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Genetics and Physiology of Multiple-Stress Tolerance in Crops
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Genetics and Physiology of Multiple-Stress Tolerance in Crops

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

Deadline for manuscript submissions: closed (20 September 2021) | Viewed by 51466

Special Issue Editor

Dr. Domagoj Šimić

E-Mail Website
Guest Editor
Department of Maize Breeding and Genetics, Agricultural Institute Osijek, 31000 Osijek, Croatia
Interests: genetics and physiology of multiple-stress tolerance; maize breeding; contents of carotenoids and tools in maize grain; genotype by environment interaction in crops
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Recent advances in crop physiology, new phenotyping techniques, genomics, and integrative gene-to-phenotype modeling have led to a better understanding of crop tolerance and resilience to individual environmental stress. This has resulted in greater knowledge of the gene networks underlying responses to a specific stress and new tools for plant improvement to increase crop performance. Due to the intrinsic complexities of most stress-tolerance traits, the investigation of crop responses to several simultaneous stresses remains a challenging task. Such research is particularly important as, in nature, concurrent stresses are commonplace. Moreover, the risk of multiple stresses occurring under climate change is expected to exacerbate.

Multidisciplinary studies are pivotal to understanding the effect of concurrent abiotic (e.g., drought, heat, elevated CO2, salinity, metal toxicity) and biotic stress conditions (e.g., pathogens, pests, weeds, plant density) on crop productivity. The aim of this Special Issue is to provide valuable insights into crop tolerance and resilience to both abiotic and biotic stresses by covering multidisciplinary studies ranging from physiological, biochemical, molecular, and modeling analyses. All studies investigating crops coping with any combination of at least two stresses are welcome.

Dr. Domagoj Šimić
Guest Editor

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Keywords

  • abiotic stress
  • biotic stress
  • crops
  • plant breeding
  • plant physiology
  • stress tolerance

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Published Papers (10 papers)

