Genome-Wide Identification and Expression Analysis for the Genetic Improvement of Forest Plants

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

Deadline for manuscript submissions: 24 June 2024 | Viewed by 12684

Special Issue Editors


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Guest Editor
Institute for Advanced Study, Chengdu University, Chengdu, China
Interests: plant genomics; comparative genomic analysis; phylogenomics; functional gene analysis; transcriptomics
Special Issues, Collections and Topics in MDPI journals

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Guest Editor
College of Forestry, Northwest A&F University, Yangling, China
Interests: saline stress; drought stress; transcriptional control; functional gene analysis

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Guest Editor
School of Marine Sciences, Ningbo University, Ningbo, China
Interests: plant genomics; population genomics; landscape genomics; adaptive evolution

Special Issue Information

Dear Colleagues,

As key components of forest ecosystems, forest plants provide valuable habitats that increase biodiversity and environmentally friendly products to fulfill human needs, and play a critical role in the global carbon cycle. With the rapid development of molecular biology and genomics, genetic breeding has become an efficient way to improve the quality and productivity of forest plants. Genome-wide identification and analysis of genes related to various important traits is essential for the genetic improvement programs of forest plants. Recent advances in high-throughput sequencing technologies have enabled us to gain insights into the genetic mechanisms that underlie growth traits in forest plant species. Multiple sequencing technologies with increased accuracy have also allowed us to perform more accurate identification of functional genes. We would like to announce this Special Issue of the journal Forests, which will concentrate on articles focused on accurate genome-wide identification and expression analysis of genes related to growth traits in various types of forest plants with ecological or economic importance. Studies concerned with the improvement of identification methods, population-level functional diversity analysis, or functional verification of candidate genes are most welcome. Both theoretical and empirical contributions will also be suitable for this Special Issue.

Dr. Mingcheng Wang
Dr. Shaofei Tong
Dr. Shanshan Zhu
Guest Editors

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Keywords

  • forest plants
  • genetic improvement
  • growth trait-related genes
  • expression analysis
  • functional diversity
  • high-throughput sequencing

Published Papers (12 papers)

