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Genetic Diversity of Tree Species in Forest and Conservation Management

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

Deadline for manuscript submissions: closed (15 July 2019) | Viewed by 54736

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Special Issue Editors

Dr. Lars Opgenoorth

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Guest Editor

Faculty of Biology, Department of Ecology, University of Marburg, Marburg, Germany
Interests: biogeography; ecology and evolution; biodiversity research

Dr. Christopher Kettle

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Guest Editor

1. Science Domain Leader, Forest Genetic Resources and Restoration, Bioversity International, Roma, Italy
2. Department of Environmental Systems Science, ETH Zurich, Zürich, Switzerland
Interests: conservation genetics; trees; forest genetics; restoration; borneo

Special Issue Information

Dear Colleagues,

Forest genetics and genomics have seen important advances in recent years, i.e., in characterizing genomic diversity of species across their ranges, or in understanding adaptive processes. As the forefront of this research field has always been tightly linked to technological and analytical advances, it often remains elusive for practitioners in forest and conservation management. Thus, while almost any forest genetic study somehow argues to be relevant in relation to climate or global change, specific guidelines for management and conservation are rarely presented, remain general, or are based on data that far precede current technological standards. Important information that are missing are, e.g., updated maps of genetic conservation units and of seed zonation. Likewise, information on the scale of gene flow and the scale of local adaptation are limited, as are information on the dimension of introgression in protected focal species, for example, from mass planted hybrids. Starting from these few examples, we here encourage manuscript submission to this Special Issue from all relevant fields. This includes classical forest genetic, and advanced forest genomic studies, as well as modelling studies, and meta-analyses if they make use of genetic or genomic data. Studies should however specifically target management and conservation of forests or forest genetic resources.

Dr. Lars Opgenoorth
Dr. Christopher Kettle
Guest Editors

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

Genetic diversity
Forest tree
Conservation management
Genetic resources
Climate change
Gene flow
Modelling

Published Papers (10 papers)

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Research

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16 pages, 4903 KiB

Open AccessArticle

Cloning, Characterization and Expression of the Phenylalanine Ammonia-Lyase Gene (PaPAL) from Spruce Picea asperata

by Yufeng Liu, Lijuan Liu, Shuai Yang, Qian Zeng, Zhiran He and Yinggao Liu

Forests 2019, 10(8), 613; https://doi.org/10.3390/f10080613 - 24 Jul 2019

Cited by 9 | Viewed by 3231

Abstract

Phenylalanine ammonia-lyase (PAL) is the crucial enzyme of the phenylpropanoid pathway, which plays an important role in plant disease resistance. To understand the function of PAL in Picea asperata, in this study, the full-length cDNA sequence of the PAL gene from this species was isolated and named PaPAL. The gene contains a 2160-bp open reading frame (ORF) encoding 720 amino acids with a calculated molecular weight of 78.7 kDa and a theoretical isoelectric point of 5.88. The deduced PaPAL protein possesses the specific signature motif (GTITASGDLVPLSYIA) of phenylalanine ammonia-lyases. Multiple alignment analysis revealed that PaPAL has high identity with other plant PALs. The tertiary structure of PaPAL was predicted using PcPAL from Petroselinum crispum as a template, and the results suggested that PaPAL may have a similar function to that of PcPAL. Furthermore, phylogenetic analysis indicated that PaPAL has a close relationship with other PALs from the Pinaceae species. The optimal expression condition of recombinant PaPAL in Escherichia coli BL21 (DE3) was 0.2 mM IPTG (isopropyl β-D-thiogalactoside) at 16 °C for 4 h, and the molecular weight of recombinant PaPAL was found to be approximately 82 kDa. Recombinant PaPAL was purified and exhibited high PAL activity at optimal conditions of pH 8.6 and 60 °C. Quantitative real-time PCR (qRT-PCR) showed the PaPAL gene to be expressed in all tissues of P. asperata tested, with the highest expression level in the needles. The PaPAL gene was induced by the pathogen (Lophodermium piceae), which caused needle cast disease, indicating that it might be involved in defense against needle cast disease. These results provide a basis for understanding the molecular mechanisms of the PAL gene in the process of P. asperata disease resistance. Full article

(This article belongs to the Special Issue Genetic Diversity of Tree Species in Forest and Conservation Management)

