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Shearman JR, Naktang C, Sonthirod C, Kongkachana W, U-Thoomporn S, Jomchai N, Maknual C, Yamprasai S, Wanthongchai P, Pootakham W, Tangphatsornruang S. De novo assembly and analysis of Sonneratia ovata genome and population analysis. Genomics 2024; 116:110837. [PMID: 38548034 DOI: 10.1016/j.ygeno.2024.110837] [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: 11/13/2023] [Revised: 02/22/2024] [Accepted: 03/24/2024] [Indexed: 04/01/2024]
Abstract
Mangroves are an important part of coastal and estuarine ecosystems where they serve as nurseries for marine species and prevent coastal erosion. Here we report the genome of Sonneratia ovata, which is a true mangrove that grows in estuarine environments and can tolerate moderate salt exposure. We sequenced the S. ovata genome and assembled it into chromosome-level scaffolds through the use of Hi-C. The genome is 212.3 Mb and contains 12 chromosomes that range in size from 12.2 to 23.2 Mb. Annotation identified 29,829 genes with a BUSCO completeness of 95.9%. We identified salt genes and found copy number expansion of salt genes such as ADP-ribosylation factor 1, and elongation factor 1-alpha. Population analysis identified a low level of genetic variation and a lack of population structure within S. ovata.
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Affiliation(s)
- Jeremy R Shearman
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
| | - Chaiwat Naktang
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
| | - Chutima Sonthirod
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
| | - Wasitthee Kongkachana
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
| | - Sonicha U-Thoomporn
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
| | - Nukoon Jomchai
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
| | - Chatree Maknual
- Department of Marine and Coastal Resources, 120 The Government Complex, Chaengwatthana Rd., Thung Song Hong, Bangkok 10210, Thailand
| | - Suchart Yamprasai
- Department of Marine and Coastal Resources, 120 The Government Complex, Chaengwatthana Rd., Thung Song Hong, Bangkok 10210, Thailand
| | - Poonsri Wanthongchai
- Department of Marine and Coastal Resources, 120 The Government Complex, Chaengwatthana Rd., Thung Song Hong, Bangkok 10210, Thailand
| | - Wirulda Pootakham
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
| | - Sithichoke Tangphatsornruang
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand.
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2
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Chen S, Du T, Huang Z, He K, Yang M, Gao S, Yu T, Zhang H, Li X, Chen S, Liu CM, Li H. The Spartina alterniflora genome sequence provides insights into the salt-tolerance mechanisms of exo-recretohalophytes. PLANT BIOTECHNOLOGY JOURNAL 2024. [PMID: 38685729 DOI: 10.1111/pbi.14368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 03/24/2024] [Accepted: 04/11/2024] [Indexed: 05/02/2024]
Abstract
Spartina alterniflora is an exo-recretohalophyte Poaceae species that is able to grow well in seashore, but the genomic basis underlying its adaptation to salt tolerance remains unknown. Here, we report a high-quality, chromosome-level genome assembly of S. alterniflora constructed through PacBio HiFi sequencing, combined with high-throughput chromosome conformation capture (Hi-C) technology and Illumina-based transcriptomic analyses. The final 1.58 Gb genome assembly has a contig N50 size of 46.74 Mb. Phylogenetic analysis suggests that S. alterniflora diverged from Zoysia japonica approximately 21.72 million years ago (MYA). Moreover, whole-genome duplication (WGD) events in S. alterniflora appear to have expanded gene families and transcription factors relevant to salt tolerance and adaptation to saline environments. Comparative genomics analyses identified numerous species-specific genes, significantly expanded genes and positively selected genes that are enriched for 'ion transport' and 'response to salt stress'. RNA-seq analysis identified several ion transporter genes including the high-affinity K+ transporters (HKTs), SaHKT1;2, SaHKT1;3 and SaHKT1;8, and high copy number of Salt Overly Sensitive (SOS) up-regulated under high salt conditions, and the overexpression of SaHKT2;4 in Arabidopsis thaliana conferred salt tolerance to the plant, suggesting specialized roles for S. alterniflora to adapt to saline environments. Integrated metabolomics and transcriptomics analyses revealed that salt stress activate glutathione metabolism, with differential expressions of several genes such as γ-ECS, GSH-S, GPX, GST and PCS in the glutathione metabolism. This study suggests several adaptive mechanisms that could contribute our understanding of evolutional basis of the halophyte.
