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Abiotic Stress in Land Plants: Molecular Genetics and Genomics

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A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: 5 July 2024 | Viewed by 14301

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Special Issue Editors

Dr. Muhammad Imran

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Guest Editor

College of Agriculture, South China Agricultural University, Guangzhou, China
Interests: crop protection; plant biotechnology; plant breeding, plant genetics; molecular genetics; plant biology

Dr. Emilie Widemann

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1. Institut de Biologie Moléculaire des Plantes, CNRS-Université de Strasbourg, 67084 Strasbourg, France
2. Department of Biology, Western University, London, ON N6A 3K7, Canada
Interests: arabidopsis; abiotic stresses
Special Issues, Collections and Topics in MDPI journals

Dr. Sarfraz Shafiq

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Guest Editor

Department of Anatomy and Cell Biology, Western University, London, ON N6A 3K7, Canada
Interests: wheat genetics; cotton genetics; crop; plant genetics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Plants in their natural environments are subjected to a variety of environmental stresses, including abiotic stresses such as low and high temperature, salinity, drought, flood, heavy metal toxicity, and oxidative stress. These environmental factors impact plant survival, yield, reproduction, and growth. To overcome these abiotic stresses, plants respond simultaneously through several tolerance mechanisms to counter the disturbances and retain protection and health. Multiple crop species now have reference and draft genome and transcriptome assemblies, and resequencing data are increasing. Scientists are using comparative genomic, epigenomic, and transcriptomic analyses to pinpoint candidate genes and provide mechanistic insight into the molecular network underlying stress responses. To maximize the potential of staple crops and introduce new crops for food and feed, high-throughput phenotyping, genome-wide association studies, and optimized genomics-assisted breeding are all gaining popularity. Plant biotechnologists and breeders need to use novel methods to increase crop plants’ abiotic stress tolerance as a result of rising abiotic stress issues. However, even though recent studies have uncovered a number of key genes, gene regulatory networks, and quantitative trait loci that mediate plant responses to different abiotic stresses, a complete view of this multifaceted trait is still missing. To better understand how plants respond and adapt to environmental stresses, molecular genetics and genomics are the focus of this discussion. Articles of any format (original research, methods, opinion, review) that shed new light on any facet of plant responses and adaptation to abiotic stresses are welcome.

Potential topics include but are not limited to:

Plant’s molecular, biochemical, and physiological responses;
Mechanisms of abiotic stress responses and tolerance;
Stress perception, signal translation, abiotic severity, and plant adaptation and defense systems;
Genomics, proteomics, and metabolomics approaches;
Genome editing for abiotic stress tolerance;
Epigenomics modifications, microRNA, long non-coding RNA;
Genome sequencing, resequencing, genome wide association studies, mapping of genetic loci governing abiotic stress;
Metabolic regulations in response to abiotic stress.

Dr. Muhammad Imran
Dr. Emilie Widemann
Dr. Sarfraz Shafiq
Guest Editors

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Keywords

abiotic stress
regulatory networks
genetic diversity
molecular genetics
genomics
functional genomics
transcriptomics
epigenomics
epitrancriptomics
miRNA

Published Papers (9 papers)

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Research

16 pages, 5017 KiB

Open AccessArticle

Multi-Omic Analysis Reveals the Molecular Mechanism of UV-B Stress Resistance in Acetylated RcMYB44 in Rhododendron chrysanthum