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Research

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18 pages, 5013 KiB  
Article
Isolation and Characterization of the Sulfate Transporter Gene Family and Its Expression Pattern in Response to Selenium and Abiotic Stress in Walnuts (Juglans regia L.)
by Simin Zhang, Yansheng Xue, Ningfang Liu, Danzeng Quzhen, De Qiong, Yongling Liao, Weiwei Zhang, Jiabao Ye, Qijian Wang and Feng Xu
Forests 2024, 15(4), 702; https://doi.org/10.3390/f15040702 - 15 Apr 2024
Viewed by 411
Abstract
The sulfate transporter (SULTR) is responsible for the transport and uptake of sulfate, which plays an indispensable role in the growth cycle of plants and adaptation to plant stress. However, there are few reports on the response and regulation of SULTR gene family [...] Read more.
The sulfate transporter (SULTR) is responsible for the transport and uptake of sulfate, which plays an indispensable role in the growth cycle of plants and adaptation to plant stress. However, there are few reports on the response and regulation of SULTR gene family members in walnuts (Juglans regia L.) to sodium selenate, low temperatures, high temperatures, and simulated drought stress. In this study, the whole genome of the SULTR genes family in walnuts was identified and analyzed by the bioinformatics method. The results show that the walnut genome contains seventeen JrSULTR genes, which are unevenly distributed on eight chromosomes and can be divided into four subfamilies. Cis-acting elements that respond to stress and participate in the regulation of plant hormones were found in the promoter sequence of the JrSULTR genes. The analysis of transcriptome data showed that the expression of JrSULTR1.2b was significantly upregulated under sodium selenate treatment, and the results of qRT-PCR analysis were basically consistent with the transcriptome data. The expression of JrSULTR3.1a and JrSULTR3.4b increased with the prolongation of simulated drought stress time. The transcription levels of JrSULTR1.2b and JrSULTR3.1a were significantly increased after low-temperature treatment. After 9 h of high-temperature treatment, the expression levels of JrSULTR3.1a and JrSULTR3.3 were significantly increased. JrSULTR1.2b and JrSULTR3.1a showed significant expression specificity under stress treatment. At the same time, we also performed subcellular localization of these two genes, which was consistent with the predicted results and was in the cell membrane, and their regulatory functions need to be further studied. These studies laid the foundation for us to explore the specific function of the JrSULTR genes in alleviating abiotic stress in walnuts. Full article
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14 pages, 4209 KiB  
Article
Identification and Analysis of Expression Patterns of the Caleosin Genes in Hickory (Carya cathayensis Sarg.)
by Yueyinglun Cao, Yang Zhan, Jiale Liu, Tianyu Tang, Juan Li, Rui Zhao, Qixiang Zhang, Shuai Hu, Wenhan Cao and Yanli Gao
Forests 2024, 15(4), 609; https://doi.org/10.3390/f15040609 - 28 Mar 2024
Viewed by 570
Abstract
The deciduous tree hickory (Carya cathayensis) holds economic significance in China due to its high oil content, particularly in unsaturated fatty acids. Oil bodies are crucial for storing triacylglycerol (TAG), with caleosin serving as a predominant oil body protein that aids [...] Read more.
The deciduous tree hickory (Carya cathayensis) holds economic significance in China due to its high oil content, particularly in unsaturated fatty acids. Oil bodies are crucial for storing triacylglycerol (TAG), with caleosin serving as a predominant oil body protein that aids in oil body formation and stability maintenance. Our study utilized bioinformatics techniques to identify caleosin genes within Carya cathayensis, Carya illinoinensis, and Juglans regia. Three caleosin genes were discovered in the genomes of Carya cathayensis, Carya illi-noinensis, and Juglans regia. These genes encode hydrophilic proteins. Additionally, all caleosin proteins feature a single Ca2+-binding EF-hand, a conserved “proline knot” motif, and a C-terminal hydrophilic region with four potential phosphorylation sites. The caleosin proteins in Carya cathayensis consist of α-helix, β-corner, extended chain, and random curl structures. Cis-acting elements related to stress response and hormone signaling were identified in Carya cathayensis, Carya illinoinensis, and Juglans regia, with distinct cis-acting elements implicated in seed-specific regulation in Carya cathayensis. Additionally, subcellular localization analysis confirmed that CcaCLO1 and CcaCLO2 were localized within oil bodies. Transcriptome analysis and quantitative real-time polymerase chain reaction (qRT-PCR) data demonstrated a significant up-regulation of CcaCLO1 expression during the developmental stages of the Carya cathayensis embryo. Furthermore, qPCR findings indicated that caleosins from Carya cathayensis were responsive to salt stress, with a significant up-regulation of CcaCLO1 following exposure to salt stress treatment. Consequently, caleosin genes in Carya cathayensis, Carya illinoinensis, and Juglans regia share similar physicochemical characteristics and conserved motifs. Specifically, CcaCLO1 in Carya cathayensis primarily responds to embryo development and salt stress. These findings offer foundational insights for future investigations into the regulatory mechanisms of oil accumulation and response to salt stress in hickory. Full article
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22 pages, 4386 KiB  
Article
