This approach not only be used to preserve Iki-no-Matsubara population (genetic diversity, genetic structure, relatedness, and resilience of the forests) but can also be applied to minimize PWN damage. These results provide a baseline for further seed sourcing as well as develop genetic management strategies within P. thunbergii populations, including Kyushu PWN-P. thunbergii resistant trees. Full article
(This article belongs to the Special Issue Genetics and Improvement of Forest Trees)
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Article
Evaluation of Responsivity to Drought Stress Using Infrared Thermography and Chlorophyll Fluorescence in Potted Clones of Cryptomeria japonica
Forests 2021, 12(1), 55; https://doi.org/10.3390/f12010055 - 02 Jan 2021
Cited by 3 | Viewed by 1256
Abstract
As climate change progresses, the breeding of drought-tolerant forest trees is necessary. Breeding drought-tolerant trees requires screening for drought stress using a large number of individuals and a high-throughput phenotyping method. The aim of this study was therefore to establish high-throughput methods for [...] Read more.
As climate change progresses, the breeding of drought-tolerant forest trees is necessary. Breeding drought-tolerant trees requires screening for drought stress using a large number of individuals and a high-throughput phenotyping method. The aim of this study was therefore to establish high-throughput methods for evaluating the clonal stress responses to drought stress using infrared thermography and chlorophyll fluorescence methods in Cryptomeria japonica. The stomatal conductance index (Ig), maximum photochemical quantum yield of photosystem II (Fv/Fm), and axial growth of four plus-tree clones of C. japonica planted in pots were measured weekly for 85 days after irrigation was stopped. The phenotypic trait responsivity to drought stress was estimated by a nonlinear mixed model and by introducing the cumulative water index, which considers the past history of the soil water environment. These methods and procedures enabled us to evaluate the clonal stress responses in C. japonica and could be applied to large-scale clone materials to promote the breeding program for drought tolerance. Full article
(This article belongs to the Special Issue Genetics and Improvement of Forest Trees)
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Article
Population Genetic Diversity and Structure of Ancient Tree Populations of Cryptomeria japonica var. sinensis Based on RAD-seq Data
Forests 2020, 11(11), 1192; https://doi.org/10.3390/f11111192 - 12 Nov 2020
Cited by 9 | Viewed by 1542
Abstract
Research highlights: Our study is the first to explore the genetic composition of ancient Cryptomeria trees across a distribution range in China. Background and objectives: Cryptomeria japonica var. sinensis is a native forest species of China; it is widely planted in the south [...] Read more.
Research highlights: Our study is the first to explore the genetic composition of ancient Cryptomeria trees across a distribution range in China. Background and objectives: Cryptomeria japonica var. sinensis is a native forest species of China; it is widely planted in the south of the country to create forests and for wood production. Unlike Cryptomeria in Japan, genetic Chinese Cryptomeria has seldom been studied, although there is ample evidence of its great ecological and economic value. Materials and methods: Because of overcutting, natural populations are rare in the wild. In this study, we investigated seven ancient tree populations to explore the genetic composition of Chinese Cryptomeria through ddRAD-seq technology. Results: The results reveal a lower genetic variation but higher genetic differentiation (Ho = 0.143, FST = 0.1204) than Japanese Cryptomeria (Ho = 0.245, FST = 0.0455). The 86% within-population variation is based on an analysis of molecular variance (AMOVA). Significant excess heterozygosity was detected in three populations and some outlier loci were found; these were considered to be the consequence of selection or chance. Structure analysis and dendrogram construction divided the seven ancient tree populations into four groups corresponding to the geographical provinces in which the populations are located, but there was no obvious correlation between genetic distance and geographic distance. A demographic history analysis conducted by a Stairway Plot showed that the effective population size of Chinese Cryptomeria had experienced a continuing decline from the mid-Pleistocene to the present. Our findings suggest that the strong genetic drift caused by climate fluctuation and intense anthropogenic disturbance together contributed to the current low diversity and structure. Considering the species’ unfavorable conservation status, strategies are urgently required to preserve the remaining genetic resources. Full article
(This article belongs to the Special Issue Genetics and Improvement of Forest Trees)
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Article
Effects of Light Intensity and Girdling Treatments on the Production of Female Cones in Japanese Larch (Larix kaempferi (Lamb.) Carr.): Implications for the Management of Seed Orchards
Forests 2020, 11(10), 1110; https://doi.org/10.3390/f11101110 - 19 Oct 2020
Cited by 2 | Viewed by 1001
Abstract
To ensure sustainable forestry, it is important to establish an efficient management procedure for improving the seed production capacity of seed orchards. In this study, we evaluated the effects of girdling and increasing light intensity on female cone production in an old L. [...] Read more.
