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Genetics and Evolution of Abiotic Stress Tolerance in Plants

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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: closed (15 November 2021) | Viewed by 37056

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Dr. Patrizia Galeffi

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Biotechnology and Agroindustry Division, Casaccia Research Center, ENEA (Italian National Agency for New Technologies, Energy and Sustainable Economic Development), Via Anguillarese 301, 00123 Rome, Italy
Interests: plant functional genomics; cereal transcriptomics; DREB gene family; plant genetics; abiotic stress tolerance in plant; antibody molecular biology; crop genetic improvement; VRN gene family; QTL related to the abiotic stresses
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Dear Colleagues,

Now more than ever, understanding the genetics and evolution of the gene mechanisms and the networks of different molecular pathways acting on plant abiotic stress tolerance has an important role in the finding of new solutions and approaches able to contribute to a good equilibrium among human needs, food security, and future strategies for mitigating the effects of global climate changes.

In this context, a major role for science and research is very welcome.

Scientists have the relevant task of increasing our knowledge in the complex area of plant genetics and genomics, the genes responsive to specific abiotic stresses (such as drought, salts, or heat) and their inducible promoters, and various gene expression control and modulation mechanisms, including alternative splicing, micro-RNA interference, post-transcriptional mRNA decay, and post-translational protein degradation. At the same time, evolution has played a key role in the establishment of the current plant molecular traits, so that major insights into the genetic diversity producing different alleles, adaptation, phylogenesis, and evolution of genomes and gene families can be translated and applied as tools for developing new tolerant plant varieties able to satisfy our needs, in terms of food security, protection of the planet, and conservation and recovery of natural resources such as water and soils.

With this Special Issue, I wish to invite the submission of high-quality original research manuscripts or review articles on any topic related to:

“Genetics and Evolution of Abiotic Stress Tolerance in Plants”.

Please submit your research and join in our Special Issue, which will represent an exciting virtual tour through plant molecular responses to the various environmental stresses.

You will find all the necessary information and instructions and a team up to the task at the Genes editorial office.

Dr. Patrizia Galeffi
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. Genes is an international peer-reviewed open access monthly journal published by MDPI.

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Keywords

Abiotic stress tolerance genes
Drought stress genes
Transcription factors
Heat stress genes
DREB gene family
AREB gene family
Myc, Myb gene family
bZip gene family
LEA gene family
Molecular mechanisms of abiotic stress tolerance
Alternative splicing of abiotic stress tolerance genes
Genetic diversity of genes involved in abiotic stresses
Phylogenesis of abiotic stress tolerance genes
Evolution studies on stress tolerance genes

Published Papers (11 papers)

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Editorial

Jump to: Research, Review

3 pages, 158 KiB

Open AccessEditorial

Genetics and Evolution of Abiotic Stress Tolerance in Plants

by Patrizia Galeffi

Genes 2022, 13(8), 1380; https://doi.org/10.3390/genes13081380 - 01 Aug 2022

Cited by 2 | Viewed by 1232

Abstract

Now more than ever, the understanding of the genetics and evolution of the gene mechanisms and the networks of different molecular pathways acting on plant abiotic stress tolerance has an important role in the finding of new solutions and approaches mitigating the effects of global climate changes, thus contributing to a correct equilibrium among human needs, food security and human health and wellbeing [...] Full article

(This article belongs to the Special Issue Genetics and Evolution of Abiotic Stress Tolerance in Plants)

Research

Jump to: Editorial, Review

15 pages, 4178 KiB

Open AccessArticle

Expression Analysis of the TdDRF1 Gene in Field-Grown Durum Wheat under Full and Reduced Irrigation

by Arianna Latini, Cristina Cantale, Karthikeyan Thiyagarajan, Karim Ammar and Patrizia Galeffi