Endogenous Phytohormone and Transcriptome Analysis Provided Insights into Seedling Height Growth of Pinus yunnanensis
by Zhuangyue Lu, Qibo Wang, Zhenxin Yang, Lin Chen, Nianhui Cai and Yulan Xu
Forests 2024, 15(3), 489; https://doi.org/10.3390/f15030489 - 06 Mar 2024
Viewed by 713
Abstract
Plant height plays a crucial role in both the structure and quality of plants. Pinus yunnanensis is a distinctive species of the forest found in Southwest China, where the height of the plants significantly influences both yield performance and plant architecture. Although the [...] Read more.
Plant height plays a crucial role in both the structure and quality of plants. Pinus yunnanensis is a distinctive species of the forest found in Southwest China, where the height of the plants significantly influences both yield performance and plant architecture. Although the phenotypes of P. yunnanensis seedlings with different plant heights were quite different at their seedling stage, the molecular mechanisms controlling the seedling differentiation remain poorly understood. This study is aimed to investigate the underlying mechanisms of P. yunnanensis seedling differentiation using phenotypic, transcriptomic, and endogenous phytohormone analyses. The P. yunnanensis seedlings were categorized into three grades, i.e., Grades A, B, and C, by mean ± 1/2 standard deviation method (H ± 1/2σ), and the seedling height and ground diameter were measured. We conducted the measurements of endogenous hormone levels in the young shoot apexes of seedlings at different grades during the fast-growth period (March). The DEGs were identified through transcriptome sequencing and analyzed by qRT-PCR validation. Significant differences were observed in the content and ratio of endogenous phytohormones among various grades of P. yunnanensis seedlings (p < 0.05). The ABA content in Grade A was prominently more than that in Grades B and C, and the order of the content of auxins was Grade B > C > A. Furthermore, when compared to Grade A, the ratios of auxins/CTKs, auxins/ABA, CTKs/ABA, and (auxins + CTKs)/ABA exhibited significant increases in Grades B and C. Moreover, GO functional annotation analysis indicated the more pronounced enrichment of DEGs in molecular functions. KEGG metabolic pathway analysis revealed notable differences in enrichment pathways between the pairwise comparisons. The “plant hormone signal transduction” pathway exhibited enrichment in the two groups, followed by “plant–pathogen interaction” pathway in the organism system that was enriched in the three groups. In addition, the results for endogenous phytohormone metabolism pathways indicate a significant up-regulation in the expression of AUX1, while AHP and PP2C exhibited significant down-regulation. To sum up, we aimed at investigating the underlying mechanisms of P. yunnanensis seedling differentiation using phenotypic, transcriptomic, and endogenous phytohormone analyses. The results suggested that individual phytohormones have a limited capacity to regulate gene expression, and seedling differentiation results from the combined regulation of multiple hormones. In addition, several candidate genes associated with phytohormone biosynthesis and signal transduction pathways were identified, including AUX1, GH3, AHP, B-ARR, PP2C, etc., which provided candidate genes for the following hormone-related gene overexpression and knockout experiments. These findings provide insights into the molecular genetic control of seedling height growth of P. yunnanensis. Full article
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19 pages, 6240 KiB  
Article
Genome-Wide Identification and Expression Analysis of Salt-Tolerance-Associated NAC Family Genes in Cyclocarya paliurus
by Ziwei Yang, Yin An, Qian Ye, Nannan Zhang, Xin Liu, Fayin He, Yue Zeng, Ming Tang, Zhengting Yang and Kun Li
Forests 2024, 15(3), 479; https://doi.org/10.3390/f15030479 - 04 Mar 2024
Viewed by 705
Abstract
Soil salinity affects approximately 20% of the world’s arable land, presenting a significant challenge for studying the mechanisms by which plants adapt to saline environments. Cyclocarya paliurus, an invaluable research model due to its ecological and medicinal significance, is primarily concentrated in [...] Read more.
Soil salinity affects approximately 20% of the world’s arable land, presenting a significant challenge for studying the mechanisms by which plants adapt to saline environments. Cyclocarya paliurus, an invaluable research model due to its ecological and medicinal significance, is primarily concentrated in central and southern China. Nevertheless, Cyclocarya paliurus faces challenges from environmental factors such as soil salinization, which adversely impacts its growth, subsequently affecting the yield and quality of its bioactive compounds. The NAC gene family, a critical group of plant-specific transcription factors, plays pivotal roles in responding to abiotic stresses. However, there has not yet been any studies on NAC genes under salt stress in Cyclocarya paliurus. In this study, we identified 132 NAC genes within the Cyclocarya paliurus genome. Our analysis of the conserved structures and gene organization revealed a high degree of conservation in the proteins of the CpNAC gene family. Cis-element analysis unveiled the participation of these genes in a variety of biological processes, including light responses, phytohormone responses, cell cycle responses, and abiotic stress responses. Under salt stress conditions, the expression of 35 CpNAC genes changed significantly, indicating a response to salt treatment. Furthermore, we provided additional evidence for the identification of the NAC gene family and revealed their potential positive regulatory role in signal transduction by conducting a transcriptional activation activity analysis of CpNAC132(D) and CpNAC040, which are homologous to Arabidopsis thaliana NAC062/91 and NAC103, respectively. This research not only advances our comprehension of the salt stress adaptation in Cyclocarya paliurus but also provides robust support for future investigations into plant responses to environmental stress and the cultivation of salt-tolerant crops. Full article
