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Forests
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Application of Biotechnology Techniques on Tree Species—Series II
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Application of Biotechnology Techniques on Tree Species—Series II

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

Deadline for manuscript submissions: closed (29 March 2024) | Viewed by 19210

Special Issue Editors

Dr. Jorge Canhoto

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Guest Editor
Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
Interests: plant breeding; plant biotechnology; in vitro culture; genomics; plant anatomy; somatic embryogenesisinterests; plant development; forestry
Special Issues, Collections and Topics in MDPI journals
Dr. Paloma Moncaleán

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Guest Editor
Department of Forestry Science, NEIKER-BRTA, 01080 Arkaute, Spain
Interests: bioeconomy; in vitro culture; physiology; forestry
Special Issues, Collections and Topics in MDPI journals
Dr. Sandra Correia

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Guest Editor
Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
Interests: plant biotechnology; plant molecular biology; plant stress biology; proteomics; transcriptomics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Trees are dominant species in many land ecosystems, and their economic relevance is well known, not only for the production of wood and other products, but also because they deliver a variety of ecosystem services, including temperature regulation, mitigation of soil erosion, and the management and filtering of rainwater, and because they are habitats for other organisms. Due to their long reproductive and life cycles, trees require specific strategies for breeding and large-scale propagation. In recent years, biotechnology has assumed an increasingly important role in tree breeding and cloning through the application of techniques such as somatic embryogenesis, propagation in bioreactors, genetic transformation, proteomics, genomics, and production of synthetic seeds, among many others. Based on these tools, improved trees displaying new features are now in the field ensuring higher productivities and helping to preserve natural forests while contributing to fixing CO2 and to avoiding desertification, both from an ecological and human perspective. This Special Issue invites works from researchers and other stakeholders on the latest developments in the field of tree biotechnology. Those interested in tree biotechnology are welcome to collaborate and share their more recent results in this field.

Dr. Jorge Canhoto
Dr. Paloma Moncaleán
Dr. Sandra Correia
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

  • acclimatization
  • bioreactors
  • breeding
  • cloning
  • genetic transformation
  • in vitro
  • molecular biology
  • omics
  • rooting

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Published Papers (8 papers)