by Meiqi Liu, Xiaoru Lin, Kun Cao, Liping Yang, Hongwei Xu and Xiaofu Zhou

Genes 2023, 14(11), 2022; https://doi.org/10.3390/genes14112022 - 30 Oct 2023

Viewed by 826

Abstract

Ultraviolet-B (UV-B) radiation is a significant environmental factor influencing the growth and development of plants. MYBs play an essential role in the processes of plant responses to abiotic stresses. In the last few years, the development of transcriptome and acetylated proteome technologies have resulted in further and more reliable data for understanding the UV-B response mechanism in plants. In this research, the transcriptome and acetylated proteome were used to analyze Rhododendron chrysanthum Pall. (R. chrysanthum) leaves under UV-B stress. In total, 2348 differentially expressed genes (DEGs) and 685 differentially expressed acetylated proteins (DAPs) were found. The transcriptome analysis revealed 232 MYB TFs; we analyzed the transcriptome together with the acetylated proteome, and screened 4 MYB TFs. Among them, only RcMYB44 had a complete MYB structural domain. To investigate the role of RcMYB44 under UV-B stress, a homology tree was constructed between RcMYB44 and Arabidopsis MYBs, and it was determined that RcMYB44 shares the same function with ATMYB44. We further constructed the hormone signaling pathway involved in RcMYB44, revealing the molecular mechanism of resistance to UV-B stress in R. chrysanthum. Finally, by comparing the transcriptome and the proteome, it was found that the expression levels of proteins and genes were inconsistent, which is related to post-translational modifications of proteins. In conclusion, RcMYB44 of R. chrysanthum is involved in mediating the growth hormone, salicylic acid, jasmonic acid, and abscisic acid signaling pathways to resist UV-B stress. Full article

(This article belongs to the Special Issue Abiotic Stress in Land Plants: Molecular Genetics and Genomics)

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19 pages, 4365 KiB

Open AccessArticle

RNA-Seq Identified Putative Genes Conferring Photosynthesis and Root Development of Melon under Salt Stress

by Tai Liu, Sikandar Amanullah, Huichun Xu, Peng Gao, Zhiqiang Du, Xixi Hu, Mo Han, Ye Che, Ling Zhang, Guochao Qi and Di Wang

Genes 2023, 14(9), 1728; https://doi.org/10.3390/genes14091728 - 29 Aug 2023

Cited by 1 | Viewed by 945

Abstract

Melon is an important fruit crop of the Cucurbitaceae family that is being cultivated over a large area in China. Unfortunately, salt stress has crucial effects on crop plants and damages photosynthesis, membranal lipid components, and hormonal metabolism, which leads to metabolic imbalance and retarded growth. Herein, we performed RNA-seq analysis and a physiological parameter evaluation to assess the salt-induced stress impact on photosynthesis and root development activity in melon. The endogenous quantification analysis showed that the significant oxidative damage in the membranal system resulted in an increased ratio of non-bilayer/bilayer lipid (MGDG/DGDG), suggesting severe irregular stability in the photosynthetic membrane. Meanwhile, root development was slowed down by a superoxidized membrane system, and downregulated genes showed significant contributions to cell wall biosynthesis and IAA metabolism. The comparative transcriptomic analysis also exhibited that major DEGs were more common in the intrinsic membrane component, photosynthesis, and metabolism. These are all processes that are usually involved in negative responses. Further, the WGCN analysis revealed the involvement of two main network modules: the thylakoid membrane and proteins related to photosystem II. The qRT-PCR analysis exhibited that two key genes (MELO3C006053.2 and MELO3C023596.2) had significant variations in expression profiling at different time intervals of salt stress treatments (0, 6, 12, 24, and 48 h), which were also consistent with the RNA-seq results, denoting the significant accuracy of molecular dataset analysis. In summary, we performed an extensive molecular and metabolic investigation to check the salt-stress-induced physiological changes in melon and proposed that the PSII reaction centre may likely be the primary stress target. Full article

(This article belongs to the Special Issue Abiotic Stress in Land Plants: Molecular Genetics and Genomics)

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15 pages, 6832 KiB

Open AccessArticle

Identification of the Light-Harvesting Chlorophyll a/b Binding Protein Gene Family in Peach (Prunus persica L.) and Their Expression under Drought Stress

by Li Wang, Jia Wei, Xingyun Shi, Weihong Qian, Jan Mehmood, Yiming Yin and Huijuan Jia