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Research

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13 pages, 1970 KiB  
Article
A Cold-Shock Protein from the South Pole-Dwelling Soil Bacterium Arthrobacter sp. Confers Cold Tolerance to Rice
by So Young Kim, Joung Sug Kim, Woosuk Cho, Kyong Mi Jun, Xiaoxuan Du, Kyung Do Kim, Yeon-Ki Kim and Gang-Seob Lee
Genes 2021, 12(10), 1589; https://doi.org/10.3390/genes12101589 - 9 Oct 2021
Cited by 9 | Viewed by 2505
Abstract
Low temperature is a critical environmental factor restricting the physiology of organisms across kingdoms. In prokaryotes, cold shock induces the expression of various genes and proteins involved in cellular processes. Here, a cold-shock protein (ArCspA) from the South Pole-dwelling soil bacterium Arthrobacter sp. [...] Read more.
Low temperature is a critical environmental factor restricting the physiology of organisms across kingdoms. In prokaryotes, cold shock induces the expression of various genes and proteins involved in cellular processes. Here, a cold-shock protein (ArCspA) from the South Pole-dwelling soil bacterium Arthrobacter sp. A2-5 was introduced into rice, a monocot model plant species. Four-week-old 35S:ArCspA transgenic rice plants grown in a cold chamber at 4 °C survived for 6 days. Cold stress significantly decreased the chlorophyll content in WT plants after 4 days compared with that in 35S:ArCspA transgenic plants. RNA-seq analysis was performed on WT and 35S:ArCspA transgenic rice with/without cold stress. GO terms such as “response to stress (GO:0006950)”, “response to cold (GO:0009409)”, and “response to heat (GO:0009408)” were significantly enriched among the upregulated genes in the 35S:ArCspA transgenic rice under normal conditions, even without cold-stress treatment. The expression of five cold stress-related genes, Rab16B (Os11g0454200), Rab21 (Os11g0454300), LEA22 (Os01g0702500), ABI5 (Os01 g0859300), and MAPK5 (Os03g0285800), was significantly upregulated in the transgenic rice compared with the WT rice. These results indicate that the ArCspA gene might be involved in the induction of cold-responsive genes and provide cold tolerance. Full article
(This article belongs to the Special Issue Genetics and Physiology of Multiple-Stress Tolerance in Crops)
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21 pages, 3045 KiB  
Article
Down-Regulation of SlGRAS10 in Tomato Confers Abiotic Stress Tolerance
by Sidra Habib, Yee Yee Lwin and Ning Li
Genes 2021, 12(5), 623; https://doi.org/10.3390/genes12050623 - 22 Apr 2021
Cited by 28 | Viewed by 2945
Abstract
Adverse environmental factors like salt stress, drought, and extreme temperatures, cause damage to plant growth, development, and crop yield. GRAS transcription factors (TFs) have numerous functions in biological processes. Some studies have reported that the GRAS protein family plays significant functions in plant [...] Read more.
Adverse environmental factors like salt stress, drought, and extreme temperatures, cause damage to plant growth, development, and crop yield. GRAS transcription factors (TFs) have numerous functions in biological processes. Some studies have reported that the GRAS protein family plays significant functions in plant growth and development under abiotic stresses. In this study, we demonstrated the functional characterization of a tomato SlGRAS10 gene under abiotic stresses such as salt stress and drought. Down-regulation of SlGRAS10 by RNA interference (RNAi) produced dwarf plants with smaller leaves, internode lengths, and enhanced flavonoid accumulation. We studied the effects of abiotic stresses on RNAi and wild-type (WT) plants. Moreover, SlGRAS10-RNAi plants were more tolerant to abiotic stresses (salt, drought, and Abscisic acid) than the WT plants. Down-regulation of SlGRAS10 significantly enhanced the expressions of catalase (CAT), peroxidase (POD), and superoxide dismutase (SOD) to reduce the effects of reactive oxygen species (ROS) such as O2− and H2O2. Malondialdehyde (MDA) and proline contents were remarkably high in SlGRAS10-RNAi plants. Furthermore, the expression levels of chlorophyll biosynthesis, flavonoid biosynthesis, and stress-related genes were also enhanced under abiotic stress conditions. Collectively, our conclusions emphasized the significant function of SlGRAS10 as a stress tolerate transcription factor in a certain variety of abiotic stress tolerance by enhancing osmotic potential, flavonoid biosynthesis, and ROS scavenging system in the tomato plant. Full article
(This article belongs to the Special Issue Genetics and Physiology of Multiple-Stress Tolerance in Crops)
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17 pages, 8539 KiB  
Article
Transcriptomic Profiling of Fe-Responsive lncRNAs and Their Regulatory Mechanism in Rice