To ensure sustainable forestry, it is important to establish an efficient management procedure for improving the seed production capacity of seed orchards. In this study, we evaluated the effects of girdling and increasing light intensity on female cone production in an old L. kaempferi (Lamb.) Carr. seed orchard. We also evaluated whether there is a genotype-specific reproductive response to these factors among clones. The results showed that female cone production was augmented by girdling and increasing light intensity. There was a difference in the effectiveness of girdling treatment levels, and the probability of producing female cones increased markedly at higher girdling levels. At light intensities where the relative photosynthetic photon flux density was higher than 50%, more than half of the trees tended to produce female cones, even in intact (ungirdled) trees, and the genotype-specific response to light intensity was more apparent in less-reproductive clones. These findings suggested that girdling less-reproductive trees combined with increasing light intensity was an effective management strategy for improving cone production in old seed orchards. Full article
(This article belongs to the Special Issue Genetics and Improvement of Forest Trees)
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Article
Ten Years of Provenance Trials and Application of Multivariate Random Forests Predicted the Most Preferable Seed Source for Silviculture of Abies sachalinensis in Hokkaido, Japan
Forests 2020, 11(10), 1058; https://doi.org/10.3390/f11101058 - 30 Sep 2020
Cited by 5 | Viewed by 1202
Abstract
Research highlights: Using 10-year tree height data obtained after planting from the range-wide provenance trials of Abies sachalinensis, we constructed multivariate random forests (MRF), a machine learning algorithm, with climatic variables. The constructed MRF enabled prediction of the optimum seed source to [...] Read more.
Research highlights: Using 10-year tree height data obtained after planting from the range-wide provenance trials of Abies sachalinensis, we constructed multivariate random forests (MRF), a machine learning algorithm, with climatic variables. The constructed MRF enabled prediction of the optimum seed source to achieve good performance in terms of height growth at every planting site on a fine scale. Background and objectives: Because forest tree species are adapted to the local environment, local seeds are empirically considered as the best sources for planting. However, in some cases, local seed sources show lower performance in height growth than that showed by non-local seed sources. Tree improvement programs aim to identify seed sources for obtaining high-quality timber products by performing provenance trials. Materials and methods: Range-wide provenance trials for one of the most important silvicultural species, Abies sachalinensis, were established in 1980 at nine transplanting experimental sites. We constructed an MRF to estimate the responses of tree height at 10 years after planting at eight climatic variables at 1 km × 1 km resolution. The model was applied for prediction of tree height throughout Hokkaido Island. Results: Our model showed that four environmental variables were major factors affecting height growth—winter solar radiation, warmth index, maximum snow depth, and spring solar radiation. A tree height prediction map revealed that local seeds showed the best performance except in the southernmost region and several parts of northern regions. Moreover, the map of optimum seed provenance suggested that deployment of distant seed sources can outperform local sources in the southernmost and northern regions. Conclusions: We predicted that local seeds showed optimum growth, whereas non-local seeds had the potential to outperform local seeds in some regions. Several deployment options were proposed to improve tree growth. Full article
(This article belongs to the Special Issue Genetics and Improvement of Forest Trees)
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Article
Do Seedlings Derived from Pinewood Nematode-Resistant Pinus thunbergii Parl. Clones Selected in Southwestern Region Perform Well in Northern Regions in Japan? Inferences from Nursery Inoculation Tests
Forests 2020, 11(9), 955; https://doi.org/10.3390/f11090955 - 01 Sep 2020
Cited by 3 | Viewed by 756
Abstract
Background and Objectives: To determine whether the progeny of pinewood nematode-resistant Pinus thunbergii Parl. clones selected in the southwestern region of Japan could be successful in reforestation in the northern region, we investigated the magnitude of the genotype–environment interaction effect on the resistance [...] Read more.
Background and Objectives: To determine whether the progeny of pinewood nematode-resistant Pinus thunbergii Parl. clones selected in the southwestern region of Japan could be successful in reforestation in the northern region, we investigated the magnitude of the genotype–environment interaction effect on the resistance against Bursaphelenchus xylophilus (Steiner and Buhrer) Nickle in P. thunbergii. Materials and Methods: We inoculated P. thunbergii seedlings of six full-sib families, with various resistance levels, with B. xylophilus in nurseries at three experimental sites in the northern and southern regions of Japan. All parental clones of the tested families originated from southwestern Japan, and selection of parental clones for resistance was performed in the same region. Sound rates after nematode inoculation were calculated, and survival analysis, correlation analysis and variance component analysis were performed. Results and Conclusions: Families with high sound rate in the southern region also showed a high sound rate in the northern region. In almost all cases, Spearman’s correlation coefficients for sound rates were more than 0.698 among sites. The variance component of the interaction between site and family was small compared to that of site and family separately. Thus, we conclude that the resistant clones selected in the southern region would retain their genetic resistance in the northern regions. Full article
(This article belongs to the Special Issue Genetics and Improvement of Forest Trees)
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Article
Genetic Diversity and Structure of Japanese Endemic Genus Thujopsis (Cupressaceae) Using EST-SSR Markers
Forests 2020, 11(9), 935; https://doi.org/10.3390/f11090935 - 27 Aug 2020
Cited by 2 | Viewed by 843
Abstract
The genus Thujopsis (Cupressaceae) comprises monoecious coniferous trees endemic to Japan. This genus includes two varieties: Thujopsis dolabrata (L.f.) Siebold et Zucc. var. dolabrata (southern variety, Td) and Thujopsis dolabrata (L.f.) Siebold et Zucc. var. hondae Makino (northern variety, Th). The aim of [...] Read more.
