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Routray D, Ghatak A, Chaturvedi P, Petijová L, Weckwerth W, Ručová D, Bačkor M, Lang I, Goga M. Comparative analysis of geotypic variations in the proteome of Nostoc commune. PLANT SIGNALING & BEHAVIOR 2024; 19:2370719. [PMID: 38913942 PMCID: PMC11197914 DOI: 10.1080/15592324.2024.2370719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Accepted: 06/02/2024] [Indexed: 06/26/2024]
Abstract
Cyanobacterium Nostoc commune is a filamentous terrestrial prokaryotic organism widely distributed, which suggest its high adaptive potential to environmental or abiotic stress. Physiological parameters and proteomic analysis were performed in two accession of N. commune with the aim to elucidate the differences of physiological trails between distant geotypes, namely Antarctic (AN) and central European (CE). The result obtained clearly showed that the AN geotype demonstrates elevated levels of total phenols, flavonoids, carotenoids, and phycobiliproteins, indicative of its adaptation to environmental stress as referred by comparison to CE sample. Additionally, we employed LC-MS analysis to investigate the proteomes of N. commune from AN and CE geotypes. In total, 1147 proteins were identified, among which 646 proteins expressed significant (up-regulation) changes in both accessions. In the AN geotype, 83 exclusive proteins were identified compared to 25 in the CE geotype. Functional classification of the significant proteins showed a large fraction involved in photosynthesis, amino acid metabolism, carbohydrate metabolism and protein biosynthesis. Further analysis revealed some defense-related proteins such as, superoxide dismutase (SOD) and glutathione reductase, which are rather explicitly expressed in the AN N. commune. The last two proteins suggest a more stressful condition in AN N. commune. In summary, our findings highlight biochemical processes that safeguard the AN geotype of N. commune from extreme environmental challenges, not recorded in CE accession, probably due to less stressful environment in Europe. This study brings the first ever proteomic analysis of N. commune, emphasizing the need for additional investigations into the climate adaptation of this species with rather plastic genome.
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Affiliation(s)
- Deepti Routray
- Department of Plant Biology, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Košice, Slovakia
| | - Arindam Ghatak
- Molecular Systems Biology Lab, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center, University of Vienna, Vienna, Austria
| | - Palak Chaturvedi
- Molecular Systems Biology Lab, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Linda Petijová
- Department of Genetics, Faculty of Science, Pavol Jozef Šafárik University in Košice, Košice, Slovakia
| | - Wolfram Weckwerth
- Molecular Systems Biology Lab, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center, University of Vienna, Vienna, Austria
| | - Dajana Ručová
- Department of Plant Biology, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Košice, Slovakia
| | - Martin Bačkor
- Department of Plant Biology, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Košice, Slovakia
- Institute of Biotechnology, Faculty of Biotechnology and Food Sciences, Slovak University of Agriculture in Nitra, Nitra, Slovakia
| | - Ingeborg Lang
- Molecular Systems Biology Lab, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Michal Goga
- Department of Plant Biology, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Košice, Slovakia
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2
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Ceasar SA, Prabhu S, Ebeed HT. Protein research in millets: current status and way forward. PLANTA 2024; 260:43. [PMID: 38958760 DOI: 10.1007/s00425-024-04478-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Accepted: 06/27/2024] [Indexed: 07/04/2024]
Abstract
MAIN CONCLUSION Millets' protein studies are lagging behind those of major cereals. Current status and future insights into the investigation of millet proteins are discussed. Millets are important small-seeded cereals majorly grown and consumed by people in Asia and Africa and are considered crops of future food security. Although millets possess excellent climate resilience and nutrient supplementation properties, their research advancements have been lagging behind major cereals. Although considerable genomic resources have been developed in recent years, research on millet proteins and proteomes is currently limited, highlighting a need for further investigation in this area. This review provides the current status of protein research in millets and provides insights to understand protein responses for climate resilience and nutrient supplementation in millets. The reference proteome data is available for sorghum, foxtail millet, and proso millet to date; other millets, such as pearl millet, finger millet, barnyard millet, kodo millet, tef, and browntop millet, do not have any reference proteome data. Many studies were reported on stress-responsive protein identification in foxtail millet, with most studies on the identification of proteins under drought-stress conditions. Pearl millet has a few reports on protein identification under drought and saline stress. Finger millet is the only other millet to have a report on stress-responsive (drought) protein identification in the leaf. For protein localization studies, foxtail millet has a few reports. Sorghum has the highest number of 40 experimentally proven crystal structures, and other millets have fewer or no experimentally proven structures. Further proteomics studies will help dissect the specific proteins involved in climate resilience and nutrient supplementation and aid in breeding better crops to conserve food security.
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Affiliation(s)
- S Antony Ceasar
- Division of Plant Molecular Biology and Biotechnology, Department of Biosciences, Rajagiri College of Social Sciences, Cochin, Kerala, 683 104, India.
| | - Srinivasan Prabhu
- Division of Phytochemistry and Drug Design, Department of Biosciences, Rajagiri College of Social Sciences, Cochin, Kerala, 683 104, India
| | - Heba T Ebeed
- Botany and Microbiology Department, Faculty of Science, Damietta University, Damietta, Egypt
- National Biotechnology Network of Expertise (NBNE), Academy of Scientific Research and Technology (ASRT), Cairo, Egypt
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3
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Moin M, Bommineni PR, Tyagi W. Exploration of the pearl millet phospholipase gene family to identify potential candidates for grain quality traits. BMC Genomics 2024; 25:581. [PMID: 38858648 PMCID: PMC11165789 DOI: 10.1186/s12864-024-10504-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Accepted: 06/06/2024] [Indexed: 06/12/2024] Open
Abstract
BACKGROUND Phospholipases constitute a diverse category of enzymes responsible for the breakdown of phospholipids. Their involvement in signal transduction with a pivotal role in plant development and stress responses is well documented. RESULTS In the present investigation, a thorough genome-wide analysis revealed that the pearl millet genome contains at least 44 phospholipase genes distributed across its 7 chromosomes, with chromosome one harbouring the highest number of these genes. The synteny analysis suggested a close genetic relationship of pearl millet phospholipases with that of foxtail millet and sorghum. All identified genes were examined to unravel their gene structures, protein attributes, cis-regulatory elements, and expression patterns in two pearl millet genotypes contrasting for rancidity. All the phospholipases have a high alpha-helix content and distorted regions within the predicted secondary structures. Moreover, many of these enzymes possess binding sites for both metal and non-metal ligands. Additionally, the putative promoter regions associated with these genes exhibit multiple copies of cis-elements specifically responsive to biotic and abiotic stress factors and signaling molecules. The transcriptional profiling of 44 phospholipase genes in two genotypes contrasting for rancidity across six key tissues during pearl millet growth revealed a predominant expression in grains, followed by seed coat and endosperm. Specifically, the genes PgPLD-alpha1-1, PgPLD-alpha1-5, PgPLD-delta1-7a, PgPLA1-II-1a, and PgPLD-delta1-2a exhibited notable expression in grains of both the genotypes while showing negligible expression in the other five tissues. The sequence alignment of putative promoters revealed several variations including SNPs and InDels. These variations resulted in modifications to the corresponding cis-acting elements, forming distinct transcription factor binding sites suggesting the transcriptional-level regulation for these five genes in pearl millet. CONCLUSIONS The current study utilized a genome-wide computational analysis to characterize the phospholipase gene family in pearl millet. A comprehensive expression profile of 44 phospholipases led to the identification of five grain-specific candidates. This underscores a potential role for at least these five genes in grain quality traits including the regulation of rancidity in pearl millet. Therefore, this study marks the first exploration highlighting the possible impact of phospholipases towards enhancing agronomic traits in pearl millet.
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Affiliation(s)
- Mazahar Moin
- Cell and Molecular Biology and Trait Engineering, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Patancheru, Telangana, 502324, India
| | - Pradeep Reddy Bommineni
- Cell and Molecular Biology and Trait Engineering, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Patancheru, Telangana, 502324, India
| | - Wricha Tyagi
- Cell and Molecular Biology and Trait Engineering, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Patancheru, Telangana, 502324, India.
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Zhang S, Ghatak A, Mohammadi Bazargani M, Kramml H, Zang F, Gao S, Ramšak Ž, Gruden K, Varshney RK, Jiang D, Chaturvedi P, Weckwerth W. Cell-type proteomic and metabolomic resolution of early and late grain filling stages of wheat endosperm. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:555-571. [PMID: 38050335 DOI: 10.1111/pbi.14203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 08/21/2023] [Accepted: 10/03/2023] [Indexed: 12/06/2023]
Abstract
The nutritional value of wheat grains, particularly their protein and metabolite composition, is a result of the grain-filling process, especially in the endosperm. Here, we employ laser microdissection (LMD) combined with shotgun proteomics and metabolomics to generate a cell type-specific proteome and metabolome inventory of developing wheat endosperm at the early (15 DAA) and late (26 DAA) grain-filling stages. We identified 1803 proteins and 41 metabolites from four different cell types (aleurone (AL), sub-aleurone (SA), starchy endosperm (SE) and endosperm transfer cells (ETCs). Differentially expressed proteins were detected, 67 in the AL, 31 in the SA, 27 in the SE and 50 in the ETCs between these two-time points. Cell-type accumulation of specific SUT and GLUT transporters, sucrose converting and starch biosynthesis enzymes correlate well with the respective sugar metabolites, suggesting sugar upload and starch accumulation via nucellar projection and ETC at 15 DAA in contrast to the later stage at 26 DAA. Changes in various protein levels between AL, SA and ETC support this metabolic switch from 15 to 26 DAA. The distinct spatial and temporal abundances of proteins and metabolites revealed a contrasting activity of nitrogen assimilation pathways, e.g. for GOGAT, GDH and glutamic acid, in the different cell types from 15 to 26 DAA, which can be correlated with specific protein accumulation in the endosperm. The integration of cell-type specific proteome and metabolome data revealed a complex metabolic interplay of the different cell types and a functional switch during grain development and grain-filling processes.