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18 pages, 3076 KiB  
Article
Insights into the Root Sprouts of Toona fargesii in a Natural Forest: From the Morphology, Physiology, and Transcriptome Levels
by Qiangqiang Cheng, Jikai Ma, Chunce Guo, Qiuwei Zhong, Wanwen Yu, Ting Jia and Lu Zhang
Forests 2024, 15(2), 335; https://doi.org/10.3390/f15020335 - 08 Feb 2024
Viewed by 646
Abstract
Toona fargesii (T. fargesii) is a deciduous tree of the Meliaceae family which is utilized for high-value timber. Interestingly, root sprouting is a typical reproductive pattern in T. fargesii. Nevertheless, the genetics underlying this phenomenon are still unclear. Here, three [...] Read more.
Toona fargesii (T. fargesii) is a deciduous tree of the Meliaceae family which is utilized for high-value timber. Interestingly, root sprouting is a typical reproductive pattern in T. fargesii. Nevertheless, the genetics underlying this phenomenon are still unclear. Here, three type of roots of T. fargesii were used for histological observation, plant endogenous hormone determination, non-structural carbohydrate (NSC) determination, and sequencing using the Illumina next-generation and PacBio SMRT platforms. Our results indicated that root sprouts originated from cork cambiums. Furthermore, indole-3-acetic acid (IAA), zeatin riboside (ZR), gibberellic acid 3 (GA3), and abscisic acid (ABA) content was significantly increased, while soluble sugar content was significantly decreased in the root sprouts. In addition, transcriptomic analysis suggested a total of 36.19 G of raw data from which 210 differentially expressed genes (DEGs) of were identified in RS vs. SR. Of these, the candidate DEGs were largely enriched in the citrate cycle, gluconeogenesis, starch and sucrose metabolism, and plant hormone signal transduction pathways. We therefore speculated that the accumulation of cytokinin and auxin might be induced by ATP-binding cassette-B 19 (ABCB19) and ABCG14, which were necessary for root sprouting. Additionally, transcription factors SQUAMOSA promoter binding protein-like 18 (SPL18) and NAM, ATAF1/2, and CUC2-14 (NAC14) were found in response to environmental water and epigenetic modification in RS. Overall, this study was to unravel the physiological and transcriptomic levels of the development of root sprouting in T. fargesii. Full article
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16 pages, 8888 KiB  
Article
Comparative Chloroplast Genome Analyses of Six Hemlock Trees in East Asia: Insights into Their Genomic Characterization and Phylogenetic Relationship
by Lin Chen, Xin Liu, Zhibei Wang, Xi Wu, Kaiyue Hong and Chunping Xie
Forests 2023, 14(11), 2136; https://doi.org/10.3390/f14112136 - 26 Oct 2023
Cited by 1 | Viewed by 976
Abstract
Hemlocks (Pinaceae: Tsuga) are widely distributed in North America and East Asia, forming a reticulate evolutionary structure in East Asia with significant ecological importance. To clarify the chloroplast genome characteristics and phylogenetic relationships among Tsuga species, we analyzed the chloroplast genomes of [...] Read more.
Hemlocks (Pinaceae: Tsuga) are widely distributed in North America and East Asia, forming a reticulate evolutionary structure in East Asia with significant ecological importance. To clarify the chloroplast genome characteristics and phylogenetic relationships among Tsuga species, we analyzed the chloroplast genomes of T. chinensis var. tchekiangensis, T. chinensis, T. diversifolia, T. dumosa, T. forrestii, and T. sieboldii, performing associated phylogenetic analyses. The results reveal that the chloroplast genome lengths among the six Tsuga species vary from 120,520 to 121,010 bp, encompassing about 108 to 112 genes, including 35/32 tRNA genes and 4 rRNA genes. A codon usage analysis highlighted a preference for A/U-ending codons, and all six nucleotide types have A/T bases and a prevalence of mononucleotides. Notably, all Tsuga species exhibit inverted repeat (IR) contractions and possess unique hexanucleotides absent in the other species of Pinaceae, potentially making them more susceptible to gene recombination or rearrangement during evolution. While most variations are observed in non-coding regions, particularly in intergenic fragments, substantial variation sites are also present within the genes. The phylogenetic tree, constructed using chloroplast genomes, substantiates the sister taxa relationship between Tsuga and Nothotsuga. Furthermore, it confirms that T. chinensis var. tchekiangensis exhibits a closer relationship with T. forrestii than with T. chinensis. These findings not only provide partial evidence that T. chinensis may not constitute a monophyletic species but also underscore the necessity of reevaluating the taxonomic status of T. chinensis var. tchekiangensis. In addition, while the RSCU cluster analysis is basically consistent with the phylogenetic analysis, it also highlights a distinct differentiation between Nothotsuga and Tsuga. This study not only provides molecular-level phylogenetic classification evidence of Pinaceous genera via chloroplast genome analyses but also offers compelling evidence for further exploring the relationships and species delimitation among the hemlocks of East Asia. Full article
