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Sonsungsan P, Suratanee A, Buaboocha T, Chadchawan S, Plaimas K. Identification of Salt-Sensitive and Salt-Tolerant Genes through Weighted Gene Co-Expression Networks across Multiple Datasets: A Centralization and Differential Correlation Analysis. Genes (Basel) 2024; 15:316. [PMID: 38540375 PMCID: PMC10970189 DOI: 10.3390/genes15030316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/18/2024] [Accepted: 02/24/2024] [Indexed: 06/14/2024] Open
Abstract
Salt stress is a significant challenge that severely hampers rice growth, resulting in decreased yield and productivity. Over the years, researchers have identified biomarkers associated with salt stress to enhance rice tolerance. However, the understanding of the mechanism underlying salt tolerance in rice remains incomplete due to the involvement of multiple genes. Given the vast amount of genomics and transcriptomics data available today, it is crucial to integrate diverse datasets to identify key genes that play essential roles during salt stress in rice. In this study, we propose an integration of multiple datasets to identify potential key transcription factors. This involves utilizing network analysis based on weighted co-expression networks, focusing on gene-centric measurement and differential co-expression relationships among genes. Consequently, our analysis reveals 86 genes located in markers from previous meta-QTL analysis. Moreover, six transcription factors, namely LOC_Os03g45410 (OsTBP2), LOC_Os07g42400 (OsGATA23), LOC_Os01g13030 (OsIAA3), LOC_Os05g34050 (OsbZIP39), LOC_Os09g29930 (OsBIM1), and LOC_Os10g10990 (transcription initiation factor IIF), exhibited significantly altered co-expression relationships between salt-sensitive and salt-tolerant rice networks. These identified genes hold potential as crucial references for further investigation into the functions of salt stress response in rice plants and could be utilized in the development of salt-resistant rice cultivars. Overall, our findings shed light on the complex genetic regulation underlying salt tolerance in rice and contribute to the broader understanding of rice's response to salt stress.
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Affiliation(s)
- Pajaree Sonsungsan
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand;
| | - Apichat Suratanee
- Department of Mathematics, Faculty of Applied Science, King Mongkut’s University of Technology North Bangkok, Bangkok 10800, Thailand;
| | - Teerapong Buaboocha
- Center of Excellence in Molecular Crop, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand;
| | - Supachitra Chadchawan
- Center of Excellence in Environment and Plant Physiology (CEEPP), Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand;
- Omics Science and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Kitiporn Plaimas
- Omics Science and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Advanced Virtual and Intelligent Computing (AVIC) Center, Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
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Reinprecht Y, Schram L, Perry GE, Morneau E, Smith TH, Pauls KP. Mapping yield and yield-related traits using diverse common bean germplasm. Front Genet 2024; 14:1246904. [PMID: 38234999 PMCID: PMC10791882 DOI: 10.3389/fgene.2023.1246904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 11/29/2023] [Indexed: 01/19/2024] Open
Abstract
Common bean (bean) is one of the most important legume crops, and mapping genes for yield and yield-related traits is essential for its improvement. However, yield is a complex trait that is typically controlled by many loci in crop genomes. The objective of this research was to identify regions in the bean genome associated with yield and a number of yield-related traits using a collection of 121 diverse bean genotypes with different yields. The beans were evaluated in replicated trials at two locations, over two years. Significant variation among genotypes was identified for all traits analyzed in the four environments. The collection was genotyped with the BARCBean6K_3 chip (5,398 SNPs), two yield/antiyield gene-based markers, and seven markers previously associated with resistance to common bacterial blight (CBB), including a Niemann-Pick polymorphism (NPP) gene-based marker. Over 90% of the single-nucleotide polymorphisms (SNPs) were polymorphic and separated the panel into two main groups of small-seeded and large-seeded beans, reflecting their Mesoamerican and Andean origins. Thirty-nine significant marker-trait associations (MTAs) were identified between 31 SNPs and 15 analyzed traits on all 11 bean chromosomes. Some of these MTAs confirmed genome regions previously associated with the yield and yield-related traits in bean, but a number of associations were not reported previously, especially those with derived traits. Over 600 candidate genes with different functional annotations were identified for the analyzed traits in the 200-Kb region centered on significant SNPs. Fourteen SNPs were identified within the gene model sequences, and five additional SNPs significantly associated with five different traits were located at less than 0.6 Kb from the candidate genes. The work confirmed associations between two yield/antiyield gene-based markers (AYD1m and AYD2m) on chromosome Pv09 with yield and identified their association with a number of yield-related traits, including seed weight. The results also confirmed the usefulness of the NPP marker in screening for CBB resistance. Since disease resistance and yield measurements are environmentally dependent and labor-intensive, the three gene-based markers (CBB- and two yield-related) and quantitative trait loci (QTL) that were validated in this work may be useful tools for simplifying and accelerating the selection of high-yielding and CBB-resistant bean cultivars.