Genes 2023, 14(7), 1475; https://doi.org/10.3390/genes14071475 - 19 Jul 2023

Cited by 1 | Viewed by 1139

Abstract

In higher plants, light-harvesting chlorophyll a/b binding (Lhc) proteins play a vital role in photosynthetic processes and are widely involved in the regulation of plant growth, development, and response to abiotic stress. However, the Lhc gene family has not been well identified in peaches (Prunus persica L.). In this study, 19 PpLhc genes were identified in the peach genome database, which were unevenly distributed on all chromosomes. Phylogenetic analysis demonstrated that PpLhc proteins could be divided into three major subfamilies, each of whose members had different exon–intron structures but shared similar conserved motifs. A total of 17 different kinds of cis-regulatory elements were identified in the promoter regions of all PpLhc genes, which could be classified into three categories: plant growth and development, stress response, and phytohormone response. In addition, transcriptomic data analysis and RT-qPCR results revealed that the expression profiles of some PpLhc genes changed under drought treatment, suggesting the crucial roles of Lhc genes in the regulation of plant tolerance to drought stress. Taken together, these findings will provide valuable information for future functional studies of PpLhc genes, especially in response to drought stress. Full article

(This article belongs to the Special Issue Abiotic Stress in Land Plants: Molecular Genetics and Genomics)

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12 pages, 1354 KiB

Open AccessArticle

Transcriptome Analysis in Pyrus betulaefolia Roots in Response to Short-Term Boron Deficiency

by Jing Liu, Tao Chen, Chun-Lei Wang and Xiao Liu

Genes 2023, 14(4), 817; https://doi.org/10.3390/genes14040817 - 29 Mar 2023

Cited by 2 | Viewed by 1240

Abstract

Boron (B) deficiency stress is frequently observed in pear orchards and causes a considerable loss of productivity and fruit quality. Pyrus betulaefolia is one of the most important rootstocks that has been widely used in pear production. The present study confirmed that the boron form of different tissues showed various changes, and the free boron content was significantly decreased under the short-term B deficiency condition. Moreover, the ABA and JA content also significantly accumulated in the root after short-term B deficiency treatment. A comprehensive transcriptome analysis of 24 h B deficiency treatment P. betulaefolia root was performed in this study. Transcriptome results revealed a total of 1230 up-regulated and 642 down-regulated differentially expressed genes (DEGs), respectively. B deficiency significantly increased the expression of the key aquaporin gene NIP5-1. In addition, B deficiency also increased the expression of ABA (ZEP and NCED) and JA (LOX, AOS and OPR) synthesis genes. Several MYB, WRKY, bHLH and ERF transcription factors were induced by B deficiency stress, which may relate to the regulation of B uptake and plant hormone synthesis. Overall, these findings suggested that P. betulaefolia root had adaptive responses to short-term B deficiency stress by improved boron absorption ability and hormone (JA and ABA) synthesis. The transcriptome analysis provided further information for understanding the mechanism of the pear rootstock responses to B deficiency stress. Full article

(This article belongs to the Special Issue Abiotic Stress in Land Plants: Molecular Genetics and Genomics)

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13 pages, 6805 KiB

Open AccessArticle

Genome-Wide Identification and Expression Analysis of TPS Gene Family in Liriodendron chinense