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17 pages, 5882 KiB  
Article
Genome-Wide Identification and Analysis of the DGAT Gene Family in Lindera glauca and Expression Analysis during Fruit Development Stages
by Xue Bai, Yongyi Yang, Lun Xie, Qingqing Li and Biao Xiong
Forests 2023, 14(8), 1633; https://doi.org/10.3390/f14081633 - 13 Aug 2023
Viewed by 940
Abstract
Diacylglycerol acyltransferase (DGAT) is a vital and sole rate-limiting enzyme involved in triacylglycerol synthesis. Identifying DGAT genes in Lindera glauca is essential for studying lipid metabolism pathways and developing novel oil crops with enhanced value. In the study reported in this paper, 15 [...] Read more.
Diacylglycerol acyltransferase (DGAT) is a vital and sole rate-limiting enzyme involved in triacylglycerol synthesis. Identifying DGAT genes in Lindera glauca is essential for studying lipid metabolism pathways and developing novel oil crops with enhanced value. In the study reported in this paper, 15 LgDGAT family genes were first obtained from the L. glauca genome via bioinformatics analysis. We comprehensively analyzed their chromosome distribution, gene structure, subcellular localization, promoter prediction, phylogenetic relationships, tissue-specific expression, and expression patterns during different stages of fruit development. Our findings revealed that LgDGATs can be classified into DGAT1, DGAT2, DGAT3, and WSD (wax ester synthase/acyl-CoA: diacylglycerol acyltransferase) subfamilies distributed across chromosome 3, 5, 6, 8 and 11. LgDGATs’ promoter region showed abundant elements linked to the light response and plant hormone response. Forms of LgDGAT1, LgDGAT2, and LgDGAT3 were primarily expressed in the early and late phases of fruit development, indicating their potential function in the growth and development of L. glauca, particularly in oil accumulation. Conversely, LgWSDs exhibited predominant expression in stems and leaves. This paper elucidates the gene structure and expression patterns of LgDGATs, providing a theoretical foundation for understanding the functionality of DGAT genes in Lindera species. Full article
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19 pages, 37786 KiB  
Article
Genome-Wide Identification and Expression Profiling of B3 Transcription Factor Genes in Prunus armeniaca
by Xiaodan Shi, Wanwen Yu, Lin Wang, Han Zhao, Jingjing Hu, Tana Wuyun and Huimin Liu
Forests 2023, 14(8), 1523; https://doi.org/10.3390/f14081523 - 26 Jul 2023
Viewed by 1148
Abstract
The B3 superfamily, which belongs to the plant-specific transcription factors, is widely involved in multiple biological processes. In apricot (Prunus armeniaca), the classification, structure, and function of the B3 superfamily are not yet clear. In this study, a total of 75 [...] Read more.
The B3 superfamily, which belongs to the plant-specific transcription factors, is widely involved in multiple biological processes. In apricot (Prunus armeniaca), the classification, structure, and function of the B3 superfamily are not yet clear. In this study, a total of 75 B3 genes were identified from the apricot genome. The apricot B3 superfamily can be divided into five subfamilies, i.e., REM, ARF, ABI3, RAV, and HSI, and genes in the same subfamily have similar structures. The distribution of B3 genes on chromosomes presents a clustering phenomenon. Tandem duplication is the main mode of apricot B3 family expansion, and gene duplication mainly occurs in the REM and ARF subfamilies. Many B3 genes originated from a common ancestor of Arabidopsis and apricot before lineage divergence, and ancestor genes expanded fewer times in apricot than in Arabidopsis. Gene ontology analysis showed that apricot B3 genes were closely related to vernalization, flower development, and shoot system development. PaABI3-1 and PaABI3-2 might play a positive regulation role in the transcription of PaOleosin, which encodes a lipid body protein. This study lays a foundation for the further study of the B3 superfamily function in apricot, especially the specific functions of the ABI3 subfamily in apricot kernel oil storage. Full article
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13 pages, 3200 KiB  
Article
Functional Characterization of a New Salt Stress Response Gene, PeCBL4, in Populus euphratica Oliv
by Meiqiao Qu, Qi Sun, Ningning Chen, Zhuoyan Chen, Hechen Zhang, Fuling Lv and Yi An
Forests 2023, 14(7), 1504; https://doi.org/10.3390/f14071504 - 23 Jul 2023
Cited by 1 | Viewed by 921
Abstract
Populus euphratica is a typical stress-resistant tree species that provides valuable natural genetic resources for breeding salt-tolerant plants. The calcineurin B-like (CBL)-interacting protein kinase (CIPK) network plays an important role in regulating plant responses to abiotic stresses. The aim of this study was [...] Read more.