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Affiliation(s)
- Shuang Zhang
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
- National Technique Innovation Center for Regional Wheat Production/Key Laboratory of Crop Ecophysiology, Ministry of Agriculture/Nanjing Agricultural University, Nanjing, China
| | - Arindam Ghatak
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
| | | | - Hannes Kramml
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Fujuan Zang
- National Technique Innovation Center for Regional Wheat Production/Key Laboratory of Crop Ecophysiology, Ministry of Agriculture/Nanjing Agricultural University, Nanjing, China
| | - Shuang Gao
- National Technique Innovation Center for Regional Wheat Production/Key Laboratory of Crop Ecophysiology, Ministry of Agriculture/Nanjing Agricultural University, Nanjing, China
| | - Živa Ramšak
- Department of Systems Biology and Biotechnology, National Institute of Biology, Ljubljana, Slovenia
| | - Kristina Gruden
- Department of Systems Biology and Biotechnology, National Institute of Biology, Ljubljana, Slovenia
| | - Rajeev K Varshney
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
| | - Dong Jiang
- National Technique Innovation Center for Regional Wheat Production/Key Laboratory of Crop Ecophysiology, Ministry of Agriculture/Nanjing Agricultural University, Nanjing, China
| | - Palak Chaturvedi
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Wolfram Weckwerth
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
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5
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Xu L, Lan Y, Lin M, Zhou H, Ying S, Chen M. Genome-Wide Identification and Transcriptional Analysis of AP2/ERF Gene Family in Pearl Millet ( Pennisetum glaucum). Int J Mol Sci 2024; 25:2470. [PMID: 38473718 DOI: 10.3390/ijms25052470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Revised: 02/14/2024] [Accepted: 02/16/2024] [Indexed: 03/14/2024] Open
Abstract
The apetala2/ethylene response factor (AP2/ERF) gene family plays a crucial role in regulating plant growth and development and responding to different abiotic stresses (e.g., drought, heat, cold, and salinity). However, the knowledge of the ERF family in pearl millet remains limited. Here, a total of 167 high-confidence PgERF genes are identified and divided into five subgroups based on gene-conserved structure and phylogenetic analysis. Forty-one pairs of segmental duplication are found using collinear analysis. Nucleotide substitution analysis reveals these duplicated pairs are under positive purification, indicating they are actively responding to natural selection. Comprehensive transcriptomic analysis reveals that PgERF genesare preferentially expressed in the imbibed seeds and stem (tilling stage) and respond to heat, drought, and salt stress. Prediction of the cis-regulatory element by the PlantCARE program indicates that PgERF genes are involved in responses to environmental stimuli. Using reverse transcription quantitative real-time PCR (RT-qPCR), expression profiles of eleven selected PgERF genes are monitored in various tissues and during different abiotic stresses. Transcript levels of each PgERF gene exhibit significant changes during stress treatments. Notably, the PgERF7 gene is the only candidate that can be induced by all adverse conditions. Furthermore, four PgERF genes (i.e., PgERF22, PgERF37, PgERF88, and PgERF155) are shown to be involved in the ABA-dependent signaling pathway. These results provide useful bioinformatic and transcriptional information for understanding the roles of the pearl millet ERF gene family in adaptation to climate change.
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Affiliation(s)
- Liang Xu
- College of Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524091, China
| | - Ying Lan
- College of Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524091, China
| | - Miaohong Lin
- College of Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524091, China
| | - Hongkai Zhou
- College of Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524091, China
| | - Sheng Ying
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48823, USA
| | - Miao Chen
- College of Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524091, China
- Shenzhen Institute, Guangdong Ocean University, Shenzhen 518120, China
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6
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Halder T, Stroeher E, Liu H, Chen Y, Yan G, Siddique KHM. Protein biomarkers for root length and root dry mass on chromosomes 4A and 7A in wheat. J Proteomics 2024; 291:105044. [PMID: 37931703 DOI: 10.1016/j.jprot.2023.105044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 10/16/2023] [Accepted: 10/22/2023] [Indexed: 11/08/2023]
Abstract
Improving the wheat (Triticum aestivum L.) root system is important for enhancing grain yield and climate resilience. Total root length (RL) and root dry mass (RM) significantly contribute to water and nutrient acquisition directly impacting grain yield and stress tolerance. This study used label-free quantitative proteomics to identify proteins associated with RL and RM in wheat near-isogenic lines (NILs). NIL pair 6 had 113 and NIL pair 9 had 30 differentially abundant proteins (DAPs). Three of identified DAPs located within the targeted genomic regions (GRs) of NIL pairs 6 (qDT.4A.1) and 9 (QHtscc.ksu-7A), showed consistent gene expressions at the protein and mRNA transcription (qRT-PCR) levels for asparagine synthetase (TraesCS4A02G109900), signal recognition particle 19 kDa protein (TraesCS7A02G333600) and 3,4-dihydroxy-2-butanone 4-phosphate synthase (TraesCS7A02G415600). This study discovered, for the first time, the involvement of these proteins as candidate biomarkers for increased RL and RM in wheat. However, further functional validation is required to ascertain their practical applicability in wheat root breeding. SIGNIFICANCE OF THE STUDY: Climate change has impacted global demand for wheat (Triticum aestivum L.). Root traits such as total root length (RL) and root dry mass (RM) are crucial for water and nutrient uptake and tolerance to abiotic stresses such as drought, salinity, and nutrient imbalance in wheat. Improving RL and RM could significantly enhance wheat grain yield and climate resilience. However, breeding for these traits has been limited by lack of appropriate root phenotyping methods, advanced genotypes, and the complex nature of the wheat genome. In this study, we used a semi-hydroponic root phenotyping system to collect accurate root data, near-isogenic lines (NILs; isolines with similar genetic backgrounds but contrasting target genomic regions (GRs)) and label-free quantitative proteomics to explore the molecular mechanisms underlying high RL and RM in wheat. We identified differentially abundant proteins (DAPs) and their molecular pathways in NIL pairs 6 (GR: qDT.4A.1) and 9 (GR: QHtscc.ksu-7A), providing a foundation for further molecular investigations. Furthermore, we identified three DAPs within the target GRs of the NIL pairs with differential expression at the transcript level, as confirmed by qRT-PCR analysis which could serve as candidate protein biomarkers for RL and RM improvement.
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Affiliation(s)
- Tanushree Halder
- UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia; The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia; Department of Genetics and Plant Breeding, Faculty of Agriculture, Sher-e-Bangla Agricultural University, Dhaka 1207, Bangladesh.
| | - Elke Stroeher
- Centre for Microscopy, Characterisation & Analysis, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Hui Liu
- UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia; The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia.
| | - Yinglong Chen
- UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia; The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Guijun Yan
- UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia; The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Kadambot H M Siddique
- UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia; The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia.
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7
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Shanmugam T, Chaturvedi P, Streit D, Ghatak A, Bergelt T, Simm S, Weckwerth W, Schleiff E. Low dose ribosomal DNA P-loop mutation affects development and enforces autophagy in Arabidopsis. RNA Biol 2024; 21:1-15. [PMID: 38156797 PMCID: PMC10761087 DOI: 10.1080/15476286.2023.2298532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2023] [Indexed: 01/03/2024] Open
Abstract
Arabidopsis contains hundreds of ribosomal DNA copies organized within the nucleolar organizing regions (NORs) in chromosomes 2 and 4. There are four major types of variants of rDNA, VAR1-4, based on the polymorphisms of 3' external transcribed sequences. The variants are known to be differentially expressed during plant development. We created a mutant by the CRISPR-Cas9-mediated excision of ~ 25 nt from predominantly NOR4 ribosomal DNA copies, obtaining mosaic mutational events on ~ 5% of all rDNA copies. The excised region consists of P-loop and Helix-82 segments of 25S rRNA. The mutation led to allelic, dosage-dependent defects marked by lateral root inhibition, reduced size, and pointy leaves, all previously observed for defective ribosomal function. The mutation in NOR4 led to dosage compensation from the NOR2 copies by elevated expression of VAR1 in mutants and further associated single-nucleotide variants, thus, resulting in altered rRNA sub-population. Furthermore, the mutants exhibited rRNA maturation defects specifically in the minor pathway typified by 32S pre-rRNA accumulation. Density-gradient fractionation and subsequent RT-PCR of rRNA analyses revealed that mutated copies were not incorporated into the translating ribosomes. The mutants in addition displayed an elevated autophagic flux as shown by the autophagic marker GFP-ATG8e, likely related to ribophagy.
