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New Advances in Tree (Epi)Genomics and Implications for Breeding and Management

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

Deadline for manuscript submissions: closed (20 October 2020) | Viewed by 20470

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Special Issue Editor

Prof. Dr. Stéphane Maury

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Guest Editor

INRA, EA1207 USC1328 Laboratoire de Biologie des Ligneux et des Grandes Cultures, Université d’Orléans, F-45067 Orléans, France
Interests: plant epigenetic mechanisms; DNA methylation; meristem; phenotypic plasticity; adaptation; drought; phytohormone and chromatin crosstalk
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Forest tree breeding programs started only a few decades ago with two main aims: to guarantee the genetic origin of the forest reproductive material used in reforestation and to improve tree characteristics. Further criteria have recently been added—notably, adaptation to abiotic and biotic factors in response to new socioeconomic needs and global changes. A decade after the first forest tree genome sequence was released, the rapidly evolving genomics and bioinformatics toolbox has advanced our understanding of tree genomes. The potential impact of these technologies is considered major for adapting forests to the changing demand from ecosystem services in terms of conservation and use, as well as climate change.

The present Special Issue in the journal Forests (ISSN 1999-4907, https://0-www-mdpi-com.brum.beds.ac.uk/journal/forests), entitled "New Advances in Tree (Epi)Genomics and Implications for Breeding and Management" encourages the submission of research as well as review papers dealing with new advances in tree genomics and epigenomics that could be related to new perspectives in tree breeding and management.

Dr. Stephane Maury
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

tree
genomes
epigenomes
breeding
conservation of genetic ressources
biotechnology
climate change

Published Papers (5 papers)

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Research

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20 pages, 6234 KiB

Open AccessArticle

Whole-Genome DNA Methylation Associated With Differentially Expressed Genes Regulated Anthocyanin Biosynthesis Within Flower Color Chimera of Ornamental Tree Prunus mume

by Liangbao Jiang, Man Zhang and Kaifeng Ma

Forests 2020, 11(1), 90; https://0-doi-org.brum.beds.ac.uk/10.3390/f11010090 - 10 Jan 2020

Cited by 16 | Viewed by 3809

Abstract

DNA methylation is one of the best-studied epigenetic modifications involved in many biological processes. However, little is known about the epigenetic mechanism for flower color chimera of Prunus mume (Japanese apricot, mei). Using bisulfate sequencing and RNA sequencing, we analyzed the white (FBW) and red (FBR) petals collected from an individual tree of Japanese apricot cv. ‘Fuban Tiaozhi’ mei to reveal the different changes in methylation patterns associated with gene expression leading to significant difference in anthocyanins accumulation of FBW (0.012 ± 0.005 mg/g) and FBR (0.078 ± 0.013 mg/g). It was found that gene expression levels were positively correlated with DNA methylation levels within gene-bodies of FBW and FBR genomes; however, negative correlations between gene expression and DNA methylation levels were detected within promoter domains. In general, the methylation level within methylome of FBW was higher; and in total, 4,618 differentially methylated regions (DMRs) and 1,212 differentially expressed genes (DEGs) were detected from FBW vs. FBR. We also identified 82 DMR-associated DEGs, and 13 of them, including PmBAHD, PmCYP450, and PmABC, were playing critical roles in phenylalanine metabolism pathway, glycosyltransferase activity, and ABC transporter. The evidence exhibited DNA methylation may regulate gene expression resulting in flower color chimera of Japanese apricot. Full article

(This article belongs to the Special Issue New Advances in Tree (Epi)Genomics and Implications for Breeding and Management)

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11 pages, 3913 KiB

Open AccessArticle

DNA Methylation of Farnesyl Pyrophosphate Synthase, Squalene Synthase, and Squalene Epoxidase Gene Promoters and Effect on the Saponin Content of Eleutherococcus Senticosus

by Zhuo Wang, Hongyu Guo, Yantong Zhang, Limei Lin, Minghui Cui, Yuehong Long and Zhaobin Xing