The genus Thujopsis (Cupressaceae) comprises monoecious coniferous trees endemic to Japan. This genus includes two varieties: Thujopsis dolabrata (L.f.) Siebold et Zucc. var. dolabrata (southern variety, Td) and Thujopsis dolabrata (L.f.) Siebold et Zucc. var. hondae Makino (northern variety, Th). The aim of this study is to understand the phylogeographic and genetic population relationships of the genus Thujopsis for the conservation of genetic resources and future breeding. A total of 609 trees from 22 populations were sampled, including six populations from the Td distribution range and 16 populations from the Th distribution range. The genotyping results for 19 expressed sequence tag (EST)-based simple sequence repeat (SSR) markers, followed by a structure analysis, neighbor-joining tree creation, an analysis of molecular variance (AMOVA), and hierarchical F statistics, supported the existence of two genetic clusters related to the distribution regions of the Td and Th varieties. The two variants, Td and Th, could be defined by their provenance, in spite of the ambiguous morphological differences between the varieties. The distribution ranges of both variants, which have been defined from their morphology, was confirmed by genetic analysis. The Th populations exhibited relatively uniform genetic diversity, most likely because Th refugia in the glacial period were scattered throughout their current distribution area. On the other hand, there was a tendency for Td’s genetic diversity to decrease from central to southern Honshu island. Notably, the structure analysis and neighbor-joining tree suggest the hybridization of the two varieties in the contact zone. More detailed studies of the genetic structure of Td are required in future analyses. Full article
(This article belongs to the Special Issue Genetics and Improvement of Forest Trees)
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Article
Effects of Temperature Factors on Resistance against Pine Wood Nematodes in Pinus thunbergii, Based on Multiple Location Sites Nematode Inoculation Tests
Forests 2020, 11(9), 922; https://doi.org/10.3390/f11090922 - 24 Aug 2020
Cited by 4 | Viewed by 1037
Abstract
Pine wilt disease (PWD) caused by the pinewood nematode (PWN) (Bursaphelenchus xylophilus (Steiner and Buhrer) Nickle) is a worldwide issue. Infection is considered to be promoted mainly by the increased air temperature, but it is important to investigate whether the effect of [...] Read more.
Pine wilt disease (PWD) caused by the pinewood nematode (PWN) (Bursaphelenchus xylophilus (Steiner and Buhrer) Nickle) is a worldwide issue. Infection is considered to be promoted mainly by the increased air temperature, but it is important to investigate whether the effect of high temperature similarly influences the different ranks of resistant clone. In the present study, we conducted PWN inoculation tests using six common open-pollinated families of resistant Pinus thunbergii Parl. The tests were conducted at nurseries of five test sites across Japanese archipelago between 2015 and 2017. Our analysis focused specifically on temperature. Firstly, we examined the effects of test sites, inoculation year, and their interaction on unaffected seedling rate and found that the unaffected seedling rate of all tested pine families decreased as the cumulative temperature increased. We found that the unaffected seedling rate decreased as the cumulative temperature increased for all tested pine families. In general, higher cumulative temperatures were required for having an effect on the unaffected seedling rates of higher PWN-resistant families. Typically, early cumulative temperatures, i.e., 19 days after inoculation, had the greatest effect on the unaffected seedling rates of PWN-resistant pines. However, the relationship between cumulative temperature and predicted unaffected seedling rate follow similar rate for all families. Thus, the order of resistance level is maintained in terms of the cumulative temperature required for having an effect. Full article
(This article belongs to the Special Issue Genetics and Improvement of Forest Trees)
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Article
SNP Genotyping with Target Amplicon Sequencing Using a Multiplexed Primer Panel and Its Application to Genomic Prediction in Japanese Cedar, Cryptomeria japonica (L.f.) D.Don
Forests 2020, 11(9), 898; https://doi.org/10.3390/f11090898 - 19 Aug 2020
Cited by 5 | Viewed by 1491
Abstract
Along with progress in sequencing technology and accumulating knowledge of genome and gene sequences, molecular breeding techniques have been developed for predicting the genetic potential of individual genotypes and for selecting superior individuals. For Japanese cedar (Cryptomeria japonica (L.f.) D.Don), which is [...] Read more.