by Shoudong Wang, Shuo Sun, Runze Guo, Wenying Liao and Huixia Shou
Genes 2021, 12(4), 567; https://doi.org/10.3390/genes12040567 - 14 Apr 2021
Cited by 7 | Viewed by 2642
Abstract
Iron (Fe) deficiency directly affects crop growth and development, ultimately resulting in reduced crop yield and quality. Recently, long non-coding RNAs (lncRNAs) have been demonstrated to play critical regulatory roles in a multitude of pathways across numerous species. However, systematic screening of lncRNAs [...] Read more.
Iron (Fe) deficiency directly affects crop growth and development, ultimately resulting in reduced crop yield and quality. Recently, long non-coding RNAs (lncRNAs) have been demonstrated to play critical regulatory roles in a multitude of pathways across numerous species. However, systematic screening of lncRNAs responding to Fe deficiency and their regulatory mechanism in plants has not been reported. In this work, 171 differently expressed lncRNAs (DE-lncRNAs) were identified based on analysis of strand-specific RNA-seq data from rice shoots and roots under Fe-deficient conditions. We also found several lncRNAs, which could generate miRNAs or act as endogenous target mimics to regulate expression of Fe-related genes. Analysis of interaction networks and gene ontology enrichment revealed that a number of DE-lncRNAs were associated with iron transport and photosynthesis, indicating a possible role of lncRNAs in regulation of Fe homeostasis. Moreover, we identified 76 potential lncRNA targets of OsbHLH156, a key regulator for transcriptional response to Fe deficiency. This study provides insight into the potential functions and regulatory mechanism of Fe-responsive lncRNAs and would be an initial and reference for any further studies regarding lncRNAs involved in Fe deficiency in plants. Full article
(This article belongs to the Special Issue Genetics and Physiology of Multiple-Stress Tolerance in Crops)
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19 pages, 7131 KiB  
Article
Genome-Wide Analysis of the Role of NAC Family in Flower Development and Abiotic Stress Responses in Cleistogenes songorica
by Xifang Zong, Qi Yan, Fan Wu, Qian Ma and Jiyu Zhang
Genes 2020, 11(8), 927; https://doi.org/10.3390/genes11080927 - 12 Aug 2020
Cited by 14 | Viewed by 3714
Abstract
Plant-specific NAC (NAM, ATAF, CUC) transcription factor (TF) family plays important roles in biological processes such as plant growth and response to stress. Nevertheless, no information is known about NAC TFs in Cleistogenes songorica, a prominent xerophyte desert [...] Read more.
Plant-specific NAC (NAM, ATAF, CUC) transcription factor (TF) family plays important roles in biological processes such as plant growth and response to stress. Nevertheless, no information is known about NAC TFs in Cleistogenes songorica, a prominent xerophyte desert grass in northwestern China. In this study, 162 NAC genes were found from the Cleistogenes songorica genome, among which 156 C. songoricaNAC (CsNAC) genes (96.3%) were mapped onto 20 chromosomes. The phylogenetic tree constructed by CsNAC and rice NAC TFs can be separated into 14 subfamilies. Syntenic and Ka/Ks analyses showed that CsNACs were primarily expanded by genomewide replication events, and purifying selection was the primary force driving the evolution of CsNAC family genes. The CsNAC gene expression profiles showed that 36 CsNAC genes showed differential expression between cleistogamous (CL) and chasmogamous (CH) flowers. One hundred and two CsNAC genes showed differential expression under heat, cold, drought, salt and ABA treatment. Twenty-three CsNAC genes were commonly differentially expressed both under stress responses and during dimorphic floret development. Gene Ontology (GO) annotation, coexpression network and qRT-PCR tests revealed that these CsNAC genes may simultaneously regulate dimorphic floret development and the response to stress. Our results may help to characterize the NAC transcription factors in C. songorica and provide new insights into the functional research and application of the NAC family in crop improvement, especially in dimorphic floret plants. Full article
(This article belongs to the Special Issue Genetics and Physiology of Multiple-Stress Tolerance in Crops)
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23 pages, 6314 KiB  
Article
Brassinosteroid Priming Improves Peanut Drought Tolerance via Eliminating Inhibition on Genes in Photosynthesis and Hormone Signaling
by Luping Huang, Lei Zhang, Ruier Zeng, Xinyue Wang, Huajian Zhang, Leidi Wang, Shiyuan Liu, Xuewen Wang and Tingting Chen
Genes 2020, 11(8), 919; https://doi.org/10.3390/genes11080919 - 11 Aug 2020
Cited by 36 | Viewed by 4909
Abstract
