Special Issue "Abiotic Stress in Plants: Current Challenges and Perspectives"

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

Deadline for manuscript submissions: 20 October 2019.

Special Issue Editor

Guest Editor
Dr. Anca Macovei Website E-Mail
Università degli Studi di Pavia, Department of Biology and Biotechnology “L. Spallanzani”, Pavia, Italy

Special Issue Information

Dear Colleagues,

In the current context of continuous climatic changes, abiotic stresses pose significant threats to both crop agricultural production and plant biodiversity. In addition to the climatic challenges, another considerable issue is represented by anthropogenic activities that result in soil erosion, as well as air and water pollution. Accordingly, to face these current challenges, sustainable methodologies for efficient crop production and safeguarding plant biodiversity need to be established and properly applied. To do so, dedicated basic and applied research studies are essential to better understand the complexity of plant responses to abiotic stresses. In the past decades, myriad studies focused on plants’ response to abiotic stresses, but these merely covered single components of the multifaceted intricacy associated with these highly complex traits. Moreover, understanding the interconnectivity between different pathways paves the way to developing plants resilient to multiple abiotic stresses.

The aim of this collection of articles is to gain further valuable insights into the plant resilience to abiotic stresses by covering multidisciplinary studies ranging from physiological, biochemical, molecular, and modelling analyses. Multiplex omics approaches designed to study pathways of plant response to single and multiple types of abiotic stresses are encouraged.

Dr. Anca Macovei
Guest Editor

Manuscript Submission Information

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Keywords

  • abiotic stress
  • agriculture
  • biodiversity
  • modelling analyses
  • omics
  • resilient plants

Published Papers (7 papers)