Genes 2022, 13(3), 555; https://doi.org/10.3390/genes13030555 - 21 Mar 2022

Cited by 2 | Viewed by 2317

Abstract

Some of the key genes and regulatory mechanisms controlling drought response in durum wheat have been identified. One of the major challenges for breeders is how to use this knowledge for the achievement of drought stress tolerance. In the present study, we report the expression profiles of the TdDRF1 gene, at consecutive plant growth stages, from different durum wheat genotypes evaluated in two different field environments. The expression of a possible target gene (Wdnh13) of the TdDRF1 gene was also investigated and analogies with the transcript profiles were found. The results of the qRT-PCR highlighted differences in molecular patterns, thus suggesting a genotype dependency of the TdDRF1 gene expression in response to the stress induced. Furthermore, a statistical association between the expression of TdDRF1 transcripts and agronomic traits was also performed and significant differences were found among genotypes, suggesting a relationship. One of the genotypes was found to combine molecular and agronomic characteristics. Full article

(This article belongs to the Special Issue Genetics and Evolution of Abiotic Stress Tolerance in Plants)

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25 pages, 2998 KiB

Open AccessArticle

Performance Prediction of Durum Wheat Genotypes in Response to Drought and Heat in Climate Change Conditions

by Marco Dettori, Carla Cesaraccio, Pierpaolo Duce and Valentina Mereu

Genes 2022, 13(3), 488; https://doi.org/10.3390/genes13030488 - 10 Mar 2022

Cited by 2 | Viewed by 2840

Abstract

With an approach combining crop modelling and biotechnology to assess the performance of three durum wheat cultivars (Creso, Duilio, Simeto) in a climate change context, weather and agronomic datasets over the period 1973–2004 from two sites, Benatzu and Ussana (Southern Sardinia, Itay), were used and the model responses were interpreted considering the role of DREB genes in the genotype performance with a focus on drought conditions. The CERES-Wheat crop model was calibrated and validated for grain yield, earliness and kernel weight. Forty-eight synthetic scenarios were used: 6 scenarios with increasing maximum air temperature; 6 scenarios with decreasing rainfall; 36 scenarios combining increasing temperature and decreasing rainfall. The simulated effects on yields, anthesis and kernel weights resulted in yield reduction, increasing kernel weight, and shortened growth duration in both sites. Creso (late cultivar) was the most sensitive to simulated climate conditions. Simeto and Duilio (early cultivars) showed lower simulated yield reductions and a larger anticipation of anthesis date. Observed data showed the same responses for the three cultivars in both sites. The CERES-Wheat model proved to be effective in representing reality and can be used in crop breeding programs with a molecular approach aiming at developing molecular markers for the resistance to drought stress. Full article

(This article belongs to the Special Issue Genetics and Evolution of Abiotic Stress Tolerance in Plants)

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19 pages, 1881 KiB

Open AccessArticle

Genome Wide Association Study Uncovers the QTLome for Osmotic Adjustment and Related Drought Adaptive Traits in Durum Wheat

by Giuseppe Emanuele Condorelli, Maria Newcomb, Eder Licieri Groli, Marco Maccaferri, Cristian Forestan, Ebrahim Babaeian, Markus Tuller, Jeffrey Westcott White, Rick Ward, Todd Mockler, Nadia Shakoor and Roberto Tuberosa