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Affiliation(s)
- Thiruvenkadam Shanmugam
- Molecular Cell Biology of Plants, Institute for Molecular Biosciences & Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Palak Chaturvedi
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Deniz Streit
- Molecular Cell Biology of Plants, Institute for Molecular Biosciences & Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Arindam Ghatak
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Thorsten Bergelt
- Molecular Cell Biology of Plants, Institute for Molecular Biosciences & Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Stefan Simm
- Molecular Cell Biology of Plants, Institute for Molecular Biosciences & Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Wolfram Weckwerth
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
| | - Enrico Schleiff
- Molecular Cell Biology of Plants, Institute for Molecular Biosciences & Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
- Frankfurt Institute for Advanced Studies, Frankfurt am Main, Germany
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8
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Pixley KV, Cairns JE, Lopez-Ridaura S, Ojiewo CO, Dawud MA, Drabo I, Mindaye T, Nebie B, Asea G, Das B, Daudi H, Desmae H, Batieno BJ, Boukar O, Mukankusi CTM, Nkalubo ST, Hearne SJ, Dhugga KS, Gandhi H, Snapp S, Zepeda-Villarreal EA. Redesigning crop varieties to win the race between climate change and food security. MOLECULAR PLANT 2023; 16:1590-1611. [PMID: 37674314 DOI: 10.1016/j.molp.2023.09.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 08/17/2023] [Accepted: 09/03/2023] [Indexed: 09/08/2023]
Abstract
Climate change poses daunting challenges to agricultural production and food security. Rising temperatures, shifting weather patterns, and more frequent extreme events have already demonstrated their effects on local, regional, and global agricultural systems. Crop varieties that withstand climate-related stresses and are suitable for cultivation in innovative cropping systems will be crucial to maximize risk avoidance, productivity, and profitability under climate-changed environments. We surveyed 588 expert stakeholders to predict current and novel traits that may be essential for future pearl millet, sorghum, maize, groundnut, cowpea, and common bean varieties, particularly in sub-Saharan Africa. We then review the current progress and prospects for breeding three prioritized future-essential traits for each of these crops. Experts predict that most current breeding priorities will remain important, but that rates of genetic gain must increase to keep pace with climate challenges and consumer demands. Importantly, the predicted future-essential traits include innovative breeding targets that must also be prioritized; for example, (1) optimized rhizosphere microbiome, with benefits for P, N, and water use efficiency, (2) optimized performance across or in specific cropping systems, (3) lower nighttime respiration, (4) improved stover quality, and (5) increased early vigor. We further discuss cutting-edge tools and approaches to discover, validate, and incorporate novel genetic diversity from exotic germplasm into breeding populations with unprecedented precision, accuracy, and speed. We conclude that the greatest challenge to developing crop varieties to win the race between climate change and food security might be our innovativeness in defining and boldness to breed for the traits of tomorrow.
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Affiliation(s)
- Kevin V Pixley
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico.
| | - Jill E Cairns
- International Maize and Wheat Improvement Center (CIMMYT), Harare, Zimbabwe
| | | | - Chris O Ojiewo
- International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya
| | | | - Inoussa Drabo
- International Maize and Wheat Improvement Center (CIMMYT), Dakar, Senegal
| | - Taye Mindaye
- Ethiopian Institute of Agricultural Research (EIAR), Addis Ababa, Ethiopia
| | - Baloua Nebie
- International Maize and Wheat Improvement Center (CIMMYT), Dakar, Senegal
| | - Godfrey Asea
- National Agricultural Research Organization (NARO), Kampala, Uganda
| | - Biswanath Das
- International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya
| | - Happy Daudi
- Tanzania Agricultural Research Institute (TARI), Naliendele, Tanzania
| | - Haile Desmae
- International Maize and Wheat Improvement Center (CIMMYT), Dakar, Senegal
| | - Benoit Joseph Batieno
- Institut de l'Environnement et de Recherches Agricoles (INERA), Ouagadougou, Burkina Faso
| | - Ousmane Boukar
- International Institute of Tropicl Agriculture (IITA), Kano, Nigeria
| | | | | | - Sarah J Hearne
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Kanwarpal S Dhugga
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Harish Gandhi
- International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya
| | - Sieglinde Snapp
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
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9
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Pandey S, Singh A, Jaiswal P, Singh MK, Meena KR, Singh SK. The potentialities of omics resources for millet improvement. Funct Integr Genomics 2023; 23:210. [PMID: 37355501 DOI: 10.1007/s10142-023-01149-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/16/2023] [Accepted: 06/21/2023] [Indexed: 06/26/2023]
Abstract
Millets are nutrient-rich (nutri-rich) cereals with climate resilience attributes. However, its full productive potential is not realized due to the lack of a focused yield improvement approach, as evidenced by the available literature. Also, the lack of well-characterized genomic resources significantly limits millet improvement. But the recent availability of genomic data and advancement in omics tools has shown its enormous potential to enhance the efficiency and precision faced by conventional breeding in millet improvement. The development of high throughput genotyping platforms based on next-generation sequencing (NGS) has provided a low-cost method for genomic information, specifically for neglected nutri-rich cereals with the availability of a limited number of reference genome sequences. NGS has created new avenues for millet biotechnological interventions such as mutation-based study, GWAS, GS, and other omics technologies. The simultaneous discovery of high-throughput markers and multiplexed genotyping platform has aggressively aided marker-assisted breeding for millet improvement. Therefore, omics technology offers excellent opportunities to explore and combine useful variations for targeted traits that could impart high nutritional value to high-yielding cultivars under changing climatic conditions. In millet improvement, an in-depth account of NGS, integrating genomics data with different biotechnology tools, is reviewed in this context.
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Affiliation(s)
- Saurabh Pandey
- Department of Agricultural, Guru Nanak Dev University, Amritsar, Punjab, 143005, India
| | - Ashutosh Singh
- Centre for Advanced Studies on Climate Change, RPCAU, Pusa, Samastipur, Bihar, 848125, India.
| | - Priyanka Jaiswal
- Lovely Professional University, Jalandhar - Delhi G.T. Road, Phagwara, Punjab, 144411, India
| | - Mithilesh Kumar Singh
- Department of Genetics and Plant Breeding, RPCAU, Pusa, Samastipur, Bihar, 848125, India
| | - Khem Raj Meena
- Department of Biotechnology, School of Life Sciences, Central University of Rajasthan, Kishangarh, Rajasthan, 305817, India
| | - Satish Kumar Singh
- Department of Genetics and Plant Breeding, RPCAU, Pusa, Samastipur, Bihar, 848125, India
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10
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Carbó M, Chaturvedi P, Álvarez A, Pineda-Cevallos D, Ghatak A, González PR, Cañal MJ, Weckwerth W, Valledor L. Ferroptosis is the key cellular process mediating Bisphenol A responses in Chlamydomonas and a promising target for enhancing microalgae-based bioremediation. JOURNAL OF HAZARDOUS MATERIALS 2023; 448:130997. [PMID: 36860062 DOI: 10.1016/j.jhazmat.2023.130997] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 01/31/2023] [Accepted: 02/09/2023] [Indexed: 06/18/2023]
Abstract
Microplastics are one of the major pollutants in aquatic environments. Among their components, Bisphenol A (BPA) is one of the most abundant and dangerous, leading to endocrine disorders deriving even in different types of cancer in mammals. However, despite this evidence, the xenobiotic effects of BPA over plantae and microalgae still need to be better understood at the molecular level. To fill this gap, we characterized the physiological and proteomic response of Chlamydomonas reinhardtii during long-term BPA exposure by analyzing physiological and biochemical parameters combined with proteomics. BPA imbalanced iron and redox homeostasis, disrupting cell function and triggering ferroptosis. Intriguingly, this microalgae defense against this pollutant is recovering at both molecular and physiological levels while starch accumulation at 72 h of BPA exposure. In this work, we addressed the molecular mechanisms involved in BPA exposure, demonstrating for the first time the induction of ferroptosis in a eukaryotic alga and how ROS detoxification mechanisms and other specific proteomic rearrangements reverted this situation. These results are of great significance not only for understanding the BPA toxicology or exploring the molecular mechanisms of ferroptosis in microalgae but also for defining novel target genes for microplastic bioremediation efficient strain development.
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Affiliation(s)
- María Carbó
- Department of Organisms and Systems Biology and University Institute of Biotechnology of Asturias (IUBA), University of Oviedo, Asturias, Spain
| | - Palak Chaturvedi
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Ana Álvarez
- Department of Organisms and Systems Biology and University Institute of Biotechnology of Asturias (IUBA), University of Oviedo, Asturias, Spain
| | | | - Arindam Ghatak
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | | | - María Jesús Cañal
- Department of Organisms and Systems Biology and University Institute of Biotechnology of Asturias (IUBA), University of Oviedo, Asturias, Spain
| | - Wolfram Weckwerth
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Luis Valledor
- Department of Organisms and Systems Biology and University Institute of Biotechnology of Asturias (IUBA), University of Oviedo, Asturias, Spain.
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11
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Retzer K, Weckwerth W. Recent insights into metabolic and signalling events of directional root growth regulation and its implications for sustainable crop production systems. FRONTIERS IN PLANT SCIENCE 2023; 14:1154088. [PMID: 37008498 PMCID: PMC10060999 DOI: 10.3389/fpls.2023.1154088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 03/06/2023] [Indexed: 06/19/2023]
Abstract
Roots are sensors evolved to simultaneously respond to manifold signals, which allow the plant to survive. Root growth responses, including the modulation of directional root growth, were shown to be differently regulated when the root is exposed to a combination of exogenous stimuli compared to an individual stress trigger. Several studies pointed especially to the impact of the negative phototropic response of roots, which interferes with the adaptation of directional root growth upon additional gravitropic, halotropic or mechanical triggers. This review will provide a general overview of known cellular, molecular and signalling mechanisms involved in directional root growth regulation upon exogenous stimuli. Furthermore, we summarise recent experimental approaches to dissect which root growth responses are regulated upon which individual trigger. Finally, we provide a general overview of how to implement the knowledge gained to improve plant breeding.