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Research

Open AccessCommunication
WGCNA Analysis of Salt-Responsive Core Transcriptome Identifies Novel Hub Genes in Rice
Genes 2019, 10(9), 719; https://doi.org/10.3390/genes10090719 - 17 Sep 2019
Abstract
Rice, being a major staple food crop and sensitive to salinity conditions, bears heavy yield losses due to saline soil. Although some salt responsive genes have been identified in rice, their applications in developing salt tolerant cultivars have resulted in limited achievements. Herein, [...] Read more.
Rice, being a major staple food crop and sensitive to salinity conditions, bears heavy yield losses due to saline soil. Although some salt responsive genes have been identified in rice, their applications in developing salt tolerant cultivars have resulted in limited achievements. Herein, we used bioinformatic approaches to perform a meta-analysis of three transcriptome datasets from salinity and control conditions in order to reveal novel genes and the molecular pathways underlying rice response to salt. From a total of 28,432 expressed genes, we identify 457 core differentially expressed genes (DEGs) constitutively responding to salt, regardless of the stress duration, genotype, or the tissue. Gene co-expression analysis divided the core DEGs into three different modules, each of them contributing to salt response in a unique metabolic pathway. Gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses highlighted key biological processes and metabolic pathways involved in the salt response. We identified important novel hub genes encoding proteins of different families including CAM, DUF630/632, DUF581, CHL27, PP2-13, LEA4-5, and transcription factors, which could be functionally characterized using reverse genetic experiments. This novel repertoire of candidate genes related to salt response in rice will be useful for engineering salt tolerant varieties. Full article
(This article belongs to the Special Issue Abiotic Stress in Plants: Current Challenges and Perspectives)
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Open AccessArticle
Identification of Maize CC-Type Glutaredoxins That Are Associated with Response to Drought Stress
Genes 2019, 10(8), 610; https://doi.org/10.3390/genes10080610 - 12 Aug 2019
Abstract
Global maize cultivation is often adversely affected by drought stress. The CC-type glutaredoxin (GRX) genes form a plant-specific subfamily that regulate plant growth and respond to environmental stresses. However, how maize CC-type GRX (ZmGRXCC) genes respond to drought stress remains unclear. [...] Read more.
Global maize cultivation is often adversely affected by drought stress. The CC-type glutaredoxin (GRX) genes form a plant-specific subfamily that regulate plant growth and respond to environmental stresses. However, how maize CC-type GRX (ZmGRXCC) genes respond to drought stress remains unclear. We performed a TBLASTN search to identify ZmGRXCCs in the maize genome and verified the identified sequences using the NCBI conservative domain database (CDD). We further established a phylogenetic tree using Mega7 and surveyed known cis-elements in the promoters of ZmGRXCCs using the PlantCARE database. We found twenty-one ZmGRXCCs in the maize genome by a genome-wide investigation and compared their phylogenetic relationships with rice, maize, and Arabidopsis. The analysis of their redox active sites showed that most of the 21 ZmGRXCCs share similar structures with their homologs. We assessed their expression at young seedlings and adult leaves under drought stress and their expression profiles in 15 tissues, and found that they were differentially expressed, indicating that different ZmGRXCC genes have different functions. Notably, ZmGRXCC14 is up-regulated at seedling, V12, V14, V16, and R1 stages. Importantly, significant associations between genetic variation in ZmGRXCC14 and drought tolerance are found at the seedling stage. These results will help to advance the study of the function of ZmGRXCCs genes under drought stress and understand the mechanism of drought resistance in maize. Full article
(This article belongs to the Special Issue Abiotic Stress in Plants: Current Challenges and Perspectives)
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Open AccessArticle
Transcriptome Analysis of Acid-Responsive Genes and Pathways Involved in Polyamine Regulation in Iron Walnut
Genes 2019, 10(8), 605; https://doi.org/10.3390/genes10080605 - 10 Aug 2019
Abstract
We reported changes in the co-regulated mRNA expression in iron walnut (Juglans sigillata) in response to soil pH treatments and identified mRNAs specific to acidic soil conditions. Phenotypic and physiological analyses revealed that iron walnut growth was greater for the pH [...] Read more.
We reported changes in the co-regulated mRNA expression in iron walnut (Juglans sigillata) in response to soil pH treatments and identified mRNAs specific to acidic soil conditions. Phenotypic and physiological analyses revealed that iron walnut growth was greater for the pH 4–5 and pH 5–6 treatments than for the pH 3–4 and pH 6–7 treatments. A total of 2768 differentially expressed genes were detected and categorized into 12 clusters by Short Time-series Expression Miner (STEM). The 994 low-expression genes in cluster III and 255 high-expression genes in cluster X were classified as acid-responsive genes on the basis of the relationships between phenotype, physiology, and STEM clustering, and the two gene clusters were analyzed by a maximum likelihood (ML) evolutionary tree with the greatest log likelihood values. No prominent sub-clusters occurred in cluster III, but three occurred in cluster X. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated that acid-responsive genes were related primarily to arginine biosynthesis and the arginine/proline metabolism pathway, implying that polyamine accumulation may enhance iron walnut acid stress tolerance. Overall, our results revealed 1249 potentially acid-responsive genes in iron walnut, indicating that its response to acid stress involves different pathways and activated genes. Full article
(This article belongs to the Special Issue Abiotic Stress in Plants: Current Challenges and Perspectives)
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Open AccessArticle
Potassium Transporter LrKUP8 Is Essential for K+ Preservation in Lycium ruthenicum, A Salt-Resistant Desert Shrub
Genes 2019, 10(8), 600; https://doi.org/10.3390/genes10080600 - 09 Aug 2019
Abstract
Salt stress is a major constraint for many crops and trees. A wild species of Goji named Lycium ruthenicum is an important economic halophyte in China and has an extremely high tolerance to salinity. L. ruthenicum grows in saline soil and is known [...] Read more.
Salt stress is a major constraint for many crops and trees. A wild species of Goji named Lycium ruthenicum is an important economic halophyte in China and has an extremely high tolerance to salinity. L. ruthenicum grows in saline soil and is known as a potash-rich species. However, its salt adaptation strategies and ion balance mechanism remains poorly understood. Potassium (K+) is one of the essential macronutrients for plant growth and development. In this study, a putative salt stress-responsive gene encoding a HAK (high-affinity K+)/KUP (K+ uptake)/KT (K+ transporter) transporter was cloned and designated as LrKUP8. This gene belongs to the cluster II group of the KT/HAK/KUP family. The expression of LrKUP8 was strongly induced under high NaCl concentrations. The OE-LrKUP8 calli grew significantly better than the vector control calli under salt stress conditions. Further estimation by ion content and micro-electrode ion flux indicated a relative weaker K+ efflux in the OE-LrKUP8 calli than in the control. Thus, a key gene involved in K+ uptake under salt condition was functionally characterized using a newly established L. ruthenicum callus transformation system. The importance of K+ regulation in L. ruthenicum under salt tolerance was highlighted. Full article
