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Functional Genomics and Molecular Genetics Studies on Plant Regulation
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Functional Genomics and Molecular Genetics Studies on Plant Regulation

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

Deadline for manuscript submissions: closed (25 October 2023) | Viewed by 12326

Special Issue Editor

Prof. Dr. Jianjun Hu

E-Mail Website
Guest Editor
Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
Interests: functional genomics; molecular genetics; plant regulation; transcriptome analysis; plant genetics

Special Issue Information

Dear Colleagues,

Plant growth, resistance, etc., is a very complex biological process that is affected by multiple influences of its own genome and complex environment. It is still difficult to understand how genotype and phenotype are related, and it is important to use genomic, transcriptomic, proteomic, and metabolomic technologies and molecular genetics to reveal the role of genes and non-coding sequences in the regulation of plant growth and development. This study, entitled "Functional Genomics and Molecular Genetics Studies on Plant Regulation", aims to collect the latest research progress and update our knowledge on the genetic basis of plant functional genomics and molecular genetics in understanding plant complex traits and promoting genetic improvement of plants.

Potential topics include, but are not limited to, the following:

  • Regulation of non-coding RNA in transcriptomics;
  • Omics analysis of agronomic traits, such as genomics, epigenomics, transcriptomics, proteomics, and metabolomics, etc.;
  • GWAS and QTL mapping, map-based cloning of plant complex traits;
  • Functional analysis and molecular mechanism of target genes;
  • Genetic diversity and trait discovery;
  • Application of gene editing in trait development and deployment.

Prof. Dr. Jianjun Hu
Guest Editor

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

  • functional genomics
  • molecular genetics
  • plant regulation
  • transcriptome analysis
  • multi-omic
  • genetic variation

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Published Papers (7 papers)