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Affiliation(s)
- Shoukun Chen
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- Nanfan Research Institute, CAAS, Sanya, Hainan, China
- Hainan Seed Industry Laboratory, Sanya, Hainan, China
| | - Tingting Du
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- Nanfan Research Institute, CAAS, Sanya, Hainan, China
| | - Zhangping Huang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- Nanfan Research Institute, CAAS, Sanya, Hainan, China
| | - Kunhui He
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- Nanfan Research Institute, CAAS, Sanya, Hainan, China
| | - Maogeng Yang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- Nanfan Research Institute, CAAS, Sanya, Hainan, China
- Key Laboratory of Plant Molecular & Developmental Biology, College of Life Sciences, Yantai University, Yantai, Shandong, China
| | - Shang Gao
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- Nanfan Research Institute, CAAS, Sanya, Hainan, China
| | - Tingxi Yu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- Nanfan Research Institute, CAAS, Sanya, Hainan, China
| | - Hao Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- Nanfan Research Institute, CAAS, Sanya, Hainan, China
| | - Xiang Li
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Shihua Chen
- Key Laboratory of Plant Molecular & Developmental Biology, College of Life Sciences, Yantai University, Yantai, Shandong, China
| | - Chun-Ming Liu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- School of Advanced Agricultural Sciences, Peking University, Beijing, China
| | - Huihui Li
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- Nanfan Research Institute, CAAS, Sanya, Hainan, China
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3
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Kumar S, Chakraborty S, Chakraborty N. Dehydration-responsive cytoskeleton proteome of rice reveals reprograming of key molecular pathways to mediate metabolic adaptation and cell survival. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 207:108359. [PMID: 38237420 DOI: 10.1016/j.plaphy.2024.108359] [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: 09/29/2023] [Revised: 12/22/2023] [Accepted: 01/10/2024] [Indexed: 03/16/2024]
Abstract
The plant cytoskeletal proteins play a key role that control cytoskeleton dynamics, contributing to crucial biological processes such as cell wall morphogenesis, stomatal conductance and abscisic acid accumulation in repercussion to water-deficit stress or dehydration. Yet, it is still completely unknown which specific biochemical processes and regulatory mechanisms the cytoskeleton uses to drive dehydration tolerance. To better understand the role of cytoskeleton, we developed the dehydration-responsive cytoskeletal proteome map of a resilient rice cultivar. Initially, four-week-old rice plants were exposed to progressive dehydration, and the magnitude of dehydration-induced compensatory physiological responses was monitored in terms of physicochemical indices. The organelle fractionation in conjunction with label-free quantitative proteome analysis led to the identification of 955 dehydration-responsive cytoskeletal proteins (DRCPs). To our knowledge, this is the first report of a stress-responsive plant cytoskeletal proteome, representing the largest inventory of cytoskeleton and cytoskeleton-associated proteins. The DRCPs were apparently involved in a wide array of intra-cellular molecules transportation, organelles positioning, cytoskeleton organization followed by different metabolic processes including amino acid metabolism. These findings presented open a unique view on global regulation of plant cytoskeletal proteome is intimately linked to cellular metabolic rewiring of adaptive responses, and potentially confer dehydration tolerance, especially in rice, and other crop species, in general.
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Affiliation(s)
- Sunil Kumar
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Subhra Chakraborty
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Niranjan Chakraborty
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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Sun Y, Shi M, Wang D, Gong Y, Sha Q, Lv P, Yang J, Chu P, Guo S. Research progress on the roles of actin-depolymerizing factor in plant stress responses. FRONTIERS IN PLANT SCIENCE 2023; 14:1278311. [PMID: 38034575 PMCID: PMC10687421 DOI: 10.3389/fpls.2023.1278311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 11/01/2023] [Indexed: 12/02/2023]
Abstract
Actin-depolymerizing factors (ADFs) are highly conserved small-molecule actin-binding proteins found throughout eukaryotic cells. In land plants, ADFs form a small gene family that displays functional redundancy despite variations among its individual members. ADF can bind to actin monomers or polymerized microfilaments and regulate dynamic changes in the cytoskeletal framework through specialized biochemical activities, such as severing, depolymerizing, and bundling. The involvement of ADFs in modulating the microfilaments' dynamic changes has significant implications for various physiological processes, including plant growth, development, and stress response. The current body of research has greatly advanced our comprehension of the involvement of ADFs in the regulation of plant responses to both biotic and abiotic stresses, particularly with respect to the molecular regulatory mechanisms that govern ADF activity during the transmission of stress signals. Stress has the capacity to directly modify the transcription levels of ADF genes, as well as indirectly regulate their expression through transcription factors such as MYB, C-repeat binding factors, ABF, and 14-3-3 proteins. Furthermore, apart from their role in regulating actin dynamics, ADFs possess the ability to modulate the stress response by influencing downstream genes associated with pathogen resistance and abiotic stress response. This paper provides a comprehensive overview of the current advancements in plant ADF gene research and suggests that the identification of plant ADF family genes across a broader spectrum, thorough analysis of ADF gene regulation in stress resistance of plants, and manipulation of ADF genes through genome-editing techniques to enhance plant stress resistance are crucial avenues for future investigation in this field.
