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Molecular Biology of Crop Abiotic Stress Resistance
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Molecular Biology of Crop Abiotic Stress Resistance

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 November 2024) | Viewed by 11594

Special Issue Editors

Prof. Dr. Yanxin Zhao

E-Mail Website
Guest Editor
Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
Interests: maize; functional genomics; abiotic stress; plant phenomics; cytoplasmic male sterility; molecular breeding
Dr. Meijie Luo

E-Mail Website
Guest Editor
Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
Interests: waxy corn; sweet corn; biofortification; salt tolerance; heavy metal stress; herbicide resistance; molecular breeding

Special Issue Information

Dear Colleagues,

Extreme environmental stimuli, such as heat, cold, drought, high salinity, heavy metal pollution and mineral nutrient deficiencies, severely constrain crop growth, development and yield. Breeding stress-resistant varieties can reduce the yield losses of crops under stress conditions and alleviate the food shortages caused by the ever-growing global population. Crop plants possess and adopt multifarious molecular strategies to cope with various environmental stresses. The identification of genetic loci and genes conferring crop stress resistance and understanding the molecular mechanism underlying crop stress response and resistance will facilitate the breeding of elite stress-resistant crops. Along with an increasing number of crop genomes being sequenced, more of the genetic and molecular basis of crop stress resistance will be uncovered soon.

This Special Issue of Genes, entitled “Molecular Biology of Crop Stress Abiotic Resistance”, will collect high-quality research articles, short communications and reviews on all aspects of the recent molecular biology research of crop stress resistance. The topics include, but are not limited to, the following aspects: 1) the identification of candidate loci/genes for a variety of crop stress resistance by QTL mapping, gene cloning and mining omics data; 2) crop stress resistance-related gene family survey, gene expression regulation and gene function validation with mutants and overexpression; 3) stress-resistant molecular marker development and molecular breeding; 4) new methods and techniques used to study crop stress resistance.

Prof. Dr. Yanxin Zhao
Dr. Meijie Luo
Guest Editors

Manuscript Submission Information

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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.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • crop
  • abiotic stress
  • gene cloning
  • QTL mapping
  • gene function analysis

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Published Papers (7 papers)