Genes 2022, 13(2), 293; https://doi.org/10.3390/genes13020293 - 02 Feb 2022

Cited by 11 | Viewed by 3160

Abstract

Osmotic adjustment (OA) is a major component of drought resistance in crops. The genetic basis of OA in wheat and other crops remains largely unknown. In this study, 248 field-grown durum wheat elite accessions grown under well-watered conditions, underwent a progressively severe drought treatment started at heading. Leaf samples were collected at heading and 17 days later. The following traits were considered: flowering time (FT), leaf relative water content (RWC), osmotic potential (ψs), OA, chlorophyll content (SPAD), and leaf rolling (LR). The high variability (3.89-fold) in OA among drought-stressed accessions resulted in high repeatability of the trait (h² = 72.3%). Notably, a high positive correlation (r = 0.78) between OA and RWC was found under severe drought conditions. A genome-wide association study (GWAS) revealed 15 significant QTLs (Quantitative Trait Loci) for OA (global R² = 63.6%), as well as eight major QTL hotspots/clusters on chromosome arms 1BL, 2BL, 4AL, 5AL, 6AL, 6BL, and 7BS, where a higher OA capacity was positively associated with RWC and/or SPAD, and negatively with LR, indicating a beneficial effect of OA on the water status of the plant. The comparative analysis with the results of 15 previous field trials conducted under varying water regimes showed concurrent effects of five OA QTL cluster hotspots on normalized difference vegetation index (NDVI), thousand-kernel weight (TKW), and/or grain yield (GY). Gene content analysis of the cluster regions revealed the presence of several candidate genes, including bidirectional sugar transporter SWEET, rhomboid-like protein, and S-adenosyl-L-methionine-dependent methyltransferases superfamily protein, as well as DREB1. Our results support OA as a valuable proxy for marker-assisted selection (MAS) aimed at enhancing drought resistance in wheat. Full article

(This article belongs to the Special Issue Genetics and Evolution of Abiotic Stress Tolerance in Plants)

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21 pages, 5009 KiB

Open AccessArticle

Transcriptome Analysis Reveals Differentially Expressed Genes That Regulate Biosynthesis of the Active Compounds with Methyl Jasmonate in Rosemary Suspension Cells

by Deheng Yao, Zihao Zhang, Yukun Chen, Yuling Lin, Xuhan Xu and Zhongxiong Lai

Genes 2022, 13(1), 67; https://doi.org/10.3390/genes13010067 - 27 Dec 2021

Cited by 6 | Viewed by 3135

Abstract

To study the effects of Methyl jasmonates (MeJA) on rosemary suspension cells, the antioxidant enzymes’ change of activities under different concentrations of MeJA, including 0 (CK), 10 (M10), 50 (M50) and 100 μM MeJA (M100). The results demonstrated that MeJA treatments increased the activities of phenylalanine ammonla-lyase (PAL), superoxide dismutase (SOD), peroxidase (POD), catalase (CAT) and polyphenol oxidase (PPO) and reduced the contents of hydrogen peroxide (H₂O₂) and malondialdehyde (MDA), thus accelerating the ROS scavenging. Comparative transcriptome analysis of different concentrations of MeJA showed that a total of 7836, 6797 and 8310 genes were differentially expressed in the comparisons of CKvsM10, CKvsM50, CKvsM100, respectively. The analysis of differentially expressed genes (DEGs) showed phenylpropanoid biosynthesis, vitamin B6, ascorbate and aldarate metabolism-related genes were significantly enriched. The transcripts of flavonoid and terpenoid metabolism pathways and plant hormone signal transduction, especially the jasmonic acid (JA) signal-related genes, were differentially expressed in CKvsM50 and CKvsM100 comparisons. In addition, the transcription factors (TFs), e.g., MYC2, DELLA, MYB111 played a key role in rosemary suspension cells under MeJA treatments. qRT-PCR of eleven DEGs showed a high correlation between the RNA-seq and the qRT-PCR result. Taken together, MeJA alleviated peroxidative damage of the rosemary suspension cells in a wide concentration range via concentration-dependent differential expression patterns. This study provided a transcriptome sequence resource responding to MeJA and a valuable resource for the genetic and genomic studies of the active compounds engineering in rosemary. Full article

(This article belongs to the Special Issue Genetics and Evolution of Abiotic Stress Tolerance in Plants)

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18 pages, 2043 KiB

Open AccessArticle

Juvenile Heat Tolerance in Wheat for Attaining Higher Grain Yield by Shifting to Early Sowing in October in South Asia

by Uttam Kumar, Ravi Prakash Singh, Susanne Dreisigacker, Marion S. Röder, Jose Crossa, Julio Huerta-Espino, Suchismita Mondal, Leonardo Crespo-Herrera, Gyanendra Pratap Singh, Chandra Nath Mishra, Gurvinder Singh Mavi, Virinder Singh Sohu, Sakuru Venkata Sai Prasad, Rudra Naik, Satish Chandra Misra and Arun Kumar Joshi