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Affiliation(s)
| | - Lyndsay Schram
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
| | - Gregory E. Perry
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
| | - Emily Morneau
- Harrow Research and Development Centre, Agriculture and Agri-Food Canada, Harrow, ON, Canada
| | - Thomas H. Smith
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
| | - K. Peter Pauls
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
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Abubakar YS, Sadiq IZ, Aarti A, Wang Z, Zheng W. Interplay of transport vesicles during plant-fungal pathogen interaction. STRESS BIOLOGY 2023; 3:35. [PMID: 37676627 PMCID: PMC10442309 DOI: 10.1007/s44154-023-00114-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 07/31/2023] [Indexed: 09/08/2023]
Abstract
Vesicle trafficking is an essential cellular process upon which many physiological processes of eukaryotic cells rely. It is usually the 'language' of communication among the components of the endomembrane system within a cell, between cells and between a cell and its external environment. Generally, cells have the potential to internalize membrane-bound vesicles from external sources by endocytosis. Plants constantly interact with both mutualistic and pathogenic microbes. A large part of this interaction involves the exchange of transport vesicles between the plant cells and the microbes. Usually, in a pathogenic interaction, the pathogen releases vesicles containing bioactive molecules that can modulate the host immunity when absorbed by the host cells. In response to this attack, the host cells similarly mobilize some vesicles containing pathogenesis-related compounds to the pathogen infection site to destroy the pathogen, prevent it from penetrating the host cell or annul its influence. In fact, vesicle trafficking is involved in nearly all the strategies of phytopathogen attack subsequent plant immune responses. However, this field of plant-pathogen interaction is still at its infancy when narrowed down to plant-fungal pathogen interaction in relation to exchange of transport vesicles. Herein, we summarized some recent and novel findings unveiling the involvement of transport vesicles as a crosstalk in plant-fungal phytopathogen interaction, discussed their significance and identified some knowledge gaps to direct future research in the field. The roles of vesicles trafficking in the development of both organisms are also established.
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Affiliation(s)
- Yakubu Saddeeq Abubakar
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Department of Biochemistry, Faculty of Life Sciences, Ahmadu Bello University, Zaria, Nigeria
| | - Idris Zubair Sadiq
- Department of Biochemistry, Faculty of Life Sciences, Ahmadu Bello University, Zaria, Nigeria
| | - Aarti Aarti
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zonghua Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.
- Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, China.
| | - Wenhui Zheng
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China.