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Affiliation(s)
- Katarzyna Retzer
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany, Czech Academy of Sciences, Prague, Czechia
| | - Wolfram Weckwerth
- Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, Molecular Systems Biology (MoSys), University of Vienna, Wien, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Wien, Austria
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12
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Chaturvedi P, Govindaraj M, Sehgal D, Weckwerth W. Editorial: Sorghum and pearl millet as climate resilient crops for food and nutrition security, volume II. FRONTIERS IN PLANT SCIENCE 2023; 14:1170103. [PMID: 36968384 PMCID: PMC10031092 DOI: 10.3389/fpls.2023.1170103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 02/23/2023] [Indexed: 06/18/2023]
Affiliation(s)
- Palak Chaturvedi
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Mahalingam Govindaraj
- HarvestPlus, Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Deepmala Sehgal
- Syngenta, Jealott’s Hill International Research Centre, Bracknell, United Kingdom
| | - Wolfram Weckwerth
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center, University of Vienna, Vienna, Austria
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13
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Kumar A, Sheoran P, Mann A, Yadav D, Kumar A, Devi S, Kumar N, Dhansu P, Sharma DK. Deciphering trait associated morpho-physiological responses in pearlmillet hybrids and inbred lines under salt stress. FRONTIERS IN PLANT SCIENCE 2023; 14:1121805. [PMID: 36938010 PMCID: PMC10018183 DOI: 10.3389/fpls.2023.1121805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 02/07/2023] [Indexed: 06/18/2023]
Abstract
Pearl millet is a staple food for more than 90 million people residing in highly vulnerable hot arid and semi-arid regions of Africa and Asia. These regions are more prone to detrimental effects of soil salinity on crop performance in terms of reduced biomass and crop yields. We investigated the physiological mechanisms of salt tolerance to irrigation induced salinity stress (ECiw ~3, 6 & 9 dSm-1) and their confounding effects on plant growth and yield in pearl millet inbred lines and hybrids. On average, nearly 30% reduction in above ground plant biomass was observed at ECiw ~6 dSm-1 which stretched to 56% at ECiw ~9 dSm-1 in comparison to best available water. With increasing salinity stress, the crop performance of test hybrids was better in comparison to inbred lines; exhibiting relatively higher stomatal conductance (gS; 16%), accumulated lower proline (Pro; -12%) and shoot Na+/K+(-31%), synthesized more protein (SP; 2%) and sugars (TSS; 32%) compensating in lower biomass (AGB; -22%) and grain yield (GY: -14%) reductions at highest salinity stress of ECiw ~9 dSm-1. Physiological traits modeling underpinning plant salt tolerance and adaptation mechanism illustrated the key role of 7 traits (AGB, Pro, SS, gS, SPAD, Pn, and SP) in hybrids and 8 traits (AGB, Pro, PH, Na+, K+, Na+/K+, SPAD, and gS) in inbred lines towards anticipated grain yield variations in salinity stressed pearl millet. Most importantly, the AGB alone, explained >91% of yield variation among evaluated hybrids and inbreed lines at ECiw ~9 dSm-1. Cumulatively, the better morpho-physiological adaptation and lesser yield reduction with increasing salinity stress in pearl millet hybrids (HHB 146, HHB 272, and HHB 234) and inbred lines (H77/833-2-202, ICMA 94555 and ICMA 843-22) substantially complemented in increased plant salt tolerance and yield stability over a broad range of salinity stress. The information generated herein will help address in deciphering the trait associated physiological alterations to irrigation induced salt stress, and developing potential hybrids in pearl millet using these parents with special characteristics.
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Affiliation(s)
- Ashwani Kumar
- Division of Crop Improvement, ICAR-Central Soil Salinity Research Institute, Karnal, India
| | - Parvender Sheoran
- Division of Social Sciences Research, ICAR-Central Soil Salinity Research Institute, Karnal, India
| | - Anita Mann
- Division of Crop Improvement, ICAR-Central Soil Salinity Research Institute, Karnal, India
| | - Devvart Yadav
- Chaudhary Charan Singh Haryana Agricultural University, Hisar, India
| | - Arvind Kumar
- Division of Crop Improvement, ICAR-Central Soil Salinity Research Institute, Karnal, India
| | - Sunita Devi
- Division of Crop Improvement, ICAR-Central Soil Salinity Research Institute, Karnal, India
| | - Naresh Kumar
- Division of Crop Improvement, ICAR-Central Soil Salinity Research Institute, Karnal, India
- Department of Chemistry and Biochemistry Eternal University, Baru, Sahib, India
| | - Pooja Dhansu
- ICAR–Sugarcane Breeding Institute, Regional Center, Karnal, India
| | - Dinesh K. Sharma
- Division of Crop Improvement, ICAR-Central Soil Salinity Research Institute, Karnal, India
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14
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Jan N, Rather AMUD, John R, Chaturvedi P, Ghatak A, Weckwerth W, Zargar SM, Mir RA, Khan MA, Mir RR. Proteomics for abiotic stresses in legumes: present status and future directions. Crit Rev Biotechnol 2023; 43:171-190. [PMID: 35109728 DOI: 10.1080/07388551.2021.2025033] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Legumes are the most important crop plants in agriculture, contributing 27% of the world's primary food production. However, productivity and production of Legumes is reduced due to increasing environmental stress. Hence, there is a pressing need to understand the molecular mechanism involved in stress response and legumes adaptation. Proteomics provides an important molecular approach to investigate proteins involved in stress response. Both the gel-based and gel-free-based techniques have significantly contributed to understanding the proteome regulatory network in leguminous plants. In the present review, we have discussed the role of different proteomic approaches (2-DE, 2 D-DIGE, ICAT, iTRAQ, etc.) in the identification of various stress-responsive proteins in important leguminous crops, including soybean, chickpea, cowpea, pigeon pea, groundnut, and common bean under variable abiotic stresses including heat, drought, salinity, waterlogging, frost, chilling and metal toxicity. The proteomic analysis has revealed that most of the identified differentially expressed proteins in legumes are involved in photosynthesis, carbohydrate metabolism, signal transduction, protein metabolism, defense, and stress adaptation. The proteomic approaches provide insights in understanding the molecular mechanism of stress tolerance in legumes and have resulted in the identification of candidate genes used for the genetic improvement of plants against various environmental stresses. Identifying novel proteins and determining their expression under different stress conditions provide the basis for effective engineering strategies to improve stress tolerance in crop plants through marker-assisted breeding.
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Affiliation(s)
- Nelofer Jan
- Division of Genetics & Plant Breeding, Faculty of Agriculture, SKUAST-Kashmir, Kashmir, India
| | | | - Riffat John
- Plant Molecular Biology Laboratory, Department of Botany, University of Kashmir, Srinagar, India
| | - Palak Chaturvedi
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Arindam Ghatak
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Wolfram Weckwerth
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, Vienna, Austria.,Vienna Metabolomics Center, University of Vienna, Vienna, Austria
| | - Sajad Majeed Zargar
- Division of Plant Biotechnology, Faculty of Horticulture, SKUAST-Kashmir, Srinagar, India
| | - Rakeeb Ahmad Mir
- Department of Biotechnology, Baba Ghulam Shah Badshah University, Jammu, India
| | - Mohd Anwar Khan
- Division of Genetics & Plant Breeding, Faculty of Agriculture, SKUAST-Kashmir, Kashmir, India
| | - Reyazul Rouf Mir
- Division of Genetics & Plant Breeding, Faculty of Agriculture, SKUAST-Kashmir, Kashmir, India
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15
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Kumar R, Ghatak A, Goyal I, Sarkar NK, Weckwerth W, Grover A, Chaturvedi P. Heat-induced proteomic changes in anthers of contrasting rice genotypes under variable stress regimes. FRONTIERS IN PLANT SCIENCE 2023; 13:1083971. [PMID: 36756226 PMCID: PMC9901367 DOI: 10.3389/fpls.2022.1083971] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 12/02/2022] [Indexed: 06/18/2023]
Abstract
Heat stress drastically affects anther tissues resulting in poor plant fertility, necessitating an urgent need to determine the key proteome regulation associated with mature anther in response to heat stress. We identified several genotype - specific protein alterations in rice anthers of Moroberekan (Japonica, heat sensitive), IR64 (Indica, moderately heat tolerant), and Nagina22 (Aus, heat tolerant) in the short-term (ST_HS; one cycle of 42°C, 4 hours before anthesis) and long-term (LT_HS; 6 cycles of 38°C, 6 hours before anthesis) heat stress. The proteins upregulated in long-term heat stress in Nagina22 were enriched in biological processes related to unfolded protein binding and carboxylic acid metabolism, including amino acid metabolism. In short-term heat stress, Nagina22 anthers were enriched in proteins associated with vitamin E biosynthesis and GTPase activator activity. In contrast, downregulated proteins were related to ribosomal proteins. The expression of different Hsp20 and DnaJ was genotype specific. Overall, the heat response in Nagina22 was associated with its capacity for adequate metabolic control and cellular homeostasis, which may be critical for its higher reproductive thermotolerance. This study improves our understanding of thermotolerance mechanisms in rice anthers during anthesis and lays a foundation for breeding thermotolerant varieties via molecular breeding.
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Affiliation(s)
- Ritesh Kumar
- Department of Plant Molecular Biology, University of Delhi, New Delhi, India
| | - Arindam Ghatak
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Isha Goyal
- Department of Plant Molecular Biology, University of Delhi, New Delhi, India
| | - Neelam K. Sarkar
- Department of Plant Molecular Biology, University of Delhi, New Delhi, India
| | - Wolfram Weckwerth
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
| | - Anil Grover
- Department of Plant Molecular Biology, University of Delhi, New Delhi, India
| | - Palak Chaturvedi
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
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16
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Abdirad S, Wu Y, Ghorbanzadeh Z, Tazangi SE, Amirkhani A, Fitzhenry MJ, Kazemi M, Ghaffari MR, Koobaz P, Zeinalabedini M, Habibpourmehraban F, Masoomi-Aladizgeh F, Atwell BJ, Mirzaei M, Salekdeh GH, Haynes PA. Proteomic analysis of the meristematic root zone in contrasting genotypes reveals new insights in drought tolerance in rice. Proteomics 2022; 22:e2200100. [PMID: 35920597 DOI: 10.1002/pmic.202200100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 07/18/2022] [Accepted: 07/21/2022] [Indexed: 12/29/2022]
Abstract
Drought is responsible for major losses in rice production. Root tips contain meristematic and elongation zones that play major roles in determination of root traits and adaptive strategies to drought. In this study we analysed two contrasting genotypes of rice: IR64, a lowland, drought-susceptible, and shallow-rooting genotype; and Azucena, an upland, drought-tolerant, and deep-rooting genotype. Samples were collected of root tips of plants grown under control and water deficit stress conditions. Quantitative proteomics analysis resulted in the identification of 7294 proteins from the root tips of IR64 and 6307 proteins from Azucena. Data are available via ProteomeXchange with identifier PXD033343. Using a Partial Least Square Discriminant Analysis on 4170 differentially abundant proteins, 1138 statistically significant proteins across genotypes and conditions were detected. Twenty two enriched biological processes showing contrasting patterns between two genotypes in response to stress were detected through gene ontology enrichment analysis. This included identification of novel proteins involved in root elongation with specific expression patterns in Azucena, including four Expansins and seven Class III Peroxidases. We also detected an antioxidant network and a metallo-sulfur cluster assembly machinery in Azucena, with roles in reactive oxygen species and iron homeostasis, and positive effects on root cell cycle, growth and elongation.