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Research

19 pages, 10599 KiB  
Article
Growth, Physiological, and Transcriptome Analyses Reveal Mongolian Oak Seedling Responses to Shading
by Xinman Li, Min Jiang, Yachao Ren, Jiushuai Pang, Junjie Ren, Guifen Li, Yangchen Yuan, Xueding Xing, Miaomiao Zhou, Jinmao Wang and Minsheng Yang
Forests 2024, 15(3), 538; https://doi.org/10.3390/f15030538 - 14 Mar 2024
Viewed by 1046
Abstract
Mongolian oak (Quercus mongolica) is a common building material and landscaping tree species in northern China, with significant economic and ecological value. Its seedling growth is inhibited by high light intensity, but the mechanism by which light stress affects the growth [...] Read more.
Mongolian oak (Quercus mongolica) is a common building material and landscaping tree species in northern China, with significant economic and ecological value. Its seedling growth is inhibited by high light intensity, but the mechanism by which light stress affects the growth and development of its seedlings remains unclear. In this study, we investigated the phenotypes, physiological processes, and molecular responses of 3-year-old Mongolian oak seedlings under different light treatments: full light (Sck), light shading (S1; 40% light), moderate shading (S2; 20% light), and severe shading (S3; 3% light). Compared to Sck, the S1 and S2 treatments resulted in higher leaf area, photosynthetic pigment content, photosynthesis rates, soluble sugar contents, and soluble protein contents in Mongolian oak seedlings. The S1 and S2 treatments also promoted seedling height and diameter growth and resulted in lower degrees of membrane lipid peroxidation, cell membrane permeability, and antioxidant enzyme activity. In contrast, severe shading (S3) significantly inhibited seedling height and diameter growth due to the lower net photosynthetic rate, and exhibiting higher degrees of membrane lipid peroxidation and cell membrane permeability. Shading treatments (S1 and S2) alleviated the negative effects of strong light on the growth and development of Mongolian oak seedlings, with the S2 treatment having the greatest effect. However, severe shading (S3) inhibited growth and development. A total of 3726 differentially expressed genes (DEGs) were detected in leaves under different shading treatments in RNA sequencing analysis. Among these, 1691, 3150, and 824 DEGs were detected in the Sck-S1, Sck-S2, and S1-S2 comparison groups, respectively. The different shading treatments determined common expression regulation pathways, including carotenoid biosynthesis, photosynthetic antenna proteins, and mitogen activated protein kinase (MAPK) signal transduction. Shading induced increases in gene expression levels in light harvesting complexes, which are related to changes in gene expression in the photosynthetic system, leading to changes in photosynthetic physiology. The expression levels of genes related to reactive oxygen species signal perception and activation enzymes were upregulated in Sck. Together, these findings revealed the response mechanisms of Mongolian oak seedlings to different shading levels at the physiological and molecular levels, providing a scientific basis and technical support for the cultivation and large-scale production of Mongolian oak seedlings. Full article
(This article belongs to the Special Issue Application of Biotechnology Techniques on Tree Species—Series II)
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13 pages, 2388 KiB  
Article
Multi-Omics Analyses Unravel Genetic Relationship of Chinese Coffee Germplasm Resources
by Yu Ge, Butian Wang, Xuedong Shi, Zhenwei Zhang, Meijun Qi, Huabo Du, Peng Qu, Kuaile Jiang, Zhihua Chen and Xuejun Li
Forests 2024, 15(1), 163; https://doi.org/10.3390/f15010163 - 12 Jan 2024
Cited by 1 | Viewed by 1034
Abstract
The genetic relationships between Coffea arabica resources were analyzed via specific length amplified fragment sequencing (SLAF-seq) and transcriptome sequencing to provide the theoretical basis for breeding new varieties. Twenty C. arabica accessions were used to analyze genetic diversity on the basis of SNPs [...] Read more.
The genetic relationships between Coffea arabica resources were analyzed via specific length amplified fragment sequencing (SLAF-seq) and transcriptome sequencing to provide the theoretical basis for breeding new varieties. Twenty C. arabica accessions were used to analyze genetic diversity on the basis of SNPs identified in SLAFs and the transcriptome data. For the SLAF-seq analysis of 20 C. arabica accessions, two Coffea canephora accessions, one Coffea liberica accession, and one Coffea racemosa accession, the number of reads ranged from 2,665,424 to 7,210,310, with a GC content of 38.49%–40.91% and a Q30 value of 94.99%–96.36%. A total of 3,347,069 SLAF tags were obtained, with an average sequencing depth of 13.90×. Moreover, the 1,048,575 SNPs identified in the polymorphic SLAFs were filtered, then the remaining 198,955 SNPs were used to construct a phylogenetic tree, perform a principal component analysis, and characterize the population structure. For the transcriptome analysis, 128.50 Gb clean reads were generated for the 20 C. arabica accessions, with a GC content of 44.36%–51.09% and a Q30 value of 94.55%–95.40%. Furthermore, 25,872 genes’ expression levels were used for the correlation analysis. The phylogenetic relationships as well as the results of the principal component analysis, population structure analysis, and correlation analysis clearly distinguished C. arabica Typica-type accessions from the C. arabica Bourbon-type accessions. Notably, several C. arabica local selections with unknown genetic backgrounds were classified according to all four clustering results. Full article