Drought negatively affects the growth and yield of terrestrial crops. Seed priming, pre-exposing seed to a compound, could induce improved tolerance and adaptation to stress in germinated plants. To understand the effects and regulatory mechanism of seed priming with brassinosteroid (BR) on peanut [...] Read more.
Drought negatively affects the growth and yield of terrestrial crops. Seed priming, pre-exposing seed to a compound, could induce improved tolerance and adaptation to stress in germinated plants. To understand the effects and regulatory mechanism of seed priming with brassinosteroid (BR) on peanut plants, we treated seeds with five BR concentrations and examined dozens of physiological and biochemical features, and transcriptomic changes in leaves under well-watered and drought conditions. We found optimal 0.15 ppm BR priming could reduce inhibitions from drought and increase the yield of peanut, and priming effects are dependent on stage of plant development and duration of drought. BR priming induced fewer differentially expressed genes (DEGs) than no BR priming under well-watered condition. Drought with BR priming reduced the number of DEGs than drought only. These DEGs were enriched in varied gene ontologies and metabolism pathways. Downregulation of DEGs involved in both light perceiving and photosynthesis in leaves is consistent with low parameters of photosynthesis. Optimal BR priming partially rescued the levels of growth promoting auxin and gibberellin which were largely reduced by drought, and increased levels of defense associated abscisic acid and salicylic acid after long-term drought. BR priming induced many DEGs which function as kinase or transcription factor for signal cascade under drought. We proposed BR priming-induced regulatory responses will be memorized and recalled for fast adaptation in later drought stress. These results provide physiological and regulatory bases of effects of seed priming with BR, which can help to guide the framing improvement under drought stress. Full article
(This article belongs to the Special Issue Genetics and Physiology of Multiple-Stress Tolerance in Crops)
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27 pages, 4995 KiB  
Article
Genetic Basis of Maize Resistance to Multiple Insect Pests: Integrated Genome-Wide Comparative Mapping and Candidate Gene Prioritization
by A. Badji, D. B. Kwemoi, L. Machida, D. Okii, N. Mwila, S. Agbahoungba, F. Kumi, A. Ibanda, A. Bararyenya, M. Solemanegy, T. Odong, P. Wasswa, M. Otim, G. Asea, M. Ochwo-Ssemakula, H. Talwana, S. Kyamanywa and P. Rubaihayo
Genes 2020, 11(6), 689; https://doi.org/10.3390/genes11060689 - 24 Jun 2020
Cited by 21 | Viewed by 7125
Abstract
Several species of herbivores feed on maize in field and storage setups, making the development of multiple insect resistance a critical breeding target. In this study, an association mapping panel of 341 tropical maize lines was evaluated in three field environments for resistance [...] Read more.
Several species of herbivores feed on maize in field and storage setups, making the development of multiple insect resistance a critical breeding target. In this study, an association mapping panel of 341 tropical maize lines was evaluated in three field environments for resistance to fall armyworm (FAW), whilst bulked grains were subjected to a maize weevil (MW) bioassay and genotyped with Diversity Array Technology’s single nucleotide polymorphisms (SNPs) markers. A multi-locus genome-wide association study (GWAS) revealed 62 quantitative trait nucleotides (QTNs) associated with FAW and MW resistance traits on all 10 maize chromosomes, of which, 47 and 31 were discovered at stringent Bonferroni genome-wide significance levels of 0.05 and 0.01, respectively, and located within or close to multiple insect resistance genomic regions (MIRGRs) concerning FAW, SB, and MW. Sixteen QTNs influenced multiple traits, of which, six were associated with resistance to both FAW and MW, suggesting a pleiotropic genetic control. Functional prioritization of candidate genes (CGs) located within 10–30 kb of the QTNs revealed 64 putative GWAS-based CGs (GbCGs) showing evidence of involvement in plant defense mechanisms. Only one GbCG was associated with each of the five of the six combined resistance QTNs, thus reinforcing the pleiotropy hypothesis. In addition, through in silico co-functional network inferences, an additional 107 network-based CGs (NbCGs), biologically connected to the 64 GbCGs, and differentially expressed under biotic or abiotic stress, were revealed within MIRGRs. The provided multiple insect resistance physical map should contribute to the development of combined insect resistance in maize. Full article
(This article belongs to the Special Issue Genetics and Physiology of Multiple-Stress Tolerance in Crops)
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Review