Along with progress in sequencing technology and accumulating knowledge of genome and gene sequences, molecular breeding techniques have been developed for predicting the genetic potential of individual genotypes and for selecting superior individuals. For Japanese cedar (Cryptomeria japonica (L.f.) D.Don), which is the most common coniferous species in Japanese forestry, we constructed a custom primer panel for target amplicon sequencing in order to simultaneously determine 3034 informative single nucleotide polymorphisms (SNPs). We performed primary evaluation of the custom primer panel with actual sequencing and in silico PCR. Genotyped SNPs had a distribution over almost the entire region of the C. japonica linkage map and verified the high reproducibility of genotype calls compared to SNPs obtained by genotyping arrays. Genotyping was performed for 576 individuals of the F1 population, and genomic prediction models were constructed for growth and wood property-related traits using the genotypes. Amplicon sequencing with the custom primer panel enables efficient obtaining genotype data in order to perform genomic prediction, manage clones, and advance forest tree breeding. Full article
(This article belongs to the Special Issue Genetics and Improvement of Forest Trees)
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Article
Profiling of Widely Targeted Metabolomics for the Identification of Secondary Metabolites in Heartwood and Sapwood of the Red-Heart Chinese Fir (Cunninghamia Lanceolata)
Forests 2020, 11(8), 897; https://doi.org/10.3390/f11080897 - 18 Aug 2020
Cited by 6 | Viewed by 1239
Abstract
The chemical composition of secondary metabolites is important for the quality control of wood products. In this study, the widely targeted metabolomics approach was used to analyze the metabolic profiles of heartwood and sapwood in the red-heart Chinese fir (Cunninghamia lanceolata), [...] Read more.
The chemical composition of secondary metabolites is important for the quality control of wood products. In this study, the widely targeted metabolomics approach was used to analyze the metabolic profiles of heartwood and sapwood in the red-heart Chinese fir (Cunninghamia lanceolata), with an ultra-performance liquid chromatography-electrospray ionization tandem mass spectrometry system. A total of 224 secondary metabolites were detected in the heartwood and sapwood, and of these, flavonoids and phenolic acids accounted for 36% and 26% of the components, respectively. The main pathways appeared to be differentially activated, including those for the biosynthesis of phenylpropanoids and flavonoids. Moreover, we observed highly significant accumulation of naringenin chalcone, dihydrokaempferol, pinocembrin, hesperetin, and other important secondary metabolites in the flavonoid biosynthesis pathway. Our results provide insight into the flavonoid pathway associated with wood color formation in Chinese fir that will be useful for further breeding programs. Full article
(This article belongs to the Special Issue Genetics and Improvement of Forest Trees)
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Article
Complete Chloroplast Genome of Japanese Larch (Larix kaempferi): Insights into Intraspecific Variation with an Isolated Northern Limit Population
Forests 2020, 11(8), 884; https://doi.org/10.3390/f11080884 - 14 Aug 2020
Cited by 7 | Viewed by 1191
Abstract
Research Highlights: The complete chloroplast genome for eight individuals of Japanese larch, including from the isolated population at the northern limit of the range (Manokami larch), revealed that Japanese larch forms a monophyletic group, within which Manokami larch can be phylogenetically placed in [...] Read more.
Research Highlights: The complete chloroplast genome for eight individuals of Japanese larch, including from the isolated population at the northern limit of the range (Manokami larch), revealed that Japanese larch forms a monophyletic group, within which Manokami larch can be phylogenetically placed in Japanese larch. We detected intraspecific variation for possible candidate cpDNA markers in Japanese larch. Background and Objectives: The natural distribution of Japanese larch is limited to the mountainous range in the central part of Honshu Island, Japan, with an isolated northern limit population (Manokami larch). In this study, we determined the phylogenetic position of Manokami larch within Japanese larch, characterized the chloroplast genome of Japanese larch, detected intraspecific variation, and determined candidate cpDNA markers. Materials and Methods: The complete genome sequence was determined for eight individuals, including Manokami larch, in this study. The genetic position of the northern limit population was evaluated using phylogenetic analysis. The chloroplast genome of Japanese larch was characterized by comparison with eight individuals. Furthermore, intraspecific variations were extracted to find candidate cpDNA markers. Results: The phylogenetic tree showed that Japanese larch forms a monophyletic group, within which Manokami larch can be phylogenetically placed, based on the complete chloroplast genome, with a bootstrap value of 100%. The value of nucleotide diversity (π) was calculated at 0.00004, based on SNP sites for Japanese larch, suggesting that sequences had low variation. However, we found three hyper-polymorphic regions within the cpDNA. Finally, we detected 31 intraspecific variations, including 19 single nucleotide polymorphisms, 8 simple sequence repeats, and 4 insertions or deletions. Conclusions: Using a distant genotype in a northern limit population (Manokami larch), we detected sufficient intraspecific variation for the possible candidates of cpDNA markers in Japanese larch. Full article
(This article belongs to the Special Issue Genetics and Improvement of Forest Trees)
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Article
Physiological Characterization and Transcriptome Analysis of Camellia oleifera Abel. during Leaf Senescence
Forests 2020, 11(8), 812; https://doi.org/10.3390/f11080812 - 28 Jul 2020
Cited by 4 | Viewed by 1043
Abstract
Camellia (C.) oleifera Abel. is an evergreen small arbor with high economic value for producing edible oil that is well known for its high level of unsaturated fatty acids. The yield formation of tea oil extracted from fruit originates from the leaves, so [...] Read more.