Genes 2021, 12(11), 1808; https://doi.org/10.3390/genes12111808 - 18 Nov 2021

Cited by 8 | Viewed by 2235

Abstract

Farmers in northwestern and central India have been exploring to sow their wheat much earlier (October) than normal (November) to sustain productivity by escaping terminal heat stress and to utilize the available soil moisture after the harvesting of rice crop. However, current popular varieties are poorly adapted to early sowing due to the exposure of juvenile plants to the warmer temperatures in the month of October and early November. Therefore, a study was undertaken to identify wheat genotypes suited to October sowing under warmer temperatures in India. A diverse collection of 3322 bread wheat varieties and elite lines was prepared in CIMMYT, Mexico, and planted in the 3rd week of October during the crop season 2012–2013 in six locations (Ludhiana, Karnal, New Delhi, Indore, Pune and Dharwad) spread over northwestern plains zone (NWPZ) and central and Peninsular zone (CZ and PZ; designated as CPZ) of India. Agronomic traits data from the seedling stage to maturity were recorded. Results indicated substantial diversity for yield and yield-associated traits, with some lines showing indications of higher yields under October sowing. Based on agronomic performance and disease resistance, the top 48 lines (and two local checks) were identified and planted in the next crop season (2013–2014) in a replicated trial in all six locations under October sowing (third week). High yielding lines that could tolerate higher temperature in October sowing were identified for both zones; however, performance for grain yield was more promising in the NWPZ. Hence, a new trial of 30 lines was planted only in NWPZ under October sowing. Lines showing significantly superior yield over the best check and the most popular cultivars in the zone were identified. The study suggested that agronomically superior wheat varieties with early heat tolerance can be obtained that can provide yield up to 8 t/ha by planting in the third to fourth week of October. Full article

(This article belongs to the Special Issue Genetics and Evolution of Abiotic Stress Tolerance in Plants)

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23 pages, 8832 KiB

Open AccessArticle

In Silico and Transcription Analysis of Trehalose-6-phosphate Phosphatase Gene Family of Wheat: Trehalose Synthesis Genes Contribute to Salinity, Drought Stress and Leaf Senescence

by Md Ashraful Islam, Md Mustafizur Rahman, Md Mizanor Rahman, Xiujuan Jin, Lili Sun, Kai Zhao, Shuguang Wang, Ashim Sikdar, Hafeez Noor, Jong-Seong Jeon, Wenjun Zhang and Daizhen Sun

Genes 2021, 12(11), 1652; https://doi.org/10.3390/genes12111652 - 20 Oct 2021

Cited by 7 | Viewed by 2719

Abstract

Trehalose-6-phosphate phosphatase (TPP) genes take part in trehalose metabolism and also in stress tolerance, which has been well documented in many species but poorly understood in wheat. The present research has identified a family of 31 TPP genes in Triticum aestivum L. through homology searches and classified them into five clades by phylogenetic tree analysis, providing evidence of an evolutionary status with Hordeum vulgare, Brachypodium distachyon and Oryza sativa. The exon-intron distribution revealed a discrete evolutionary history and projected possible gene duplication occurrences. Furthermore, different computational approaches were used to analyze the physical and chemical properties, conserved domains and motifs, subcellular and chromosomal localization, and three-dimensional (3-D) protein structures. Cis-regulatory elements (CREs) analysis predicted that TaTPP promoters consist of CREs related to plant growth and development, hormones, and stress. Transcriptional analysis revealed that the transcription levels of TaTPPs were variable in different developmental stages and organs. In addition, qRT-PCR analysis showed that different TaTPPs were induced under salt and drought stresses and during leaf senescence. Therefore, the findings of the present study give fundamental genomic information and possible biological functions of the TaTPP gene family in wheat and will provide the path for a better understanding of TaTPPs involvement in wheat developmental processes, stress tolerance, and leaf senescence. Full article

(This article belongs to the Special Issue Genetics and Evolution of Abiotic Stress Tolerance in Plants)

