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Advances in Forest Tree Physiology, Breeding and Genetic Research: 2nd Edition

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: closed (20 February 2025) | Viewed by 8816

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Prof. Dr. Chenghao Li

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School of Forest, Northeast Forestry University, Harbin 150040, China
Interests: tree genetics and breeding; poplar
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Recently, there has been much progress in research on trees. However, it remains vital to deepen our knowledge of forest trees’ molecular mechanisms. From metabolism and compounds to genetic exploration and the regulation of key traits, all have largely extended our understanding of trees’ molecular biology. Exploring trees’ molecular mechanisms may provide us with strategies to promote tree adaptation and benefit human society. This Special Issue of IJMS, titled “Advances in Forest Tree Physiology, Breeding and Genetic Research”, covers many physiological, cellular and molecular research topics, including growth, development, and biotic and abiotic stress responses in trees. A major criterion for acceptance of papers is the study providing substantial insight into molecular mechanisms or describing new pathways governing trees’ biological processes. We also welcome submissions related to research into woody species.

This Special Issue will be supervised by Prof. Dr. Chenghao Li and assisted by our Topical Advisory Panel Member Dr. Jingli Yang (Northeast Forestry University).

Prof. Dr. Chenghao Li
Guest Editor

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Keywords

forest tree
physiology
genetic
biotic and abiotic stress
poplar
growth

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20 pages, 6233 KiB

Open AccessArticle

Functional Characterization of PmDXR, a Critical Rate-Limiting Enzyme, for Turpentine Biosynthesis in Masson Pine (Pinus massoniana Lamb.)

by Rong Li, Lingzhi Zhu, Peizhen Chen, Yu Chen, Qingqing Hao, Peihuang Zhu and Kongshu Ji

Int. J. Mol. Sci. 2024, 25(8), 4415; https://doi.org/10.3390/ijms25084415 - 17 Apr 2024

Cited by 3 | Viewed by 1438

Abstract

As one of the largest and most diverse classes of specialized metabolites in plants, terpenoids (oprenoid compounds, a type of bio-based material) are widely used in the fields of medicine and light chemical products. They are the most important secondary metabolites in coniferous species and play an important role in the defense system of conifers. Terpene synthesis can be promoted by regulating the expressions of terpene synthase genes, and the terpene biosynthesis pathway has basically been clarified in Pinus massoniana, in which there are multiple rate-limiting enzymes and the rate-limiting steps are difficult to determine, so the terpene synthase gene regulation mechanism has become a hot spot in research. Herein, we amplified a PmDXR gene (GenBank accession no. MK969119.1) of the MEP pathway (methyl-erythritol 4-phosphate) from Pinus massoniana. The DXR enzyme activity and chlorophyll a, chlorophyll b and carotenoid contents of overexpressed Arabidopsis showed positive regulation. The PmDXR gene promoter was a tissue-specific promoter and can respond to ABA, MeJA and GA stresses to drive the expression of the GUS reporter gene in N. benthamiana. The DXR enzyme was identified as a key rate-limiting enzyme in the MEP pathway and an effective target for terpene synthesis regulation in coniferous species, which can further lay the theoretical foundation for the molecularly assisted selection of high-yielding lipid germplasm of P. massoniana, as well as provide help in the pathogenesis of pine wood nematode disease. Full article

(This article belongs to the Special Issue Advances in Forest Tree Physiology, Breeding and Genetic Research: 2nd Edition)

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18 pages, 8812 KiB

Open AccessArticle

Uncovering PheCLE1 and PheCLE10 Promoting Root Development Based on Genome-Wide Analysis

by Changhong Mu, Wenlong Cheng, Hui Fang, Ruiman Geng, Jutang Jiang, Zhanchao Cheng and Jian Gao

Int. J. Mol. Sci. 2024, 25(13), 7190; https://doi.org/10.3390/ijms25137190 - 29 Jun 2024