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Matsumoto T, Higaki T, Takatsuka H, Kutsuna N, Ogata Y, Hasezawa S, Umeda M, Inada N. Arabidopsis thaliana Subclass I ACTIN DEPOLYMERIZING FACTORs Regulate Nuclear Organization and Gene Expression. PLANT & CELL PHYSIOLOGY 2023; 64:1231-1242. [PMID: 37647615 DOI: 10.1093/pcp/pcad092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 07/28/2023] [Accepted: 08/09/2023] [Indexed: 09/01/2023]
Abstract
ACTIN DEPOLYMERIZING FACTOR (ADF) is a conserved protein that regulates the organization and dynamics of actin microfilaments. Eleven ADFs in the Arabidopsis thaliana genome are grouped into four subclasses, and subclass I ADFs, ADF1-4, are all expressed throughout the plant. Previously, we showed that subclass I ADFs function in the regulation of the response against powdery mildew fungus as well as in the regulation of cell size and endoreplication. Here, we report a new role of subclass I ADFs in the regulation of nuclear organization and gene expression. Through microscopic observation of epidermal cells in mature leaves, we found that the size of chromocenters in both adf4 and transgenic lines where expression of subclass I ADFs is downregulated (ADF1-4Ri) was reduced compared with that of wild-type Col-0. Arabidopsis thaliana possesses eight ACTIN (ACT) genes, among which ACT2, -7 and -8 are expressed in vegetative organs. The chromocenter size in act7, but not in the act2/8 double mutant, was enlarged compared with that in Col-0. Microarray analysis revealed that 1,818 genes were differentially expressed in adf4 and ADF1-4Ri. In particular, expression of 22 nucleotide-binding leucine-rich repeat genes, which are involved in effector-triggered plant immunity, was reduced in adf4 and ADF1-4Ri. qRT-PCR confirmed the altered expressions shown with microarray analysis. Overall, these results suggest that ADF regulates various aspects of plant physiology through its role in regulation of nuclear organization and gene expression. The mechanism how ADF and ACT regulate nuclear organization and gene expression is discussed.
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Affiliation(s)
- Tomoko Matsumoto
- Graduate School of Agriculture, Osaka Metropolitan University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531 Japan
| | - Takumi Higaki
- Graduate School of Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuou-ku, Kumamoto, 860-8555 Japan
- International Research Organization for Advanced Science and Technology (IROAST), Kumamoto University, 2-39-1 Kurokami, Chuou-ku, Kumamoto, 860-8555 Japan
| | | | | | - Yoshiyuki Ogata
- Graduate School of Agriculture, Osaka Metropolitan University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531 Japan
| | - Seiichiro Hasezawa
- Graduate School of Science and Engineering, Hosei University, Kajino-cho 3-7-2 Koganei, Tokyo, 184-8584 Japan
| | - Masaaki Umeda
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Takayama-cho 8916-5 Ikoma, Nara, 630-0192 Japan
| | - Noriko Inada
- Graduate School of Agriculture, Osaka Metropolitan University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531 Japan
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Takayama-cho 8916-5 Ikoma, Nara, 630-0192 Japan
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6
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Sun Y, Wang D, Shi M, Gong Y, Yin S, Jiao Y, Guo S. Genome-wide identification of actin-depolymerizing factor gene family and their expression patterns under various abiotic stresses in soybean ( Glycine max). FRONTIERS IN PLANT SCIENCE 2023; 14:1236175. [PMID: 37575943 PMCID: PMC10413265 DOI: 10.3389/fpls.2023.1236175] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 07/14/2023] [Indexed: 08/15/2023]
Abstract
The actin-depolymerizing factor (ADF) encoded by a family of genes is highly conserved among eukaryotes and plays critical roles in the various processes of plant growth, development, and stress responses via the remodeling of the architecture of the actin cytoskeleton. However, the ADF family and the encoded proteins in soybean (Glycine max) have not yet been systematically investigated. In this study, 18 GmADF genes (GmADF1 - GmADF18) were identified in the soybean genome and were mapped to 14 different chromosomes. Phylogenetic analysis classified them into four groups, which was confirmed by their structure and the distribution of conserved motifs in the encoded proteins. Additionally, 29 paralogous gene pairs were identified in the GmADF family, and analysis of their Ka/Ks ratios indicated their purity-based selection during the evolutionary expansion of the soybean genome. The analysis of the expression profiles based on the RNA-seq and qRT-PCR data indicated that GmADFs were diversely expressed in different organs and tissues, with most of them responding actively to drought- and salt-induced stresses, suggesting the critical roles played by them in various biological processes. Overall, our study shows that GmADF genes may play a crucial role in response to various abiotic stresses in soybean, and the highly inducible candidate genes could be used for further functional studies and molecular breeding in soybean.