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Ganotra J, Sharma B, Biswal B, Bhardwaj D, Tuteja N. Emerging role of small GTPases and their interactome in plants to combat abiotic and biotic stress. PROTOPLASMA 2023; 260:1007-1029. [PMID: 36525153 DOI: 10.1007/s00709-022-01830-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 12/05/2022] [Indexed: 06/07/2023]
Abstract
Plants are frequently subjected to abiotic and biotic stress which causes major impediments in their growth and development. It is emerging that small guanosine triphosphatases (small GTPases), also known as monomeric GTP-binding proteins, assist plants in managing environmental stress. Small GTPases function as tightly regulated molecular switches that get activated with the aid of guanosine triphosphate (GTP) and deactivated by the subsequent hydrolysis of GTP to guanosine diphosphate (GDP). All small GTPases except Rat sarcoma (Ras) are found in plants, including Ras-like in brain (Rab), Rho of plant (Rop), ADP-ribosylation factor (Arf) and Ras-like nuclear (Ran). The members of small GTPases in plants interact with several downstream effectors to counteract the negative effects of environmental stress and disease-causing pathogens. In this review, we describe processes of stress alleviation by developing pathways involving several small GTPases and their associated proteins which are important for neutralizing fungal infections, stomatal regulation, and activation of abiotic stress-tolerant genes in plants. Previous reviews on small GTPases in plants were primarily focused on Rab GTPases, abiotic stress, and membrane trafficking, whereas this review seeks to improve our understanding of the role of all small GTPases in plants as well as their interactome in regulating mechanisms to combat abiotic and biotic stress. This review brings to the attention of scientists recent research on small GTPases so that they can employ genome editing tools to precisely engineer economically important plants through the overexpression/knock-out/knock-in of stress-related small GTPase genes.
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Affiliation(s)
- Jahanvi Ganotra
- Department of Botany, Central University of Jammu, Jammu and Kashmir, Jammu, 181143, India
| | - Bhawana Sharma
- Department of Botany, Central University of Jammu, Jammu and Kashmir, Jammu, 181143, India
| | - Brijesh Biswal
- Department of Botany, Central University of Jammu, Jammu and Kashmir, Jammu, 181143, India
| | - Deepak Bhardwaj
- Department of Botany, Central University of Jammu, Jammu and Kashmir, Jammu, 181143, India.
| | - Narendra Tuteja
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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Ahouvi Y, Haber Z, Zach YY, Rosental L, Toubiana D, Sharma D, Alseekh S, Tajima H, Fernie AR, Brotman Y, Blumwald E, Sade N. The Alteration of Tomato Chloroplast Vesiculation Positively Affects Whole-Plant Source-Sink Relations and Fruit Metabolism under Stress Conditions. PLANT & CELL PHYSIOLOGY 2023; 63:2008-2026. [PMID: 36161338 DOI: 10.1093/pcp/pcac133] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 09/14/2022] [Accepted: 09/23/2022] [Indexed: 06/16/2023]
Abstract
Changes in climate conditions can negatively affect the productivity of crop plants. They can induce chloroplast degradation (senescence), which leads to decreased source capacity, as well as decreased whole-plant carbon/nitrogen assimilation and allocation. The importance, contribution and mechanisms of action regulating source-tissue capacity under stress conditions in tomato (Solanum lycopersicum) are not well understood. We hypothesized that delaying chloroplast degradation by altering the activity of the tomato chloroplast vesiculation (CV) under stress would lead to more efficient use of carbon and nitrogen and to higher yields. Tomato CV is upregulated under stress conditions. Specific induction of CV in leaves at the fruit development stage resulted in stress-induced senescence and negatively affected fruit yield, without any positive effects on fruit quality. Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein 9 (CRISPR/CAS9) knockout CV plants, generated using a near-isogenic tomato line with enhanced sink capacity, exhibited stress tolerance at both the vegetative and the reproductive stages, leading to enhanced fruit quantity, quality and harvest index. Detailed metabolic and transcriptomic network analysis of sink tissue revealed that the l-glutamine and l-arginine biosynthesis pathways are associated with stress-response conditions and also identified putative novel genes involved in tomato fruit quality under stress. Our results are the first to demonstrate the feasibility of delayed stress-induced senescence as a stress-tolerance trait in a fleshy fruit crop, to highlight the involvement of the CV pathway in the regulation of source strength under stress and to identify genes and metabolic pathways involved in increased tomato sink capacity under stress conditions.
