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Forest-Tree Gene Regulation in Response to Abiotic and Biotic Stress

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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 (15 October 2022) | Viewed by 40673

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Special Issue Editor

Dr. Yuepeng Song

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National Engineering Laboratory for Tree Breeding & Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, China
Interests: DNA methylation; transcription; genomics; epigenetics

Special Issue Information

Dear Colleagues,

Forests are a critical component of the global terrestrial ecosystem, covering a diverse geographical environment. As perennial plants, forests must adapt to simultaneous exposure to various abiotic and biotic stresses, which can affect their growth and survival. However, the mechanisms for stress-specific adaption in response to different abiotic and biotic stresses remain unclear. Thus, understanding the unique acclimation process for each abiotic treatment will require a comprehensive and systematic comparison of the responses of different trees to different abiotic and biotic stresses.

This Special Issue seeks contributions on all kinds of abiotic and biotic stress adaptation in trees, with the aim to provide an up-to-date compendium of recent research in this field from around the world. It provides an opportunity for researchers to present the results of studies on the genetic basis, transcriptional regulation mechanisms and physiological response of abiotic and biotic tolerant trees, with benefits for tree genetic improvement, forestation and forest management in the future.

Dr. Yuepeng Song
Guest Editor

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Keywords

trees
abiotic and biotic stresses
heat stress
cold stress
salt stress
metal stress
forest disease
environmental adaptation

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Published Papers (10 papers)

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Editorial

Jump to: Research, Review

3 pages, 1095 KiB

Open AccessEditorial

Abiotic and Biotic Stress Cascades in the Era of Climate Change Pose a Challenge to Genetic Improvements in Plants

by Yue Xiao, Menglei Wang and Yuepeng Song

Forests 2022, 13(5), 780; https://doi.org/10.3390/f13050780 - 18 May 2022

Cited by 6 | Viewed by 2504

Abstract

Forest ecosystems are vast, second in expanse only to marine ecosystems [...] Full article

(This article belongs to the Special Issue Forest-Tree Gene Regulation in Response to Abiotic and Biotic Stress)

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Research

Jump to: Editorial, Review

22 pages, 4608 KiB

Open AccessArticle

Genome-Wide Identification of miRNAs and Its Downstream Transcriptional Regulatory Network during Seed Maturation in Tilia tuan

by Xuri Hao, Lei Liu, Peng Liu, Menglei Wang and Yuepeng Song

Forests 2022, 13(11), 1750; https://doi.org/10.3390/f13111750 - 24 Oct 2022

Cited by 3 | Viewed by 1398

Abstract

Seed maturation not only determines the qualities and yields of seeds, but also affects seed storage and quality preservation. MicroRNAs (miRNAs) are a ubiquitous regulatory factor of gene expression in eukaryotes, which participate in the complex regulatory network of gene expression during seed maturation. However, miRNAs involved in maturation of Tilia tuan are still unknown. To reveal the role of miRNAs in T. tuan, small RNAs were profiled by high-throughput sequencing during seed maturation at five developmental stages. By predicting the target genes of miRNAs, the expression patterns of miRNAs during seed maturation were analyzed to identify those related to seed maturation. A total of 187 known miRNAs belonging to 42 miRNA families were found at five different seed maturation stages. Based on the analysis of unknown sequences, eight novel miRNAs were identified; 11,775 targets of 195 miRNAs were identified. Large numbers of miRNAs with diverse expression patterns, multiple-targeting and co-targeting of many miRNAs, and a complex regulatory network of miRNA-target genes were identified during seed maturation. These miRNAs and their targets may be involved in fatty acid, ABA, and lignin biosynthesis. Our study provides more information about the miRNA regulatory network and deepens our understanding of the function of miRNAs in T. tuan. miRNAs are revealed to be crucial during seed maturation, which provides a basis for further study of the regulatory role of miRNAs during seed maturation. Full article

(This article belongs to the Special Issue Forest-Tree Gene Regulation in Response to Abiotic and Biotic Stress)