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11 pages, 2965 KiB

Open AccessArticle

Complete Chloroplast Genome of Pinus densiflora Siebold & Zucc. and Comparative Analysis with Five Pine Trees

by Hye-In Kang, Hyun Oh Lee, Il Hwan Lee, In Sik Kim, Seok-Woo Lee, Tae Jin Yang and Donghwan Shim

Forests 2019, 10(7), 600; https://doi.org/10.3390/f10070600 - 19 Jul 2019

Cited by 16 | Viewed by 4740

Abstract

Pinus densiflora (Korean red pine) is widely distributed in East Asia and considered one of the most important species in Korea. In this study, the complete chloroplast genome of P. densiflora was sequenced by combining the advantages of Oxford Nanopore MinION and Illumina MiSeq. The sequenced genome was then compared with that of a previously published conifer plastome. The chloroplast genome was found to be circular and comprised of a quadripartite structure, including 113 genes encoding 73 proteins, 36 tRNAs and 4 rRNAs. It had short inverted repeat regions and lacked ndh gene family genes, which is consistent with other Pinaceae species. The gene content of P. densiflora was found to be most similar to that of P. sylvestris. The newly attempted sequencing method could be considered an alternative method for obtaining accurate genetic information, and the chloroplast genome sequence of P. densiflora revealed in this study can be used in the phylogenetic analysis of Pinus species. Full article

(This article belongs to the Special Issue Genetic Diversity of Tree Species in Forest and Conservation Management)

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20 pages, 4032 KiB

Open AccessArticle

Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Quercus bawanglingensis Huang, Li et Xing, a Vulnerable Oak Tree in China

by Xue Liu, Er-Mei Chang, Jian-Feng Liu, Yue-Ning Huang, Ya Wang, Ning Yao and Ze-Ping Jiang

Forests 2019, 10(7), 587; https://doi.org/10.3390/f10070587 - 15 Jul 2019

Cited by 34 | Viewed by 4891

Abstract

Quercus bawanglingensis Huang, Li et Xing, an endemic evergreen oak of the genus Quercus (Fagaceae) in China, is currently listed in the Red List of Chinese Plants as a vulnerable (VU) plant. No chloroplast (cp) genome information is currently available for Q. bawanglingensis, which would be essential for the establishment of guidelines for its conservation and breeding. In the present study, the cp genome of Q. bawanglingensis was sequenced and assembled into double-stranded circular DNA with a length of 161,394 bp. Two inverted repeats (IRs) with a total of 51,730 bp were identified, and the rest of the sequence was separated into two single-copy regions, namely, a large single-copy (LSC) region (90,628 bp) and a small single-copy (SSC) region (19,036 bp). The genome of Q. bawanglingensis contains 134 genes (86 protein-coding genes, 40 tRNAs and eight rRNAs). More forward (29) than inverted long repeats (21) are distributed in the cp genome. A simple sequence repeat (SSR) analysis showed that the genome contains 82 SSR loci, involving 84.15% A/T mononucleotides. Sequence comparisons among the nine complete cp genomes, including the genomes of Q. bawanglingensis, Q. tarokoensis Hayata (NC036370), Q. aliena var. acutiserrata Maxim. ex Wenz. (KU240009), Q. baronii Skan (KT963087), Q. aquifolioides Rehd. et Wils. (KX911971), Q. variabilis Bl. (KU240009), Fagus engleriana Seem. (KX852398), Lithocarpus balansae (Drake) A. Camus (KP299291) and Castanea mollissima Bl. (HQ336406), demonstrated that the diversity of SC regions was higher than that of IR regions, which might facilitate identification of the relationships within this extremely complex family. A phylogenetic analysis showed that Fagus engleriana and Trigonobalanus doichangensis form the basis of the produced evolutionary tree. Q. bawanglingensis and Q. tarokoensis, which belong to the group Ilex, share the closest relationship. The analysis of the cp genome of Q. bawanglingensis provides crucial genetic information for further studies of this vulnerable species and the taxonomy, phylogenetics and evolution of Quercus. Full article

(This article belongs to the Special Issue Genetic Diversity of Tree Species in Forest and Conservation Management)