Camellia (C.) oleifera Abel. is an evergreen small arbor with high economic value for producing edible oil that is well known for its high level of unsaturated fatty acids. The yield formation of tea oil extracted from fruit originates from the leaves, so leaf senescence, the final stage of leaf development, is an important agronomic trait affecting the production and quality of tea oil. However, the physiological characteristics and molecular mechanism underlying leaf senescence of C. oleifera are poorly understood. In this study, we performed physiological observation and de novo transcriptome assembly for annual leaves and biennial leaves of C. oleifera. The physiological assays showed that the content of chlorophyll (Chl), soluble protein, and antioxidant enzymes including superoxide dismutase, peroxide dismutase, and catalase in senescing leaves decreased significantly, while the proline and malondialdehyde concentration increased. By analyzing RNA-Seq data, we identified 4645 significantly differentially expressed unigenes (DEGs) in biennial leaves with most associated with flavonoid and phenylpropanoid biosynthesis and phenylalanine metabolism pathways. Among these DEGs, 77 senescence-associated genes (SAGs) including NOL, ATAF1, MDAR, and SAG12 were classified to be related to Chl degradation, plant hormone, and oxidation pathways. The further analysis of the 77 SAGs based on the Spearman correlation algorithm showed that there was a significant expression correlation between these SAGs, suggesting the potential connections between SAGs in jointly regulating leaf senescence. A total of 162 differentially expressed transcription factors (TFs) identified during leaf senescence were mostly distributed in MYB (myeloblastosis), ERF (Ethylene-responsive factor), WRKY, and NAC (NAM, ATAF1/2 and CUCU2) families. In addition, qRT-PCR analysis of 19 putative SAGs were in accordance with the RNA-Seq data, further confirming the reliability and accuracy of the RNA-Seq. Collectively, we provide the first report of the transcriptome analysis of C. oleifera leaves of two kinds of age and a basis for understanding the molecular mechanism of leaf senescence. Full article
(This article belongs to the Special Issue Genetics and Improvement of Forest Trees)
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Article
Transcriptomic Profiling of Cryptomeria fortunei Hooibrenk Vascular Cambium Identifies Candidate Genes Involved in Phenylpropanoid Metabolism
Forests 2020, 11(7), 766; https://doi.org/10.3390/f11070766 - 17 Jul 2020
Cited by 4 | Viewed by 1052
Abstract
Cryptomeria fortunei Hooibrenk (Chinese cedar) is a coniferous tree from southern China that has an important function in landscaping and timber production. Lignin is one of the key components of secondary cell walls, which have a crucial role in conducting water and providing [...] Read more.
Cryptomeria fortunei Hooibrenk (Chinese cedar) is a coniferous tree from southern China that has an important function in landscaping and timber production. Lignin is one of the key components of secondary cell walls, which have a crucial role in conducting water and providing mechanical support for the upward growth of plants. It is mainly biosynthesized via the phenylpropanoid metabolic pathway, of which the molecular mechanism remains so far unresolved in C. fortunei. In order to obtain further insight into this pathway, we performed transcriptome sequencing of the C. fortunei cambial zone at 5 successive growth stages. We generated 78,673 unigenes from transcriptome data, of which 45,214 (57.47%) were successfully annotated in the non-redundant protein database (NR). A total of 8975 unigenes were identified to be significantly differentially expressed between Sample_B and Sample_A after analyzing their expression profiles. Of the differentially expressed genes (DEGs), 6817 (75.96%) and 2158 (24.04%) were up- and down-regulated, respectively. 83 DEGs were involved in phenylpropanoid metabolism, 37 DEGs that encoded v-Myb avian myeloblastosis viral oncogene homolog (MYB) transcription factor (TF), and many candidates that encoded lignin synthesizing enzymes. These findings contribute to understanding the expression pattern of C. fortunei cambial zone transcriptome. Furthermore, our results provide additional insight towards understanding the molecular mechanisms of wood formation in C. fortunei. Full article
(This article belongs to the Special Issue Genetics and Improvement of Forest Trees)
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Article
Marker-Assisted Selection of Trees with MALE STERILITY 1 in Cryptomeria japonica D. Don
Forests 2020, 11(7), 734; https://doi.org/10.3390/f11070734 - 06 Jul 2020
Cited by 8 | Viewed by 1253
Abstract
The practical use of marker-assisted selection (MAS) is limited in conifers because of the difficulty with developing markers due to a rapid decrease in linkage disequilibrium, the limited genomic information available, and the diverse genetic backgrounds among the breeding material collections. First, in [...] Read more.