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Research

13 pages, 7132 KiB  
Article
Molecular Characterization of Peroxidase (PRX) Gene Family in Cucumber
by Weirong Luo, Junjun Liu, Wenchen Xu, Shenshen Zhi, Xudong Wang and Yongdong Sun
Genes 2024, 15(10), 1245; https://doi.org/10.3390/genes15101245 - 25 Sep 2024
Viewed by 685
Abstract
Background: The Peroxidase (PRX) gene family is essential for plant growth and significantly contributes to defense against stresses. However, information about PRX genes in cucumber (Cucumis sativus L.) remains limited. Methods: In this present study, CsPRX genes were [...] Read more.
Background: The Peroxidase (PRX) gene family is essential for plant growth and significantly contributes to defense against stresses. However, information about PRX genes in cucumber (Cucumis sativus L.) remains limited. Methods: In this present study, CsPRX genes were identified and characterized using bioinformatics analysis. The expression pattern analysis of CsPRX genes were examined utilizing the RNA-seq data of cucumber from public databases and real-time quantitative PCR (qRT-PCR) analysis. Results: Here, we identified 60 CsPRX genes and mapped them onto seven chromosomes of cucumber. The CsPRX proteins exhibited the presence of 10 conserved motifs, with motif 8, motif 2, motif 5, and motif 3 consistently appearing across all 60 CsPRX protein sequences, indicating the conservation of CsPRX proteins. Furthermore, RNA-seq analysis revealed that differential expression of CsPRX genes in various tissues. Notably, a majority of the CsPRX genes exhibited significantly higher expression levels in the root compared to the other plant tissues, suggesting a potential specialization of these genes in root function. In addition, qRT-PCR analysis for four selected CsPRX genes under different stress conditions indicated that these selected CsPRX genes demonstrated diverse expression levels when subjected to NaCl, CdCl2, and PEG treatments, and the CsPRX17 gene was significantly induced by NaCl, CdCl2, and PEG stresses, suggesting a vital role of the CsPRX17 gene in response to environmental stresses. Conclusions: These findings will contribute valuable insights for future research into the functions and regulatory mechanisms associated with CsPRX genes in cucumber. Full article
(This article belongs to the Special Issue Molecular Biology of Crop Abiotic Stress Resistance)
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21 pages, 1382 KiB  
Article
Differential Gene Expression in Contrasting Common Bean Cultivars for Drought Tolerance during an Extended Dry Period
by Talita Pijus Ponce, Michely da Silva Bugança, Victória Stern da Silva, Rogério Fernandes de Souza, Vânia Moda-Cirino and Juarez Pires Tomaz
Genes 2024, 15(7), 935; https://doi.org/10.3390/genes15070935 - 17 Jul 2024
Viewed by 1109
Abstract
Common beans (Phaseolus vulgaris L.), besides being an important source of nutrients such as iron, magnesium, and protein, are crucial for food security, especially in developing countries. Common bean cultivation areas commonly face production challenges due to drought occurrences, mainly during the [...] Read more.
Common beans (Phaseolus vulgaris L.), besides being an important source of nutrients such as iron, magnesium, and protein, are crucial for food security, especially in developing countries. Common bean cultivation areas commonly face production challenges due to drought occurrences, mainly during the reproductive period. Dry spells last approximately 20 days, enough time to compromise production. Hence, it is crucial to understand the genetic and molecular mechanisms that confer drought tolerance to improve common bean cultivars’ adaptation to drought. Sixty six RNASeq libraries, generated from tolerant and sensitive cultivars in drought time sourced from the R5 phenological stage at 0 to 20 days of water deficit were sequenced, generated over 1.5 billion reads, that aligned to 62,524 transcripts originating from a reference transcriptome, as well as 6673 transcripts obtained via de novo assembly. Differentially expressed transcripts were functionally annotated, revealing a variety of genes associated with molecular functions such as oxidoreductase and transferase activity, as well as biological processes related to stress response and signaling. The presence of regulatory genes involved in signaling cascades and transcriptional control was also highlighted, for example, LEA proteins and dehydrins associated with dehydration protection, and transcription factors such as WRKY, MYB, and NAC, which modulate plant response to water deficit. Additionally, genes related to membrane and protein protection, as well as water and ion uptake and transport, were identified, including aquaporins, RING-type E3 ubiquitin transferases, antioxidant enzymes such as GSTs and CYPs, and thioredoxins. This study highlights the complexity of plant response to water scarcity, focusing on the functional diversity of the genes involved and their participation in the biological processes essential for plant adaptation to water stress. The identification of regulatory and cell protection genes offers promising prospects for genetic improvement aiming at the production of common bean varieties more resistant to drought. These findings have the potential to drive sustainable agriculture, providing valuable insights to ensure food security in a context of climate change. Full article
(This article belongs to the Special Issue Molecular Biology of Crop Abiotic Stress Resistance)
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13 pages, 4622 KiB  
Article
Heat-Resistant Inbred Lines Coordinate the Heat Response Gene Expression Remarkably in Maize (Zea mays L.)
by Ming Xue, Xiaoyue Han, Luyao Zhang and Saihua Chen
Genes 2024, 15(3), 289; https://doi.org/10.3390/genes15030289 - 25 Feb 2024
