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Molecular Genetics of Forest Trees and Applications in Breeding, Conservation...
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Molecular Genetics of Forest Trees and Applications in Breeding, Conservation and Management of Genetic Resources

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

Deadline for manuscript submissions: closed (30 September 2022) | Viewed by 17230

Special Issue Editor

Prof. Dr. Paraskevi Alizoti

E-Mail Website
Guest Editor
Laboratory of Forest Genetics and Tree Improvement, School of Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
Interests: forests genetics; tree breeding and selection strategies; conservation and use of forest genetic resources; forest genetic monitoring; quantitative, evolutionary and ecological genetics; classical and molecular breeding; genetic adaptation to climate change, assisted migration; application of GIS in conservation of genetic resources
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Molecular genetics is a key scientific area providing tools and applications to study the vast genetic diversity of forest tree species and their complex life histories; dissect complex traits; apply marker-based breeding strategies aiming towards tailored selection of parents and acceleration of breeding cycles; characterize forest genetic resources, in situ conservation networks, and ex situ collections; identify genetic lineages, endangered populations, and untapped genetic resources; and study the genetics/genomics of adaptation to changing environments to mitigate the climate change effects. Cutting-edge results on the above topics are urgently needed given the overarching threat of climate change and the need to better understand the extent of genetic variation and the spatial distribution of unique genes or gene families for specific adaptations that could guide us toward better characterization, conservation, and management of forest genetic resources, while results on the genomic prediction of breeding values, and the extension at the genome-wide scale, may contribute to high accuracy in genetic prediction and reduction in breeding cycle duration in breeding programs.

This Special Issue aims to publish cutting-edge results from across the globe on the above topics and synthesize the recent knowledge obtained from applying molecular genetics on tree breeding, conservation, and management of forest genetic resources in the face of climate change.

Prof. Dr. Evi Alizoti
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 submissions that pass pre-check are 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 2600 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

  • molecular characterization of forest genetic resources
  • molecular signatures of adaptation
  • marker-based breeding strategies
  • molecular dissection of complex traits
  • life histories of forest trees and genetic lineages
  • unique or specific genes/alleles for better adaptation to climate change

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Related Special Issue

Published Papers (6 papers)