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29 pages, 8312 KiB

Open AccessEditor’s ChoiceArticle

Transcriptome Profiling of Maize (Zea mays L.) Leaves Reveals Key Cold-Responsive Genes, Transcription Factors, and Metabolic Pathways Regulating Cold Stress Tolerance at the Seedling Stage

by Joram Kiriga Waititu, Quan Cai, Ying Sun, Yinglu Sun, Congcong Li, Chunyi Zhang, Jun Liu and Huan Wang

Genes 2021, 12(10), 1638; https://doi.org/10.3390/genes12101638 - 18 Oct 2021

Cited by 22 | Viewed by 3519

Abstract

Cold tolerance is a complex trait that requires a critical perspective to understand its underpinning mechanism. To unravel the molecular framework underlying maize (Zea mays L.) cold stress tolerance, we conducted a comparative transcriptome profiling of 24 cold-tolerant and 22 cold-sensitive inbred lines affected by cold stress at the seedling stage. Using the RNA-seq method, we identified 2237 differentially expressed genes (DEGs), namely 1656 and 581 annotated and unannotated DEGs, respectively. Further analysis of the 1656 annotated DEGs mined out two critical sets of cold-responsive DEGs, namely 779 and 877 DEGs, which were significantly enhanced in the tolerant and sensitive lines, respectively. Functional analysis of the 1656 DEGs highlighted the enrichment of signaling, carotenoid, lipid metabolism, transcription factors (TFs), peroxisome, and amino acid metabolism. A total of 147 TFs belonging to 32 families, including MYB, ERF, NAC, WRKY, bHLH, MIKC MADS, and C₂H₂, were strongly altered by cold stress. Moreover, the tolerant lines’ 779 enhanced DEGs were predominantly associated with carotenoid, ABC transporter, glutathione, lipid metabolism, and amino acid metabolism. In comparison, the cold-sensitive lines’ 877 enhanced DEGs were significantly enriched for MAPK signaling, peroxisome, ribosome, and carbon metabolism pathways. The biggest proportion of the unannotated DEGs was implicated in the roles of long non-coding RNAs (lncRNAs). Taken together, this study provides valuable insights that offer a deeper understanding of the molecular mechanisms underlying maize response to cold stress at the seedling stage, thus opening up possibilities for a breeding program of maize tolerance to cold stress. Full article

(This article belongs to the Special Issue Genetics and Evolution of Abiotic Stress Tolerance in Plants)

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16 pages, 1449 KiB

Open AccessArticle

Biochemical and Molecular Effects Induced by Triacontanol in Acquired Tolerance of Rice to Drought Stress

by Basmah M. Alharbi, Awatif Mahfouz Abdulmajeed and Heba Hassan

Genes 2021, 12(8), 1119; https://doi.org/10.3390/genes12081119 - 23 Jul 2021

Cited by 11 | Viewed by 2282

Abstract

To assess the effect of triacontanol (TRIA) on rice plants grown under normal or drought conditions, rice seeds were presoaked in TRIA (35 ppm) for two hours. After 20 days of sowing, rice seedlings developed from TRIA-treated or untreated seeds were subjected to drought stress. After 10 days of plant exposure to drought stress, data of major growth attributes and the content of photosynthetic pigments were recorded. Moreover, the effect of drought stress on stomatal conductance and the photochemical efficiency of PSII (Fv/Fm) were followed. The data obtained indicated that the species of rice (Oryza sativa L.) cultivar Giza 177 under investigation was sensitive to drought stress where there were significant decreases in the fresh and dry weights of shoots and roots and in stomatal conductance, as well as in the content of chlorophyll a, chlorophyll b, and carotenoids. Seed priming with TRIA enhanced both growth and acquired plant tolerance to drought stress. Thus, TRIA via the enhancement of stomatal conductance through the regulation of stomatal closure, the rate of water loss, ABA metabolism, the accumulation of osmolytes, and the regulation of aquaporins genes improved the water status of plants grown under water scarcity. Moreover, TRIA via increasing the content of free amino acids and sugars under drought stress may increase the chance of plant tissues to retain more water under scarcity conditions. Full article