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14 pages, 2984 KiB

Open AccessArticle

Transcriptome Analysis of Apricot Kernel Pistils Reveals the Mechanisms Underlying ROS-Mediated Freezing Resistance

by Xiaojuan Liu, Yingying Yang, Huihui Xu, Dan Yu, Quanxin Bi and Libing Wang

Forests 2022, 13(10), 1655; https://doi.org/10.3390/f13101655 - 9 Oct 2022

Cited by 2 | Viewed by 1664

Abstract

Spring frost is a major limiting factor in the production and cultivation of apricot kernels, an ecological and economic dry-fruit tree in China. The frequent occurrence of spring frost often coincides with the blooming period of apricot kernels, resulting in significant damage to floral organs and reductions in yield. We investigated the molecular signature of pistils from two apricot kernel cultivars with different frost-resistance levels using transcriptome data. A total of 3223 differently expressed genes (DEGs) were found between two apricot kernel cultivars under freezing stress, including the bHLH and AP2/ERF-ERF transcription factors. Based on KEGG analysis, DEGs were mostly enriched in the biosynthesis of the secondary metabolites, in the metabolic pathways, and in plant-hormone signal transduction. The co-expression network, which included 81 hub genes, revealed that transcription factors, protein kinases, ubiquitin ligases, hormone components, and Ca²⁺-related proteins coregulated the ROS-mediated freezing response. Moreover, gene interaction relationships, such as ERF109-HMGCR1, ERF109-GRXC9, and bHLH13-JAZ8, were predicted. These findings revealed the regulatory factors for differences in frost resistance between the two tested apricot kernel cultivars and contributed to a deeper understanding of the comprehensive regulatory program during freezing stress. Some of the hub genes identified in this work provide new choices and directions for breeding apricot kernels with a high frost resistance. Full article

(This article belongs to the Special Issue Forest-Tree Gene Regulation in Response to Abiotic and Biotic Stress)

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19 pages, 9878 KiB

Open AccessArticle

Identification of AP2/ERF Transcription Factor Family Genes and Expression Patterns in Response to Drought Stress in Pinusmassoniana

by Shuang Sun, Xingxing Liang, Hu Chen, La Hu and Zhangqi Yang

Forests 2022, 13(9), 1430; https://doi.org/10.3390/f13091430 - 6 Sep 2022

Cited by 3 | Viewed by 1831

Abstract

Pinus massoniana Lamb. is found in 17 Chinese provinces and is an important timber tree species in southern China. The current seasonal drought climate is becoming increasingly severe, threatening P. massoniana growth and limiting the development of the P. massoniana industry. Plant growth, development, and stress were all regulated by AP2/ERF. We identified 124 AP2/ERF transcription factor family members in this study and discovered that all the genes had their own conserved structural domains and that PmAP2/ERFs were divided into 12 subfamilies with high conservation and similarity in gene structure and evolutionary level. Nine PmAP2/ERF genes were constitutively expressed under drought treatment, and it was hypothesized that the PmAP2/ERF96 gene negatively regulated drought stress, PmAP2/ERF46 and PmAP2/ERF49 genes showed a positive or negative response to drought in different tissues, while the remaining six genes were positively regulated. The PmAP2/ERF genes responded to drought stress following treatment with the exogenous hormones SA, ABA, and MeJA, but the expression patterns differed, with each gene responding to at least one exogenous hormone to induce up-regulation of expression under drought stress, with PmAP2/ERF11, PmAP2/ERF44, PmAP2/ERF77, and PmAP2/ERF80 genes significantly induced by three hormones. The genes mentioned above may be involved in hormone signaling pathways in response to drought stress. The results indicate that the PmAP2/ERF genes may positively or negatively regulate the corresponding signaling pathways in P. massoniana to improve drought resistance. Full article

(This article belongs to the Special Issue Forest-Tree Gene Regulation in Response to Abiotic and Biotic Stress)