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20 pages, 9086 KiB  
Review
Genetic Approaches to Enhance Multiple Stress Tolerance in Maize
by Nenad Malenica, Jasenka Antunović Dunić, Lovro Vukadinović, Vera Cesar and Domagoj Šimić
Genes 2021, 12(11), 1760; https://doi.org/10.3390/genes12111760 - 4 Nov 2021
Cited by 19 | Viewed by 5076
Abstract
The multiple-stress effects on plant physiology and gene expression are being intensively studied lately, primarily in model plants such as Arabidopsis, where the effects of six stressors have simultaneously been documented. In maize, double and triple stress responses are obtaining more attention, such [...] Read more.
The multiple-stress effects on plant physiology and gene expression are being intensively studied lately, primarily in model plants such as Arabidopsis, where the effects of six stressors have simultaneously been documented. In maize, double and triple stress responses are obtaining more attention, such as simultaneous drought and heat or heavy metal exposure, or drought in combination with insect and fungal infestation. To keep up with these challenges, maize natural variation and genetic engineering are exploited. On one hand, quantitative trait loci (QTL) associated with multiple-stress tolerance are being identified by molecular breeding and genome-wide association studies (GWAS), which then could be utilized for future breeding programs of more resilient maize varieties. On the other hand, transgenic approaches in maize have already resulted in the creation of many commercial double or triple stress resistant varieties, predominantly weed-tolerant/insect-resistant and, additionally, also drought-resistant varieties. It is expected that first generation gene-editing techniques, as well as recently developed base and prime editing applications, in combination with the routine haploid induction in maize, will pave the way to pyramiding more stress tolerant alleles in elite lines/varieties on time. Full article
(This article belongs to the Special Issue Genetics and Physiology of Multiple-Stress Tolerance in Crops)
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31 pages, 2982 KiB  
Review
CRISPR-Based Genome Editing Tools: Insights into Technological Breakthroughs and Future Challenges
by Muntazir Mushtaq, Aejaz Ahmad Dar, Milan Skalicky, Anshika Tyagi, Nancy Bhagat, Umer Basu, Basharat Ahmad Bhat, Abbu Zaid, Sajad Ali, Tanvir-Ul-Hassan Dar, Gyanendra Kumar Rai, Shabir Hussain Wani, Muhammad Habib-Ur-Rahman, Vaclav Hejnak, Pavla Vachova, Marian Brestic, Arzu Çığ, Fatih Çığ, Murat Erman and Ayman EL Sabagh
Genes 2021, 12(6), 797; https://doi.org/10.3390/genes12060797 - 24 May 2021
Cited by 40 | Viewed by 11308
Abstract
Genome-editing (GE) is having a tremendous influence around the globe in the life science community. Among its versatile uses, the desired modifications of genes, and more importantly the transgene (DNA)-free approach to develop genetically modified organism (GMO), are of special interest. The recent [...] Read more.
Genome-editing (GE) is having a tremendous influence around the globe in the life science community. Among its versatile uses, the desired modifications of genes, and more importantly the transgene (DNA)-free approach to develop genetically modified organism (GMO), are of special interest. The recent and rapid developments in genome-editing technology have given rise to hopes to achieve global food security in a sustainable manner. We here discuss recent developments in CRISPR-based genome-editing tools for crop improvement concerning adaptation, opportunities, and challenges. Some of the notable advances highlighted here include the development of transgene (DNA)-free genome plants, the availability of compatible nucleases, and the development of safe and effective CRISPR delivery vehicles for plant genome editing, multi-gene targeting and complex genome editing, base editing and prime editing to achieve more complex genetic engineering. Additionally, new avenues that facilitate fine-tuning plant gene regulation have also been addressed. In spite of the tremendous potential of CRISPR and other gene editing tools, major challenges remain. Some of the challenges are related to the practical advances required for the efficient delivery of CRISPR reagents and for precision genome editing, while others come from government policies and public acceptance. This review will therefore be helpful to gain insights into technological advances, its applications, and future challenges for crop improvement. Full article