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Research

16 pages, 4281 KiB  
Article
HS-SPEM-GC-MS Analyses of Volatiles and Transcriptome Analysis of Camellia tetracocca in Response to Feeding by Empoasca onukii Matsuda
by Ni Zhang, Jinqiu Wang, Tianyi Pu, Zhibing Zhao, Weiwen Tan, Zhengwen Yu and Yuehua Song
Forests 2023, 14(10), 2059; https://doi.org/10.3390/f14102059 - 15 Oct 2023
Viewed by 1336
Abstract
The tea leafhopper (Empoasca (Matsumurasca) onukii Matsuda, 1952) is the predominant pest infesting tea and causes significant losses in yield. Plants have evolved multiple defense responses to protect themselves from insect herbivores. Camellia tetracocca, a kind of ancient tea [...] Read more.
The tea leafhopper (Empoasca (Matsumurasca) onukii Matsuda, 1952) is the predominant pest infesting tea and causes significant losses in yield. Plants have evolved multiple defense responses to protect themselves from insect herbivores. Camellia tetracocca, a kind of ancient tea with local popularity, is unique to southwest China. This ancient tea is often attacked by the tea leafhopper. However, there are no relevant reports on changes in volatile components and defense signaling pathways after Camellia tetracocca has been attacked by E. onukii. To reveal changes in the responses of the volatile components of C. tetracocca to E. onukii, the headspace sampling technique and GC-MS were adopted to determine and analyze the volatiles. Furthermore, to unveil the defense mechanisms of C. tetracocca in response to E. onukii, transcriptome analysis was applied to damaged tea leaves and healthy leaves. The GC-MS analysis showed significant increases in the linalool and (E)-2-hexenal contents. The transcriptome analysis revealed a set of core pest-responsive genes (3074 upregulated and 5098 downregulated). Most of the enriched pest-responsive genes are mainly involved in plant hormone signal transduction photosynthesis, terpenoid backbone biosynthesis, alpha-linolenic acid metabolism, and the NF-κB signaling pathway. A conjoint analysis of the transcriptome and metabolome indicated that N2-acetylornithine, D-malic acid, theogallin, fucosyllactose, 5-caffeoylquinic acid, fumarprotocetraric acid, and arabinogalactose have a significant correlation with LOC114279735, LOC114317534, LOC114282078, LOC114317768, and LOC114263181. This study lays a foundation for further research on the breeding and cultivation of insect-resistant germplasm resources for C. tetracocca and on the promotion and development of the plant. Full article
(This article belongs to the Special Issue Functional Genomics and Molecular Genetics Studies on Plant Regulation)
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12 pages, 5662 KiB  
Article
Establishment of a Transient Transformation Protocol in Cinnamomum camphora
by Siyi Zhang, Rong Hu, Lin Yang and Zhaojiang Zuo
Forests 2023, 14(9), 1872; https://doi.org/10.3390/f14091872 - 14 Sep 2023
Cited by 3 | Viewed by 1640
Abstract
Cinnamomum camphora is an excellent evergreen broad-leaved tree species with strong stress tolerance, but its molecular character revelation as well as ecological and economic value improvement were limited due to the lack of a genetic transformation system. To establish a simple and efficient [...] Read more.
Cinnamomum camphora is an excellent evergreen broad-leaved tree species with strong stress tolerance, but its molecular character revelation as well as ecological and economic value improvement were limited due to the lack of a genetic transformation system. To establish a simple and efficient transient transformation system for uncovering the molecular mechanism of plant tolerating stresses and promoting the selective breeding of good varieties, the infection method, co-cultivation time, infection solution concentration, and growth density of Agrobacterium tumefaciens containing green fluorescent protein (GFP)-based calmodulin protein 3 gene (GCaMP3) were identified by monitoring the fluorescence emitted from GCaMP3 bound to Ca2+. Meanwhile, the transient transformation effects were evaluated via cytoplasmic Ca2+ concentration variations at high temperatures of 35 °C and 40 °C. When C. camphora leaves were infected with A. tumefaciens containing GCaMP3 via injection and soaking, no significant difference was detected in the fluorescence intensity over 48 h, indicating that the two infection methods had the same transient transformation efficiency. By prolonging the co-cultivation time, the fluorescence intensity gradually increased, reached its strongest at the 48th h, and then gradually declined. For the infection solution concentration, an OD600 of 0.7 led to the strongest fluorescence intensity, with an increase of 42.2%, 13.7%, 4.2%, and 14.2%, respectively, compared to that at OD600 of 0.5, 0.6, 0.8, and 0.9. When A. tumefaciens growth density OD600 was 0.5–0.7, the strongest fluorescence intensity was detected after transient transformation. Combining these optimum conditions, GCaMP3 was transferred into C. camphora, which indicated the variations in cytoplasmic Ca2+ concentration at high temperatures, with the fluorescence intensity at 35 °C and 40 °C increasing by 12.6% and 30.6%, respectively, in contrast to that at 28 °C. Therefore, it should be an efficient transient transformation system for C. camphora, with A. tumefaciens growth density OD600 of 0.5–0.7, infection solution concentration OD600 of 0.7, and co-cultivation time of 48 h by using both injection and soak infection methods, which is beneficial for uncovering the Ca2+ signal transduction in the plant tolerating stresses and promoting its molecular biology development and selective breeding of good varieties. Full article
(This article belongs to the Special Issue Functional Genomics and Molecular Genetics Studies on Plant Regulation)
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19 pages, 7938 KiB  