Viewed by 1193

Abstract

Moso bamboo (Phyllostachys edulis), renowned for its rapid growth, is attributed to the dynamic changes in its apical meristem. The CLAVATA3/EMBRYO SURROUNDING REGION-RELATED (CLE) family genes are known to play crucial roles in regulating meristem and organ formation in model plants, but their functions in Moso bamboo remain unclear. Here, we conducted a genome-wide identification of the CLE gene family of Moso bamboo and investigated their gene structure, chromosomal localization, evolutionary relationships, and expression patterns. A total of 11 PheCLE genes were identified, all of which contained a conserved CLE peptide core functional motif (Motif 1) at their C-termini. Based on Arabidopsis classification criteria, these genes were predominantly distributed in Groups A–C. Collinearity analysis unveiled significant synteny among CLE genes in Moso bamboo, rice, and maize, implying potential functional conservation during monocot evolution. Transcriptomic analysis showed significant expression of these genes in the apical tissues of Moso bamboo, including root tips, shoot tips, rhizome buds, and flower buds. Particularly, single-cell transcriptomic data and in situ hybridization further corroborated the heightened expression of PheCLE1 and PheCLE10 in the apical tissue of basal roots. Additionally, the overexpression of PheCLE1 and PheCLE10 in rice markedly promoted root growth. PheCLE1 and PheCLE10 were both located on the cell membrane. Furthermore, the upstream transcription factors NAC9 and NAC6 exhibited binding affinity toward the promoters of PheCLE1 and PheCLE10, thereby facilitating their transcriptional activation. In summary, this study not only systematically identified the CLE gene family in Moso bamboo for the first time but also emphasized their central roles in apical tissue development. This provides a valuable theoretical foundation for the further exploration of functional peptides and their signaling regulatory networks in bamboo species. Full article

(This article belongs to the Special Issue Advances in Forest Tree Physiology, Breeding and Genetic Research: 2nd Edition)

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17 pages, 14317 KiB

Open AccessArticle

Genome-Wide Analysis of the Gibberellin-Oxidases Family Members in Four Prunus Species and a Functional Analysis of PmGA2ox8 in Plant Height

by Xue Li, Jie Zhang, Xiaoyu Guo, Like Qiu, Ke Chen, Jia Wang, Tangren Cheng, Qixiang Zhang and Tangchun Zheng

Int. J. Mol. Sci. 2024, 25(16), 8697; https://doi.org/10.3390/ijms25168697 - 9 Aug 2024

Cited by 1 | Viewed by 1315

Abstract

Gibberellins (GAs), enzymes that play a significant role in plant growth and development, and their levels in plants could be regulated by gibberellin-oxidases (GAoxs). As important fruit trees and ornamental plants, the study of the mechanism of plant architecture formation of the Prunus genus is crucial. Here, 85 GAox genes were identified from P. mume, P. armeniaca, P. salicina, and P. persica, and they were classified into six subgroups. Conserved motif and gene structure analysis showed that GAoxs were conserved in the four Prunus species. Collinearity analysis revealed two fragment replication events of PmGAoxs in the P. mume genome. Promoter cis-elements analysis revealed 24 PmGAoxs contained hormone-responsive elements and development regulatory elements. The expression profile indicated that PmGAoxs have tissue expression specificity, and GA levels during the dormancy stage of flower buds were controlled by certain PmGAoxs. After being treated with IAA or GA₃, the transcription level of PmGA2ox8 in stems was significantly increased and showed a differential expression level between upright and weeping stems. GUS activity driven by PmGA2ox8 promoter was detected in roots, stems, leaves, and flower organs of Arabidopsis. PmGA2ox8 overexpression in Arabidopsis leads to dwarfing phenotype, increased number of rosette leaves but decreased leaf area, and delayed flowering. Our results showed that GAoxs were conserved in Prunus species, and PmGA2ox8 played an essential role in regulating plant height. Full article

(This article belongs to the Special Issue Advances in Forest Tree Physiology, Breeding and Genetic Research: 2nd Edition)

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16 pages, 6882 KiB

Open AccessArticle

Unbalanced Expression of Structural Genes in Carotenoid Pathway Contributes to the Flower Color Formation of the Osmanthus Cultivar ‘Yanzhi Hong’

by Min Zhang, Zi-Han Chai, Cheng Zhang and Lin Chen

Int. J. Mol. Sci. 2024, 25(18), 10198; https://doi.org/10.3390/ijms251810198 - 23 Sep 2024

Viewed by 1073

Abstract

Carotenoids are important natural pigments that are responsible for the fruit and flower colors of many plants. The composition and content of carotenoid can greatly influence the color phenotype of plants. However, the regulatory mechanism underling the divergent behaviors of carotenoid accumulation, especially in flower, remains unclear. In this study, a new cultivar Osmanthus fragrans ‘Yanzhi Hong’ was used to study the regulation of carotenoid pigmentation in flower. Liquid chromatograph–mass spectrometer (LC-MS) analysis showed that β-carotene, phytoene, lycopene, γ-carotene, and lutein were the top five pigments enriched in the petals of ‘Yanzhi Hong’. Through transcriptome analysis, we found that the expression of the structural genes in carotenoid pathway was imbalanced: most of the structural genes responsible for lycopene biosynthesis were highly expressed throughout the flower developmental stages, while those for lycopene metabolism kept at a relatively lower level. The downregulation of LYCE, especially at the late developmental stages, suppressed the conversion from lycopene to α-carotene but promoted the accumulation of β-carotene, which had great effect on the carotenoid composition of ‘Yanzhi Hong’. Ethylene response factor (ERF), WRKY, basic helix-loop-helix (bHLH), v-myb avian myeloblastosis viral oncogene homolog (MYB), N-Acetylcysteine (NAC), auxin response factor (ARF), and other transcription factors (TFs) have participated in the flower color regulation of ‘Yanzhi Hong’, which formed co-expression networks with the structural genes and functioned in multiple links of the carotenoid pathway. The results suggested that the cyclization of lycopene is a key link in determining flower color. The modification of the related TFs will break the expression balance between the upstream and downstream genes and greatly influence the carotenoid profile in flowers, which can be further used for creating colorful plant germplasms. Full article