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9 pages, 2913 KiB

Open AccessArticle

Genome Survey Sequencing of Acer truncatum Bunge to Identify Genomic Information, Simple Sequence Repeat (SSR) Markers and Complete Chloroplast Genome

by Rongkai Wang, Jinshuan Fan, Pan Chang, Ling Zhu, Mengran Zhao and Lingli Li

Forests 2019, 10(2), 87; https://doi.org/10.3390/f10020087 - 23 Jan 2019

Cited by 22 | Viewed by 3784

Abstract

The Acer truncatum Bunge is a particular forest tree species found in the north of China. Due to the recent discovery that its seeds contain a considerable amount of nervonic acid, this species has received more and more attention. However, there have been no reports of the genome in this species. In this study, we report on the Acer truncatum genome sequence produced by genome survey sequencing. In total, we obtained 61.90 Gbp of high-quality data, representing approximately 116x coverage of the Acer truncatum genome. The genomic characteristics of Acer truncatum include a genome size of 529.88 Mbp, a heterozygosis rate of 1.06% and a repeat rate of 48.8%. A total of 392,961 high-quality genomic SSR markers were developed and a graphical map of the annotated circular chloroplast genome was generated. Thus far, this is the first report of de novo whole genome sequencing and assembly of Acer truncatum. We believe that this genome sequence dataset may provide a new resource for future genomic analysis and molecular breeding studies of Acer truncatum. Full article

(This article belongs to the Special Issue Genetic Diversity of Tree Species in Forest and Conservation Management)

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15 pages, 2020 KiB

Open AccessArticle

An RNA Sequencing Transcriptome Analysis and Development of EST-SSR Markers in Chinese Hawthorn through Illumina Sequencing

by Suliya Ma, Wenxuan Dong, Tong Lyu and Yingmin Lyu

Forests 2019, 10(2), 82; https://doi.org/10.3390/f10020082 - 22 Jan 2019

Cited by 19 | Viewed by 3423

Abstract

Chinese hawthorn (Crataegus pinnatifida) is an important ornamental and economic horticultural plant. However, the lack of molecular markers has limited the development and utilization of hawthorn germplasm resources. Simple sequence repeats (SSRs) derived from expressed sequence tags (ESTs) allow precise and effective cultivar characterization and are routinely used for genetic diversity analysis. Thus, we first reported the development of polymorphic EST-SSR markers in C. pinnatifida with perfect repeats using Illumina RNA-Seq technique. In total, we investigated 14,364 unigenes, from which 5091 EST-SSR loci were mined. Di-nucleotides (2012, 39.52%) were the most abundant SSRs, followed by mono- (1989, 39.07%), and tri-nucleotides (1024, 20.11%). On the basis of these EST-SSRs, a total of 300 primer pairs were designed and used for polymorphism analysis in 70 accessions collected from different geographical regions of China. Of 239 (79.67%) pairs of primer-generated amplification products, 163 (54.33%) pairs of primers showed polymorphism. Finally, 33 primers with high polymorphism were selected for genetic diversity analysis and tested on 70 individuals with low-cost fluorescence-labeled M13 primers using capillary electrophoresis genotyping platform. A total of 108 alleles were amplified by 33 SSR markers, with the number of alleles (Na) ranging from 2 to 14 per locus (mean: 4.939), and the effective number of alleles (Ne) ranging from 1.258 to 3.214 (mean: 2.221). The mean values of gene diversity (He), observed heterozygosity (Ho), and polymorphism information content (PIC) were 0.524 (range 0.205–0.689), 0.709 (range 0.132–1.000), and 0.450 (range 0.184–0.642), respectively. Furthermore, the dendrogram constructed based on the EST-SSR separated the cultivars into two main clusters. In sum, our study was the first comprehensive study on the development and analysis of a large set of SSR markers in hawthorn. The results suggested that the use of NGS techniques for SSR development represented a powerful tool for genetic studies. Additionally, fluorescence-labeled M13 markers proved to be a valuable method for genotyping. All of these EST-SSR markers have agronomic potential and constitute a scientific basis for future studies on the identification, classification, and innovation of hawthorn germplasms. Full article

(This article belongs to the Special Issue Genetic Diversity of Tree Species in Forest and Conservation Management)

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13 pages, 2637 KiB

Open AccessArticle

RAD-Seq Data Point to a Distinct Split in Liriodendron (Magnoliaceae) and Obvious East–West Genetic Divergence in L. chinense

by Yongda Zhong, Aihong Yang, Shujuan Liu, Lipan Liu, Yanqiang Li, Zhaoxiang Wu and Faxin Yu