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Affiliation(s)
- Yoav Ahouvi
- School of Plant Sciences and Food Security, Tel Aviv University, P.O.B. 39040, 55 Haim Levanon St., Tel Aviv 6139001, Israel
| | - Zechariah Haber
- School of Plant Sciences and Food Security, Tel Aviv University, P.O.B. 39040, 55 Haim Levanon St., Tel Aviv 6139001, Israel
| | - Yair Yehoshua Zach
- School of Plant Sciences and Food Security, Tel Aviv University, P.O.B. 39040, 55 Haim Levanon St., Tel Aviv 6139001, Israel
| | - Leah Rosental
- Department of Life Sciences, Ben-Gurion University of the Negev, P.O.B. 653, 1 David Ben Gurion Blvd., Beer-Sheva 8410501, Israel
| | - David Toubiana
- School of Plant Sciences and Food Security, Tel Aviv University, P.O.B. 39040, 55 Haim Levanon St., Tel Aviv 6139001, Israel
| | - Davinder Sharma
- School of Plant Sciences and Food Security, Tel Aviv University, P.O.B. 39040, 55 Haim Levanon St., Tel Aviv 6139001, Israel
| | - Saleh Alseekh
- Department of Root Biology and Symbiosis, Max Planck Institute of Molecular Plant Physiology, 1 Am Mühlenberg, Golm, Potsdam 14476, Germany
- Department of Plant Metabolomics, Center for Plant Systems Biology and Biotechnology, 139 Ruski Blvd., Plovdiv 4000, Bulgaria
| | - Hiromi Tajima
- Department of Plant Sciences, University of California, 1 Shields Ave., Davis, CA 95616, USA
| | - Alisdair R Fernie
- Department of Root Biology and Symbiosis, Max Planck Institute of Molecular Plant Physiology, 1 Am Mühlenberg, Golm, Potsdam 14476, Germany
- Department of Plant Metabolomics, Center for Plant Systems Biology and Biotechnology, 139 Ruski Blvd., Plovdiv 4000, Bulgaria
| | - Yariv Brotman
- Department of Life Sciences, Ben-Gurion University of the Negev, P.O.B. 653, 1 David Ben Gurion Blvd., Beer-Sheva 8410501, Israel
| | - Eduardo Blumwald
- Department of Plant Sciences, University of California, 1 Shields Ave., Davis, CA 95616, USA
| | - Nir Sade
- School of Plant Sciences and Food Security, Tel Aviv University, P.O.B. 39040, 55 Haim Levanon St., Tel Aviv 6139001, Israel
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6
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Domozych DS, Bagdan K. The cell biology of charophytes: Exploring the past and models for the future. PLANT PHYSIOLOGY 2022; 190:1588-1608. [PMID: 35993883 PMCID: PMC9614468 DOI: 10.1093/plphys/kiac390] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 07/26/2022] [Indexed: 06/15/2023]
Abstract
Charophytes (Streptophyta) represent a diverse assemblage of extant green algae that are the sister lineage to land plants. About 500-600+ million years ago, a charophyte progenitor successfully colonized land and subsequently gave rise to land plants. Charophytes have diverse but relatively simple body plans that make them highly attractive organisms for many areas of biological research. At the cellular level, many charophytes have been used for deciphering cytoskeletal networks and their dynamics, membrane trafficking, extracellular matrix secretion, and cell division mechanisms. Some charophytes live in challenging habitats and have become excellent models for elucidating the cellular and molecular effects of various abiotic stressors on plant cells. Recent sequencing of several charophyte genomes has also opened doors for the dissection of biosynthetic and signaling pathways. While we are only in an infancy stage of elucidating the cell biology of charophytes, the future application of novel analytical methodologies in charophyte studies that include a broader survey of inclusive taxa will enhance our understanding of plant evolution and cell dynamics.