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Affiliation(s)
| | | | | | | | | | | | - Shangjing Guo
- School of Agricultural Science and Engineering, Liaocheng University, Liaocheng, China
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7
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Characterization of a Stress-Enhanced Promoter from the Grass Halophyte, Spartina alterniflora L. BIOLOGY 2022; 11:biology11121828. [PMID: 36552337 PMCID: PMC9775435 DOI: 10.3390/biology11121828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/12/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]
Abstract
Stress-inducible promoters are vital for the desirable expression of genes, especially transcription factors, which could otherwise compromise growth and development when constitutively overexpressed in plants. Here, we report on the characterization of the promoter region of a stress-responsive gene SaAsr1 from monocot halophyte cordgrass (Spartina alterniflora). Several cis-acting elements, such as ABRE (ABA-responsive element), DRE-CRT (dehydration responsive-element/C-Repeat), LTRE (low temperature-responsive element), ERE (ethylene-responsive element), LRE (light-responsive element), etc. contributed at varying degrees to salt-, drought- and ABA-enhanced expression of gusA reporter gene in Arabidopsis thaliana under the full-length promoter, pAsr11875 and its deletion derivatives with an assortment of cis-regulatory motifs. The smallest promoter, pAsr1491, with three cis-acting elements (a CCAAT box-heat responsive, an LRE, and a copper responsive element) conferred drought-enhanced expression of gusA; pAsr1755 (with an ABRE and a DRE) presented the highest expression in ABA and drought; and pAsr1994 with seven ABREs and two DREs conferred optimal induction of gusA, especially under drought and ABA. Arabidopsis transgenics expressing a known abiotic stress-responsive gene, SaADF2 (actin depolymerization factor 2), under both pAsr11875 and p35S promoters outperformed the wild type (WT) with enhanced drought and salt tolerance contributed by higher relative water content and membrane stability with no significant difference between pAsr11875:SaADF2 or p35S:SaADF2 lines. However, pAsr11875:SaADF2 lines produced healthy plants with robust shoot systems under salt stress and control compared to slightly stunted growth of the p35S:SaADF2 plants. This reestablished the evidence that transgene expression under a stress-inducible promoter is a better strategy for the genetic manipulation of crops.
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Liu Z, Østerlund I, Ruhnow F, Cao Y, Huang G, Cai W, Zhang J, Liang W, Nikoloski Z, Persson S, Zhang D. Fluorescent cytoskeletal markers reveal associations between the actin and microtubule cytoskeleton in rice cells. Development 2022; 149:275467. [DOI: 10.1242/dev.200415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 05/09/2022] [Indexed: 11/20/2022]
Abstract
ABSTRACT
Rice (Oryza sativa) is one of our main food crops, feeding ∼3.5 billion people worldwide. An increasing number of studies note the importance of the cytoskeleton, including actin filaments and microtubules, in rice development and environmental responses. Yet, reliable in vivo cytoskeleton markers are lacking in rice, which limits our knowledge of cytoskeletal functions in living cells. Therefore, we generated bright fluorescent marker lines of the actin and microtubule cytoskeletons in rice, suitable for live-cell imaging in a wide variety of rice tissues. Using these lines, we show that actin bundles and microtubules engage and co-function during pollen grain development, how the cytoskeletal components are coordinated during root cell development, and that the actin cytoskeleton is robust and facilitates microtubule responses during salt stress. Hence, we conclude that our cytoskeletal marker lines, highlighted by our findings of cytoskeletal associations and dynamics, will substantially further future investigations in rice biology.