Forests 2019, 10(12), 1053; https://0-doi-org.brum.beds.ac.uk/10.3390/f10121053 - 20 Nov 2019

Cited by 9 | Viewed by 2144

Abstract

Eleutherococcus senticosus (Ruper. et Maxim.) Maxim is a traditional Chinese medicine. The saponin components of E. senticosus have several biological effects, including reduction of blood lipids; protection against liver, heart, and vascular disease; and antitumor activity. The DNA methylation of E. senticosus farnesyl pyrophosphate synthase (FPS), squalene synthase (SS), and squalene epoxidase (SE) gene promoters and the mechanism of the influence of these enzymes on saponin synthesis and accumulation in E. senticosus were explored using bisulfite sequencing technology, real-time PCR, the vanillin-concentrated sulfuric acid chromogenic method, and LC-MS. There are 19 DNA methylation sites and 8 methylation types in the FPS gene. The SS gene has nine DNA methylation sites and two DNA methylation types. The SE gene has 16 DNA methylation sites and 7 methylation types. The total saponin content in the high and low DNA methylation groups were 1.07 ± 0.12 and 2.92 ± 0.32 mg/g, respectively. Statistical analysis indicated that the gene expression of the FPS, SS, and SE genes was significantly positively correlated with the saponin content (p < 0.05), and that the methylation ratio was significantly negatively correlated with the saponin content (p < 0.01), while the expression of the SS and SE genes was significantly positively correlated (p < 0.01). A total of 488 metabolites were detected from E. senticosus and 100 different metabolites were screened out by extensive targeted metabolomics. The amount of most metabolites related to the mevalonate pathway was higher in the low DNA methylation group than in the high DNA methylation group. It was demonstrated that there are DNA methylation sites in the promoter regions of the FPS, SS, and SE genes of E. senticosus, and DNA methylation in this region could significantly inhibit synthesis in the mevalonate pathway, thus reducing the content of the final product E. senticosus saponin. Full article

(This article belongs to the Special Issue New Advances in Tree (Epi)Genomics and Implications for Breeding and Management)

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22 pages, 12708 KiB

Open AccessArticle

PacBio Long-Read Sequencing Reveals the Transcriptomic Complexity and Aux/IAA Gene Evolution in Gnetum (Gnetales)

by Chen Hou, Nan Deng and Yingjuan Su

Forests 2019, 10(11), 1043; https://0-doi-org.brum.beds.ac.uk/10.3390/f10111043 - 18 Nov 2019

Cited by 6 | Viewed by 3611

Abstract

The genus Gnetum includes pantropical trees, shrubs and lianas, with unresolved phylogenetic relationships with other seed plant groups. Despite the reference genome for this genus being recently published, the molecular mechanisms that regulate the reproductive organ development of Gnetum remain unclear. A previous study showed that indole-3-acetic acid is involved in the regulation of female strobili of Gnetum, while the diversity and evolution of indole-3-acetic acid-related genes—the Aux/IAA genes—have never been investigated in Gnetales. Thus, a pooled sample from different developmental stages of female strobili in Gnetum luofuense C.Y. Cheng was sequenced using PacBio single-molecular long-read technology (SMRT) sequencing. PacBio SMRT sequencing generated a total of 53,057 full-length transcripts, including 2043 novel genes. Besides this, 10,454 alternative splicing (AS) events were detected with intron retention constituting the largest proportion (46%). Moreover, 1196 lncRNAs were identified, and 8128 genes were found to possess at least one poly (A) site. A total of 3179 regulatory proteins, including 1413 transcription factors (e.g., MADS-box and bHLHs), 477 transcription regulators (e.g., SNF2), and 1289 protein kinases (e.g., RLK/Pelles) were detected, and these protein regulators probably participated in the female strobili development of G. luofuense. In addition, this is the first study of the Aux/IAA genes of the Gnetales, and we identified 6, 7 and 12 Aux/IAA genes from Gnetum luofuense, Welwitschia mirabilis, and Ephedra equistina, respectively. Our phylogenetic analysis reveals that Aux/IAA genes from the gymnosperms tended to cluster and possessed gene structures as diverse as those in angiosperms. Moreover, the Aux/IAA genes of the Gnetales might possess higher molecular evolutionary rates than those in other gymnosperms. The sequencing of the full-length transcriptome paves the way to uncovering molecular mechanisms that regulate reproductive organ development in gymnosperms. Full article