Populus euphratica is a typical stress-resistant tree species that provides valuable natural genetic resources for breeding salt-tolerant plants. The calcineurin B-like (CBL)-interacting protein kinase (CIPK) network plays an important role in regulating plant responses to abiotic stresses. The aim of this study was to characterize the function of a new CBL member, PeCBL4, in response to abiotic stresses. PeCBL4 was cloned, and sequence analysis was performed. The subcellular localization of PeCBL4 was determined using the fusion expression vector of GFP. Yeast two-hybrid assays and bimolecular fluorescence complementation were performed to identify PeCIPK members that interacted with PeCBL4. PeCBL4 was then transformed into the corresponding Arabidopsis thaliana mutants. Na+ and K+ content as well as their net fluxes were determined under high salt stress and low K+ stress. Phylogenetic tree analysis showed that PeCBL4 was clustered together with PtCBL4 and belonged to the same subgroup as AtCBL4. Subcellular localization indicated that PeCBL4 was expressed on the plasma membrane. Yeast two-hybrid assays and bimolecular fluorescence complementation showed that PeCBL4 interacted with PeCIPK24 and PeCIPK26. In addition, under high salt stress, the Na+ efflux capacities of seedlings decreased in sos3 mutants, and transgenic plants of PeCBL4 enhanced efflux capacities. In addition, the overexpression of PeCBL4 negatively influenced the influx capacity of K+. PeCBL4 interacts with PeCIPK24 and PeCIPK26 and regulates Na+/K+ balance under low K+ and high salt stress. Full article
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12 pages, 1753 KiB  
Article
Stilbene Content and Expression of Stilbene Synthase Genes in Korean Pine Pinus koraiensis Siebold & Zucc
by Andrey R. Suprun, Alexandra S. Dubrovina, Valeria P. Grigorchuk and Konstantin V. Kiselev
Forests 2023, 14(6), 1239; https://doi.org/10.3390/f14061239 - 15 Jun 2023
Viewed by 1174
Abstract
Stilbenes are a large group of plant phenolic compounds that have a wide range of biologically active properties, such as antioxidant, immunomodulatory, anti-inflammatory, and anti-angiogenic effects. In plants, stilbenes are involved in the defense against environmental stresses, including fungal infections and insect attacks. [...] Read more.
Stilbenes are a large group of plant phenolic compounds that have a wide range of biologically active properties, such as antioxidant, immunomodulatory, anti-inflammatory, and anti-angiogenic effects. In plants, stilbenes are involved in the defense against environmental stresses, including fungal infections and insect attacks. The biosynthesis of stilbenes is well described for those plant species where resveratrol and its derivatives are the predominant stilbenes. However, there is little information on stilbene biosynthesis in the Pinaceae family, although the highest content of stilbenes was found in plants of this family. In this study, seasonal variations in stilbene compositions and contents in different parts of Pinus koraiensis was described (needles, bark, wood, young branches, and strobiles). HPLC-ESI-MS analysis showed the presence of seven stilbenes in P. koraiensis: t-astringin; t-piceid; cis-piceid; t-isorapontin; t-pinostilbenoside; t-resveratrol; and t-pinostilbene. Glycosylated and methylated forms of stilbenes, such as t-astringin, t-piceid, and t-pinostilbenoside, prevailed over other stilbenoids. The highest content of stilbenes was detected in the bark collected in spring and winter (up to 54.8 mg/g dry weight). The complete protein-coding sequences of three stilbene synthase genes, PkSTS1, PkSTS2, and PkSTS3, were obtained from the RNA isolated from the P. koraiensis needles. The expression of the PkSTS1, PkSTS2, and PkSTS3 genes was analyzed using real-time PCR and frequency analysis of cloned RT-PCR products in the needles of P. koraiensis collected in different seasons. Thus, we first analyzed stilbene biosynthesis in the different organs of pine P. koraiensis and PkSTS expression depending on the year seasons. Full article
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13 pages, 6644 KiB  
Article
Genome-Wide Analysis, Identification, and Characterization of the PFK Gene Family Members of Populus deltoides
by Tae-Lim Kim, Michael Immanuel Jesse Denison, Hyemin Lim, Hoyong Chung and Changyoung Oh
Forests 2023, 14(6), 1104; https://doi.org/10.3390/f14061104 - 26 May 2023
Cited by 1 | Viewed by 1204
Abstract
Plants produce two phosphorylated enzymes: pyrophosphate-dependent fructose-6-phosphate phosphotransferase (PFP) and ATP-dependent phosphofructokinase (PFK). However, the characterization of phosphofructokinase (PFK) family members and their functions remains unexplored in Eastern Cottonwood (Populus deltoides). This study comprehensively analyzed 17 phosphofructokinase genes in the P. [...] Read more.
Plants produce two phosphorylated enzymes: pyrophosphate-dependent fructose-6-phosphate phosphotransferase (PFP) and ATP-dependent phosphofructokinase (PFK). However, the characterization of phosphofructokinase (PFK) family members and their functions remains unexplored in Eastern Cottonwood (Populus deltoides). This study comprehensively analyzed 17 phosphofructokinase genes in the P. deltoides genome, including their gene structure, conserved domains, evolutionary relationships, and expression patterns. Genome-wide analysis of the poplar genome identified 11 genes belonging to PdPFK and 6 genes belonging to PdPFP. Phylogenetic, gene structure, and motif analyses revealed two main categories of PFK genes: PFK with eleven genes and PFP with six genes. Quantitative PCR (qPCR) analysis demonstrated that all 17 phosphofructokinase genes were induced in various tissues and developmental stages of P. deltoides. PFPs were strongly expressed throughout P. deltoides’ growth and development, notably in the roots, according to the transcript analysis. This genome-wide analysis provides insights into PFK and PFP genes and establishes a foundation for future investigations into the role of genes in P. deltoids. Full article
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Review

