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Functional Genomics of Forest Trees

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

Deadline for manuscript submissions: closed (23 July 2023) | Viewed by 16805

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Special Issue Editors

Dr. Zhong Chen

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Guest Editor

Department of Silviculture, College of Forestry, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
Interests: functional genomics; tree genetics and molecular biology; floral development; triterpenoid saponin

Dr. Meixia Ye

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Guest Editor

Center of Computational Biology, Beijing Forestry University, Beijing, China
Interests: quantitative genetics; statistical genetics; system biology

Special Issue Information

Dear Colleagues,

Forest trees make a significant contribution to sustainability with renewable resources, the supply of ecosystem services and the global economy. In over a decade since the sequencing and release of the first forest tree genome, black cottonwood (Populus trichocarpa Torr. and Gray), we have witnessed tremendous advances in forest tree physiology, genetics and molecular biology derived from genomic resources. With the rapid development of high-throughput, next-generation sequencing technologies and novel biostatistical tools, the related research of forest trees has entered the functional genomics era. The challenge faced will be to identify genes underlying important traits and to analyze the functions of these genes.

The present Special Issue in the journal Forests, entitled "Functional Genomics of Forest Trees" encourages the submission of research as well as review papers dealing with new advances in functional genomics of forest trees. The main contents could be related to new perspectives in tree physiology, growth, development, and breeding, especially in wood formation and quality, floral development, sex differentiation, secondary metabolism, and stress tolerance. The topics covered include but are not limited to the identification and functional characterization of coding and non-coding features in genomes, multi-omics analysis, gene expression profiling, SNP technologies, genetic engineering approaches, such as transformation systems, or cutting-edge technologies, such as CRISPR/Cas9 gene editing, as well as bioinformatics, QTL mapping, phenomics, quantitative genetics, and system biology.

As the Guest Editors of this Special Issue, we would like to invite you to participate in this venture by contributing a paper on the topic of your choice within the broad area covered by "Functional Genomics of Forest Trees". We look forward to receiving your contribution.

Dr. Zhong Chen
Dr. Meixia Ye
Guest Editors

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Keywords

functional genomics
multi-omics analysis
tree genetics
regulation of gene expression
tree molecular biology
tree breeding
bioinformatics
quantitative genetics

Published Papers (10 papers)

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Research

21 pages, 18832 KiB

Open AccessArticle

The MYB Transcription Factor Family in Eucommia ulmoides: Genome-Wide Identification, Characterization, and Network Analysis in Relation to the Rubber Biosynthetic Genes

by Xiaotong Hu, Yun Li, Yufei Xia and Yanjun Ma

Forests 2023, 14(10), 2064; https://doi.org/10.3390/f14102064 - 16 Oct 2023

Viewed by 945

Abstract

The MYB transcription factor family is one of the largest families of plant transcription factors (TFs), and it plays a vital role in the entire process of a plant’s growth and development. Well known in China, Eucommia ulmoides (E. ulmoides) produces a form of natural rubber called Eucommia ulmoides gum (EUG). Nevertheless, there is little research on the evolutionary history and expression patterns of its MYBs, as well as on the regulation of EUG by MYB TFs. This research provides a comprehensive description, classification, and potential functional analysis of the EuMYB gene family. A total of 119 MYB members of E. ulmoides were identified based on the whole genome sequencing data, and their gene structure, phylogenetics, chromosome location, conserved motifs, etc., were analyzed. Based on the phylogenetic tree results, EuMYBs could be divided into 35 sub-groups. In addition, chromosomal localization and collinearity analysis revealed the heterogeneous distribution of the MYB family in the E. ulmoides’ genome, indicating the expansion of its gene family. Moreover, promoter cis-acting elements showed that the promoter contained abundant light-responsive elements, anaerobic-induction-responsive elements, and abscisic-acid-responsive elements. A co-expression regulatory network between the EUG biosynthesis genes and the EuMYBs was built. Meanwhile, regarding the six EuMYBs with high expression in the gum-forming tissues selected that correlated with the farnesyl diphosphate synthase (FPS1) structural gene, RT-qPCR experiments showed a possible regulatory relationship between EuMYBs and FPS1, which played an important role in EUG biosynthesis. In conclusion, this paper defines a research gap and lays a foundation for further studies on the biological functions of EuMYBs. Full article

(This article belongs to the Special Issue Functional Genomics of Forest Trees)