The practical use of marker-assisted selection (MAS) is limited in conifers because of the difficulty with developing markers due to a rapid decrease in linkage disequilibrium, the limited genomic information available, and the diverse genetic backgrounds among the breeding material collections. First, in this study, two families were produced by artificial crossing between two male-sterile trees, ‘Shindai11’ and ‘Shindai12’, and a plus tree, ‘Suzu-2’ (Ms1/ms1) (S11-S and S12-S families, respectively). The segregation ratio between the male-sterile and male-fertile trees did not deviate significantly from the expected 1:1 ratio in either family. These results clearly suggested that the male-sterile gene of ‘Shindai11’ and ‘Shindai12’ is MALE STERILITY 1 (MS1). Since it is difficult to understand the relative positions of each marker, due to the lack of a linkage map which all the closely linked markers previously reported are mapped on, we constructed a partial linkage map of the region encompassing MS1 using the S11-S and S12-S families. For the S11-S and S12-S families, 19 and 18 markers were mapped onto the partial linkage maps of the MS1 region, respectively. There was collinearity (conserved gene order) between the two partial linkage maps. Two markers (CJt020762_ms1-1 and reCj19250_2335) were mapped to the same position as the MS1 locus on both maps. Of these markers, we used CJt020762 for the MAS in this study. According to the MAS results for 650 trees from six prefectures of Japan (603 trees from breeding materials and 47 trees from the Ishinomaki natural population), five trees in Niigata Prefecture and one tree in Yamagata Prefecture had heterozygous ms1-1, and three trees in Miyagi Prefecture had heterozygous ms1-2. The results obtained in this study suggested that ms1-1 and ms1-2 have different geographical distributions. Since MAS can be used effectively to reduce the labor and time required for selection of trees with a male-sterile gene, the research should help ensure that the quantity of breeding materials will increase to assist future tree-breeding efforts. Full article
(This article belongs to the Special Issue Genetics and Improvement of Forest Trees)
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Article
Transcriptome Analysis in Male Strobilus Induction by Gibberellin Treatment in Cryptomeria japonica D. Don
Forests 2020, 11(6), 633; https://doi.org/10.3390/f11060633 - 03 Jun 2020
Cited by 4 | Viewed by 1184
Abstract
The plant hormone gibberellin (GA) is known to regulate elongating growth, seed germination, and the initiation of flower bud formation, and it has been postulated that GAs originally had functions in reproductive processes. Studies on the mechanism of induction of flowering by GA [...] Read more.
The plant hormone gibberellin (GA) is known to regulate elongating growth, seed germination, and the initiation of flower bud formation, and it has been postulated that GAs originally had functions in reproductive processes. Studies on the mechanism of induction of flowering by GA have been performed in Arabidopsis and other model plants. In coniferous trees, reproductive organ induction by GAs is known to occur, but there are few reports on the molecular mechanism in this system. To clarify the gene expression dynamics of the GA induction of the male strobilus in Cryptomeria japonica, we performed comprehensive gene expression analysis using a microarray. A GA-treated group and a nontreated group were allowed to set, and individual trees were sampled over a 6-week time course. A total of 881 genes exhibiting changed expression was identified. In the GA-treated group, genes related to ‘stress response’ and to ‘cell wall’ were initially enriched, and genes related to ‘transcription’ and ‘transcription factor activity’ were enriched at later stages. This analysis also clarified the dynamics of the expression of genes related to GA signaling transduction following GA treatment, permitting us to compare and contrast with the expression dynamics of genes implicated in signal transduction responses to other plant hormones. These results suggested that various plant hormones have complex influences on the male strobilus induction. Additionally, principal component analysis (PCA) using expression patterns of the genes that exhibited sequence similarity with flower bud or floral organ formation-related genes of Arabidopsis was performed. PCA suggested that gene expression leading to male strobilus formation in C. japonica became conspicuous within one week of GA treatment. Together, these findings help to clarify the evolution of the mechanism of induction of reproductive organs by GA. Full article
(This article belongs to the Special Issue Genetics and Improvement of Forest Trees)
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Article
Geographical Gradients of Genetic Diversity and Differentiation among the Southernmost Marginal Populations of Abies sachalinensis Revealed by EST-SSR Polymorphism
Forests 2020, 11(2), 233; https://doi.org/10.3390/f11020233 - 20 Feb 2020
Cited by 13 | Viewed by 1355
Abstract
Research Highlights: We detected the longitudinal gradients of genetic diversity parameters, such as the number of alleles, effective number of alleles, heterozygosity, and inbreeding coefficient, and found that these might be attributable to climatic conditions, such as temperature and snow depth. Background [...] Read more.