(This article belongs to the Special Issue Application of Biotechnology Techniques on Tree Species—Series II)
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21 pages, 4545 KiB  
Article
Enhanced Photosynthetic Efficiency for Increased Carbon Assimilation and Woody Biomass Production in Engineered Hybrid Poplar
by Yumin Tao, Li-Wei Chiu, Jacob W. Hoyle, Rebecca A. Dewhirst, Christian Richey, Karli Rasmussen, Jessica Du, Patrick Mellor, Julie Kuiper, Dominick Tucker, Alex Crites, Gary A. Orr, Matthew J. Heckert, Damaris Godinez-Vidal, Martha L. Orozco-Cardenas and Madeline E. Hall
Forests 2023, 14(4), 827; https://doi.org/10.3390/f14040827 - 18 Apr 2023
Cited by 5 | Viewed by 6902
Abstract
Increasing CO2 levels in the atmosphere and the resulting negative impacts of climate change have compelled global efforts to achieve carbon neutrality or negativity. Most such efforts focus on carbon sequestration through chemical or physical approaches. Harnessing the power of synthetic biology [...] Read more.
Increasing CO2 levels in the atmosphere and the resulting negative impacts of climate change have compelled global efforts to achieve carbon neutrality or negativity. Most such efforts focus on carbon sequestration through chemical or physical approaches. Harnessing the power of synthetic biology to enhance the natural ability of carbon sequestration in plants, especially non-annuals, provides a biological approach to further reduce CO2 levels in the air. Here, we selected a photorespiration bypass pathway and tested its effectiveness on photosynthetic enhancement in a hybrid poplar, INRA717-IB4. The design includes an RNAi strategy to reduce the transportation of the photorespiration byproduct, glycolate, out of chloroplast and a shunt pathway to metabolize the retained glycolate back to CO2 for fixation through the Calvin-Benson cycle. Molecular and physiological data collected from two separate growth experiments indicate that transgenic plants expressing genes in the photorespiration bypass pathway have increased photosynthetic efficiency, leading to faster plant growth and elevated biomass production. One lead transgenic event accumulated 35%–53% more above-ground dry biomass over four months of growth in a controlled environment. Our results provide a proof of concept for engineering trees to help combat climate change. Full article
(This article belongs to the Special Issue Application of Biotechnology Techniques on Tree Species—Series II)
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10 pages, 2952 KiB  
Article
Efficient Virus-Induced Gene Silencing in Ilex dabieshanensis Using Tobacco Rattle Virus
by Xinran Chong, Yue Wang, Xiaoyang Xu, Fan Zhang, Chuanyong Wang, Yanwei Zhou, Ting Zhou, Yunlong Li, Xiaoqing Lu and Hong Chen
Forests 2023, 14(3), 488; https://doi.org/10.3390/f14030488 - 28 Feb 2023
Cited by 8 | Viewed by 1842
Abstract
Ilex dabieshanensis is not only an important ornamental plant, but can also be used to produce Kuding tea, owing to its lipid-lowering and anti-inflammatory medicinal properties. The genetic transformation of I. dabieshanensis is currently difficult, which restricts functional gene studies and molecular breeding [...] Read more.
Ilex dabieshanensis is not only an important ornamental plant, but can also be used to produce Kuding tea, owing to its lipid-lowering and anti-inflammatory medicinal properties. The genetic transformation of I. dabieshanensis is currently difficult, which restricts functional gene studies and molecular breeding research on this species. Virus-induced gene silencing (VIGS) is a powerful tool for determining gene functions in plants. The present study reports the first application of VIGS mediated by a tobacco rattle virus (TRV) vector in I. dabieshanensis. We tested the efficiency of the VIGS system to silence Mg-chelatase H subunit (ChlH) gene through agroinfiltration. The agroinfiltrated leaves of I. dabieshanensis exhibited a typical yellow-leaf phenotype of ChlH gene silencing at 21 days post infiltration. Endogenous ChlH expression levels in the leaves of yellow-leaf phenotype plants were all significantly lower than that in the leaves of mock-infected and control plants. Overall, our results indicated that the TRV-based VIGS system can efficiently silence genes in I. dabieshanensis, and this system will contribute to efficient functional genomics research in I. dabieshanensis. Full article
(This article belongs to the Special Issue Application of Biotechnology Techniques on Tree Species—Series II)
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13 pages, 2757 KiB  