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17 pages, 10029 KiB

Open AccessArticle

Comprehensive Analysis of GRAS Gene Family and Their Expression under GA3, Drought Stress and ABA Treatment in Larix kaempferi

by Miaomiao Ma, Lu Li, Xuhui Wang, Chunyan Zhang, Solme Pak and Chenghao Li

Forests 2022, 13(9), 1424; https://doi.org/10.3390/f13091424 - 5 Sep 2022

Cited by 3 | Viewed by 1606

Abstract

The GRAS family transcription factors play important roles in regulating plant growth and responses to abiotic stress, which can be utilized to breed novel plants with improved abiotic stress resistance. However, the GRAS gene family has been largely unexplored for tree species, particularly for Larix kaempferi, which has high economic and ecological values, challenging practices for breeding abiotic stress-resistant L. kaempferi. In order to improve the stress resistance by regulating the transcription factors in L. kaempferi, we identified 11 GRAS genes in L. kaempferi and preliminarily characterized them through comprehensive analyses of phylogenetic relationships, conserved motifs, promoter cis-elements, and expression patterns, as well as protein interaction network prediction. The phylogenetic analysis showed that the LkGRAS family proteins were classified into four subfamilies, including DELLA, HAM, SCL, and PAT1, among which the SCL subfamily was the largest one. Conserved motif analysis revealed many putative motifs such as LHRI-VHIID-LHRII-PFYRE-SAW at C-terminals of the LkGRAS proteins; we discovered a unique motif of the LkGRAS genes. Promoter cis-acting element analysis exhibited several putative elements associated with abiotic stresses and phytohormones; the abscisic acid-responsive elements (ABRE) and G-box are the most enriched elements in the promoters. Through expression profiles of LkGRAS genes in different tissues and under drought-stress and phytohormones (GA₃ and ABA) treatments, it was demonstrated that LkGRAS genes are most active in the needles, and they rapidly respond to environmental cues such as drought-stress and phytohormone treatments within 24 h. Protein interaction network prediction analysis revealed that LkGRAS proteins interact with various proteins, among which examples are the typical GA, ABA, and drought-stress signaling factors. Taken together, our work identifies the novel LkGRAS gene family in L. kaempferi and provides preliminary information for further in-depth functional characterization studies and practices of breeding stress-resistant L. kaempferi. Full article

(This article belongs to the Special Issue Forest-Tree Gene Regulation in Response to Abiotic and Biotic Stress)

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21 pages, 3665 KiB

Open AccessArticle

Coexpression Network Analysis Based Characterisation of the R2R3-MYB Family Genes in Tolerant Poplar Infected with Melampsora larici-populina

by Qiaoli Chen, Feng Wang and Danlei Li

Forests 2022, 13(8), 1255; https://doi.org/10.3390/f13081255 - 9 Aug 2022

Cited by 3 | Viewed by 1883

Abstract

R2R3-MYB protein is the most abundant class of MYB transcription factor family in plants. The transcript profiles of two E4 races of Melampsora larici-populina-tolerant poplars and an intolerant poplar were investigated to characterise the role of the R2R3-MYB family genes in the poplar–E4 interaction. In this study, 217 R2R3-MYBs were identified, and 83 R2R3-MYB genes were assigned to 22 different coexpression modules by weighted gene coexpression network analysis. Most R2R3-MYB genes were unchanged in the early period of E4 infection in both tolerant and intolerant poplars. However, there were obvious increases in differentially expressed R2R3-MYB genes in tolerant poplars at 2 and 4 dpi when defence responses occurred, suggesting that differently expressed R2R3-MYB genes at these time points may play an important role in poplar resistance to E4 infection. In total, 34 R2R3-MYB genes showed differential expression at 2 and 4 dpi between tolerant and intolerant poplars. Among them, 16 differentially expressed R2R3-MYB genes were related to 43 defence-related genes that had significant differences between tolerant and intolerant poplars. There might be coregulatory relationships between R2R3-MYBs and other TFs during poplar–E4 interaction. Some differentially expressed R2R3-MYB genes were related to genes involved in flavonoid biosynthesis and IAA or free SA signal transduction and might help activate defence response during poplar–E4 interaction. MYB194 could be an important node in the convergence of IAA and SA signalling. Full article

(This article belongs to the Special Issue Forest-Tree Gene Regulation in Response to Abiotic and Biotic Stress)