(This article belongs to the Special Issue New Advances in Tree (Epi)Genomics and Implications for Breeding and Management)

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21 pages, 5685 KiB

Open AccessArticle

A Complete Transcriptional Landscape Analysis of Pinus elliottii Engelm. Using Third-Generation Sequencing and Comparative Analysis in the Pinus Phylogeny

by Shu Diao, Xianying Ding, Qifu Luan and Jingmin Jiang

Forests 2019, 10(11), 942; https://0-doi-org.brum.beds.ac.uk/10.3390/f10110942 - 24 Oct 2019

Cited by 9 | Viewed by 3216

Abstract

The planting of Pinus elliottii Engelm. has now reached close to three million ha in China. Molecular breeding as part of the improvement program for P. elliottii in southern China has been carried out in recent years. Third-generation sequencing (Pacbio sequencing technology, TGS) was used to obtain the exome of P. elliottii for molecular breeding. A total of 35.8 Gb clean reads were generated using TGS. After removing the redundant reads, we obtained 80,339 high-accuracy transcripts. Significantly, a total of 76,411 transcripts (95.1%) were blasted to public annotation databases. We predicted 65,062 intact coding sequences (CDSs), 8916 alternative splicing events, 1937 long non-coding RNAs, and 22,109 simple sequence repeats (SSRs) based on these obtained transcripts. Using the public databases and the data obtained above, 23 orthologous single-copy genes were identified to analyze the phylogenetic relationships for Pinus firstly including P. elliottii. Many positive selection genes involved in important biological processes and metabolism pathways were identified between P. elliottii and other pines. These positive selection genes could be candidate genes to be researched on the genetic basis of superior performance. Our study is the first to reveal the full-length and well-annotated transcripts of P. elliottii, which could provide reference for short transcriptome sequences in the research of genetics, phylogenetics, and genetic improvement for the non-reference genome species. Full article

(This article belongs to the Special Issue New Advances in Tree (Epi)Genomics and Implications for Breeding and Management)

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Review

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21 pages, 1677 KiB

Open AccessReview

Advances and Promises of Epigenetics for Forest Trees

by Joana Amaral, Zoé Ribeyre, Julien Vigneaud, Mamadou Dia Sow, Régis Fichot, Christian Messier, Gloria Pinto, Philippe Nolet and Stéphane Maury

Forests 2020, 11(9), 976; https://0-doi-org.brum.beds.ac.uk/10.3390/f11090976 - 10 Sep 2020

Cited by 47 | Viewed by 7032

Abstract

The importance of tree genetic variability in the ability of forests to respond and adapt to environmental changes is crucial in forest management and conservation. Along with genetics, recent advances have highlighted “epigenetics” as an emerging and promising field of research for the understanding of tree phenotypic plasticity and adaptive responses. In this paper, we review recent advances in this emerging field and their potential applications for tree researchers and breeders, as well as for forest managers. First, we present the basics of epigenetics in plants before discussing its potential for trees. We then propose a bibliometric and overview of the literature on epigenetics in trees, including recent advances on tree priming. Lastly, we outline the promises of epigenetics for forest research and management, along with current gaps and future challenges. Research in epigenetics could use highly diverse paths to help forests adapt to global change by eliciting different innovative silvicultural approaches for natural- and artificial-based forest management. Full article

(This article belongs to the Special Issue New Advances in Tree (Epi)Genomics and Implications for Breeding and Management)

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