Cited by 1 | Viewed by 1687
Abstract
High temperatures are increasingly becoming a prominent environmental factor accelerating the adverse influence on the growth and development of maize (Zea mays L.). Therefore, it is critical to identify the key genes and pathways related to heat stress (HS) tolerance in maize. [...] Read more.
High temperatures are increasingly becoming a prominent environmental factor accelerating the adverse influence on the growth and development of maize (Zea mays L.). Therefore, it is critical to identify the key genes and pathways related to heat stress (HS) tolerance in maize. Great challenges have been faced in dissecting genetic mechanisms and uncovering master genes for HS tolerance. Here, Z58D showed more thermotolerance than AF171 at the seedling stage with a lower wilted leaf rate and H2O2 accumulation under HS conditions. Transcriptomic analysis identified 3006 differentially expressed genes (DEGs) in AF171 and 4273 DEGs in Z58D under HS treatments, respectively. Subsequently, GO enrichment analysis showed that commonly upregulated genes in AF171 and Z58D were significantly enriched in the following biological processes, including protein folding, response to heat, response to temperature stimulus and response to hydrogen peroxide. Moreover, the comparison between the two inbred lines under HS showed that response to heat and response to temperature stimulus were significantly over-represented for the 1234 upregulated genes in Z58D. Furthermore, more commonly upregulated genes exhibited higher expression levels in Z58D than AF171. In addition, maize inbred CIMBL55 was verified to be more tolerant than B73, and more commonly upregulated genes also showed higher expression levels in CIMBL55 than B73 under HS. These consistent results indicate that heat-resistant inbred lines may coordinate the remarkable expression of genes in order to recover from HS. Additionally, 35 DEGs were conserved among five inbred lines via comparative transcriptomic analysis. Most of them were more pronounced in Z58D than AF171 at the expression levels. These candidate genes may confer thermotolerance in maize. Full article
(This article belongs to the Special Issue Molecular Biology of Crop Abiotic Stress Resistance)
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15 pages, 2906 KiB  
Article
Identification of Novel QTL for Mercury Accumulation in Maize Using an Enlarged SNP Panel
by Jionghao Gao, Jianxin Li, Jihong Zhang, Yan Sun, Xiaolong Ju, Wenlong Li, Haiyang Duan, Zhengjie Xue, Li Sun, Javed Hussain Sahito, Zhiyuan Fu, Xuehai Zhang and Jihua Tang
Genes 2024, 15(2), 257; https://doi.org/10.3390/genes15020257 - 19 Feb 2024
Cited by 3 | Viewed by 1740
Abstract
Mercury (Hg) pollution not only poses a threat to the environment but also adversely affects the growth and development of plants, with potential repercussions for animals and humans through bioaccumulation in the food chain. Maize, a crucial source of food, industrial materials, and [...] Read more.
Mercury (Hg) pollution not only poses a threat to the environment but also adversely affects the growth and development of plants, with potential repercussions for animals and humans through bioaccumulation in the food chain. Maize, a crucial source of food, industrial materials, and livestock feed, requires special attention in understanding the genetic factors influencing mercury accumulation. Developing maize varieties with low mercury accumulation is vital for both maize production and human health. In this study, a comprehensive genome-wide association study (GWAS) was conducted using an enlarged SNP panel comprising 1.25 million single nucleotide polymorphisms (SNPs) in 230 maize inbred lines across three environments. The analysis identified 111 significant SNPs within 78 quantitative trait loci (QTL), involving 169 candidate genes under the Q model. Compared to the previous study, the increased marker density and optimized statistical model led to the discovery of 74 additional QTL, demonstrating improved statistical power. Gene ontology (GO) enrichment analysis revealed that most genes participate in arsenate reduction and stress responses. Notably, GRMZM2G440968, which has been reported in previous studies, is associated with the significant SNP chr6.S_155668107 in axis tissue. It encodes a cysteine proteinase inhibitor, implying its potential role in mitigating mercury toxicity by inhibiting cysteine. Haplotype analyses provided further insights, indicating that lines carrying hap3 exhibited the lowest mercury content compared to other haplotypes. In summary, our study significantly enhances the statistical power of GWAS, identifying additional genes related to mercury accumulation and metabolism. These findings offer valuable insights into unraveling the genetic basis of mercury content in maize and contribute to the development of maize varieties with low mercury accumulation. Full article
(This article belongs to the Special Issue Molecular Biology of Crop Abiotic Stress Resistance)
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14 pages, 2229 KiB  
Article
Phenotypic and Proteomic Insights into Differential Cadmium Accumulation in Maize Kernels
by Huanle Guo, Min Deng, Feng Yu, Han Li, Zhongyang Cao, Qiang Zeng, Zhihui Chen, Hongbing Luo and Bin Tang
Genes 2023, 14(12), 2204; https://doi.org/10.3390/genes14122204 - 13 Dec 2023
Viewed by 1423
Abstract
The contamination of agricultural soil with cadmium (Cd), a heavy metal, poses a significant environmental challenge, affecting crop growth, development, and human health. Previous studies have established the pivotal role of the ZmHMA3 gene, a P-type ATPase heavy metal transporter, in determining variable [...] Read more.