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13 pages, 2465 KiB

Open AccessArticle

Transcriptome Analysis of Response to Aluminum Stress in Pinus massoniana

by Ting Wang, Ying Hu, Hu Chen, Jianhui Tan, Huilan Xu, Peng Li, Dongshan Wu, Jie Jia and Zhangqi Yang

Forests 2022, 13(6), 837; https://doi.org/10.3390/f13060837 - 27 May 2022

Cited by 9 | Viewed by 2292

Abstract

Pinus massoniana is a vital kind of coniferous species rich in rosin. Aluminum stress is a severe problem for P. massoniana growth in acidic soil causing root poisoning. However, the molecular mechanisms of aluminum-responsive are still unclear. We performed a transcriptome analysis of the P. massoniana root in response to aluminum stress. Through WGCNA analysis, we identified 338 early and 743 late response genes to aluminum stress. Gene Ontology analysis found many critical functional pathways, such as carbohydrate binding, cellulase activity, and phenylalanine ammonia-lyase activity. In addition, KEGG analysis revealed a significant enrichment of phenylpropanoid biosynthesis pathways. Further analysis showed that the expression of lignin synthesis genes 4CL, CAD, and COMT were up-regulated, indicating that they may play a crucial role in the process of aluminum tolerance in P. massoniana roots. These results provide method support for studying the regulation mechanism of P. massoniana aluminum stress. Full article

(This article belongs to the Special Issue Forest-Tree Gene Regulation in Response to Abiotic and Biotic Stress)

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19 pages, 6006 KiB

Open AccessArticle

Genomic Survey and Cold-Induced Expression Patterns of bHLH Transcription Factors in Liriodendron chinense (Hemsl) Sarg.

by Rongxue Li, Baseer Ahmad, Delight Hwarari, Dong’ao Li, Ye Lu, Min Gao, Jinhui Chen and Liming Yang

Forests 2022, 13(4), 518; https://doi.org/10.3390/f13040518 - 28 Mar 2022

Cited by 12 | Viewed by 2597

Abstract

bHLH transcription factors play an animated role in the plant kingdom during growth and development, and responses to various abiotic stress. In this current study, we conducted, the genome-wide survey of bHLH transcription factors in Liriodendron chinense (Hemsl) Sarg., 91 LcbHLH family members were identified. Identified LcbHLH gene family members were grouped into 19 different subfamilies based on the conserved motifs and phylogenetic analysis. Our results showed that LcbHLH genes clustered in the same subfamily exhibited a similar conservative exon-intron pattern. Hydrophilicity value analysis showed that all LcbHLH proteins were hydrophilic. The Molecular weight (Mw) of LcbHLH proteins ranged from 10.19 kD (LcbHLH15) to 88.40 kD (LcbHLH50). A greater proportion, ~63%, of LcbHLH proteins had a theoretical isoelectric point (pI) less than seven. Additional analysis on the collinear relationships within species and among dissimilar species illustrated that tandem and fragment duplication are the foremost factors of amplification of this family in the evolution process, and they are all purified and selected. RNA-seq and real-time quantitative PCR analysis of LcbHLH members showed that the expression of LcbHLH35, 55, and 86 are up-regulated, and the expression of LcbHLH9, 20, 39, 54, 56, and 69 is down-regulated during cold stress treatments while the expression of LcbHLH24 was up-regulated in the short term and then later down-regulated. From our results, we concluded that LcbHLH genes might participate in cold-responsive processes of L. chinense. These findings provide the basic information of bHLH gene in L. chinense and their regulatory roles in plant development and cold stress response. Full article

(This article belongs to the Special Issue Forest-Tree Gene Regulation in Response to Abiotic and Biotic Stress)

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20 pages, 4520 KiB

Open AccessArticle

Identification of Aquaporin Gene Family in Response to Natural Cold Stress in Ligustrum × vicaryi Rehd.