(This article belongs to the Special Issue Genetics and Evolution of Abiotic Stress Tolerance in Plants)

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18 pages, 3008 KiB

Open AccessArticle

The Seed Development Factors TT2 and MYB5 Regulate Heat Stress Response in Arabidopsis

by Pierre Jacob, Gwilherm Brisou, Marion Dalmais, Johanne Thévenin, Froukje van der Wal, David Latrasse, Ravi Suresh Devani, Moussa Benhamed, Bertrand Dubreucq, Adnane Boualem, Loic Lepiniec, Richard G. H. Immink, Heribert Hirt and Abdelhafid Bendahmane

Genes 2021, 12(5), 746; https://doi.org/10.3390/genes12050746 - 15 May 2021

Cited by 13 | Viewed by 4306

Abstract

HEAT SHOCK FACTOR A2 (HSFA2) is a regulator of multiple environmental stress responses required for stress acclimation. We analyzed HSFA2 co-regulated genes and identified 43 genes strongly co-regulated with HSFA2 during multiple stresses. Motif enrichment analysis revealed an over-representation of the site II element (SIIE) in the promoters of these genes. In a yeast 1-hybrid screen with the SIIE, we identified the closely related R2R3-MYB transcription factors TT2 and MYB5. We found overexpression of MYB5 or TT2 rendered plants heat stress tolerant. In contrast, tt2, myb5, and tt2/myb5 loss of function mutants showed heat stress hypersensitivity. Transient expression assays confirmed that MYB5 and TT2 can regulate the HSFA2 promoter together with the other members of the MBW complex, TT8 and TRANSPARENT TESTA GLABRA 1 (TTG1) and that the SIIE was involved in this regulation. Transcriptomic analysis revealed that TT2/MYB5 target promoters were enriched in SIIE. Overall, we report a new function of TT2 and MYB5 in stress resistance and a role in SIIE-mediated HSFA2 regulation. Full article

(This article belongs to the Special Issue Genetics and Evolution of Abiotic Stress Tolerance in Plants)

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Review

Jump to: Editorial, Research

22 pages, 1184 KiB

Open AccessEditor’s ChoiceReview

HD-ZIP Gene Family: Potential Roles in Improving Plant Growth and Regulating Stress-Responsive Mechanisms in Plants

by Rahat Sharif, Ali Raza, Peng Chen, Yuhong Li, Enas M. El-Ballat, Abdur Rauf, Christophe Hano and Mohamed A. El-Esawi

Genes 2021, 12(8), 1256; https://doi.org/10.3390/genes12081256 - 17 Aug 2021

Cited by 67 | Viewed by 6956

Abstract

Exploring the molecular foundation of the gene-regulatory systems underlying agronomic parameters or/and plant responses to both abiotic and biotic stresses is crucial for crop improvement. Thus, transcription factors, which alone or in combination directly regulated the targeted gene expression levels, are appropriate players for enlightening agronomic parameters through genetic engineering. In this regard, homeodomain leucine zipper (HD-ZIP) genes family concerned with enlightening plant growth and tolerance to environmental stresses are considered key players for crop improvement. This gene family containing HD and LZ domain belongs to the homeobox superfamily. It is further classified into four subfamilies, namely HD-ZIP I, HD-ZIP II, HD-ZIP III, and HD-ZIP IV. The first HD domain-containing gene was discovered in maize cells almost three decades ago. Since then, with advanced technologies, these genes were functionally characterized for their distinct roles in overall plant growth and development under adverse environmental conditions. This review summarized the different functions of HD-ZIP genes in plant growth and physiological-related activities from germination to fruit development. Additionally, the HD-ZIP genes also respond to various abiotic and biotic environmental stimuli by regulating defense response of plants. This review, therefore, highlighted the various significant aspects of this important gene family based on the recent findings. The practical application of HD-ZIP biomolecules in developing bioengineered plants will not only mitigate the negative effects of environmental stresses but also increase the overall production of crop plants. Full article

(This article belongs to the Special Issue Genetics and Evolution of Abiotic Stress Tolerance in Plants)

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