Article
Effects of Polyploidy on Physiological Performance of Acclimatized Solanum betaceum Cav. Plants under Water Deficit
by Sandra Correia, Ana Braga, João Martins, Barbara Correia, Glória Pinto and Jorge Canhoto
Forests 2023, 14(2), 208; https://doi.org/10.3390/f14020208 - 21 Jan 2023
Cited by 3 | Viewed by 1796
Abstract
The urgent need to identify stress-tolerant genotypes and understand their inherent genetic plasticity is one of the major targets of research and breeding programs. Species that are cultivated in areas that are prone to drought need to be able to tolerate water stress [...] Read more.
The urgent need to identify stress-tolerant genotypes and understand their inherent genetic plasticity is one of the major targets of research and breeding programs. Species that are cultivated in areas that are prone to drought need to be able to tolerate water stress (WS) while still displaying features that are economically valuable. Tamarillo (Solanum betaceum) is a solanaceous fruit crop with increasing agronomic interest due to the nutritional properties of its edible fruits and its biotechnological potential. Several protocols have been established for the in vitro culture of this species and controlled hybridization, as well as for the induction of tetraploidy. Nevertheless, the impact of WS on S. betaceum performance has been poorly studied, and nothing is known about the role of ploidy status on this response. Since no morphological differences were noticed between diploids and tetraploids at the end of the acclimatization period, we hypothesized that ploidy level may have a role in plant drought responses. Thus, micropropagated and acclimatized tamarillo diploid (2n = 2x = 24) and tetraploid (4n = 4x = 48) plants were exposed to WS, and several physiological parameters were evaluated, such as plant growth, water potential, photosynthetic performance, sugars, proline, and MDA levels. Water stress did not affect plant growth in both diploids and tetraploids, but it induced stomatal closure and reduced the net CO2 assimilation rate. Water stress also reduced the photosynthetic efficiency of PSII, but no differences were found in the total chlorophyll content. From all the parameters analyzed, tetraploid plants showed a better response under water shortage conditions when considering water potential (WP). Metabolite analysis indicated no significant differences in the accumulation of soluble sugars and MDA in WS plants but a significant increase in proline accumulation in diploids exposed to WS. These observed differences in parameters such as WP and proline accumulation point to mechanisms of osmoregulation and stress signaling that differ between diploid and tetraploid plants, particularly in WS conditions, demonstrating that tetraploids can adapt better to water shortage conditions than their diploid counterparts. Full article
(This article belongs to the Special Issue Application of Biotechnology Techniques on Tree Species—Series II)
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12 pages, 2975 KiB  
Article
Machine Learning-Assisted In Vitro Rooting Optimization in Passiflora caerulea
by Marziyeh Jafari, Mohammad Hosein Daneshvar, Sahar Jafari and Mohsen Hesami
Forests 2022, 13(12), 2020; https://doi.org/10.3390/f13122020 - 29 Nov 2022
Cited by 17 | Viewed by 1987
Abstract
In vitro rooting as one of the most critical steps of micropropagation is affected by various extrinsic (e.g., medium composition, auxins) and intrinsic factors (e.g., species, explant). In Passiflora species, in vitro adventitious rooting is a difficult, complex, and non-linear process. Since in [...] Read more.
In vitro rooting as one of the most critical steps of micropropagation is affected by various extrinsic (e.g., medium composition, auxins) and intrinsic factors (e.g., species, explant). In Passiflora species, in vitro adventitious rooting is a difficult, complex, and non-linear process. Since in vitro rooting is a multivariable complex biological process, efficient and reliable computational approaches such as machine learning (ML) are required to model, predict, and optimize this non-linear biological process. Therefore, in the current study, a hybrid of generalized regression neural network (GRNN) and genetic algorithm (GA) was employed to predict in vitro rooting responses (rooting percentage, number of roots, and root length) of Passiflora caerulea based on the optimization of the level of auxins (indole-3-acetic acid (IAA), indolebutyric acid (IBA), and 1-naphthaleneacetic acid (NAA)) and the type of explant (microshoots derived from leaf, node, and internode). Based on the results, the GRNN model was accurate in predicting all in vitro rooting responses of P. caerulea (R2 > 0.92) in either training or testing sets. The result of the validation experiment also showed that there was a negligible difference between the predicted-optimized values and the validated results demonstrating the reliability of the developed GRNN-GA model. Generally, the results of the current study showed that GRNN-GA is a reliable and accurate model to predict and optimize in vitro rooting of P. caerulea. Full article