(This article belongs to the Special Issue Advances in Forest Tree Physiology, Breeding and Genetic Research: 2nd Edition)

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18 pages, 8167 KiB

Open AccessArticle

Genome-Wide Analysis of the PYL Gene Family in Betula platyphylla and Its Responses to Abiotic Stresses

by Jiajie Yu, Ruiqi Wang, Xiang Zhang and Su Chen

Int. J. Mol. Sci. 2024, 25(24), 13728; https://doi.org/10.3390/ijms252413728 - 23 Dec 2024

Viewed by 688

Abstract

Abscisic acid (ABA) is a key phytohormone that participates in various plant biological processes, such as seed germination, senescence, stomatal movement, and flowering. In the ABA signal transduction pathway, Pyrabactin Resistance 1 (PYR1)/PYR1-Like (PYL)/Regulatory Component is the core module for ABA perception. In this study, a total of 12 PYL family members were identified in birch (Betula platyphylla Suk.) from a genome-wide range that can be divided into 3 subgroups according to their evolutionary relationships. The physiochemical properties of the 12 BpPYLs were characterized, and the members of the same subgroups share more similar exon–intron and motif patterns. The results of synteny analysis showed two syntenic gene pairs within BpPYL family members and 12, 8, 19, and 6 syntenic gene pairs between BpPYLs and AtPYLs, OsPYLs, PtPYLs, and ZmPYLs, respectively. Multiple cis-acting elements were identified in the promoters of BpPYLs, including stress response, phytohormone signaling, and growth and development. The results of GO and KEGG enrichment analysis showed that BpPYLs were enriched in the pathways mainly related to ABA signaling and cell communication. The results of RT-qPCR verified the expressional responses of BpPYLs to ABA, salt, and PEG treatments. Furthermore, the positive roles of BpPYL3 and BpPYL11 were proven by using salt-tolerant yeast transformation. This study provides a reference for research on ABA signal transduction and forest tree responses upon abiotic stresses. Full article

(This article belongs to the Special Issue Advances in Forest Tree Physiology, Breeding and Genetic Research: 2nd Edition)

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22 pages, 6621 KiB

Open AccessArticle

Orogeny and High Pollen Flow as Driving Forces for High Genetic Diversity of Endangered Acer griseum (Franch.) Pax Endemic to China

by Xinhe Xia, Xuedan Yu, Yuxia Wu, Jia Liao, Xinyue Pan, Yongqi Zheng and Chuanhong Zhang

Int. J. Mol. Sci. 2025, 26(2), 574; https://doi.org/10.3390/ijms26020574 - 11 Jan 2025

Viewed by 907

Abstract

Acer griseum (Franch.) Pax is an endangered species endemic to China, mainly scattered in the Qinling–Daba Mountains. The genetic diversity of 17 natural populations were analyzed by nuclear DNA (nDNA) and chloroplast DNA (cpDNA) to explore the driving forces for its microevolution. A high level of genetic diversity (nDNA: He = 0.296, cpDNA: Ht = 0.806) was found in A. griseum. Genetic variation was mainly within populations (92.52%) based on nDNA, while it was mainly among populations (96.26%) based on cpDNA. The seventeen populations were divided into two groups, corresponding to the subtropical zone (Group I) and temperate zone (Group II), with haplotype 4 (Hap4) and Hap5 being the most common haplotypes, respectively. Consequently, genes associated with heat and heavy metal stress were identified in Group I, while genes related to salt and drought stress were identified in Group II. Haplotype differentiation was driven by the heterogeneous microenvironment caused by the uplifting of the Qinling-Daba Mountains, which was a vital source of its high genetic diversity. Furthermore, the uplifted Qinling–Daba mountains may bridge high pollen flow among populations, whereas rivers can result in low seed flow among populations, which has led to the incongruent genetic structure between nDNA and cpDNA. This study represents a new perspective that geological events, especially orogeny, play an important role in plant microevolution through the establishment of maternal genetic structure and provides a meaningful conservation strategy for A. griseum. Overall, the Qinling–Daba Mountains not only are cradles for the genetic diversity of A. griseum but also provided refugia for it during the Quaternary glacial period. Full article