Forests 2019, 10(1), 13; https://doi.org/10.3390/f10010013 - 26 Dec 2018

Cited by 11 | Viewed by 4465

Abstract

Liriodendron is a Tertiary period relic tree genus with a typical East Asian and North American disjunction distribution pattern. As an angiosperm base group of trees, Liriodendron provides a valuable resource for the study of evolution processes. Here, we reconstruct the phylogeny and population genetic structure of Liriodendron based on the restriction site-associated DNA sequencing (RAD-Seq) of a wide collection of individuals from 16 populations. Our results reveal a clear phylogenetic break between L. chinense and L. tulipifera and obvious genetic divergence between the eastern and western populations of L. chinense, which are consistent with the patterns of geographical distributions. The phylogeographic history and long-term geographical isolation of the genus may be responsible for this pattern. Furthermore, a closer relationship was found between L. tulipifera and the eastern populations of L. chinense, indicating the ancient phylogeny of L. chinense in this area. The results of this study will aid in the development of scientific strategies for the conservation and utilization of the Liriodendron germplasm. Full article

(This article belongs to the Special Issue Genetic Diversity of Tree Species in Forest and Conservation Management)

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22 pages, 3072 KiB

Open AccessArticle

Population Structure, Genetic Diversity, and Gene Introgression of Two Closely Related Walnuts (Juglans regia and J. sigillata) in Southwestern China Revealed by EST-SSR Markers

by Xiao-Ying Yuan, Yi-Wei Sun, Xu-Rong Bai, Meng Dang, Xiao-Jia Feng, Saman Zulfiqar and Peng Zhao

Forests 2018, 9(10), 646; https://doi.org/10.3390/f9100646 - 16 Oct 2018

Cited by 27 | Viewed by 5053

Abstract

The common walnut (Juglans regia L.) and iron walnut (J. sigillata Dode) are well-known economically important species cultivated for their edible nuts, high-quality wood, and medicinal properties and display a sympatric distribution in southwestern China. However, detailed research on the genetic diversity and introgression of these two closely related walnut species, especially in southwestern China, are lacking. In this study, we analyzed a total of 506 individuals from 28 populations of J. regia and J. sigillata using 25 EST-SSR markers to determine if their gene introgression was related to sympatric distribution. In addition, we compared the genetic diversity estimates between them. Our results indicated that all J. regia populations possess slightly higher genetic diversity than J. sigillata populations. The Geostatistical IDW technique (H_O, PPL, N_A and PrA) revealed that northern Yunnan and Guizhou provinces had high genetic diversity for J. regia while the northwestern Yunnan province had high genetic diversity for J. sigillata. AMOVA analysis revealed that significant genetic variation was mainly distributed within population as 73% in J. regia and 76% in J. sigillata. The genetic differentiation (F_ST) was 0.307 between the two walnut species (p < 0.0001), which was higher than F_ST values within populations (J. regia F_ST = 0.265 and J. sigillata F_ST = 0.236). However, the STRUCTURE analysis of the J. regia and J. sigillata populations revealed two genetic clusters in which gene introgression exists, therefore, the boundary of separation between these two walnut species is not clear. Moreover, these results were validated by NJ and UPGMA analysis with additional conformation from the PCoA. Based on the SSR data, our results indicate that J. sigillata is an ecotype of J. regia. Taken together, these results reveal novel information on population genetics and provide specific geographical regions containing high genetic diversity of the Juglans species sampled, which will assist in future conservation management. Full article

(This article belongs to the Special Issue Genetic Diversity of Tree Species in Forest and Conservation Management)

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9 pages, 1161 KiB

Open AccessArticle

Fatty Acids Variation in Seed of Eucommia ulmoides Populations Collected from Different Regions in China

by Qingxin Du, Lu Wang, Panfeng Liu, Jun Qing, Caowen Sun, Zhiqiang Sun and Hongyan Du