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Research

16 pages, 2704 KiB  
Article
Transcriptome Analysis Reveals Putative Genes Involved in the Lipid Metabolism of Chaulmoogra Oil Biosynthesis in Carpotroche brasiliensis (Raddi) A.Gray, a Tropical Tree Species
by Letícia Maróstica de Vasconcelos, Flora Bittencourt, Ramon Oliveira Vidal, Edson Mario de Andrade Silva, Eduardo Almeida Costa, Fabienne Micheli, Matias Kirst, Carlos Priminho Pirovani and Fernanda Amato Gaiotto
Forests 2022, 13(11), 1806; https://doi.org/10.3390/f13111806 - 29 Oct 2022
Viewed by 1966
Abstract
Chaulmoogra oil is found in the seeds of Carpotroche brasiliensis (Raddi) Endl. (syn. Mayna brasiliensis Raddi), an oil tree of the Achariaceae family and native to Brazil’s Atlantic Forest biome, which is considered the fifth most important biodiversity hotspot in the world. Its [...] Read more.
Chaulmoogra oil is found in the seeds of Carpotroche brasiliensis (Raddi) Endl. (syn. Mayna brasiliensis Raddi), an oil tree of the Achariaceae family and native to Brazil’s Atlantic Forest biome, which is considered the fifth most important biodiversity hotspot in the world. Its main constituents are cyclopentenic fatty acids. Chaulmoogra oil has economic potential because of its use in the cosmetics industry and as a drug with anti-tumor activity. The mechanisms related to the regulation of oil biosynthesis in C. brasiliensis seeds are not fully understood, especially from a tissue-specific perspective. In this study, we applied a de novo transcriptomic approach to investigate the transcripts involved in the lipid pathways of C. brasiliensis and to identify genes involved in lipid biosynthesis. Comparative analysis of gene orthology, expression analysis and visualization of metabolic lipid networks were performed, using data obtained from high-throughput sequencing (RNAseq) of 24 libraries of vegetative and reproductive tissues of C. brasiliensis. Approximately 10.4 million paired-end reads (Phred (Q) > 20) were generated and re-assembled into 107,744 unigenes, with an average length of 340 base pairs (bp). The analysis of transcripts from different tissues identified 1131 proteins involved in lipid metabolism and transport and 13 pathways involved in lipid biosynthesis, degradation, transport, lipid bodies, and lipid constituents of membranes. This is the first transcriptome study of C. brasiliensis, providing basic information for biotechnological applications of great use for the species, which will help understand chaulmoogra oil biosynthesis. Full article
(This article belongs to the Special Issue Molecular Genetics of Forest Trees and Applications in Breeding, Conservation and Management of Genetic Resources)
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16 pages, 2415 KiB  
Article
Genetic Diversity and Structure of a Diverse Population of Picea sitchensis Using Genotyping-by-Sequencing
by Tomás Byrne, Niall Farrelly, Colin Kelleher, Trevor R. Hodkinson, Stephen L. Byrne and Susanne Barth
Forests 2022, 13(9), 1511; https://doi.org/10.3390/f13091511 - 17 Sep 2022
Cited by 1 | Viewed by 3860
Abstract
Picea sitchensis, Sitka spruce, is of interest to forestry as both a conservation species and a highly productive crop. Its native range stretches from Alaska to California, and it is hence distributed across a large environmental cline with areas of local adaptation. [...] Read more.
Picea sitchensis, Sitka spruce, is of interest to forestry as both a conservation species and a highly productive crop. Its native range stretches from Alaska to California, and it is hence distributed across a large environmental cline with areas of local adaptation. The IUFRO collection, established in 1968–1970, consists of 81 provenances of commercial and scientific interest spanning this native range. We used genotyping-by-sequencing on 1177 genotypes, originating from 80 of the IUFRO provenances which occupy 19 geographic regions of the Pacific Northwest, resulting in an SNP database of 36,567 markers. We detected low levels of genetic differentiation across this broad environmental cline, in agreement with other studies. However, we discovered island effects on geographically distant populations, such as those on Haida Gwaii and Kodiak Island. Using glaciation data, alongside this database, we see apparent post-glacial recolonization of the mainland from islands and the south of the range. Genotyping the IUFRO population expands upon the use of the collection in three ways: (i) providing information to breeders on genetic diversity which can be implemented into breeding programs, optimizing genetic gain for important traits; (ii) serving a scientific resource for studying spruce species; and (iii) utilizing provenances in breeding programs which are more tolerant to climate change. Full article
(This article belongs to the Special Issue Molecular Genetics of Forest Trees and Applications in Breeding, Conservation and Management of Genetic Resources)
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21 pages, 2976 KiB  
Article
New Insight into Genetic Structure and Diversity of Scots Pine (Pinus sylvestris L.) Populations in Lithuania Based on Nuclear, Chloroplast and Mitochondrial DNA Markers
by Darius Kavaliauskas, Darius Danusevičius and Virgilijus Baliuckas
Forests 2022, 13(8), 1179; https://doi.org/10.3390/f13081179 - 25 Jul 2022
Cited by 12 | Viewed by 2958
Abstract
We studied the genetic differentiation, structure, and diversity of Scots pine populations in Lithuania based on nuclear, chloroplast microsatellite, and mitochondrial DNA markers. We focused on revealing evolutionary history, country-wide geneflow patterns, and structuring among the Scots pine populations. We genotyped 439 Scots [...] Read more.
We studied the genetic differentiation, structure, and diversity of Scots pine populations in Lithuania based on nuclear, chloroplast microsatellite, and mitochondrial DNA markers. We focused on revealing evolutionary history, country-wide geneflow patterns, and structuring among the Scots pine populations. We genotyped 439 Scots pine individuals of mature age from 23 natural Scots pine stands in Lithuania and used the AMOVA and a set of genetic-clustering methods. The among-population differentiation was weak for nuclear microsatellite loci (nSSRs) (FST = 0.005) but much stronger for cpSSRs (PhiST = 0.240). The populations were structured into highland and lowland populations based on cpSSRs and eastern highland versus the rest for nSSRs. We detected two mtDNA mitotypes—the universal type A and northeastern type B, and the latter occurred at a markedly higher frequency in eastern Lithuania. Within-population genetic diversity was higher in large pine-dominated forest tracts in the eastern highlands than in fragmented forests in the western highlands. We concluded that phenology-based genetic networks following the temperature climate gradients have a strong effect on shaping the genetic structure of otherwise rather homogeneous gene pools of Scots pine populations in Lithuania. The possible effects of human interference with forests on genetic diversity of Scots pine populations in Lithuania are discussed. Full article