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Affiliation(s)
- Somayeh Abdirad
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran
| | - Yunqi Wu
- Australian Proteome Analysis Facility, Macquarie University, North Ryde, New South Wales, Australia
| | - Zahra Ghorbanzadeh
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran
| | - Sara Esmaeili Tazangi
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran
| | - Ardeshir Amirkhani
- Australian Proteome Analysis Facility, Macquarie University, North Ryde, New South Wales, Australia
| | - Matthew J Fitzhenry
- Australian Proteome Analysis Facility, Macquarie University, North Ryde, New South Wales, Australia
| | - Mehrbano Kazemi
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran
| | - Mohammad Reza Ghaffari
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran
| | - Parisa Koobaz
- Department of Molecular Physiology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran
| | - Mehrshad Zeinalabedini
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran
| | | | | | - Brian J Atwell
- School of Natural Sciences, Macquarie University, North Ryde, New South Wales, Australia
| | - Mehdi Mirzaei
- Australian Proteome Analysis Facility, Macquarie University, North Ryde, New South Wales, Australia.,School of Natural Sciences, Macquarie University, North Ryde, New South Wales, Australia
| | - Ghasem Hosseini Salekdeh
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran.,School of Natural Sciences, Macquarie University, North Ryde, New South Wales, Australia
| | - Paul A Haynes
- School of Natural Sciences, Macquarie University, North Ryde, New South Wales, Australia
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17
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Faye A, Barnaud A, Kane NA, Cubry P, Mariac C, Burgarella C, Rhoné B, Faye A, Olodo KF, Cisse A, Couderc M, Dequincey A, Zekraouï L, Moussa D, Tidjani M, Vigouroux Y, Berthouly-Salazar C. Genomic footprints of selection in early-and late-flowering pearl millet landraces. FRONTIERS IN PLANT SCIENCE 2022; 13:880631. [PMID: 36311100 PMCID: PMC9597309 DOI: 10.3389/fpls.2022.880631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 08/11/2022] [Indexed: 06/16/2023]
Abstract
Pearl millet is among the top three-cereal production in one of the most climate vulnerable regions, sub-Saharan Africa. Its Sahelian origin makes it adapted to grow in poor sandy soils under low soil water regimes. Pearl millet is thus considered today as one of the most interesting crops to face the global warming. Flowering time, a trait highly correlated with latitude, is one of the key traits that could be modulated to face future global changes. West African pearl millet landraces, can be grouped into early- (EF) and late-flowering (LF) varieties, each flowering group playing a specific role in the functioning and resilience of Sahelian smallholders. The aim of this study was thus to detect genes linked to flowering but also linked to relevant traits within each flowering group. We thus investigated genomic and phenotypic diversity in 109 pearl millet landrace accessions, i.e., 66 early-flowering and 43 late-flowering, grown in the groundnut basin, the first area of rainfed agriculture in Senegal dominated by dry cereals (millet, maize, and sorghum) and legumes (groundnuts, cowpeas). We were able to confirm the role of PhyC gene in pearl millet flowering and identify several other genes that appear to be as much as important, such as FSR12 and HAC1. HAC1 and two other genes appear to be part of QTLs previously identified and deserve further investigation. At the same time, we were able to highlight a several genes and variants that could contribute to the improvement of pearl millet yield, especially since their impact was demonstrated across flowering cycles.
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Affiliation(s)
- Adama Faye
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
- LNRPV, Institut Sénégalais de Recherches Agricoles (ISRA), Dakar, Senegal
- Laboratoire Mixte International LAPSE, Campus de Bel Air, route des Hydrocarbures, Dakar, Senegal
| | - Adeline Barnaud
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
- Laboratoire Mixte International LAPSE, Campus de Bel Air, route des Hydrocarbures, Dakar, Senegal
| | - Ndjido Ardo Kane
- LNRPV, Institut Sénégalais de Recherches Agricoles (ISRA), Dakar, Senegal
- Laboratoire Mixte International LAPSE, Campus de Bel Air, route des Hydrocarbures, Dakar, Senegal
- CERAAS, Institut Sénégalais de Recherches Agricoles, Thiès, Senegal
| | - Philippe Cubry
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Cédric Mariac
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Concetta Burgarella
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Bénédicte Rhoné
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
- CIRAD, UMR AGAP Institut, Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Aliou Faye
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
- LNRPV, Institut Sénégalais de Recherches Agricoles (ISRA), Dakar, Senegal
- Laboratoire Mixte International LAPSE, Campus de Bel Air, route des Hydrocarbures, Dakar, Senegal
| | - Katina Floride Olodo
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
- LNRPV, Institut Sénégalais de Recherches Agricoles (ISRA), Dakar, Senegal
- Laboratoire Mixte International LAPSE, Campus de Bel Air, route des Hydrocarbures, Dakar, Senegal
- CERAAS, Institut Sénégalais de Recherches Agricoles, Thiès, Senegal
| | - Aby Cisse
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
- LNRPV, Institut Sénégalais de Recherches Agricoles (ISRA), Dakar, Senegal
- Laboratoire Mixte International LAPSE, Campus de Bel Air, route des Hydrocarbures, Dakar, Senegal
- CERAAS, Institut Sénégalais de Recherches Agricoles, Thiès, Senegal
| | - Marie Couderc
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Anaïs Dequincey
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Leïla Zekraouï
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Djibo Moussa
- DIADE, Institut de Recherche pour le Développement (IRD), Niamey, Niger
| | - Moussa Tidjani
- DIADE, Institut de Recherche pour le Développement (IRD), Niamey, Niger
| | - Yves Vigouroux
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Cécile Berthouly-Salazar
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
- LNRPV, Institut Sénégalais de Recherches Agricoles (ISRA), Dakar, Senegal
- Laboratoire Mixte International LAPSE, Campus de Bel Air, route des Hydrocarbures, Dakar, Senegal
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18
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Mansoor S, Khan T, Farooq I, Shah LR, Sharma V, Sonne C, Rinklebe J, Ahmad P. Drought and global hunger: biotechnological interventions in sustainability and management. PLANTA 2022; 256:97. [PMID: 36219256 DOI: 10.1007/s00425-022-04006-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 09/22/2022] [Indexed: 06/16/2023]
Abstract
Drought may be efficiently managed using the following strategies: prevention, mitigation, readiness, recovery, and transformation. Biotechnological interventions may become highly important in reducing plants' drought stress in order to address key plant challenges such as population growth and climate change. Drought is a multidimensional construct with several triggering mechanisms or contributing factors working at various spatiotemporal scales, making it one of the known natural catastrophes. Drought is among the causes of hunger and malnutrition, decreasing agricultural output, and poor nutrition. Many deaths caused in children are due to hunger situations, and one in four children face stunted growth. All this hunger and malnutrition may be responsible for the reduction in agricultural productivity caused due to the drought situations affecting food security. Global Hunger Index has been accelerating due to under-nutrition and under-5 deaths. Drought has been covering more than 20% of the world's agricultural areas, leading to significantly less food production than what is required for consumption. Drought reduces soil fertility and adversely affects soil biological activity reducing the inherent capacity of the soil to support vegetation. Recent droughts have had a much greater effect on people's lives, even beyond causing poverty and hunger. Drought may have substantial financial consequences across the globe it may cause a severe impact on the world economy. It is a natural feature of the environment that will appear and disappear as it has in history. Due to increasing temperatures and growing vulnerabilities, it will undoubtedly occur more often and seriously in the coming years. To ensure sustainable socio-economic and social development, it is critical to reducing the effects of potential droughts worldwide using different biotechnological interventions. It's part of a long-term growth plan, and forecasting is essential for early warnings and global hunger management.
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Affiliation(s)
- Sheikh Mansoor
- Division of Biochemistry, Faculty of Basic Sciences, Sher e Kashmir University of Agricultural Sciences and Technology, Jammu, J&K, 180009, India
| | - Tamana Khan
- Division of Vegetable Science, Faculty of Horticulture, Sher e Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, J&K, 190025, India
| | - Iqra Farooq
- Division of Floriculture and Landscape Architecture, Sher e Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, J&K, 190025, India
| | - Labiba Riyaz Shah
- Division of Vegetable Science, Faculty of Horticulture, Sher e Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, J&K, 190025, India
| | - Vikas Sharma
- Division of Soil Science and Agricultural Chemistry, Sher e Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu, J&K, 180009, India
| | - Christian Sonne
- Department of Ecoscience, Arctic Research Centre (ARC), Faculty of Science and Technology, Aarhus University, Frederiksborgvej 399, PO Box 358, 4000, Roskilde, Denmark
| | - Jörg Rinklebe
- Laboratory of Soil and Groundwater Management, Institute of Foundation Engineering, Water and Waste Management, School of Architecture and Civil Engineering, University of Wuppertal, Pauluskirchstraße 7, 42285, Wuppertal, Germany
| | - Parvaiz Ahmad
- Department of Botany, GDC Pulwama, Jammu and Kashmir, 192301, India.