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Affiliation(s)
| | - Kaylee Bagdan
- Department of Biology, Skidmore Microscopy Imaging Center, Skidmore College, Saratoga Springs, New York 12866, USA
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Chen S, Peng Y, Lv Q, Liu J, Wu Z, Wang H, Wang X. Characterization of two constitutive promoters RPS28 and EIF1 for studying soybean growth, development, and symbiotic nodule development. ABIOTECH 2022; 3:99-109. [PMID: 36312443 PMCID: PMC9590564 DOI: 10.1007/s42994-022-00073-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 04/25/2022] [Indexed: 06/03/2023]
Abstract
Native promoters that can drive high and stable transgene expression are important tools for modifying plant traits. Although several such promoters have been reported in soybean (Glycine max), few of them function at multiple growth and development stages and during nodule development. Here, we report that the promoters of 40S RIBOSOMAL PROTEIN SMALL SUBUNIT S28 (RPS28) and EUKARYOTIC TRANSLATION INITIATION FACTOR 1 (EIF1) are ideal for high expression of transgene. Through bioinformatic analysis, we determined that RPS28 and EIF1 were highly expressed during soybean growth and development, nodule development, and various biotic and abiotic stresses. Fusion of both RPS28 and EIF1 promoters, with or without their first intron, with the reporter gene β-GLUCURONIDASE (uidA) in transgenic soybean, resulted in high GUS activity in seedlings, seeds, and nodules. Fluorimetric GUS assays showed that the RPS28 promoter and the EIF1 promoter yielded high expression, comparable to the soybean Ubiquitin (GmUbi) promoter. RPS28 and EIF1 promoters were also highly expressed in Arabidopsis thaliana and Nicotiana benthamiana. Our results indicate the potential of RPS28 and EIF1 promoters to facilitate future genetic engineering and breeding to improve the quality and yield of soybean, as well as in a wide variety of other plant species. Supplementary Information The online version contains supplementary material available at 10.1007/s42994-022-00073-6.
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Affiliation(s)
- Shengcai Chen
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Yaqi Peng
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Key Laboratory of Plant Stress Biology, Henan University, Kaifeng, 475001 China
- Sanya Institute of Henan University, Sanya, 572025 China
| | - Qi Lv
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Key Laboratory of Plant Stress Biology, Henan University, Kaifeng, 475001 China
- Sanya Institute of Henan University, Sanya, 572025 China
| | - Jing Liu
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Key Laboratory of Plant Stress Biology, Henan University, Kaifeng, 475001 China
- Sanya Institute of Henan University, Sanya, 572025 China
| | - Zhihua Wu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, Key Laboratory of State Ethnic Affairs Commission for Biological Technology, College of Life Sciences, South-Central University for Nationalities, Wuhan, 430074 China
| | - Haijiao Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Key Laboratory of Plant Stress Biology, Henan University, Kaifeng, 475001 China
- Sanya Institute of Henan University, Sanya, 572025 China
| | - Xuelu Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Key Laboratory of Plant Stress Biology, Henan University, Kaifeng, 475001 China
- Sanya Institute of Henan University, Sanya, 572025 China
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8
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Genome-wide analysis of pathogenesis-related protein 1 (PR-1) gene family from Musa spp. and its role in defense response during stresses. Gene X 2022; 821:146334. [PMID: 35181501 DOI: 10.1016/j.gene.2022.146334] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 01/31/2022] [Accepted: 02/11/2022] [Indexed: 12/17/2022] Open
Abstract
Pathogenesis related protein-1 (PR-1) is the most abundantly produced protein during defense response against many biotic and abiotic stresses. However, knowledge on PR-1 gene family and its evolutionary relationship in banana is very limited. In order to study the potential role of PR-1 genes in banana, genome wide identification, structure analysis and expressions were performed. A total of 15 and 11 PR-1 genes were identified from A and B genomes of banana and the proteins encoded by this gene family are of varying lengths and harbor conserved domains and motifs. PR-1 genes are unevenly dispersed on 11 chromosomes with segmental duplication in both A and B genome, suggesting an important contribution of duplication in expansion of PR-1 gene family in banana. qRT-PCR analysis of PR-1 gene showed positive correlation with the RNAseq data under various stresses and examination of expression pattern of selected MaPR-1 genes in banana revealed its role in biotic and abiotic stresses in general and fusarium wilt in particular. This study provides significant insight into the functions of PR-1 genes which can be further exploited as a promising candidate for developing multiple stress tolerant banana varieties.