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22 pages, 1886 KiB  
Review
Multi-Omics Techniques in Genetic Studies and Breeding of Forest Plants
by Mingcheng Wang, Rui Li and Qi Zhao
Forests 2023, 14(6), 1196; https://doi.org/10.3390/f14061196 - 09 Jun 2023
Cited by 2 | Viewed by 1794
Abstract
In recent years, the ecological and economic values of forest plants have been gradually recognized worldwide. However, the growing global demand for new forest plant varieties with higher wood production capacity and better stress tolerance cannot be satisfied by conventional phenotype-based breeding, marker-assisted [...] Read more.
In recent years, the ecological and economic values of forest plants have been gradually recognized worldwide. However, the growing global demand for new forest plant varieties with higher wood production capacity and better stress tolerance cannot be satisfied by conventional phenotype-based breeding, marker-assisted selection, and genomic selection. In the recent past, diverse omics technologies, including genomics, transcriptomics, epigenomics, proteomics, and metabolomics, have been developed rapidly, providing powerful tools for the precision genetic breeding of forest plants. Genomics lays a solid foundation for understanding complex biological regulatory networks, while other omics technologies provide different perspectives at different levels. Multi-omics integration combines the different omics technologies, becoming a powerful tool for genome-wide functional element identification in forest plant breeding. This review summarizes the recent progress of omics technologies and their applications in the genetic studies on forest plants. It will provide forest plant breeders with an elementary knowledge of multi-omics techniques for future breeding programs. Full article
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