(This article belongs to the Special Issue Application of Biotechnology Techniques on Tree Species—Series II)
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11 pages, 1931 KiB  
Article
Localization of TWISTED NEEDLES Locus on Linkage Map of Japanese Cedar (Cryptomeria japonica D. Don)
by Yoshinari Moriguchi, Ryunosuke Saito, Saneyoshi Ueno, Yoichi Hasegawa, Hiroyuki Kakui and Asako Matsumoto
Forests 2022, 13(9), 1524; https://doi.org/10.3390/f13091524 - 19 Sep 2022
Viewed by 1961
Abstract
Sugi (Cryptomeria japonica D. Don) is an important forestry species in Japan. C. japonica ‘Spiralis’ is a mutant with twisted needles. The mutant is called Yore-sugi in Japan and is known as ‘Rasen’ in other countries. The twisted trait is regulated by [...] Read more.
Sugi (Cryptomeria japonica D. Don) is an important forestry species in Japan. C. japonica ‘Spiralis’ is a mutant with twisted needles. The mutant is called Yore-sugi in Japan and is known as ‘Rasen’ in other countries. The twisted trait is regulated by a dominant gene called TWISTED NEEDLES, and it can be identified by observing the needles within 1 to 2 months after germination. The TWISTED NEEDLES gene may be useful for improving the efficiency of genome editing technology in C. japonica. In this study, we attempted to identify the linkage group of the TWISTED NEEDLES locus and investigate markers that sandwich this locus using the mapping family. First, we identified the linkage group containing the TWISTED NEEDLES locus based on the distortion from the expected segregation ratio using 32 mutant individuals of the mapping family. The segregation distortion showed that the TWISTED NEEDLES locus was located on the 11th linkage group (LG11). Next, a linkage map of LG11 was constructed based on genotype data from the single-nucleotide polymorphism (SNP) markers and double digested restriction site-associated DNA sequencing (ddRAD-seq) using 123 individuals of the MMY-1 family. On this map, six markers were located at the same position as the TWISTED NEEDLES locus. To investigate markers sandwiching the TWISTED NEEDLES locus, a partial linkage map around the TWISTED NEEDLES locus was constructed using 643 individuals of the MMY-1 family. The TWISTED NEEDLES locus was located in the 0.6 cM region between gSNP01822 and the other five markers (Contig_4705-179, Contig_4518-93, Contig_4398-118, gSNP04056, and Contig_4970-113). Full article
(This article belongs to the Special Issue Application of Biotechnology Techniques on Tree Species—Series II)
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22 pages, 3654 KiB  
Article
Influence of Physico-Chemical Factors on the Efficiency and Metabolite Profile of Adult Pinus radiata D. Don Bud Organogenesis
by Alejandra Rojas-Vargas, Ander Castander-Olarieta, Itziar A. Montalbán and Paloma Moncaleán
Forests 2022, 13(9), 1455; https://doi.org/10.3390/f13091455 - 10 Sep 2022
Cited by 3 | Viewed by 1580
Abstract
Genetic improvement programs for conifer forest species face the challenge of propagating elite individuals with superior characteristics in the present landscape of climate change; the problem is focused on the fact that when these individuals have shown the desirable traits, they have changed [...] Read more.
Genetic improvement programs for conifer forest species face the challenge of propagating elite individuals with superior characteristics in the present landscape of climate change; the problem is focused on the fact that when these individuals have shown the desirable traits, they have changed phase and therefore have lost the ability to be propagated by traditional methods. Based on our previous works on Pinus spp. regeneration of adult trees through organogenesis and trying to improve the protocol in Pinus radiata, our objective was to analyze the influence of collection dates and different 6-benzyladenine (BA) concentrations in the first phase of shoot induction, as well as the effect of different light types on the success of root induction. Moreover, we were interested in studying the effect of the abovementioned physico-chemical factors on the amino acid and carbohydrate content in the shoots developed in vitro. Reinvigorated shoots were obtained in both BA concentrations (22 or 44 μM), although the highest BA concentration showed the best results in terms of shoot induction (explants forming shoots (46%) and number of shoots per explant (1.95 ± 0.52)) when using initial explants collected in the first week of February. The percentage of explants forming shoots (EFS) was genotype-dependent. Explants from genotype A induced with the highest BA concentration showed the highest EFS (91%). With respect to the light treatment applied, significant differences in root induction (20%) and in the number of roots per explant (4.62 ± 0.65) were observed in shoots cultured under white FL. Finally, significant differences in different phases of the rooting process were detected in the amounts of fructose, glucose and sucrose and in the content of threonine and tyrosine. Full article
(This article belongs to the Special Issue Application of Biotechnology Techniques on Tree Species—Series II)
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