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Babele PK, Kudapa H, Singh Y, Varshney RK, Kumar A. Mainstreaming orphan millets for advancing climate smart agriculture to secure nutrition and health. FRONTIERS IN PLANT SCIENCE 2022; 13:902536. [PMID: 36035707 PMCID: PMC9412166 DOI: 10.3389/fpls.2022.902536] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 07/18/2022] [Indexed: 05/29/2023]
Abstract
The ever-changing climate and the current COVID-19 pandemic compound the problems and seriously impact agriculture production, resulting in socio-economic insecurities and imposing health implications globally. Most of the poor and malnourished population in the developing countries depends on agriculture for food, income, and employment. Impact of climate change together with the COVID-19 outbreak revealed immense problems highlighting the importance of mainstreaming climate-resilient and low input crops with more contemporary agriculture practices. Orphan millets play a vital role in the poor and malnourished population's livelihood, food and nutrition security. Recognizing their unique potential, the United Nations-Food and Agriculture Organization has announced the year 2023 as the "International Year of Millets". However, despite the unique properties for present and future agriculture of orphan millets, their cultivation is declining in many countries. As a result, millets have gained attention from researchers which eventually decelerated "multi-omics" resource generation. This review summarizes the benefits of millets and major barriers/ bottlenecks in their improvement. We also discuss the pre- and post-harvest technologies; policies required to introduce and establish millets in mainstream agriculture. To improve and ensure the livelihood of the poor/malnourished population, intensive efforts are urgently needed in advancing the research and development, implementing pre- and post-harvest technological intervention strategies, and making favorable policies for orphan crops to accomplish food and nutrition security. National and international collaborations are also indispensable to address the uncertain effects of climate change and COVID-19.
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Affiliation(s)
- Piyoosh K. Babele
- College of Agriculture, Rani Lakshmi Bai Central Agricultural University, Jhansi, Uttar Pradesh, India
| | - Himabindu Kudapa
- Centre of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Yogeshwar Singh
- College of Agriculture, Rani Lakshmi Bai Central Agricultural University, Jhansi, Uttar Pradesh, India
| | - Rajeev K. Varshney
- Centre of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
- Murdoch's Centre for Crop Research & Food Innovation, State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA, Australia
| | - Anil Kumar
- College of Agriculture, Rani Lakshmi Bai Central Agricultural University, Jhansi, Uttar Pradesh, India
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20
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Jiang M, Ning W, Wu S, Wang X, Zhu K, Li A, Li Y, Cheng S, Song B. Three-nucleotide periodicity of nucleotide diversity in a population enables the identification of open reading frames. Brief Bioinform 2022; 23:6607611. [PMID: 35698834 PMCID: PMC9294425 DOI: 10.1093/bib/bbac210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 04/25/2022] [Accepted: 05/06/2022] [Indexed: 11/14/2022] Open
Abstract
Accurate prediction of open reading frames (ORFs) is important for studying and using genome sequences. Ribosomes move along mRNA strands with a step of three nucleotides and datasets carrying this information can be used to predict ORFs. The ribosome-protected footprints (RPFs) feature a significant 3-nt periodicity on mRNAs and are powerful in predicting translating ORFs, including small ORFs (sORFs), but the application of RPFs is limited because they are too short to be accurately mapped in complex genomes. In this study, we found a significant 3-nt periodicity in the datasets of populational genomic variants in coding sequences, in which the nucleotide diversity increases every three nucleotides. We suggest that this feature can be used to predict ORFs and develop the Python package ‘OrfPP’, which recovers ~83% of the annotated ORFs in the tested genomes on average, independent of the population sizes and the complexity of the genomes. The novel ORFs, including sORFs, identified from single-nucleotide polymorphisms are supported by protein mass spectrometry evidence comparable to that of the annotated ORFs. The application of OrfPP to tetraploid cotton and hexaploid wheat genomes successfully identified 76.17% and 87.43% of the annotated ORFs in the genomes, respectively, as well as 4704 sORFs, including 1182 upstream and 2110 downstream ORFs in cotton and 5025 sORFs, including 232 upstream and 234 downstream ORFs in wheat. Overall, we propose an alternative and supplementary approach for ORF prediction that can extend the studies of sORFs to more complex genomes.
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Affiliation(s)
- Mengyun Jiang
- Chinese Academy of Agricultural Sciences and Henan University, China
| | - Weidong Ning
- Chinese Academy of Agricultural Sciences and Huazhong Agricultural University, China
| | - Shishi Wu
- Chinese Academy of Agricultural Sciences and Henan University, China
| | - Xingwei Wang
- Chinese Academy of Agricultural Sciences and Henan University, China
| | - Kun Zhu
- Chinese Academy of Agricultural Sciences and Henan University, China
| | - Aomei Li
- Chinese Academy of Agricultural Sciences, China
| | - Yongyao Li
- Chinese Academy of Agricultural Sciences, China
| | | | - Bo Song
- Chinese Academy of Agricultural Sciences, China
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21
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Meena RP, Ghosh G, Vishwakarma H, Padaria JC. Expression of a Pennisetum glaucum gene DREB2A confers enhanced heat, drought and salinity tolerance in transgenic Arabidopsis. Mol Biol Rep 2022; 49:7347-7358. [PMID: 35666421 DOI: 10.1007/s11033-022-07527-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 04/26/2022] [Indexed: 11/24/2022]
Abstract
BACKGROUND Pearl millet (Pennisetum glaucum) is an essential cereal crop, whose growth and yield are not impacted by abiotic stresses, such as drought, heat, and cold. The DREB transcription factors (TF) are some of the largest groups of TFs in plants and play varied roles in plant stress response and signal transduction. METHODS AND RESULTS In the present study, PgDREB2A gene encoding a DREB transcription factor in pearl millet was functionally characterized in Arabidopsis. DREB2A proteins contain a conserved domain that binds toethylene responsive element binding factors. Three different T1 transgenic lines overexpressing PgDREB2A gene were identified by Southern blot. Quantitative real-time polymerase chain reaction exhibited that PgDREB2A could be induced under drought conditions. As compared with the control, PgDREB2A overexpressing transgenic Arabidopsis showed increased rate of seed germination and root growth in transgenic lines under higher concentrations of mannitol, NaCl, ABA, heat and cold stress. Additionally, PgDREB2A transgenic lines showed enhanced durability after rehydration and tolerance to drought and salt stress was augmented with increased proline and reduced MDA build-up and diminishing water loss. CONCLUSIONS Results from this study suggested that PgDREB2A as a transcription factor may improve endurance to various abiotic stresses and can be employed for developing crops tolerant to abiotic stresses.
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Affiliation(s)
- Rajendra Prasad Meena
- National Institute for Plant Biotechnology, Pusa Campus, New Delhi, India.,PG School, ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110012, India
| | - Gourab Ghosh
- National Institute for Plant Biotechnology, Pusa Campus, New Delhi, India
| | | | - Jasdeep Chatrath Padaria
- National Institute for Plant Biotechnology, Pusa Campus, New Delhi, India. .,PG School, ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110012, India.
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22
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Wheat Proteomics for Abiotic Stress Tolerance and Root System Architecture: Current Status and Future Prospects. Proteomes 2022; 10:proteomes10020017. [PMID: 35645375 PMCID: PMC9150004 DOI: 10.3390/proteomes10020017] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 05/03/2022] [Accepted: 05/11/2022] [Indexed: 02/06/2023] Open
Abstract
Wheat is an important staple cereal for global food security. However, climate change is hampering wheat production due to abiotic stresses, such as heat, salinity, and drought. Besides shoot architectural traits, improving root system architecture (RSA) traits have the potential to improve yields under normal and stressed environments. RSA growth and development and other stress responses involve the expression of proteins encoded by the trait controlling gene/genes. Hence, mining the key proteins associated with abiotic stress responses and RSA is important for improving sustainable yields in wheat. Proteomic studies in wheat started in the early 21st century using the two-dimensional (2-DE) gel technique and have extensively improved over time with advancements in mass spectrometry. The availability of the wheat reference genome has allowed the exploration of proteomics to identify differentially expressed or abundant proteins (DEPs or DAPs) for abiotic stress tolerance and RSA improvement. Proteomics contributed significantly to identifying key proteins imparting abiotic stress tolerance, primarily related to photosynthesis, protein synthesis, carbon metabolism, redox homeostasis, defense response, energy metabolism and signal transduction. However, the use of proteomics to improve RSA traits in wheat is in its infancy. Proteins related to cell wall biogenesis, carbohydrate metabolism, brassinosteroid biosynthesis, and transportation are involved in the growth and development of several RSA traits. This review covers advances in quantification techniques of proteomics, progress in identifying DEPs and/or DAPs for heat, salinity, and drought stresses, and RSA traits, and the limitations and future directions for harnessing proteomics in wheat improvement.
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23
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Proteomic Investigation of Molecular Mechanisms in Response to PEG-Induced Drought Stress in Soybean Roots. PLANTS 2022; 11:plants11091173. [PMID: 35567174 PMCID: PMC9100407 DOI: 10.3390/plants11091173] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 04/20/2022] [Accepted: 04/25/2022] [Indexed: 11/25/2022]
Abstract
Roots are generally the critical drought sensors, but little is known about their molecular response to drought stress. We used the drought-tolerant soybean variety ‘Jiyu 47’ to investigate the differentially expressed proteins (DEPs) in soybean roots during the seedling stage based on the tandem mass tag (TMT) proteomics analysis. Various expression patterns were observed in a total of six physiological parameters. A total of 468 DEPs (144 up-regulated and 324 down-regulated) among a total of 8687 proteins were identified in response to drought stress in 24 h. The expression of DEPs was further validated based on quantitative real-time PCR of a total of five genes (i.e., GmGSH, GmGST1, GmGST2 k GmCAT, and Gm6PGD) involved in the glutathione biosynthesis. Results of enrichment analyses revealed a coordinated expression pattern of proteins involved in various cellular metabolisms responding to drought stress in soybean roots. Our results showed that drought stress caused significant alterations in the expression of proteins involved in several metabolic pathways in soybean roots, including carbohydrate metabolism, metabolism of the osmotic regulation substances, and antioxidant defense system (i.e., the glutathione metabolism). Increased production of reduced glutathione (GSH) enhanced the prevention of the damage caused by reactive oxygen species and the tolerance of the abiotic stress. The glutathione metabolism played a key role in modifying the antioxidant defense system in response to drought stress in soybean roots. Our proteomic study suggested that the soybean plants responded to drought stress by coordinating their protein expression during the vegetative stage, providing novel insights into the molecular mechanisms regulating the response to abiotic stress in plants.