(This article belongs to the Special Issue Abiotic Stress in Plants: Current Challenges and Perspectives)
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Open AccessArticle
Comparative Genomic Analysis of Rice with Contrasting Photosynthesis and Grain Production under Salt Stress
Genes 2019, 10(8), 562; https://doi.org/10.3390/genes10080562 - 25 Jul 2019
Abstract
Unfavourable environmental conditions, including soil salinity, lead to decreased rice (Oryza sativa L.) productivity, especially at the reproductive stage. In this study, we examined 30 rice varieties, which revealed significant differences in the photosynthetic performance responses under salt stress conditions during the [...] Read more.
Unfavourable environmental conditions, including soil salinity, lead to decreased rice (Oryza sativa L.) productivity, especially at the reproductive stage. In this study, we examined 30 rice varieties, which revealed significant differences in the photosynthetic performance responses under salt stress conditions during the reproductive stage, which ultimately affected yield components after recovery. In rice with a correlation between net photosynthetic rate (PN) and intercellular CO2 concentration (Ci) under salt stress, PN was found to be negatively correlated with filled grain number after recovery. Applying stringent criteria, we identified 130,317 SNPs and 15,396 InDels between two “high-yield rice” varieties and two “low-yield rice” varieties with contrasting photosynthesis and grain yield characteristics. A total of 2089 genes containing high- and moderate-impact SNPs or InDels were evaluated by gene ontology (GO) enrichment analysis, resulting in over-represented terms in the apoptotic process and kinase activity. Among these genes, 262 were highly expressed in reproductive tissues, and most were annotated as receptor-like protein kinases. These findings highlight the importance of variations in signaling components in the genome and these loci can serve as potential genes in rice breeding to produce a variety with salt avoidance that leads to increased yield in saline soil. Full article
(This article belongs to the Special Issue Abiotic Stress in Plants: Current Challenges and Perspectives)
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Open AccessArticle
Complex Gene Regulation Underlying Mineral Nutrient Homeostasis in Soybean Root Response to Acidity Stress
Genes 2019, 10(5), 402; https://doi.org/10.3390/genes10050402 - 27 May 2019
Abstract
Proton toxicity is one of the major environmental stresses limiting crop production and becomes increasingly serious because of anthropogenic activities. To understand acid tolerance mechanisms, the plant growth, mineral nutrients accumulation, and global transcriptome changes in soybean (Glycine max) in response [...] Read more.
Proton toxicity is one of the major environmental stresses limiting crop production and becomes increasingly serious because of anthropogenic activities. To understand acid tolerance mechanisms, the plant growth, mineral nutrients accumulation, and global transcriptome changes in soybean (Glycine max) in response to long-term acidity stress were investigated. Results showed that acidity stress significantly inhibited soybean root growth but exhibited slight effects on the shoot growth. Moreover, concentrations of essential mineral nutrients were significantly affected by acidity stress, mainly differing among soybean organs and mineral nutrient types. Concentrations of phosphorus (P) and molybdenum (Mo) in both leaves and roots, nitrogen (N), and potassium (K) in roots and magnesium (Mg) in leaves were significantly decreased by acidity stress, respectively. Whereas, concentrations of calcium (Ca), sulfate (S), and iron (Fe) were increased in both leaves and roots. Transcriptome analyses in soybean roots resulted in identification of 419 up-regulated and 555 down-regulated genes under acid conditions. A total of 38 differentially expressed genes (DEGs) were involved in mineral nutrients transportation. Among them, all the detected five GmPTs, four GmZIPs, two GmAMTs, and GmKUPs, together with GmIRT1, GmNramp5, GmVIT2.1, GmSKOR, GmTPK5, and GmHKT1, were significantly down-regulated by acidity stress. Moreover, the transcription of genes encoding transcription factors (e.g., GmSTOP2s) and associated with pH stat metabolic pathways was significantly up-regulated by acidity stress. Taken together, it strongly suggests that maintaining pH stat and mineral nutrient homeostasis are adaptive strategies of soybean responses to acidity stress, which might be regulated by a complex signaling network. Full article
(This article belongs to the Special Issue Abiotic Stress in Plants: Current Challenges and Perspectives)
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Open AccessArticle
Protein Changes in Response to Lead Stress of Lead-Tolerant and Lead-Sensitive Industrial Hemp Using SWATH Technology
Genes 2019, 10(5), 396; https://doi.org/10.3390/genes10050396 - 22 May 2019
Abstract
Hemp is a Pb-tolerant and Pb-accumulating plant and the study of its tolerance mechanisms could facilitate the breeding of hemp with enhanced Pb tolerance and accumulation. In the present study, we took advantage of sequential window acquisition of all theoretical mass spectra (SWATH) [...] Read more.
Hemp is a Pb-tolerant and Pb-accumulating plant and the study of its tolerance mechanisms could facilitate the breeding of hemp with enhanced Pb tolerance and accumulation. In the present study, we took advantage of sequential window acquisition of all theoretical mass spectra (SWATH) technology to study the difference in proteomics between the leaves of Pb-tolerant seed-type hemp variety Bamahuoma (BM) and the Pb-sensitive fiber-type hemp variety Yunma 1 (Y1) under Pb stress (3 g/kg soil). A total of 63 and 372 proteins differentially expressed under Pb stress relative to control conditions were identified with liquid chromatography electro spray ionization tandem mass spectrometry in BM and Y1, respectively; with each of these proteins being classified into 14 categories. Hemp adapted to Pb stress by: accelerating adenosine triphosphate (ATP) metabolism; enhancing respiration, light absorption and light energy transfer; promoting assimilation of intercellular nitrogen (N) and carbon (C); eliminating reactive oxygen species; regulating stomatal development and closure; improving exchange of water and CO2 in leaves; promoting intercellular transport; preventing aggregation of unfolded proteins; degrading misfolded proteins; and increasing the transmembrane transport of ATP in chloroplasts. Our results provide an important reference protein and gene information for future molecular studies into the resistance and accumulation of Pb in hemp. Full article
(This article belongs to the Special Issue Abiotic Stress in Plants: Current Challenges and Perspectives)
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