The contamination of agricultural soil with cadmium (Cd), a heavy metal, poses a significant environmental challenge, affecting crop growth, development, and human health. Previous studies have established the pivotal role of the ZmHMA3 gene, a P-type ATPase heavy metal transporter, in determining variable Cd accumulation in maize grains among 513 inbred lines. To decipher the molecular mechanism underlying mutation-induced phenotypic differences mediated by ZmHMA3, we conducted a quantitative tandem mass tag (TMT)-based proteomic analysis of immature maize kernels. This analysis aimed to identify differentially expressed proteins (DEPs) in wild-type B73 and ZmHMA3 null mutant under Cd stress. The findings demonstrated that ZmHMA3 accumulated higher levels of Cd compared to B73 when exposed to varying Cd concentrations in the soil. In comparison to soil with a low Cd concentration, B73 and ZmHMA3 exhibited 75 and 142 DEPs, respectively, with 24 common DEPs shared between them. ZmHMA3 showed a higher induction of upregulated genes related to Cd stress than B73. Amino sugar and nucleotide sugar metabolism was specifically enriched in B73, while phenylpropanoid biosynthesis, nitrogen metabolism, and glyoxylate and dicarboxylate metabolism appeared to play a more significant role in ZmHMA3. This study provides proteomics insights into unraveling the molecular mechanism underlying the differences in Cd accumulation in maize kernels. Full article
(This article belongs to the Special Issue Molecular Biology of Crop Abiotic Stress Resistance)
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20 pages, 4032 KiB  
Article
Using High-Throughput Phenotyping Analysis to Decipher the Phenotypic Components and Genetic Architecture of Maize Seedling Salt Tolerance
by Shangjing Guo, Lujia Lv, Yanxin Zhao, Jinglu Wang, Xianju Lu, Minggang Zhang, Ronghuan Wang, Ying Zhang and Xinyu Guo
Genes 2023, 14(9), 1771; https://doi.org/10.3390/genes14091771 - 7 Sep 2023
Cited by 2 | Viewed by 1777
Abstract
Soil salinization is a worldwide problem that limits agricultural production. It is important to understand the salt stress tolerance ability of maize seedlings and explore the underlying related genetic resources. In this study, we used a high-throughput phenotyping platform with a 3D laser [...] Read more.
Soil salinization is a worldwide problem that limits agricultural production. It is important to understand the salt stress tolerance ability of maize seedlings and explore the underlying related genetic resources. In this study, we used a high-throughput phenotyping platform with a 3D laser sensor (Planteye F500) to identify the digital biomass, plant height and normalized vegetation index under normal and saline conditions at multiple time points. The result revealed that a three-leaf period (T3) was identified as the key period for the phenotypic variation in maize seedlings under salt stress. Moreover, we mapped the salt-stress-related SNPs and identified candidate genes in the natural population via a genome-wide association study. A total of 44 candidate genes were annotated, including 26 candidate genes under normal conditions and 18 candidate genes under salt-stressed conditions. This study demonstrates the feasibility of using a high-throughput phenotyping platform to accurately, continuously quantify morphological traits of maize seedlings in different growing environments. And the phenotype and genetic information of this study provided a theoretical basis for the breeding of salt-resistant maize varieties and the study of salt-resistant genes. Full article
(This article belongs to the Special Issue Molecular Biology of Crop Abiotic Stress Resistance)
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15 pages, 4094 KiB  
Article
Nutrient Metabolism Pathways Analysis and Key Candidate Genes Identification Corresponding to Cadmium Stress in Buckwheat through Multiomics Analysis
by Dengxiang Du, Hanxian Xiong, Congping Xu, Wanyong Zeng, Jinhua Li and Guoqing Dong
Genes 2023, 14(7), 1462; https://doi.org/10.3390/genes14071462 - 18 Jul 2023
Cited by 4 | Viewed by 1970
Abstract
Fagopylum tatarium (L.) Gaertn (buckwheat) can be used both as medicine and food and is also an important food crop in barren areas and has great economic value. Exploring the molecular mechanisms of the response to cadmium (Cd) stress can provide the theoretical [...] Read more.
Fagopylum tatarium (L.) Gaertn (buckwheat) can be used both as medicine and food and is also an important food crop in barren areas and has great economic value. Exploring the molecular mechanisms of the response to cadmium (Cd) stress can provide the theoretical reference for improving the buckwheat yield and quality. In this study, perennial tartary buckwheat DK19 was used as the experimental material, its key metabolic pathways in the response to Cd stress were identified and verified through transcriptomic and metabolomic data analysis. In this investigation, 1798 metabolites were identified through non-targeted metabolomic analysis containing 1091 up-regulated and 984down-regulated metabolites after treatment. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of differential metabolites was significantly enriched in galactose metabolism, glycerol metabolism, phenylpropane biosynthesis, glutathione metabolism, starch and sucrose metabolism. Linkage analysis detected 11 differentially expressed genes (DEGs) in the galactose metabolism pathway, 8 candidate DEGs in the lipid metabolism pathway, and 20 candidate DEGs in the glutathione metabolism pathway. The results of our study provided useful clues for genetically improving the resistance to cadmium by analyzing the molecular mechanism of cadmium tolerance in buckwheat. Full article
(This article belongs to the Special Issue Molecular Biology of Crop Abiotic Stress Resistance)
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