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24
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Ndiaye A, Diallo AO, Fall NC, Diouf RD, Diouf D, Kane NA. Transcriptomic analysis of methyl jasmonate treatment reveals gene networks involved in drought tolerance in pearl millet. Sci Rep 2022; 12:5158. [PMID: 35338214 PMCID: PMC8956577 DOI: 10.1038/s41598-022-09152-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 03/16/2022] [Indexed: 11/09/2022] Open
Abstract
Water deficit stress at the early stage of development is one of the main factors limiting pearl millet production. One practice to counteract this limitation would be to resort to the application of hormones to stimulate plant growth and development at critical stages. Exogenous methyl jasmonate (MeJA) can improve drought tolerance by modulating signaling, metabolism, and photosynthesis pathways, therefore, we assumed that can occur in pearl millet during the early stage of development. To decipher the molecular mechanisms controlling these pathways, RNAseq was conducted in two pearl millet genotypes, drought-sensitive SosatC88 and drought-tolerant Souna3, in response to 200 μM of MeJA. Pairwise comparison between the MeJA-treated and non-treated plants revealed 3270 differentially expressed genes (DEGs) among 20,783 transcripts in SosatC88 and 127 DEGs out of 20,496 transcripts in Souna3. Gene ontology (GO) classification assigned most regulated DEGs in SosatC88 to heme binding, oxidation-reduction process, response to oxidative stress and membrane, and in Souna3 to terpene synthase activity, lyase activity, magnesium ion binding, and thylakoid. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis reveals that DEGs in SosatC88 are related to the oxidation-reduction process, the biosynthesis of other secondary metabolites, the signal transduction, and the metabolism of terpenoids, while in Souna3, DEGs are related to the metabolism of terpenoids and the energy metabolism. Two genes encoding a diterpenoid biosynthesis-related (Pgl_GLEAN_10009413) and a Glutathione S transferase T3 (Pgl_GLEAN_10034098) were contra-regulated between SosatC88 and Souna3. Additionally, five random genes differentially expressed by RNAseq were validated using qPCR, therefore, they are potential targets for the development of novel strategies breeding schemes for plant growth under water deficit stress. These insights into the molecular mechanisms of pearl millet genotype tolerance at the early stage of development contribute to the understanding of the role of hormones in adaptation to drought-prone environments.
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Affiliation(s)
- Adama Ndiaye
- Centre d'Étude Régional Pour L'Amélioration de L'Adaptation À La Sècheresse (CERAAS), Institut Sénégalais de Recherches Agricoles (ISRA), Route de Khombole, Thiès, BP 3320, Sénégal.,Laboratoire Campus de Biotechnologies Végétales, Département de Biologie Végétale, Faculté Des Sciences Et Techniques, Université Cheikh Anta Diop (UCAD), 10700, Dakar-Fann, Dakar, Sénégal.,Laboratoire Mixte International Adaptation Des Plantes Et Des Microorganismes Associés Aux Stress Environnementaux (LAPSE), Dakar, Sénégal
| | - Amadou Oury Diallo
- Centre d'Étude Régional Pour L'Amélioration de L'Adaptation À La Sècheresse (CERAAS), Institut Sénégalais de Recherches Agricoles (ISRA), Route de Khombole, Thiès, BP 3320, Sénégal.,Laboratoire Mixte International Adaptation Des Plantes Et Des Microorganismes Associés Aux Stress Environnementaux (LAPSE), Dakar, Sénégal
| | - Ndèye Coura Fall
- Centre d'Étude Régional Pour L'Amélioration de L'Adaptation À La Sècheresse (CERAAS), Institut Sénégalais de Recherches Agricoles (ISRA), Route de Khombole, Thiès, BP 3320, Sénégal
| | - Rose Diambogne Diouf
- Centre d'Étude Régional Pour L'Amélioration de L'Adaptation À La Sècheresse (CERAAS), Institut Sénégalais de Recherches Agricoles (ISRA), Route de Khombole, Thiès, BP 3320, Sénégal
| | - Diaga Diouf
- Laboratoire Campus de Biotechnologies Végétales, Département de Biologie Végétale, Faculté Des Sciences Et Techniques, Université Cheikh Anta Diop (UCAD), 10700, Dakar-Fann, Dakar, Sénégal.,Laboratoire Mixte International Adaptation Des Plantes Et Des Microorganismes Associés Aux Stress Environnementaux (LAPSE), Dakar, Sénégal
| | - Ndjido Ardo Kane
- Centre d'Étude Régional Pour L'Amélioration de L'Adaptation À La Sècheresse (CERAAS), Institut Sénégalais de Recherches Agricoles (ISRA), Route de Khombole, Thiès, BP 3320, Sénégal. .,Laboratoire Mixte International Adaptation Des Plantes Et Des Microorganismes Associés Aux Stress Environnementaux (LAPSE), Dakar, Sénégal.
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Singh PK, Indoliya Y, Agrawal L, Awasthi S, Deeba F, Dwivedi S, Chakrabarty D, Shirke PA, Pandey V, Singh N, Dhankher OP, Barik SK, Tripathi RD. Genomic and proteomic responses to drought stress and biotechnological interventions for enhanced drought tolerance in plants. CURRENT PLANT BIOLOGY 2022; 29:100239. [DOI: 10.1016/j.cpb.2022.100239] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/27/2023]
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26
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Lacek J, García-González J, Weckwerth W, Retzer K. Lessons Learned from the Studies of Roots Shaded from Direct Root Illumination. Int J Mol Sci 2021; 22:12784. [PMID: 34884591 PMCID: PMC8657594 DOI: 10.3390/ijms222312784] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/22/2021] [Accepted: 11/24/2021] [Indexed: 11/16/2022] Open
Abstract
The root is the below-ground organ of a plant, and it has evolved multiple signaling pathways that allow adaptation of architecture, growth rate, and direction to an ever-changing environment. Roots grow along the gravitropic vector towards beneficial areas in the soil to provide the plant with proper nutrients to ensure its survival and productivity. In addition, roots have developed escape mechanisms to avoid adverse environments, which include direct illumination. Standard laboratory growth conditions for basic research of plant development and stress adaptation include growing seedlings in Petri dishes on medium with roots exposed to light. Several studies have shown that direct illumination of roots alters their morphology, cellular and biochemical responses, which results in reduced nutrient uptake and adaptability upon additive stress stimuli. In this review, we summarize recent methods that allow the study of shaded roots under controlled laboratory conditions and discuss the observed changes in the results depending on the root illumination status.
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Affiliation(s)
- Jozef Lacek
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany, Czech Academy of Sciences, 165 02 Prague, Czech Republic; (J.L.); (J.G.-G.)
- Department of Experimental Plant Biology, Faculty of Science, Charles University, 128 00 Prague, Czech Republic
| | - Judith García-González
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany, Czech Academy of Sciences, 165 02 Prague, Czech Republic; (J.L.); (J.G.-G.)
- Department of Experimental Plant Biology, Faculty of Science, Charles University, 128 00 Prague, Czech Republic
| | - Wolfram Weckwerth
- Department of Functional and Evolutionary Ecology, Molecular Systems Biology (MoSys), Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030 Wien, Austria;
- Vienna Metabolomics Center (VIME), University of Vienna, Djerassiplatz 1, 1030 Wien, Austria
| | - Katarzyna Retzer
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany, Czech Academy of Sciences, 165 02 Prague, Czech Republic; (J.L.); (J.G.-G.)
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Satyavathi CT, Ambawat S, Khandelwal V, Srivastava RK. Pearl Millet: A Climate-Resilient Nutricereal for Mitigating Hidden Hunger and Provide Nutritional Security. FRONTIERS IN PLANT SCIENCE 2021; 12:659938. [PMID: 34589092 PMCID: PMC8475763 DOI: 10.3389/fpls.2021.659938] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 08/03/2021] [Indexed: 06/03/2023]
Abstract
Pearl millet [Pennisetum glaucum (L.) R. Br.] is the sixth most important cereal crop after rice, wheat, maize, barley and sorghum. It is widely grown on 30 million ha in the arid and semi-arid tropical regions of Asia and Africa, accounting for almost half of the global millet production. Climate change affects crop production by directly influencing biophysical factors such as plant and animal growth along with the various areas associated with food processing and distribution. Assessment of the effects of global climate changes on agriculture can be helpful to anticipate and adapt farming to maximize the agricultural production more effectively. Pearl millet being a climate-resilient crop is important to minimize the adverse effects of climate change and has the potential to increase income and food security of farming communities in arid regions. Pearl millet has a deep root system and can survive in a wide range of ecological conditions under water scarcity. It has high photosynthetic efficiency with an excellent productivity and growth in low nutrient soil conditions and is less reliant on chemical fertilizers. These attributes have made it a crop of choice for cultivation in arid and semi-arid regions of the world; however, fewer efforts have been made to study the climate-resilient features of pearl millet in comparison to the other major cereals. Several hybrids and varieties of pearl millet were developed during the past 50 years in India by both the public and private sectors. Pearl millet is also nutritionally superior and rich in micronutrients such as iron and zinc and can mitigate malnutrition and hidden hunger. Inclusion of minimum standards for micronutrients-grain iron and zinc content in the cultivar release policy-is the first of its kind step taken in pearl millet anywhere in the world, which can lead toward enhanced food and nutritional security. The availability of high-quality whole-genome sequencing and re-sequencing information of several lines may aid genomic dissection of stress tolerance and provide a good opportunity to further exploit the nutritional and climate-resilient attributes of pearl millet. Hence, more efforts should be put into its genetic enhancement and improvement in inheritance to exploit it in a better way. Thus, pearl millet is the next-generation crop holding the potential of nutritional richness and the climate resilience and efforts must be targeted to develop nutritionally dense hybrids/varieties tolerant to drought using different omics approaches.