(This article belongs to the Special Issue Advances in Forest Tree Physiology, Breeding and Genetic Research: 2nd Edition)

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21 pages, 5209 KiB

Open AccessArticle

Agrobacterium rhizogenes-Mediated Hairy Root Genetic Transformation Using Agrobacterium Gel Inoculation and RUBY Reporter Enables Efficient Gene Function Analysis in Sacha Inchi (Plukenetia volubilis)

by Kai Lin, Li-Xin Lu, Bang-Zhen Pan, Xia Chai, Qian-Tang Fu, Xian-Chen Geng, Yi Mo, Yu-Chong Fei, Jia-Jing Xu, Meng Li, Jun Ni and Zeng-Fu Xu

Int. J. Mol. Sci. 2025, 26(6), 2496; https://doi.org/10.3390/ijms26062496 - 11 Mar 2025

Viewed by 838

Abstract

Plukenetia volubilis L., a woody oilseed plant rich in α-linolenic acid, represents a promising source of polyunsaturated fatty acids. However, the lack of an efficient genetic transformation system has significantly hindered gene function research and molecular breeding in P. volubilis. In this study, we developed a highly efficient Agrobacterium rhizogenes-mediated hairy root transformation system for P. volubilis via the use of Agrobacterium gel in combination with the visually detectable RUBY reporter for gene function analysis in roots. The results indicate that the optimal transformation method involves infecting P. volubilis seedlings with Agrobacterium gel containing acetosyringone and inducing hairy root formation in perlite. This approach resulted in more than 18.97% of the seedlings producing positive hairy roots overexpressing the RUBY gene. Using this genetic transformation system, we successfully overexpressed the antimicrobial peptide-encoding gene CEMA in hairy roots, which enhanced the resistance of P. volubilis to Fusarium oxysporum. Furthermore, by combining this transformation system with the CRISPR-Cas9 tool, we validated the regulatory role of PvoSHR in the development of root epidermal cells in P. volubilis. Unexpectedly, a 123-bp DNA fragment from the T-DNA region of the A. rhizogenes Ri plasmid was found to be knocked in to the P. volubilis genome, replacing a 110-bp fragment of PvoSHR at CRISPR-Cas9 induced double-strand DNA breaks. Conclusively, this system provides a powerful tool for gene function research in P. volubilis and provides novel insights into the development of transformation and gene editing systems for other woody plants. Full article

(This article belongs to the Special Issue Advances in Forest Tree Physiology, Breeding and Genetic Research: 2nd Edition)

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25 pages, 6934 KiB

Open AccessArticle

Genome-Wide Identification and Characterization of the Growth-Regulating Factor Gene Family Responsive to Abiotic Stresses and Phytohormone Treatments in Populus ussuriensis

by Ying Zhao, Yuqi Liu, Yuan Chai, Hedan Zhang, Ming Wei and Chenghao Li

Int. J. Mol. Sci. 2025, 26(7), 3288; https://doi.org/10.3390/ijms26073288 - 1 Apr 2025

Viewed by 429

Abstract

As a unique class of plant-specific transcription factors, the GROWTH-REGULATING FACTORs (GRFs) play pivotal roles in regulating plant growth, development, and stress responses. In this study, the woody plant Populus ussuriensis was taken as the research object. Nineteen PuGRFs were identified and classified into six clades, and their potential evolutionary relationships were analyzed. The possible biological functions of PuGRFs were speculated through bioinformatics analysis. Combining real-time fluorescence quantitative PCR, PuGRFs were determined to be actively expressed in young tissues, and there are distinct tissue-specific expressions in the mature tissues of woody plants. We also conducted RT-qPCR of PuGRFs under different abiotic stresses and phytohormone treatments, most of the family members were induced under the treatments of methyl jasmonate (MEJA) and salicylic acid (SA), and we also found that 4 of 19 PuGRFs might participate in abscisic acid (ABA)-mediated osmotic stress in roots. Protein–protein interaction prediction analysis showed that six PuGRFs can interact with two types of growth-regulating interaction factors (GIFs). Further prediction and verification revealed that PuGRF1/2c and PuGRF1/2d, which belong to the same clade and have highly similar sequences, exhibited divergent interaction capabilities with GIFs, indicating evolutionary fine-tuning and functional redundancy within the GRF family. These findings lay a foundation for studying the molecular mechanisms of PuGRFs in P. ussuriensis, suggest that PuGRFs play important roles in responding to hormones and environmental changes, and the potential interaction relationships are worthy of exploration. Full article

(This article belongs to the Special Issue Advances in Forest Tree Physiology, Breeding and Genetic Research: 2nd Edition)

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