by Jiahui Dong, Shance Niu, Ji Qian, Juan Zhou, Mengnan Zhao, Yu Meng and Bao Di

Forests 2022, 13(2), 182; https://doi.org/10.3390/f13020182 - 26 Jan 2022

Cited by 2 | Viewed by 3575

Abstract

Plants are susceptible to a variety of abiotic stresses during the growing period, among which low temperature is one of the more frequent stress factors. Maintaining water balance under cold stress is a difficult and critical challenge for plants. Studies have shown that aquaporins located on the cytomembrane play an important role in controlling water homeostasis under cold stress, and are involved in the tolerance mechanism of plant cells to cold stress. In addition, the aquaporin gene family is closely related to the cold resistance of plants. As a major greening tree species in urban landscaping, Ligustrum× vicaryi Rehd. is more likely to be harmed by low temperature after a harsh winter and a spring with fluctuating temperatures. Screening the target aquaporin genes of Ligustrum × vicaryi responding to cold resistance under natural cold stress will provide a scientific theoretical basis for cold resistance breeding of Ligustrum × vicaryi. In this study, the genome-wide identification of the aquaporin gene family was performed at four different overwintering periods in September, November, January and April, and finally, 58 candidate Ligustrum × vicaryi aquaporin (LvAQP) genes were identified. The phylogenetic analysis revealed four subfamilies of the LvAQP gene family: 32 PIPs, 11 TIPs, 11 NIPs and 4 SIPs. The number of genes in PIPs subfamily was more than that in other plants. Through the analysis of aquaporin genes related to cold stress in other plants and LvAQP gene expression patterns identified 20 LvAQP genes in response to cold stress, and most of them belonged to the PIPs subfamily. The significantly upregulated LvAQP gene was Cluster-9981.114831, and the significantly downregulated LvAQP genes were Cluster-9981.112839, Cluster-9981.107281, and Cluster-9981.112777. These genes might play a key role in responding to cold tolerance in the natural low-temperature growth stage of Ligustrum × vicaryi. Full article

(This article belongs to the Special Issue Forest-Tree Gene Regulation in Response to Abiotic and Biotic Stress)

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Review

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16 pages, 2065 KiB

Open AccessReview

Physiology of Plant Responses to Water Stress and Related Genes: A Review

by Jiaojiao Wu, Jingyan Wang, Wenkai Hui, Feiyan Zhao, Peiyun Wang, Chengyi Su and Wei Gong

Forests 2022, 13(2), 324; https://doi.org/10.3390/f13020324 - 16 Feb 2022

Cited by 94 | Viewed by 20216

Abstract

Drought and waterlogging seriously affect the growth of plants and are considered severe constraints on agricultural and forestry productivity; their frequency and degree have increased over time due to global climate change. The morphology, photosynthetic activity, antioxidant enzyme system and hormone levels of plants could change in response to water stress. The mechanisms of these changes are introduced in this review, along with research on key transcription factors and genes. Both drought and waterlogging stress similarly impact leaf morphology (such as wilting and crimping) and inhibit photosynthesis. The former affects the absorption and transportation mechanisms of plants, and the lack of water and nutrients inhibits the formation of chlorophyll, which leads to reduced photosynthetic capacity. Constitutive overexpression of 9-cis-epoxydioxygenase (NCED) and acetaldehyde dehydrogenase (ALDH), key enzymes in abscisic acid (ABA) biosynthesis, increases drought resistance. The latter forces leaf stomata to close in response to chemical signals, which are produced by the roots and transferred aboveground, affecting the absorption capacity of CO₂, and reducing photosynthetic substrates. The root system produces adventitious roots and forms aerenchymal to adapt the stresses. Ethylene (ETH) is the main response hormone of plants to waterlogging stress, and is a member of the ERFVII subfamily, which includes response factors involved in hypoxia-induced gene expression, and responds to energy expenditure through anaerobic respiration. There are two potential adaptation mechanisms of plants (“static” or “escape”) through ETH-mediated gibberellin (GA) dynamic equilibrium to waterlogging stress in the present studies. Plant signal transduction pathways, after receiving stress stimulus signals as well as the regulatory mechanism of the subsequent synthesis of pyruvate decarboxylase (PDC) and alcohol dehydrogenase (ADH) enzymes to produce ethanol under a hypoxic environment caused by waterlogging, should be considered. This review provides a theoretical basis for plants to improve water stress tolerance and water-resistant breeding. Full article

(This article belongs to the Special Issue Forest-Tree Gene Regulation in Response to Abiotic and Biotic Stress)

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