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Affiliation(s)
- Zengyu Liu
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University 1 , Minhang 200240, Shanghai , China
| | - Isabella Østerlund
- University of Copenhagen 2 Department of Plant and Environmental Sciences (PLEN) , , 1870 Frederiksberg , Denmark
- Max Planck Institute of Molecular Plant Physiology 3 Systems Biology and Mathematical Modelling , , Am Mühlenberg 1, 14476 Potsdam-Golm , Germany
| | - Felix Ruhnow
- University of Copenhagen 2 Department of Plant and Environmental Sciences (PLEN) , , 1870 Frederiksberg , Denmark
| | - Yiran Cao
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University 1 , Minhang 200240, Shanghai , China
| | - Guoqiang Huang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University 1 , Minhang 200240, Shanghai , China
| | - Wenguo Cai
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University 1 , Minhang 200240, Shanghai , China
| | - Jiao Zhang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University 1 , Minhang 200240, Shanghai , China
| | - Wanqi Liang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University 1 , Minhang 200240, Shanghai , China
| | - Zoran Nikoloski
- Max Planck Institute of Molecular Plant Physiology 3 Systems Biology and Mathematical Modelling , , Am Mühlenberg 1, 14476 Potsdam-Golm , Germany
| | - Staffan Persson
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University 1 , Minhang 200240, Shanghai , China
- University of Copenhagen 2 Department of Plant and Environmental Sciences (PLEN) , , 1870 Frederiksberg , Denmark
- Copenhagen Plant Science Center (CPSC) 4 , , 1870 Frederiksberg , Denmark
- University of Copenhagen 4 , , 1870 Frederiksberg , Denmark
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University 1 , Minhang 200240, Shanghai , China
- School of Agriculture, Food, and Wine 5 , , Waite Campus, Urrbrae, SA 5064 , Australia
- University of Adelaide 5 , , Waite Campus, Urrbrae, SA 5064 , Australia
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Kouhen M, García-Caparrós P, Twyman RM, Abdelly C, Mahmoudi H, Schillberg S, Debez A. Improving environmental stress resilience in crops by genome editing: insights from extremophile plants. Crit Rev Biotechnol 2022; 43:559-574. [PMID: 35606905 DOI: 10.1080/07388551.2022.2042481] [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] [Indexed: 12/20/2022]
Abstract
In basic and applied sciences, genome editing has become an indispensable tool, especially the versatile and adaptable CRISPR/Cas9 system. Using CRISPR/Cas9 in plants has enabled modifications of many valuable traits, including environmental stress tolerance, an essential aspect when it comes to ensuring food security under climate change pressure. The CRISPR toolbox enables faster and more precise plant breeding by facilitating: multiplex gene editing, gene pyramiding, and de novo domestication. In this paper, we discuss the most recent advances in CRISPR/Cas9 and alternative CRISPR-based systems, along with the technical challenges that remain to be overcome. A revision of the latest proof-of-concept and functional characterization studies has indeed provided more insight into the quantitative traits affecting crop yield and stress tolerance. Additionally, we focus on the applications of CRISPR/Cas9 technology in regard to extremophile plants, due to their significance on: industrial, ecological and economic levels. These still unexplored genetic resources could provide the means to harden our crops against the threat of climate change, thus ensuring food security over the next century.