Article
Comprehensive Analysis of the DNA Methyltransferase Genes and Their Association with Salt Response in Pyrus betulaefolia
by Yufeng Zhang, Chunxiao Liu, Xiaoyang Xu, Jialiang Kan, Hui Li, Jing Lin, Zongming Cheng and Youhong Chang
Forests 2023, 14(9), 1751; https://doi.org/10.3390/f14091751 - 30 Aug 2023
Cited by 2 | Viewed by 1622
Abstract
DNA methylation plays an indispensable role in genome stability, regulation of gene expression and plant stress response. It is mediated by DNA methyltransferases (MTases). Twelve putative MTases of P. betulaefolia were identified and were classified into MET1, CMT, DRM2 and Dnmt2 groups based [...] Read more.
DNA methylation plays an indispensable role in genome stability, regulation of gene expression and plant stress response. It is mediated by DNA methyltransferases (MTases). Twelve putative MTases of P. betulaefolia were identified and were classified into MET1, CMT, DRM2 and Dnmt2 groups based on the organization of various characteristic domains. Three pairs of paralogous genes were identified with the Ka/Ks ratio varied from 0.232 for PbeMET1a and PbeMET1b to 0.251 for PbeCMT2 and PbeCMT3, respectively. In addition, the Ka/Ks ratio for nine pairs of orthologous gene pairs between P. betulaefolia and apple were varied from 0.053 for PbeDRM3 and MD17G1031900 to 0.278 for PbeDnmt2b and MD15G1120500, respectively. All the 12 members of MTase genes were located on nine chromosomes out of 17 P. betulaefolia chromosomes with highly conserved protein sequence structures. The isoelectric points (pI) of MTases ranged from 4.74 to 7.24, while molecular weight varied from 35.99 to 174.32. The expression profiles of MTase and other salt-responsive genes under salt stress treatment revealed their important roles involved in salt response in P. betulaefolia. Furthermore, three selected salt-responsive genes (PbeNHX2.1, PbeCBL2 and PbeAKT2) were found altered in methylation level of promoters (which contain CpG islands) under salt stress. Especially, the PbeAKT2 promoter regions showed high CHG and CHH methylation types. Our study provided a genome-wide survey of the MTase gene family and highlighted their roles in salt response. These results also provided an effective way for the breeding and improvement of salt-tolerant pear varieties. Full article
(This article belongs to the Special Issue Functional Genomics and Molecular Genetics Studies on Plant Regulation)
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17 pages, 5562 KiB  
Article
Alternative First Exons Drive Enzymatic Activity Variation in Chalcone Synthase 3 of Dendrobium sinense
by Yu Wang, Liyan Liu, Qiongjian Ou, Huiyan You, Jia Wang and Jun Niu
Forests 2023, 14(9), 1702; https://doi.org/10.3390/f14091702 - 24 Aug 2023
Cited by 1 | Viewed by 1542
Abstract
Dendrobium sinense, a native orchid species of Hainan Island, is cultivated for its ornamental flowers. Recently, this species has gained significant attention due to its medicinal value. This study focuses on the identification of type III polyketide synthase (PKS), which catalyzes the [...] Read more.
Dendrobium sinense, a native orchid species of Hainan Island, is cultivated for its ornamental flowers. Recently, this species has gained significant attention due to its medicinal value. This study focuses on the identification of type III polyketide synthase (PKS), which catalyzes the formation of crucial intermediates in secondary metabolites. Through analysis of previous transcriptome data, a total of ten type III DsPKS genes were identified. Phylogenetic analysis categorized the type III PKS proteins into CHS, BBS, and PKS groups. Interestingly, the DsCHS3 gene exhibited alternative first exons, resulting in two splice variants, namely DsCHS3-1 and DsCHS3-2. Full-length cDNA sequencing revealed that DsCHS3-1 was the more prevalent splice variant. Prokaryotic expression and purification of DsCHS3-1 and DsCHS3-2 proteins were successfully achieved. Enzyme activity analysis demonstrated significantly higher catalytic activity in DsCHS3-2 compared to DsCHS3-1, particularly in the conversion of p-coumaryol-CoA and malonyl-CoA to naringin chalcone. Functional complementation assays in Arabidopsis mutants confirmed the higher catalytic activity of DsCHS3-2, as it restored flavonoid biosynthesis to a greater extent compared to DsCHS3-1. Overall, these findings offer valuable insights into the alternative splicing patterns and functional divergence of DsCHS3 genes in D. sinense. Full article
(This article belongs to the Special Issue Functional Genomics and Molecular Genetics Studies on Plant Regulation)
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14 pages, 3919 KiB  
Article
Integrated Transcriptome and Biochemical Analysis Provides New Insights into the Leaf Color Change in Acer fabri
by Guohua Liu, Heng Gu, Hongyu Cai, Congcong Guo, Ying Chen, Lianggui Wang and Gongwei Chen
Forests 2023, 14(8), 1638; https://doi.org/10.3390/f14081638 - 14 Aug 2023
Cited by 7 | Viewed by 1564
Abstract
Acer fabri is a widely distributed ornamental tree with colorful leaves and high ornamental value. Its young leaves change from red to red and green until turning fully green. To understand the mechanism of leaf color change, transcriptome sequencing and pigment content determination [...] Read more.