by Zijian Cao, Qianxi Ma, Yuhao Weng, Jisen Shi, Jinhui Chen and Zhaodong Hao

Genes 2023, 14(3), 770; https://doi.org/10.3390/genes14030770 - 22 Mar 2023

Cited by 2 | Viewed by 2663

Abstract

Terpenoids play a key role in plant growth and development, supporting resistance regulation and terpene synthase (TPS), which is the last link in the synthesis process of terpenoids. Liriodendron chinense, commonly called the Chinese tulip tree, is a rare and endangered tree species of the family Magnoliaceae. However, the genome-wide identification of the TPS gene family and its transcriptional responses to development and abiotic stress are still unclear. In the present study, we identified a total of 58 TPS genes throughout the L. chinense genome. A phylogenetic tree analysis showed that they were clustered into five subfamilies and unevenly distributed across six chromosomes. A cis-acting element analysis indicated that LcTPSs were assumed to be highly responsive to stress hormones, such as methyl jasmonate (MeJA) and abscisic acid (ABA). Consistent with this, transcriptome data showed that most LcTPS genes responded to abiotic stress, such as cold, drought, and hot stress, at the transcriptional level. Further analysis showed that LcTPS genes were expressed in a tissue-dependent manner, especially in buds, leaves, and bark. Quantitative reverse transcription PCR (qRT-PCR) analysis confirmed that LcTPS expression was significantly higher in mature leaves compared to young leaves. These results provide a reference for understanding the function and role of the TPS family, laying a foundation for further study of the regulation of TPS in terpenoid biosynthesis in L. chinense. Full article

(This article belongs to the Special Issue Abiotic Stress in Land Plants: Molecular Genetics and Genomics)

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14 pages, 5717 KiB

Open AccessArticle

Loss of Rose Fragrance under Chilling Stress Is Associated with Changes in DNA Methylation and Volatile Biosynthesis

by Limei Xie, Xue Bai, Hao Zhang, Xianqin Qiu, Hongying Jian, Qigang Wang, Huichun Wang, Dedang Feng, Kaixue Tang and Huijun Yan

Genes 2023, 14(3), 692; https://doi.org/10.3390/genes14030692 - 10 Mar 2023

Cited by 2 | Viewed by 1709

Abstract

Rose plants are widely cultivated as cut flowers worldwide and have economic value as sources of natural fragrance and flavoring. Rosa ‘Crimson Glory’, whose petals have a pleasant fragrance, is one of the most important cultivars of edible rose plants. Flower storage at low-temperature is widely applied in production to maintain quality; however, chilling results in a decrease in aromatic volatiles. To determine the molecular basis underlying the changes in aromatic volatile emissions, we investigated the changes in volatile compounds, DNA methylation patterns, and patterns of the transcriptome in response to chilling temperature. The results demonstrated that chilling roses substantially reduced aromatic volatile emissions. We found that these reductions were correlated with the changes in the methylation status of the promoters and genic regions of the genes involved in volatile biosynthesis. These changes mainly occurred for CHH (H = A, T, or C) which accounted for 51% of the total methylation. Furthermore, transcript levels of scent-related gene Germacrene D synthase (RhGDS), Nudix hydrolase 1 (RhNUDX1), and Phenylacetaldehyde reductase (RhPAR) of roses were strikingly depressed after 24 h at low-temperature and remained low-level after 24 h of recovery at 20 °C. Overall, our findings indicated that epigenetic regulation plays an important role in the chilling tolerance of roses and lays a foundation for practical significance in the production of edible roses. Full article

(This article belongs to the Special Issue Abiotic Stress in Land Plants: Molecular Genetics and Genomics)

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21 pages, 3148 KiB

Open AccessArticle

Identification of Small RNAs Associated with Salt Stress in Chrysanthemums through High-Throughput Sequencing and Bioinformatics Analysis

by Jiefei Nai, Tieming Ma, Yingjie Liu and Yunwei Zhou

Genes 2023, 14(3), 561; https://doi.org/10.3390/genes14030561 - 23 Feb 2023

Cited by 1 | Viewed by 1155

Abstract

The Chrysanthemum variety “Niu 9717” exhibits excellent characteristics as an ornamental plant and has good salt resistance. In this study, this plant was treated with 200 mM NaCl for 12 h followed by high-throughput sequencing of miRNA and degradome. Subsequently, the regulatory patterns of potential miRNAs and their target genes were searched to elucidate how Chrysanthemum miRNAs respond to salt. From the root and leaf samples, we identified a total of 201 known miRNAs belonging to 40 families; furthermore, we identified 79 new miRNAs, of which 18 were significantly differentially expressed (p < 0.05). The expressed miRNAs, which targeted a total of 144 mRNAs in the leaf and 215 mRNAs in the root, formed 144 and 226 miRNA–target pairs in roots and leaves, respectively. Combined with the miRNA expression profile, degradome and transcriptome data were then analyzed to understand the possible effects of the miRNA target genes and their pathways on salt stress. The identified genes were mostly located in pathways related to hormone signaling during plant growth and development. Overall, these findings suggest that conserved and novel miRNAs may improve salt tolerance through the regulation of hormone signal synthesis or expression of genes involved in hormone synthesis. Full article