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Affiliation(s)
- Mohamed Kouhen
- Centre of Biotechnology of Borj-Cedria (CBBC), Laboratory of Extremophile Plants (LPE), Hammam-Lif, Tunisia.,Department of Biosciences and Territory, University of Molise, Pesche, Italy
| | - Pedro García-Caparrós
- Agronomy Department of Superior School Engineering, University of Almeria, CIAIMBITAL, Almería, Spain
| | | | - Chedly Abdelly
- Centre of Biotechnology of Borj-Cedria (CBBC), Laboratory of Extremophile Plants (LPE), Hammam-Lif, Tunisia
| | - Henda Mahmoudi
- International Center for Biosaline Agriculture, Academic City, Near Zayed University, Dubai, United Arab Emirates
| | - Stefan Schillberg
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany
| | - Ahmed Debez
- Centre of Biotechnology of Borj-Cedria (CBBC), Laboratory of Extremophile Plants (LPE), Hammam-Lif, Tunisia
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10
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Joshi S, Nath J, Singh AK, Pareek A, Joshi R. Ion transporters and their regulatory signal transduction mechanisms for salinity tolerance in plants. PHYSIOLOGIA PLANTARUM 2022; 174:e13702. [PMID: 35524987 DOI: 10.1111/ppl.13702] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 05/03/2022] [Accepted: 05/06/2022] [Indexed: 06/14/2023]
Abstract
Soil salinity is one of the most serious threats to plant growth and productivity. Due to global climate change, burgeoning population and shrinking arable land, there is an urgent need to develop crops with minimum reduction in yield when cultivated in salt-affected areas. Salinity stress imposes osmotic stress as well as ion toxicity, which impairs major plant processes such as photosynthesis, cellular metabolism, and plant nutrition. One of the major effects of salinity stress in plants includes the disturbance of ion homeostasis in various tissues. In the present study, we aimed to review the regulation of uptake, transport, storage, efflux, influx, and accumulation of various ions in plants under salinity stress. We have summarized major research advancements towards understanding the ion homeostasis at both cellular and whole-plant level under salinity stress. We have also discussed various factors regulating the function of ion transporters and channels in maintaining ion homeostasis and ionic interactions under salt stress, including plant antioxidative defense, osmo-protection, and osmoregulation. We further elaborated on stress perception at extracellular and intracellular levels, which triggers downstream intracellular-signaling cascade, including secondary messenger molecules generation. Various signaling and signal transduction mechanisms under salinity stress and their role in improving ion homeostasis in plants are also discussed. Taken together, the present review focuses on recent advancements in understanding the regulation and function of different ion channels and transporters under salt stress, which may pave the way for crop improvement.
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Affiliation(s)
- Shubham Joshi
- Division of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad, Uttar Pradesh, India
| | - Jhilmil Nath
- Division of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad, Uttar Pradesh, India
| | - Anil Kumar Singh
- ICAR-National Institute for Plant Biotechnology, LBS Centre, New Delhi, India
| | - Ashwani Pareek
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
- National Agri-Food Biotechnology Institute, Mohali, India
| | - Rohit Joshi
- Division of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad, Uttar Pradesh, India
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Kumari A, Dogra V, Joshi R, Kumar S. Stress-Responsive cis-Regulatory Elements Underline Podophyllotoxin Biosynthesis and Better Performance of Sinopodophyllum hexandrum Under Water Deficit Conditions. FRONTIERS IN PLANT SCIENCE 2022; 12:751846. [PMID: 35058943 PMCID: PMC8764236 DOI: 10.3389/fpls.2021.751846] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 11/09/2021] [Indexed: 06/09/2023]
Abstract
Sinopodophyllum hexandrum is an endangered medicinal herb known for its bioactive lignan podophyllotoxin (PTOX), which is used for the preparation of anticancer drugs. In its natural habitat, S. hexandrum is exposed to a multitude of adversities, such as fluctuating temperatures, water deficit, and high UV radiations. Transcriptional regulation of genes, which is regulated by the condition-specific binding of transcriptional factors to precise motifs in the promoter region, underlines responses to an environmental cue. Therefore, analysis of promoter sequences could ascertain the spatio-temporal expression of genes and overall stress responses. Unavailability of genomic information does not permit such analysis in S. hexandrum, especially on regulation of PTOX pathway. Accordingly, this study describes isolation and in silico analysis of 5'-upstream regions of ShPLR (PINORESINOL-LARICIRESINOL REDUCTASE) and ShSLD (SECOISOLARICIRESINOL DEHYDROGENASE), the two key genes of the PTOX biosynthetic pathway. Data showed a range of motifs related to basal transcription, stress-responsive elements, such as those for drought, low temperature, and light, suggesting that the expression of these genes and resulting PTOX accumulation would be affected by, at least, these environmental cues. While the impact of temperature and light on PTOX accumulation is well studied, the effect of water deficit on the physiology of S. hexandrum and PTOX accumulation remains obscure. Given the presence of drought-responsive elements in the promoters of the key genes, the impact of water deficit on growth and development and PTOX accumulation was studied. The results showed decline in relative water content and net photosynthetic rate, and increase in relative electrolyte leakage with stress progression. Plants under stress exhibited a reduction in transpiration rate and chlorophyll content, with a gradual increase in osmoprotectant content. Besides, stressed plants showed an increase in the expression of genes involved in the phenylpropanoid pathway and PTOX biosynthesis, and an increase in PTOX accumulation. Upon re-watering, non-irrigated plants showed a significant improvement in biochemical and physiological parameters. Summarily, our results demonstrated the importance of osmoprotectants during water deficit and the revival capacity of the species from water deficit, wherein PTOX synthesis was also modulated. Moreover, isolated promoter sequences could be employed in genetic transformation to mediate the expression of stress-induced genes in other plant systems.