Acer fabri is a widely distributed ornamental tree with colorful leaves and high ornamental value. Its young leaves change from red to red and green until turning fully green. To understand the mechanism of leaf color change, transcriptome sequencing and pigment content determination were performed in three stages during the leaf color change of A. fabri. In total, 53,550 genes, including 838 transcription factors (TFs), were identified by transcriptome sequencing. In addition, the results of orthogonal partial least squares-discriminant analysis (OPLS-DA) of three pigments in the three stages of leaf color development suggested that carotenoids played a major role in the process of leaf color change from red to red-green, whereas anthocyanins played an important role in the process of leaf color change from red to green. Based on weighted gene co-expression network analysis (WGCNA), Af0034384 (HSFB2A), Af0051627 (NMT1), and Af0052541 (THY-1) were selected as hub genes from characteristic modules with significant correlation between carotenoids and anthocyanins. The results of gene network regulation maps and real-time fluorescence quantitative PCR (qRT-PCR) showed that Af0010511 (NAC100) upregulated the expression of Af0034384 (HSFB2A), leading to an increase in carotenoid content and the gradual greening of leaves during the transition from red to green. However, during the transition from red to green leaves, Af0033232 (NAC83) and Af0049421 (WRKY24) downregulated the expression of Af0051627 (NMT1) and Af0052541 (THY-1), respectively, leading to a decrease in anthocyanin content and the complete greening of leaves. These results could provide new ideas for studying the molecular mechanism of leaf color change in A. fabri and other species. Full article
(This article belongs to the Special Issue Functional Genomics and Molecular Genetics Studies on Plant Regulation)
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15 pages, 4867 KiB  
Article
Transcriptome Sequencing and Analysis of Genes Related to Disease Resistance in Pinus thunbergii
by Yu Zhang, Guicai Du, Qunqun Guo, Guosong Dong, Min Wang, Tingting Zhang and Ronggui Li
Forests 2023, 14(3), 650; https://doi.org/10.3390/f14030650 - 22 Mar 2023
Cited by 3 | Viewed by 2088
Abstract
Pinus thunbergii (P. thunbergii) is a gymnosperm with important economic and ecological value. In order to investigate the diagnosis and defense mechanism of P. thunbergii against Bursaphelenchus xylophilus (the pinewood nematode, PWN), the needles of P. thunbergii seedlings on the fifth [...] Read more.
Pinus thunbergii (P. thunbergii) is a gymnosperm with important economic and ecological value. In order to investigate the diagnosis and defense mechanism of P. thunbergii against Bursaphelenchus xylophilus (the pinewood nematode, PWN), the needles of P. thunbergii seedlings on the fifth day after being infected by PWN were taken as samples for transcriptome sequencing analysis. Compared with the control group, 647 genes were differentially expressed in the treatment group, of which 277 genes were upregulated and 370 genes were downregulated. Enrichment analysis showed that most of these differentially expressed genes were abundant in the biosynthesis of secondary metabolites, pathogen interaction and hormone signal transduction. In addition, among the differential genes, NBS-LRR genes, thiamine-metabolizing enzymes, phenylalanine ammonia lyase and acetaldehyde dehydrogenase were screened and analyzed. The analysis of the response of P. thunbergii to PWN stress and its disease resistance genes lays a foundation for the breeding of disease-resistant P. thunbergii in the future. Full article
(This article belongs to the Special Issue Functional Genomics and Molecular Genetics Studies on Plant Regulation)
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16 pages, 5064 KiB  
Article
Comparative Analysis of the Characteristics, Phylogenetic Relationships of the Complete Chloroplast Genome, and Maternal Origin Track of White Poplar Interspecific Hybrid GM107
by Bin Guo, Tingting Chen, Ying Li, Shanwen Li, Wasif Ullah Khan, Ren-Gang Zhang, Kai-Hua Jia and Xinmin An
Forests 2023, 14(3), 587; https://doi.org/10.3390/f14030587 - 16 Mar 2023
Cited by 1 | Viewed by 1973
Abstract
White poplars are a dominant tree species in natural ecosystems throughout China, where they are also widely planted for agroforestry and industrial uses. However, the phylogenetic relationships among poplars in section Populus have a complex genetic background influenced by frequent hybridization events and, [...] Read more.
White poplars are a dominant tree species in natural ecosystems throughout China, where they are also widely planted for agroforestry and industrial uses. However, the phylogenetic relationships among poplars in section Populus have a complex genetic background influenced by frequent hybridization events and, to date, only a few studies have attempted to clarify this background. In this study, we performed de novo assembly of the whole chloroplast (cp) genome of an elite individual GM107 with the size of 156,493 bp, which consists of a large single-copy (LSR) (84,610 bp), a small single-copy (SSC) (16,567 bp), and a pair of inverted repeats (27,658 bp). It comprises 127 genes, including 85 protein-coding genes, 36 tRNAs, and 6 rRNAs. Comparative analysis of the cp genomes was conducted among 7 poplars in section Populus and 4 cp DNA markers with >1% variable sites were detected. We found that Populus alba was the most closely related species to GM107 by phylogenetic analyses. RNA sequencing detected 66 genes that participated in translation, transcription, and photosynthesis. The expression levels of almost all 66 genes were higher in leaves than in other tissues, except for PtatpF and PtatpH. In all tissues, we detected higher transcript abundances of PtndhF, PtpsbA, PtpsbB, Ptrps14, PtatpF, and PtatpH than of other genes. Both cp genome and transcriptome data help understand evolution events in section Populus and unravel the origin of Chinese white poplars, and may contribute to the molecular genetic improvement of wood properties and carbon sink capacities in the breeding of poplars in this section. Full article
(This article belongs to the Special Issue Functional Genomics and Molecular Genetics Studies on Plant Regulation)
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