Research Highlights: We detected the longitudinal gradients of genetic diversity parameters, such as the number of alleles, effective number of alleles, heterozygosity, and inbreeding coefficient, and found that these might be attributable to climatic conditions, such as temperature and snow depth. Background and Objectives: Genetic diversity among local populations of a plant species at its distributional margin has long been of interest in ecological genetics. Populations at the distribution center grow well in favorable conditions, but those at the range margins are exposed to unfavorable environments, and the environmental conditions at establishment sites might reflect the genetic diversity of local populations. This is known as the central-marginal hypothesis in which marginal populations show lower genetic variation and higher differentiation than in central populations. In addition, genetic variation in a local population is influenced by phylogenetic constraints and the population history of selection under environmental constraints. In this study, we investigated this hypothesis in relation to Abies sachalinensis, a major conifer species in Hokkaido. Materials and Methods: A total of 1189 trees from 25 natural populations were analyzed using 19 EST-SSR loci. Results: The eastern populations, namely, those in the species distribution center, showed greater genetic diversity than did the western peripheral populations. Another important finding is that the southwestern marginal populations were genetically differentiated from the other populations. Conclusions: These differences might be due to genetic drift in the small and isolated populations at the range margin. Therefore, our results indicated that the central-marginal hypothesis held true for the southernmost A. sachalinensis populations in Hokkaido. Full article
(This article belongs to the Special Issue Genetics and Improvement of Forest Trees)
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Article
Development and Deployment of High-Throughput Retrotransposon-Based Markers Reveal Genetic Diversity and Population Structure of Asian Bamboo
Forests 2020, 11(1), 31; https://doi.org/10.3390/f11010031 - 24 Dec 2019
Cited by 19 | Viewed by 1898
Abstract
Bamboo, a non-timber grass species, known for exceptionally fast growth is a commercially viable crop. Long terminal repeat (LTR) retrotransposons, the main class I mobile genetic elements in plant genomes, are highly abundant (46%) in bamboo, contributing to genome diversity. They play significant [...] Read more.
Bamboo, a non-timber grass species, known for exceptionally fast growth is a commercially viable crop. Long terminal repeat (LTR) retrotransposons, the main class I mobile genetic elements in plant genomes, are highly abundant (46%) in bamboo, contributing to genome diversity. They play significant roles in the regulation of gene expression, chromosome size and structure as well as in genome integrity. Due to their random insertion behavior, interspaces of retrotransposons can vary significantly among bamboo genotypes. Capitalizing this feature, inter-retrotransposon amplified polymorphism (IRAP) is a high-throughput marker system to study the genetic diversity of plant species. To date, there are no transposon based markers reported from the bamboo genome and particularly using IRAP markers on genetic diversity. Phyllostachys genus of Asian bamboo is the largest of the Bambusoideae subfamily, with great economic importance. We report structure-based analysis of bamboo genome for the LTR-retrotransposon superfamilies, Ty3-gypsy and Ty1-copia, which revealed a total of 98,850 retrotransposons with intact LTR sequences at both the ends. Grouped into 64,281 clusters/scaffold using CD-HIT-EST software, only 13 clusters of retroelements were found with more than 30 LTR sequences and with at least one copy having all intact protein domains such as gag and polyprotein. A total of 16 IRAP primers were synthesized, based on the high copy numbers of conserved LTR sequences. A study using these IRAP markers on genetic diversity and population structure of 58 Asian bamboo accessions belonging to the genus Phyllostachys revealed 3340 amplicons with an average of 98% polymorphism. The bamboo accessions were collected from nine different provinces of China, as well as from Italy and America. A three phased approach using hierarchical clustering, principal components and a model based population structure divided the bamboo accessions into four sub-populations, PhSP1, PhSP2, PhSP3 and PhSP4. All the three analyses produced significant sub-population wise consensus. Further, all the sub-populations revealed admixture of alleles. The analysis of molecular variance (AMOVA) among the sub-populations revealed high intra-population genetic variation (75%) than inter-population. The results suggest that Phyllostachys bamboos are not well evolutionarily diversified, although geographic speciation could have occurred at a limited level. This study highlights the usability of IRAP markers in determining the inter-species variability of Asian bamboos. Full article
(This article belongs to the Special Issue Genetics and Improvement of Forest Trees)
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Article
Variability and Plasticity in Cuticular Transpiration and Leaf Permeability Allow Differentiation of Eucalyptus Clones at an Early Age
Forests 2020, 11(1), 9; https://doi.org/10.3390/f11010009 - 18 Dec 2019
Cited by 7 | Viewed by 1210
Abstract
Background and Objectives. Water stress is a major constraining factor of Eucalyptus plantations’ growth. Within a genetic improvement program, the selection of genotypes that improve drought resistance would help to improve productivity and to expand plantations. Leaf characteristics, among others, are important [...] Read more.