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14 pages, 3707 KiB

Open AccessArticle

Transcriptomic and Non-Targeted Metabolomic Analyses Reveal Changes in Metabolic Networks during Leaf Coloration in Cyclocarya paliurus (Batalin) Iljinsk

by Caowen Sun, Shengzuo Fang and Xulan Shang

Forests 2023, 14(10), 1948; https://doi.org/10.3390/f14101948 - 25 Sep 2023

Viewed by 958

Abstract

Secondary metabolites in Cyclocarya paliurus (Batalin) Iljinsk. leaves are beneficial for human health. The synthesis and accumulation of secondary metabolites form a complex process that is influenced by the trade-off between primary and secondary metabolism and by the biosynthetic pathways themselves. In this study, we explored the relationship between secondary metabolite accumulation and the activity of metabolic networks in leaves of C. paliurus. Leaves at three different growth stages were subjected to transcriptomic and non-targeted metabolomic analyses. The results revealed that nitrogen assimilation increased and carbon assimilation decreased as leaves matured, and the patterns of secondary metabolite accumulation and gene expression differed among the leaves at different growth stages. Mature green leaves had higher nitrogen assimilation and lower carbon assimilation, which were correlated with variations in secondary metabolite accumulation. As a major source of carbon and nitrogen, glutamine accumulated in the mature green leaves of C. paliurus. The accumulation of glutamine inhibited phenylalanine biosynthesis by modulating the pentose phosphate pathway but promoted acetyl-CoA biosynthesis through the tricarboxylic acid cycle. These changes led to decreased flavonoid contents and increased triterpenoid contents in mature leaves. These metabolomic and transcriptomic data reveal the differential expression of metabolic regulatory networks during three stages of leaf development and highlight the trade-off between primary and secondary metabolism. Our results provide a comprehensive picture of the metabolic pathways that are active in the leaves of C. paliurus at different growth stages. Full article

(This article belongs to the Special Issue Functional Genomics of Forest Trees)

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16 pages, 3034 KiB

Open AccessArticle

The Construction of a High-Density Genetic Map for the Interspecific Cross of Castanea mollissima × C. henryi and the Identification of QTLs for Leaf Traits

by Xibing Jiang, Yanpeng Wang, Junsheng Lai, Jian Wu, Conglian Wu, Weiyun Hu, Xiaolong Wu and Bangchu Gong

Forests 2023, 14(8), 1684; https://doi.org/10.3390/f14081684 - 20 Aug 2023

Viewed by 894

Abstract

Chinese chestnut is an economically and ecologically valuable tree species that is extensively cultivated in China. Leaf traits play a vital role in the photosynthetic capacity, chestnut yield, and quality, making them important breeding objectives. However, there has been limited research on constructing high-density linkage maps of Chinese chestnut and conducting quantitative trait loci (QTL) analyses for these leaf traits. This knowledge gap has hindered the progress of selection in Chinese chestnut breeding. In this study, we selected a well-established interspecific F₁ population, consisting of Castanea mollissima ‘Kuili’ × C. henryi ‘YLZ1’, to construct comprehensive genetic maps for chestnut. Through the use of a genotyping-by-sequencing (GBS) technique, we successfully created a high-density linkage map based on single-nucleotide polymorphisms (SNPs) from the F₁ cross. The results showed that 4578 SNP markers were identified in the genetic linkage map, and the total length was 1812.46 cM, which was distributed throughout 12 linkage groups (LGs) with an average marker distance of 0.4 cM. Furthermore, we identified a total of 71 QTLs associated with nine chestnut leaf traits: chlorophyll b content (chlb), stomatal conductance (Gs), leaf area (LA), leaf dry weight (LDW), leaf fresh weight (LFW), leaf length (LL), leaf width (LW), petiole length (PL), and specific leaf weight (SLW). These QTLs were identified based on phenotypic data collected from 2017 to 2018. Notably, among the 71 QTLs, 29 major QTLs were found to control leaf area (LA), leaf dry weight (LDW), and leaf width (LW). The high-density genetic mapping and QTL identification related to leaf traits in this study will greatly facilitate marker-assisted selection (MAS) in chestnut breeding programs. Full article

(This article belongs to the Special Issue Functional Genomics of Forest Trees)

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30 pages, 17626 KiB

Open AccessArticle

Genome-Wide Identification, Characterization, and Expression Profiling of the Glutaredoxin Gene Family in Tea Plant (Camellia sinensis)

by Dong Jiang, Wenhai Yang, Jianhui Pi, Guoqun Yang, Yong Luo, Shenxiu Du, Ning Li and Li-Jun Huang