(This article belongs to the Special Issue Abiotic Stress in Land Plants: Molecular Genetics and Genomics)

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18 pages, 6429 KiB

Open AccessFeature PaperArticle

The NtSPL Gene Family in Nicotiana tabacum: Genome-Wide Investigation and Expression Analysis in Response to Cadmium Stress

by Linshen He, Xiang Peng, Hanping Cao, Kunjian Yang, Lien Xiang, Rui Li, Fangyuan Zhang and Wanhong Liu

Genes 2023, 14(1), 183; https://doi.org/10.3390/genes14010183 - 10 Jan 2023

Cited by 4 | Viewed by 1834

Abstract

The SQUAMOSA promoter binding protein-like (SPL)SPL family genes play an important role in regulating plant growth and development, synthesis of secondary metabolites, and resistance to stress. Understanding of the role of the SPL family in tobacco is still limited. In this study, 42 NtSPL genes were identified from the genome of the tobacco variety TN90. According to the results of the conserved motif and phylogenetic tree, the NtSPL genes were divided into eight subgroups, and the genes in the same subgroup showed similar gene structures and conserved domains. The cis-acting element analysis of the NtSPL promoters showed that the NtSPL genes were regulated by plant hormones and stresses. Twenty-eight of the 42 NtSPL genes can be targeted by miR156. Transcriptome data and qPCR results indicated that the expression pattern of miR156-targeted NtSPL genes was usually tissue specific. The expression level of miR156 in tobacco was induced by Cd stress, and the expression pattern of NtSPL4a showed a significant negative correlation with that of miR156. These results suggest that miR156-NtSPL4a may mediate the tobacco response to Cd stress. This study lays a foundation for further research on the function of the NtSPL gene and provides new insights into the involvement of NtSPL genes in the plant response to heavy metal stress. Full article

(This article belongs to the Special Issue Abiotic Stress in Land Plants: Molecular Genetics and Genomics)

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13 pages, 2034 KiB

Open AccessArticle

Co-Expression of ZmVPP1 with ZmNAC111 Confers Robust Drought Resistance in Maize

by Shengxue Liu, Xiaohu Liu, Xiaomin Zhang, Shujie Chang, Chao Ma and Feng Qin

Genes 2023, 14(1), 8; https://doi.org/10.3390/genes14010008 - 20 Dec 2022

Cited by 7 | Viewed by 1916

Abstract

Drought is a primary environmental factor limiting maize production globally. Although transferring a single gene to maize can enhance drought resistance, maize response to water deficit requires further improvement to accommodate the steadily intensifying drought events worldwide. Here, we generated dual transgene lines simultaneously overexpressing two drought-resistant genes, ZmVPP1 (encoding a vacuolar-type H+ pyrophosphatase) and ZmNAC111 (encoding a NAM, ATAF, and CUC (NAC)-type transcription factor). Following drought stress, survival rates of the pyramided transgenic seedlings reached 62–66%, while wild-type and single transgene seedling survival rates were 23% and 37–42%, respectively. Maize seedlings co-expressing ZmVPP1 and ZmNAC111 exhibited higher photosynthesis rates, antioxidant enzyme activities, and root-shoot ratios than the wild type, and anthesis-silking intervals were shorter while grain yields were higher under water deficit conditions in field trials. Additionally, RNA-sequencing analysis confirmed that photosynthesis and stress-related metabolic processes were stimulated in the dual transgene plants under drought conditions. The findings in this work illustrate how high co-expression of different drought-related genes can reinforce drought resistance over that of individual transgene lines, providing a path for developing arid climate-adapted elite maize varieties. Full article

(This article belongs to the Special Issue Abiotic Stress in Land Plants: Molecular Genetics and Genomics)

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