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Affiliation(s)
- C. Tara Satyavathi
- Indian Council of Agricultural Research - All India Coordinated Research Project on Pearl Millet, Jodhpur, India
| | - Supriya Ambawat
- Indian Council of Agricultural Research - All India Coordinated Research Project on Pearl Millet, Jodhpur, India
| | - Vikas Khandelwal
- Indian Council of Agricultural Research - All India Coordinated Research Project on Pearl Millet, Jodhpur, India
| | - Rakesh K. Srivastava
- Department of Molecular Breeding (Genomics Trait Discovery), International Crops Research Institute for Semi-arid Tropics, Patancheru, India
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28
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Zhang S, Ghatak A, Bazargani MM, Bajaj P, Varshney RK, Chaturvedi P, Jiang D, Weckwerth W. Spatial distribution of proteins and metabolites in developing wheat grain and their differential regulatory response during the grain filling process. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:669-687. [PMID: 34227164 PMCID: PMC9291999 DOI: 10.1111/tpj.15410] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 06/06/2021] [Accepted: 06/25/2021] [Indexed: 05/03/2023]
Abstract
Grain filling and grain development are essential biological processes in the plant's life cycle, eventually contributing to the final seed yield and quality in all cereal crops. Studies of how the different wheat (Triticum aestivum L.) grain components contribute to the overall development of the seed are very scarce. We performed a proteomics and metabolomics analysis in four different developing components of the wheat grain (seed coat, embryo, endosperm, and cavity fluid) to characterize molecular processes during early and late grain development. In-gel shotgun proteomics analysis at 12, 15, 20, and 26 days after anthesis (DAA) revealed 15 484 identified and quantified proteins, out of which 410 differentially expressed proteins were identified in the seed coat, 815 in the embryo, 372 in the endosperm, and 492 in the cavity fluid. The abundance of selected protein candidates revealed spatially and temporally resolved protein functions associated with development and grain filling. Multiple wheat protein isoforms involved in starch synthesis such as sucrose synthases, starch phosphorylase, granule-bound and soluble starch synthase, pyruvate phosphate dikinase, 14-3-3 proteins as well as sugar precursors undergo a major tissue-dependent change in abundance during wheat grain development suggesting an intimate interplay of starch biosynthesis control. Different isoforms of the protein disulfide isomerase family as well as glutamine levels, both involved in the glutenin macropolymer pattern, showed distinct spatial and temporal abundance, revealing their specific role as indicators of wheat gluten quality. Proteins binned into the functional category of cell growth/division and protein synthesis/degradation were more abundant in the early stages (12 and 15 DAA). At the metabolome level all tissues and especially the cavity fluid showed highly distinct metabolite profiles. The tissue-specific data are integrated with biochemical networks to generate a comprehensive map of molecular processes during grain filling and developmental processes.
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Affiliation(s)
- Shuang Zhang
- Department of Functional and Evolutionary EcologyMolecular Systems Biology Lab (MOSYS)University of ViennaAlthanstrasse 14ViennaA‐1090Austria
| | - Arindam Ghatak
- Department of Functional and Evolutionary EcologyMolecular Systems Biology Lab (MOSYS)University of ViennaAlthanstrasse 14ViennaA‐1090Austria
| | | | - Prasad Bajaj
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)Hyderabad502324India
| | - Rajeev K. Varshney
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)Hyderabad502324India
- State Agricultural Biotechnology CentreCentre for Crop and Food InnovationMurdoch UniversityMurdochWA6150Australia
| | - Palak Chaturvedi
- Department of Functional and Evolutionary EcologyMolecular Systems Biology Lab (MOSYS)University of ViennaAlthanstrasse 14ViennaA‐1090Austria
| | - Dong Jiang
- National Technique Innovation Center for Regional Wheat Production/Key Laboratory of Crop EcophysiologyMinistry of Agriculture/Nanjing Agricultural UniversityNanjing210095China
| | - Wolfram Weckwerth
- Department of Functional and Evolutionary EcologyMolecular Systems Biology Lab (MOSYS)University of ViennaAlthanstrasse 14ViennaA‐1090Austria
- Vienna Metabolomics Center (VIME)University of ViennaAlthanstrasse 14ViennaA‐1090Austria
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29
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Zenda T, Liu S, Dong A, Duan H. Advances in Cereal Crop Genomics for Resilience under Climate Change. Life (Basel) 2021; 11:502. [PMID: 34072447 PMCID: PMC8228855 DOI: 10.3390/life11060502] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 05/21/2021] [Accepted: 05/25/2021] [Indexed: 12/12/2022] Open
Abstract
Adapting to climate change, providing sufficient human food and nutritional needs, and securing sufficient energy supplies will call for a radical transformation from the current conventional adaptation approaches to more broad-based and transformative alternatives. This entails diversifying the agricultural system and boosting productivity of major cereal crops through development of climate-resilient cultivars that can sustainably maintain higher yields under climate change conditions, expanding our focus to crop wild relatives, and better exploitation of underutilized crop species. This is facilitated by the recent developments in plant genomics, such as advances in genome sequencing, assembly, and annotation, as well as gene editing technologies, which have increased the availability of high-quality reference genomes for various model and non-model plant species. This has necessitated genomics-assisted breeding of crops, including underutilized species, consequently broadening genetic variation of the available germplasm; improving the discovery of novel alleles controlling important agronomic traits; and enhancing creation of new crop cultivars with improved tolerance to biotic and abiotic stresses and superior nutritive quality. Here, therefore, we summarize these recent developments in plant genomics and their application, with particular reference to cereal crops (including underutilized species). Particularly, we discuss genome sequencing approaches, quantitative trait loci (QTL) mapping and genome-wide association (GWAS) studies, directed mutagenesis, plant non-coding RNAs, precise gene editing technologies such as CRISPR-Cas9, and complementation of crop genotyping by crop phenotyping. We then conclude by providing an outlook that, as we step into the future, high-throughput phenotyping, pan-genomics, transposable elements analysis, and machine learning hold much promise for crop improvements related to climate resilience and nutritional superiority.
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Affiliation(s)
- Tinashe Zenda
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding 071001, China; (S.L.); (A.D.)
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China
- Department of Crop Science, Faculty of Agriculture and Environmental Science, Bindura University of Science Education, Bindura P. Bag 1020, Zimbabwe
| | - Songtao Liu
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding 071001, China; (S.L.); (A.D.)
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China
| | - Anyi Dong
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding 071001, China; (S.L.); (A.D.)
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China
| | - Huijun Duan
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding 071001, China; (S.L.); (A.D.)
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China
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Modulation of photosynthesis and other proteins during water-stress. Mol Biol Rep 2021; 48:3681-3693. [PMID: 33856605 DOI: 10.1007/s11033-021-06329-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 03/31/2021] [Indexed: 10/25/2022]
Abstract
Protein changes under drought or water stress conditions have been widely investigated. These investigations have given us enormous understanding of how drought is manifested in plants and how plants respond and adopt to such conditions. Chlorophyll fluoroescence, gas exchange, OMICS, biochemical and molecular analyses have shed light on regulation of physiology and photosynthesis of plants under drought. Use of proteomics has greatly increased the repertoire of drought-associated proteins which nevertheless, need to be investigated for their mechanistic and functional roles. Roles of such proteins have been succinctly discussed in various review articles, however more information on their functional role in countering drought is needed. In this review, recent developments in the field, alterations in the abundance of plant proteins in response to drought, monitored through numerous proteomic and immuno-blot analyses, and how these could affect plants growth and development, are discussed.
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Shabrangy A, Ghatak A, Zhang S, Priller A, Chaturvedi P, Weckwerth W. Magnetic Field Induced Changes in the Shoot and Root Proteome of Barley ( Hordeum vulgare L.). FRONTIERS IN PLANT SCIENCE 2021; 12:622795. [PMID: 33708230 PMCID: PMC7940674 DOI: 10.3389/fpls.2021.622795] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 01/13/2021] [Indexed: 05/04/2023]
Abstract
The geomagnetic field (GMF) has been present since the beginning of plant evolution. Recently, some researchers have focused their efforts on employing magnetic fields (MFs) higher than GMF to improve the seed germination, growth, and harvest of agriculturally important crop plants, as the use of MFs is an inexpensive and environment-friendly technique. In this study, we have employed different treatments of MF at 7 mT (milliTesla) at different time points of exposure, including 1, 3, and 6 h. The extended exposure was followed by five consecutive days at 6 h per day in barley seeds. The results showed a positive impact of MF on growth characteristics for 5-day-old seedlings, including seed germination rate, root and shoot length, and biomass weight. Furthermore, ~5 days of delay of flowering in pre-treated plants was also observed. We used a shotgun proteomics approach to identify changes in the protein signatures of root and shoot tissues under MF effects. In total, we have identified 2,896 proteins. Thirty-eight proteins in the shoot and 15 proteins in the root showed significant changes under the MF effect. Proteins involved in primary metabolic pathways were increased in contrast to proteins with a metal ion binding function, proteins that contain iron ions in their structure, and proteins involved in electron transfer chain, which were all decreased significantly in the treated tissues. The upregulated proteins' overall biological processes included carbohydrate metabolic process, oxidation-reduction process, and cell redox homeostasis, while down-regulated processes included translation and protein refolding. In general, shoot response was more affected by MF effect than root tissue, leading to the identification of 41 shoot specific proteins. This study provides an initial insight into the proteome regulation response to MF during barley's seedling stage.
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Affiliation(s)
- Azita Shabrangy
- Molecular Systems Biology Lab, Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, Vienna, Austria
- Azita Shabrangy
| | - Arindam Ghatak
- Molecular Systems Biology Lab, Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Shuang Zhang
- Molecular Systems Biology Lab, Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Alfred Priller
- VERA Laboratory, Isotope Physics, Faculty of Physics, University of Vienna, Vienna, Austria
| | - Palak Chaturvedi
- Molecular Systems Biology Lab, Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Wolfram Weckwerth
- Molecular Systems Biology Lab, Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center, University of Vienna, Vienna, Austria
- *Correspondence: Wolfram Weckwerth
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