Forests 2023, 14(8), 1647; https://doi.org/10.3390/f14081647 - 15 Aug 2023

Cited by 1 | Viewed by 1278

Abstract

Glutaredoxins (GRXs) are a widely distributed group of small oxidoreductases that play an important role in responding to oxidative stress and maintaining redox homeostasis in living organisms. However, there has been no report on the GRX gene family in tea plants (Camellia sinensis). In this study, we conducted a systematic analysis of the CsGRX gene family in tea plants and identified a total of 86 CsGRX genes. Based on phylogenetic and conserved active site analyses, these genes were classified into four categories: CC-type, CPYC-type, CGFS-type, and GRL-type. These subtypes showed distinct characteristics in terms of gene structure, conserved motif, chromosome distribution, subcellular localization, cis-regulatory elements, and expression pattern, indicating functional differences among CsGRX family members. Collinearity analysis showed that the CsGRX family may have undergone member expansion using tandem and segmental duplication along with overwhelmingly strict purifying selection. Protein tertiary structure analysis supported the conserved site-specific binding of CsGRX family members to glutathione. Protein interaction network analysis revealed that CsGRX may interact with glutathione reductase (GR), 2-Cys Peroxiredoxin BAS1, TGA3, and others to participate in the oxidative stress response in tea plants. GO and KEGG enrichment analyses also supported the important role of the CsGRX family in maintaining intracellular redox homeostasis. Expression analysis based on RNA-seq revealed differential expression patterns of CsGRX genes under drought, cold stress, and in different tissues, which were further confirmed by RT-qPCR analysis, indicating their broad-spectrum functionality. This study provides a new perspective for further exploring the evolution and molecular functions of specific CsGRX genes. Full article

(This article belongs to the Special Issue Functional Genomics of Forest Trees)

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23 pages, 7340 KiB

Open AccessArticle

Comprehensive Bioinformatics and Expression Analysis of TCP Transcription Factors in Liriodendron chinense Reveals Putative Abiotic Stress Regulatory Roles

by Delight Hwarari, Yuanlin Guan, Rongxue Li, Ali Movahedi, Jinhui Chen and Liming Yang

Forests 2022, 13(9), 1401; https://doi.org/10.3390/f13091401 - 1 Sep 2022

Cited by 9 | Viewed by 1667

Abstract

As a magnoliid angiosperm, the Liriodendron chinense (Hamsl) Sarg in the Magnoliaceae family is susceptible to external environmental factors. The TEOSINTE BRANCHED 1/CYCLOIDEA/PROLIFERATING CELL FACTORS (TCP) proteins known for their growth and developmental biological roles have been identified in various plant species but not in the Liriodendron chinense. In this study, 15 TCP genes were identified in the L. chinense genome, and categorized into two classes, termed class I (PCF) and class II (CIN and CYC/TB1). A total of 14 TCP genes were located on the 10 chromosomes, and the remaining one, on a contig. Multispecies phylogenetic tree analysis supported the classification of identified LcTCP genes and exhibited that the expansion of the LcTCP gene family was before the angiosperm evolutionary divergence times. Additional gene duplication investigations revealed a purifying selection pressure during evolution history. Moreover, the LcTCP genes were also observed to have various cis-acting elements related to plant growth and development, phytohormone regulations, and abiotic stress responses. Gene expression pattern analysis also paraded that LcTCP genes play a crucial role in abiotic stress regulations. In particular, LcTCP1 in all stresses investigated. Overall, our findings suggest a pivotal role for the TCP gene family during external environmental stresses in L. chinense. This study will provide valuable information on the identification and function of the LcTCPs during abiotic stresses, paving the way for further research on the functional verification of L. chinense TCPs. Full article

(This article belongs to the Special Issue Functional Genomics of Forest Trees)

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15 pages, 3536 KiB

Open AccessArticle

Transcriptome Analysis Reveals Gene Expression Changes during Repair from Mechanical Wounding in Aquilaria sinensis