(This article belongs to the Special Issue Genetics and Physiology of Multiple-Stress Tolerance in Crops)
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21 pages, 730 KiB  
Review
Alternative Strategies for Multi-Stress Tolerance and Yield Improvement in Millets
by Muhammad Numan, Desalegn D. Serba and Ayalew Ligaba-Osena
Genes 2021, 12(5), 739; https://doi.org/10.3390/genes12050739 - 14 May 2021
Cited by 30 | Viewed by 6291
Abstract
Millets are important cereal crops cultivated in arid and semiarid regions of the world, particularly Africa and southeast Asia. Climate change has triggered multiple abiotic stresses in plants that are the main causes of crop loss worldwide, reducing average yield for most crops [...] Read more.
Millets are important cereal crops cultivated in arid and semiarid regions of the world, particularly Africa and southeast Asia. Climate change has triggered multiple abiotic stresses in plants that are the main causes of crop loss worldwide, reducing average yield for most crops by more than 50%. Although millets are tolerant to most abiotic stresses including drought and high temperatures, further improvement is needed to make them more resilient to unprecedented effects of climate change and associated environmental stresses. Incorporation of stress tolerance traits in millets will improve their productivity in marginal environments and will help in overcoming future food shortage due to climate change. Recently, approaches such as application of plant growth-promoting rhizobacteria (PGPRs) have been used to improve growth and development, as well as stress tolerance of crops. Moreover, with the advance of next-generation sequencing technology, genome editing, using the clustered regularly interspaced short palindromic repeats (CRISPR/Cas9) system are increasingly used to develop stress tolerant varieties in different crops. In this paper, the innate ability of millets to tolerate abiotic stresses and alternative approaches to boost stress resistance were thoroughly reviewed. Moreover, several stress-resistant genes were identified in related monocots such as rice (Oryza sativa), wheat (Triticum aestivum), and maize (Zea mays), and other related species for which orthologs in millets could be manipulated by CRISPR/Cas9 and related genome-editing techniques to improve stress resilience and productivity. These cutting-edge alternative strategies are expected to bring this group of orphan crops at the forefront of scientific research for their potential contribution to global food security. Full article
(This article belongs to the Special Issue Genetics and Physiology of Multiple-Stress Tolerance in Crops)
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20 pages, 1089 KiB  
Review
Aquaporins in Cereals—Important Players in Maintaining Cell Homeostasis under Abiotic Stress
by Marzena Małgorzata Kurowska
Genes 2021, 12(4), 477; https://doi.org/10.3390/genes12040477 - 25 Mar 2021
Cited by 18 | Viewed by 3288
Abstract
Cereal productivity is reduced by environmental stresses such as drought, heat, elevated CO2, salinity, metal toxicity and cold. Sometimes, plants are exposed to multiple stresses simultaneously. Plants must be able to make a rapid and adequate response to these environmental stimuli [...] Read more.
Cereal productivity is reduced by environmental stresses such as drought, heat, elevated CO2, salinity, metal toxicity and cold. Sometimes, plants are exposed to multiple stresses simultaneously. Plants must be able to make a rapid and adequate response to these environmental stimuli in order to restore their growing ability. The latest research has shown that aquaporins are important players in maintaining cell homeostasis under abiotic stress. Aquaporins are membrane intrinsic proteins (MIP) that form pores in the cellular membranes, which facilitate the movement of water and many other molecules such as ammonia, urea, CO2, micronutrients (silicon and boron), glycerol and reactive oxygen species (hydrogen peroxide) across the cell and intercellular compartments. The present review primarily focuses on the diversity of aquaporins in cereal species, their cellular and subcellular localisation, their expression and their functioning under abiotic stresses. Lastly, this review discusses the potential use of mutants and plants that overexpress the aquaporin-encoding genes to improve their tolerance to abiotic stress. Full article
(This article belongs to the Special Issue Genetics and Physiology of Multiple-Stress Tolerance in Crops)
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