Forests 2018, 9(9), 505; https://doi.org/10.3390/f9090505 - 21 Aug 2018

Cited by 13 | Viewed by 2903

Abstract

Fruits of 240 Eucommia ulmoides Oliver individuals were collected from 12 different geographical regions across a wide area of China. The seed oil content ranged from 28.54% in Guilin and Lueyang to 31.35% in Chaoyang. Gas chromatography–mass spectrometry analysis of the seed oil revealed that linolenic acid (56.68–60.70%), oleic acid (16.31–17.80%), and linoleic acid (11.02–13.32%) were the major components, and the oil showed good potential for the food and health care industries. Three levels (high, medium, and low) of linolenic acid and oil content were observed among the 12 populations according to principal component analysis. Canonical correspondence analysis showed that environmental factors had a large influence on oil content and fatty acids composition and explained 89.33% of the total variance. Latitude and precipitation were key environmental factors and were significantly correlated with the fatty acid composition of E. ulmoides seeds. Full article

(This article belongs to the Special Issue Genetic Diversity of Tree Species in Forest and Conservation Management)

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13 pages, 1660 KiB

Open AccessArticle

An Assessment of the Environmental Impacts of Transgenic Triploid Populus tomentosa in Field Condition

by Qi Guo, Nan Lu, Zijing Luo, Yuhan Sun, Shaowu Jin, Shaoming Wang, Zhimin Guo, Feifei Li, Shouyi Chen, Wanke Zhang, Qingju Ji and Yun Li

Forests 2018, 9(8), 482; https://doi.org/10.3390/f9080482 - 08 Aug 2018

Cited by 3 | Viewed by 3455

Abstract

Populus tomentosa grow rapidly, but are salt susceptible. To quickly and efficiently gain new poplar breeds with better salt resistance, a DREB transcription factor derived from Atriplex hortensis was transformed into triploid Populus tomentosa by our lab, which significantly improved the salt tolerance of host plants. However, environmental impacts of transgenic plants must be assessed before large-scale cultivation in China. Here, we conducted a field trial of AhDREB1 transgenic and non-transgenic triploid Populus tomentosa to assess the impact of transgenic trees on rhizospheric soil microbial communities and allelopathic activity of leaves. No significant differences in the number of soil microbes present were detected between the transgenic lines and the non-transgenic controls. The allelopathic activity of leaves from both the transgenic and non-transgenic lines varied with sampling time, but did not differ significantly between the transgenic and non-transgenic lines. These results indicate that the impact on the environment of AhDREB1 transgenic P. tomentosa did not differ significantly from that of the non-transformed controls for the variables observed in this field trial. We also investigated the persistence of AhDREB1 genes in decomposing transgenic poplar leaf on the soil under natural conditions for five months, and our data indicated that fragments of the genetically modified DNA were not detectable in the field after more than two months. We used a triphenyl tetrazolium chloride test (TTC) (or pollen germination method) and hybridization to test the pollen viability and fertility, respectively, of the transgenic and non-transgenic trees and the results showed that the pollen viability of both the transgenic and non-transgenic trees was extremely low in 2016; the receptor plant may have been sterile. Full article

(This article belongs to the Special Issue Genetic Diversity of Tree Species in Forest and Conservation Management)

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Review

Jump to: Research

18 pages, 3580 KiB

Open AccessReview

Medicinal Potential, Utilization and Domestication Status of Bitter Kola (Garcinia kola Heckel) in West and Central Africa

by Anna Maňourová, Olga Leuner, Zacharie Tchoundjeu, Patrick Van Damme, Vladimír Verner, Ondřej Přibyl and Bohdan Lojka

Forests 2019, 10(2), 124; https://doi.org/10.3390/f10020124 - 04 Feb 2019

Cited by 30 | Viewed by 17960

Abstract

Garcinia kola Heckel (Clusiaceae), known as bitter kola, is a multipurpose tree indigenous to West and Central Africa. This highly preferred species is called “wonder plant” because all of its parts can be used as medicine. Its seeds, the most valued product of the tree, are commonly eaten to prevent/cure gastric disorders and for their typical astringent taste. There is a vast evidence that bioactive components of the seeds can serve as alternative medicine to treat/prevent severe illnesses such as malaria, hepatitis and immune-destructive diseases. Despite the species’ pharmaceutical potential and its high preference by West and Central African communities, G. kola is still at the beginning of its domestication process. Even though, there are numerous scientific articles published on species‘ biological activities, it is a difficult task to find basic information on its diversity, distribution, genetics, silvicultural management or botany. Therefore, in this very first review published on G. kola, we summarize all relevant information known about the species, target some of the challenges connected with its cultivation and propose a leading direction for future research and domestication process. Full article

(This article belongs to the Special Issue Genetic Diversity of Tree Species in Forest and Conservation Management)

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