by Ruyue Du, Yanjing Zhuo, Jieru Xu, Cheng Ming and Jinhui Chen

Forests 2022, 13(8), 1258; https://doi.org/10.3390/f13081258 - 9 Aug 2022

Cited by 1 | Viewed by 1664

Abstract

Plants repair their mechanical wounds by reprogramming secondary metabolism. However, which genes are reprogrammed during this repair process in Aquilaria sinensis has rarely been studied. Here, we used high-throughput RNA sequencing to explore the changes in the transcriptome of Aquilaria’s xylem, six months after the stem was subjected to mechanical wounding. In total, 1165 transcripts were differentially accumulated, of which 1002 transcripts were increased and 163 were decreased in their abundances (|log₂ (fold change)| ≥ 1 and FDR ≤ 0.05). The majority of these genes encode products involved in plant secondary metabolism, transcription regulation, and phytohormone metabolism and signaling. The up-regulated genes were classified into 15 significantly enriched GO terms and were involved in 83 pathways, whereas the down-regulated genes were classified into 5 significantly enriched GO terms and represented 43 pathways. Gene annotation demonstrated that 100 transcripts could encode transcription factors (TFs), such as WRKY, AP2, MYB, and Helix-loop-helix (HLH) TFs. We inferred that the differential expression of TFs, genes associated with plant hormones, phenylpropanoid biosynthesis, and sesquiterpenoid biosynthesis may contribute to the repair of the stem after mechanical wounding in A. sinensis. Using co-expression analysis and prediction of TF binding sites, a TF–gene regulatory network for Aquilaria lignin biosynthesis was constructed. This included the MYB, HLH, WRKY, and AP2 TFs, and the COMT1, 4CLL7, and CCR1 genes. The changes in 10 candidate genes were validated by quantitative reverse-transcription PCR, indicating significant differences between the treated and untreated areas. Our study provides global gene expression patterns under mechanical wounding and would be valuable to further studies on the molecular mechanisms of plant repair in A. sinensis. Full article

(This article belongs to the Special Issue Functional Genomics of Forest Trees)

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26 pages, 15479 KiB

Open AccessArticle

Histological, Morpho-Physiological, and Biochemical Changes during Adventitious Rooting Induced by Exogenous Auxin in Magnolia wufengensis Cuttings

by Yi Wang, Muhammad Asif Khan, Zhonglong Zhu, Tiemei Hai, Ziyang Sang, Zhongkui Jia and Luyi Ma

Forests 2022, 13(6), 925; https://doi.org/10.3390/f13060925 - 13 Jun 2022

Cited by 3 | Viewed by 2131

Abstract

Magnolia wufengensis, a rare ornamental tree species, is now in a huge gap between market demand and actual supply of seedlings. As cutting propagation is one of the most important means to solve the shortage of seedling supply, this study developed an efficient cutting propagation procedure of M. wufengensis, revealed the morphological and histological changes of adventitious root formation, and explored the rhythm correlation between rooting process and physiological and biochemical changes. Cuttings pre-treated with NAA:IBA (2:1) exhibited the best rooting performance. Anatomical analysis demonstrated that adventitious root primordia of M. wufengensis were initiated from cambial and parenchyma cells of xylem, with no relationship to the callus formed on the epidermis. The rooting process of M. wufengenis can be divided into four periods: induction phase (0–8 dap) (dap means days after planting), initiation phase (8–13 dap), expression phase (13–18 dap), and extension phase (18–28 dap). NAA:IBA (2:1) induced the accumulations of 3-indoleacetic-acid and increased the contents of peroxidase and polyphenol-oxidase near the wounding at induction phase. The initiation phase, with the first histological modifications to the formation of meristemoids, correspond to the increase of peroxidase, polyphenol-oxidase, and soluble protein contents. The synergistic reaction of low 3-indoleacetic-acid and high levels of gibberellins and zeatin also stimulates the initiation phase. In the expression and extension phase, high activities of polyphenol-oxidase, IAA-oxidase, and increased contents of soluble protein co-stimulate the emergence and outgrowth of adventitious roots. The present study not only provides optimized protocol by application of auxin combination but also presents insights in the histological, morpho-physiological, and biochemical changes in stem cuttings of M. wufengensis. Full article

(This article belongs to the Special Issue Functional Genomics of Forest Trees)

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14 pages, 4639 KiB

Open AccessArticle

Integrated Analysis of Fatty Acid Metabolism and Transcriptome Involved in Olive Fruit Development to Improve Oil Composition