(This article belongs to the Special Issue Molecular Genetics of Forest Trees and Applications in Breeding, Conservation and Management of Genetic Resources)
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13 pages, 2200 KiB  
Article
Xylem Transcriptome Analysis in Contrasting Wood Phenotypes of Eucalyptus urophylla × tereticornis Hybrids
by Xianliang Zhu, Jiayue He, Changpin Zhou, Qijie Weng, Shengkan Chen, David Bush and Fagen Li
Forests 2022, 13(7), 1102; https://doi.org/10.3390/f13071102 - 13 Jul 2022
Cited by 2 | Viewed by 1941
Abstract
An investigation of the effects of two important post-transcriptional regulatory mechanisms, gene transcription and alternative splicing (AS), on the wood formation of Eucalyptusurophylla × tereticornis, an economic tree species widely planted in southern China, was carried out. We performed RNA-seq on [...] Read more.
An investigation of the effects of two important post-transcriptional regulatory mechanisms, gene transcription and alternative splicing (AS), on the wood formation of Eucalyptusurophylla × tereticornis, an economic tree species widely planted in southern China, was carried out. We performed RNA-seq on E. urophylla × tereticornis hybrids with highly contrasting wood basic density (BD), cellulose content (CC), hemicellulose content (HC), and lignin content (LC). Signals of strong differentially expressed genes (DEGs) and differentially spliced genes (DSGs) were detected in all four groups of wood properties, suggesting that gene transcription and selective splicing may have important regulatory roles in wood properties. We found that there was little overlap between DEGs and DSGs in groups of the same trait. Furthermore, the key DEGs and DSGs that were detected simultaneously in the four groups tended to be enriched in different Gene Ontology terms, Kyoto Encyclopedia of Genes and Genomes pathways, and transcription factors. These results implied that regulation of gene transcription and AS is controlled by independent regulatory systems in wood formation. Lastly, we detected transcript levels of known wood biosynthetic genes and found that 79 genes encoding mainly enzymes or proteins such as UGT, LAC, CAD, and CESA may be involved in the positive or negative regulation of wood properties. This study reveals potential molecular mechanisms that may regulate wood formation and will contribute to the genetic improvement of Eucalyptus. Full article
(This article belongs to the Special Issue Molecular Genetics of Forest Trees and Applications in Breeding, Conservation and Management of Genetic Resources)
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16 pages, 1959 KiB  
Article
SNP Detection in Pinus pinaster Transcriptome and Association with Resistance to Pinewood Nematode
by Inês Modesto, Vera Inácio, Polina Novikova, Isabel Carrasquinho, Yves Van de Peer and Célia M. Miguel
Forests 2022, 13(6), 946; https://doi.org/10.3390/f13060946 - 17 Jun 2022
Cited by 2 | Viewed by 2665
Abstract
Pinewood nematode (PWN, Bursaphelenchus xylophilus) is the causal agent of pine wilt disease (PWD), which severely affects Pinus pinaster stands in southwestern Europe. Despite the high susceptibility of P. pinaster, individuals of selected half-sib families have shown genetic variability in survival [...] Read more.
Pinewood nematode (PWN, Bursaphelenchus xylophilus) is the causal agent of pine wilt disease (PWD), which severely affects Pinus pinaster stands in southwestern Europe. Despite the high susceptibility of P. pinaster, individuals of selected half-sib families have shown genetic variability in survival after PWN inoculation, indicating that breeding for resistance can be a valuable strategy to control PWD. In this work, RNA-seq data from susceptible and resistant plants inoculated with PWN were used for SNP discovery and analysis. A total of 186,506 SNPs were identified, of which 31 were highly differentiated between resistant and susceptible plants, including SNPs in genes involved in cell wall lignification, a process previously linked to PWN resistance. Fifteen of these SNPs were selected for validation through Sanger sequencing and 14 were validated. To evaluate SNP-phenotype associations, 40 half-sib plants were genotyped for six validated SNPs. Associations with phenotype after PWN inoculation were found for two SNPs in two different genes (MEE12 and PCMP-E91), as well as two haplotypes of HIPP41, although significance was not maintained following Bonferroni correction. SNPs here detected may be useful for the development of molecular markers for PWD resistance and should be further investigated in future association studies. Full article
(This article belongs to the Special Issue Molecular Genetics of Forest Trees and Applications in Breeding, Conservation and Management of Genetic Resources)
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11 pages, 2740 KiB  
Article
Revealing the Genetic Structure and Differentiation in Endangered Pinus bungeana by Genome-Wide SNP Markers
by Qian Tian, Yousry A. El-Kassaby and Wei Li
Forests 2022, 13(2), 326; https://doi.org/10.3390/f13020326 - 17 Feb 2022
Cited by 8 | Viewed by 2107
Abstract
Understanding the genetic variation and differentiation of natural populations is essential for their protection, specifically if the species status is endangered as with Pinus bungeana. Here, we used 346,840 high density and strong specificity SNP loci to carry out genetic analyses (i.e., [...] Read more.
Understanding the genetic variation and differentiation of natural populations is essential for their protection, specifically if the species status is endangered as with Pinus bungeana. Here, we used 346,840 high density and strong specificity SNP loci to carry out genetic analyses (i.e., genetic diversity, genetic structure, phylogeny, and geographical differentiation) on 52 P. bungeana individuals from 5 populations (4 natural and one artificial) representing the main regions of the species distribution in China. Genetic diversity assessment indicated a trend of genetic diversity gradual decrease from west to east across the species distribution areas. Population genetic structure, PCA and phylogenetic analyses consistently indicated that populations in the central and eastern regions were clustered together, while those from the western regions were separated. Mantel test values indicated the presence of geographic isolation among populations, an important factor contributing to the observed genetic differentiation. The maximum likelihood tree and potential migration events inferred from TreeMix analysis indicated the presence of historical genetic exchanges between the west of Qinling Mountains and the Lvliang Mountains populations. Based on the generated genetic information, in situ and ex situ conservation strategies for P.bungeana germplasm resources are proposed, these strategies could be valuable for the conservation, protection and genetic improvement of this endangered species. Full article
(This article belongs to the Special Issue Molecular Genetics of Forest Trees and Applications in Breeding, Conservation and Management of Genetic Resources)
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