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Liu C, Kong M, Yang F, Zhu J, Qi X, Weng J, Di D, Xie C. Targeted generation of Null Mutants in ZmGDIα confers resistance against maize rough dwarf disease without agronomic penalty. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:803-805. [PMID: 35178853 PMCID: PMC9055807 DOI: 10.1111/pbi.13793] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/22/2021] [Accepted: 02/07/2022] [Indexed: 06/14/2023]
Affiliation(s)
- Changlin Liu
- Institute of Crop ScienceChinese Academy of Agricultural SciencesNational Key Facility for Crop Gene Resources and Genetic ImprovementBeijingChina
- Hainan Yazhou Bay Seed LabHainan ProvinceChina
| | - Ming Kong
- Institute of Crop ScienceChinese Academy of Agricultural SciencesNational Key Facility for Crop Gene Resources and Genetic ImprovementBeijingChina
| | - Fei Yang
- Institute of Plant ProtectionHebei Academy of Agriculture and Forestry SciencesBaodingHebeiChina
| | - Jinjie Zhu
- Institute of Crop ScienceChinese Academy of Agricultural SciencesNational Key Facility for Crop Gene Resources and Genetic ImprovementBeijingChina
- Hainan Yazhou Bay Seed LabHainan ProvinceChina
| | - Xiantao Qi
- Institute of Crop ScienceChinese Academy of Agricultural SciencesNational Key Facility for Crop Gene Resources and Genetic ImprovementBeijingChina
- Hainan Yazhou Bay Seed LabHainan ProvinceChina
| | - Jianfeng Weng
- Institute of Crop ScienceChinese Academy of Agricultural SciencesNational Key Facility for Crop Gene Resources and Genetic ImprovementBeijingChina
| | - Dianping Di
- Institute of Plant ProtectionHebei Academy of Agriculture and Forestry SciencesBaodingHebeiChina
| | - Chuanxiao Xie
- Institute of Crop ScienceChinese Academy of Agricultural SciencesNational Key Facility for Crop Gene Resources and Genetic ImprovementBeijingChina
- Hainan Yazhou Bay Seed LabHainan ProvinceChina
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10
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Masoomi‐Aladizgeh F, Kamath KS, Haynes PA, Atwell BJ. Genome survey sequencing of wild cotton (Gossypium robinsonii) reveals insights into proteomic responses of pollen to extreme heat. PLANT, CELL & ENVIRONMENT 2022; 45:1242-1256. [PMID: 35092006 PMCID: PMC9415111 DOI: 10.1111/pce.14268] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 01/04/2022] [Indexed: 06/14/2023]
Abstract
Heat stress specifically affects fertility by impairing pollen viability but cotton wild relatives successfully reproduce in hot savannas where they evolved. An Australian arid-zone cotton (Gossypium robinsonii) was exposed to heat events during pollen development then mature pollen was subjected to deep proteomic analysis using 57 023 predicted genes from a genomic database we assembled for the same species. Three stages of pollen development, including tetrads (TEs), uninucleate microspores (UNs) and binucleate microspores (BNs) were exposed to 36°C or 40°C for 5 days and the resulting mature pollen was collected at anthesis (p-TE, p-UN and p-BN, respectively). Using the sequential windowed acquisition of all theoretical mass spectra proteomic analysis, 2704 proteins were identified and quantified across all pollen samples analysed. Proteins predominantly decreased in abundance at all stages in response to heat, particularly after exposure of TEs to 40°C. Functional enrichment analyses demonstrated that extreme heat increased the abundance of proteins that contributed to increased messenger RNA splicing via spliceosome, initiation of cytoplasmic translation and protein refolding in p-TE40. However, other functional categories that contributed to intercellular transport were inhibited in p-TE40, linked potentially to Rab proteins. We ascribe the resilience of reproductive processes in G. robinsonii at temperatures up to 40°C, relative to commercial cotton, to a targeted reduction in protein transport.