Background and Objectives. Water stress is a major constraining factor of Eucalyptus plantations’ growth. Within a genetic improvement program, the selection of genotypes that improve drought resistance would help to improve productivity and to expand plantations. Leaf characteristics, among others, are important factors to consider when evaluating drought resistance evaluation, as well as the clone’s ability to modify leaf properties (e.g., stomatal density (d) and size, relative water content at the time of stomatal closure (RWCc), cuticular transpiration (Ec), specific leaf area (SLA)) according to growing conditions. Therefore, this study aimed at analyzing these properties in nursery plants of nine high-productivity Eucalyptus clones. Material and Methods: Five Eucalyptus globulus Labill. clones and four hybrids clones (Eucalyptus urophylla S.T. Blake × Eucalyptus grandis W. Hill ex Maiden, 12€; Eucalyptus urograndis × E. globulus, HE; Eucalyptus dunnii Maiden–E. grandis × E. globulus, HG; Eucalyptus saligna Sm. × Eucalyptus maidenii F. Muell., HI) were studied. Several parameters relating to the aforementioned leaf traits were evaluated for 2.5 years. Results: Significant differences in stomatal d and size, RWCc, Ec, and SLA among clones (p < 0.001) and according to the dates (p < 0.001) were obtained. Each clone varied seasonally the characteristics of its new developing leaves to acclimatize to the growth conditions. The pore opening surface potential (i.e., the stomatal d × size) did not affect transpiration rates with full open stomata, so the water transpired under these conditions might depend on other leaf factors. The clones HE, HG, and 12€ were the ones that differed the most from the drought resistant E. globulus control clone (C14). Those three clones showed lower leaf epidermis impermeability (HE, HG, 12€), higher SLA (12€, HG), and lower stomatal control under moderate water stress (HE, HG) not being, therefore, good candidates to be selected for drought resistance, at least for these measured traits. Conclusions: These parameters can be incorporated into genetic selection and breeding programs, especially Ec, SLA, RWCc, and stomatal control under moderate water stress. Full article
(This article belongs to the Special Issue Genetics and Improvement of Forest Trees)
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Review

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Review
Genomic Selection for Forest Tree Improvement: Methods, Achievements and Perspectives
Forests 2020, 11(11), 1190; https://doi.org/10.3390/f11111190 - 11 Nov 2020
Cited by 24 | Viewed by 1825
Abstract
The breeding of forest trees is only a few decades old, and is a much more complicated, longer, and expensive endeavor than the breeding of agricultural crops. One breeding cycle for forest trees can take 20–30 years. Recent advances in genomics and molecular [...] Read more.
The breeding of forest trees is only a few decades old, and is a much more complicated, longer, and expensive endeavor than the breeding of agricultural crops. One breeding cycle for forest trees can take 20–30 years. Recent advances in genomics and molecular biology have revolutionized traditional plant breeding based on visual phenotype assessment: the development of different types of molecular markers has made genotype selection possible. Marker-assisted breeding can significantly accelerate the breeding process, but this method has not been shown to be effective for selection of complex traits on forest trees. This new method of genomic selection is based on the analysis of all effects of quantitative trait loci (QTLs) using a large number of molecular markers distributed throughout the genome, which makes it possible to assess the genomic estimated breeding value (GEBV) of an individual. This approach is expected to be much more efficient for forest tree improvement than traditional breeding. Here, we review the current state of the art in the application of genomic selection in forest tree breeding and discuss different methods of genotyping and phenotyping. We also compare the accuracies of genomic prediction models and highlight the importance of a prior cost-benefit analysis before implementing genomic selection. Perspectives for the further development of this approach in forest breeding are also discussed: expanding the range of species and the list of valuable traits, the application of high-throughput phenotyping methods, and the possibility of using epigenetic variance to improve of forest trees. Full article
(This article belongs to the Special Issue Genetics and Improvement of Forest Trees)
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