by Xiaoxia Liu, Liqin Guo, Jianguo Zhang, Li Xue, Ying Luo and Guodong Rao

Forests 2021, 12(12), 1773; https://doi.org/10.3390/f12121773 - 14 Dec 2021

Cited by 9 | Viewed by 2213

Abstract

Olea europaea L. is an important oil crop with excellent nutritional properties. In this study, a full-length transcriptome combined with fatty acid composition was used to investigate the molecular mechanism of fatty acid (FA) metabolism of olive fruits at various stages of development (S1–S5). A total of 34 fatty acids (FAs) were measured using gas chromatography-mass spectrometry (GC-MS). All transcripts of FA metabolism during olive fruit development were studied, including glycolysis, fatty acid synthesis, triacylglycerol synthesis, and FA degradation. A total of 100 transcripts of 11 gene families, 68 transcripts of 12 gene families, 55 transcripts of 7 gene families, and 28 transcripts of 7 gene families were identified as encoding for enzymes involved in FA metabolism. Furthermore, one of the critical reactions in TAG metabolism is the activation of fatty acyl chains to fatty acyl CoA, which is catalyzed by long-chain acyl CoA synthetases (LACS). Phylogenetic analysis showed that 13 putative LACS-encoding genes clustered into five groups, of which two putative transcripts encoding LACS6/7 may participate in FA degradation. The aim of this study was to evaluate the fatty acid from synthesis to degradation pathways during olive fruit development to provide a better understanding of the molecular mechanism of FA metabolism during olive fruit maturation and provide information to improve the synthesis of oil components that are beneficial to human health. Full article

(This article belongs to the Special Issue Functional Genomics of Forest Trees)

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11 pages, 2111 KiB

Open AccessArticle

Triterpenoids Biosynthesis Regulation for Leaf Coloring of Wheel Wingnut (Cyclocaryapaliurus)

by Caowen Sun, Shengzuo Fang and Xulan Shang

Forests 2021, 12(12), 1733; https://doi.org/10.3390/f12121733 - 9 Dec 2021

Cited by 4 | Viewed by 2078

Abstract

Cyclocaryapaliurus leaves are rich in triterpenoids with positive results in the treatment of diabetes, antioxidation, and scavenging free radicals. C. paliurus red leaves have been found to contain higher flavonoids including anthocyanin, however, the triterpenoids accumulation pattern is still unclear. For the purpose of researching the triterpenoid accumulating mechanism during red new leaf development, transcriptome and metabolome analysis was conducted during C. paliurus the red leaf development process. The results uncovered that most triterpenoid ingredients were found to accumulate during leaves turning green, while the unique ingredients content including cyclocaric acid A, cyclocarioside I, cyclocarioside Ⅱand cyclocarioside Ⅲ decreased or remained unchanged. Functional structure genes (hydroxymethylglutaryl-CoA synthase, hydroxymethylglutaryl-CoA reductase, and farnesyl-diphosphate synthase) were identified for promoting triterpenoids accumulation mainly in the mevalonic acid pathway (MVA). Moreover, glycosyltransferase (UGT73C, UGT85A, and UGT85K) was also found attributed to triterpenoids accumulation. These findings provide information for a better understanding of the triterpenoid biosynthesis mechanism during leaf development and will be useful for targeted breeding. Full article

(This article belongs to the Special Issue Functional Genomics of Forest Trees)

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12 pages, 2670 KiB

Open AccessArticle

Detecting the Different Responses of Roots and Shoots to Gravity in Salix matsudana (Koidz)

by Guoyuan Liu, Yixin Li, Junfeng Gao, Zhicong Feng, Hongyi Guo, Hang Zou, Xintong Chu, Yaqi Li, Yanhong Chen, Chunmei Yu, Fei Zhong, Hui Wei and Jian Zhang

Forests 2021, 12(12), 1715; https://doi.org/10.3390/f12121715 - 7 Dec 2021

Cited by 4 | Viewed by 1948

Abstract

The study of the gravity response of roots and shoots is of great significance when exploring the polarity of plants and the development of the forest industry. In our study, normal and inverted cuts of Salix matsudana (Koidz) were cultured. The total RNAs of roots and shoots were extracted. Based on the comparative transcriptome, 412 and 668 genes were differentially expressed. The plasma membrane-, cell wall-, and extracellular region-related genes were up-regulated in the shoots, while the carbon metabolism and the nitrogen metabolism were up-regulated in the roots. Combining the alternative splicing genes, we found a potential gravity response network: in the shoots, LecRLKs were highly sensitive to gravity and further affected the alternative splicing of SNARE, as well as inducing an inhomogeneous distribution of auxin and a negative geotropism curve. In the roots, AP2/ERFs and STRKs were highly sensitive to gravity and regulated the expression level of STPKs and WAKs, finally resulting in a geotropism curve. Moreover, cell division was suppressed in both the roots and the shoots under inverted conditions with different mechanisms. Cell division inhibitors (KRPs) were up-regulated in the roots, while DNA helicase MCMs were down-regulated in the shoots. These results provide an important foundation for further studies of the molecular mechanisms and genetic regulation of plant responses to gravity and the plant polarity of forest trees. Full article

(This article belongs to the Special Issue Functional Genomics of Forest Trees)

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