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Affiliation(s)
| | | | - Paul A. Haynes
- School of Natural SciencesMacquarie UniversityNorth RydeNew South WalesAustralia
| | - Brian J. Atwell
- School of Natural SciencesMacquarie UniversityNorth RydeNew South WalesAustralia
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11
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Ambastha V, Matityahu I, Tidhar D, Leshem Y. RabA2b Overexpression Alters the Plasma-Membrane Proteome and Improves Drought Tolerance in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2021; 12:738694. [PMID: 34691115 PMCID: PMC8526897 DOI: 10.3389/fpls.2021.738694] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 09/13/2021] [Indexed: 06/07/2023]
Abstract
Rab proteins are small GTPases that are important in the regulation of vesicle trafficking. Through data mining, we identified RabA2b to be stress responsive, though little is known about the involvement of RabA in plant responses to abiotic stresses. Analysis of the RabA2b native promoter showed strong activity during osmotic stress, which required the stress hormone Abscisic acid (ABA) and was restricted to the vasculature. Sequence analysis of the promoter region identified predicted binding motifs for several ABA-responsive transcription factors. We cloned RabA2b and overexpressed it in Arabidopsis. The resulting transgenic plants were strikingly drought resistant. The reduced water loss observed in detached leaves of the transgenic plants could not be explained by stomatal aperture or density, which was similar in all the genotypes. Subcellular localization studies detected strong colocalization between RabA2b and the plasma membrane (PM) marker PIP2. Further studies of the PM showed, for the first time, a distinguished alteration in the PM proteome as a result of RabA2b overexpression. Proteomic analysis of isolated PM fractions showed enrichment of stress-coping proteins as well as cell wall/cuticle modifiers in the transgenic lines. Finally, the cuticle permeability of transgenic leaves was significantly reduced compared to the wild type, suggesting that it plays a role in its drought resistant properties. Overall, these data provide new insights into the roles and modes of action of RabA2b during water stresses, and indicate that increased RabA2b mediated PM trafficking can affect the PM proteome and increase drought tolerance.
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Affiliation(s)
- Vivek Ambastha
- Department of Plant Sciences, MIGAL – Galilee Research Institute, Kiryat Shmona, Israel
| | - Ifat Matityahu
- Department of Plant Sciences, MIGAL – Galilee Research Institute, Kiryat Shmona, Israel
| | - Dafna Tidhar
- Department of Plant Sciences, MIGAL – Galilee Research Institute, Kiryat Shmona, Israel
- Faculty of Sciences and Technology, Tel-Hai College, Upper Galilee, Israel
| | - Yehoram Leshem
- Department of Plant Sciences, MIGAL – Galilee Research Institute, Kiryat Shmona, Israel
- Faculty of Sciences and Technology, Tel-Hai College, Upper Galilee, Israel
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Pandey GK, Chinnusamy V, Lenka SK. Genes, Genomes and Germplasm for Climate-Smart Agriculture- Part-I. Curr Genomics 2021; 22:2-3. [PMID: 34045919 PMCID: PMC8142346 DOI: 10.2174/138920292201210412161326] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Affiliation(s)
- Girdhar K. Pandey
- Address correspondence to this author at the Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi 110021, India; E-mail:
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