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Affiliation(s)
- Anita Kumari
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Vivek Dogra
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Rohit Joshi
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Sanjay Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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12
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Guo J, Qu L, Hu Y, Lu W, Lu D. Proteomics reveals the effects of drought stress on the kernel development and starch formation of waxy maize. BMC PLANT BIOLOGY 2021; 21:434. [PMID: 34556041 PMCID: PMC8461923 DOI: 10.1186/s12870-021-03214-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 09/14/2021] [Indexed: 05/15/2023]
Abstract
BACKGROUND Kernel development and starch formation are the primary determinants of maize yield and quality, which are considerably influenced by drought stress. To clarify the response of maize kernel to drought stress, we established well-watered (WW) and water-stressed (WS) conditions at 1-30 days after pollination (dap) on waxy maize (Zea mays L. sinensis Kulesh). RESULTS Kernel development, starch accumulation, and activities of starch biosynthetic enzymes were significantly reduced by drought stress. The morphology of starch granules changed, whereas the grain filling rate was accelerated. A comparative proteomics approach was applied to analyze the proteome change in kernels under two treatments at 10 dap and 25 dap. Under the WS conditions, 487 and 465 differentially accumulated proteins (DAPs) were identified at 10 dap and 25 dap, respectively. Drought induced the downregulation of proteins involved in the oxidation-reduction process and oxidoreductase, peroxidase, catalase, glutamine synthetase, abscisic acid stress ripening 1, and lipoxygenase, which might be an important reason for the effect of drought stress on kernel development. Notably, several proteins involved in waxy maize endosperm and starch biosynthesis were upregulated at early-kernel stage under WS conditions, which might have accelerated endosperm development and starch synthesis. Additionally, 17 and 11 common DAPs were sustained in the upregulated and downregulated DAP groups, respectively, at 10 dap and 25 dap. Among these 28 proteins, four maize homologs (i.e., A0A1D6H543, B4FTP0, B6SLJ0, and A0A1D6H5J5) were considered as candidate proteins that affected kernel development and drought stress response by comparing with the rice genome. CONCLUSIONS The proteomic changes caused by drought were highly correlated with kernel development and starch accumulation, which were closely related to the final yield and quality of waxy maize. Our results provided a foundation for the enhanced understanding of kernel development and starch formation in response to drought stress in waxy maize.
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Affiliation(s)
- Jian Guo
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Key Laboratory of Crop Cultivation and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, P. R. China
| | - Lingling Qu
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Key Laboratory of Crop Cultivation and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, P. R. China
| | - Yifan Hu
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Key Laboratory of Crop Cultivation and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, P. R. China
| | - Weiping Lu
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Key Laboratory of Crop Cultivation and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, P. R. China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, P. R. China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, P. R. China
| | - Dalei Lu
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Key Laboratory of Crop Cultivation and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, P. R. China.
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, P. R. China.
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, P. R. China.
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Natarajan P, Murugesan AK, Govindan G, Gopalakrishnan A, Kumar R, Duraisamy P, Balaji R, Tanuja, Shyamli PS, Parida AK, Parani M. A reference-grade genome identifies salt-tolerance genes from the salt-secreting mangrove species Avicennia marina. Commun Biol 2021; 4:851. [PMID: 34239036 PMCID: PMC8266904 DOI: 10.1038/s42003-021-02384-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 06/18/2021] [Indexed: 02/06/2023] Open
Abstract
Water scarcity and salinity are major challenges facing agriculture today, which can be addressed by engineering plants to grow in the boundless seawater. Understanding the mangrove plants at the molecular level will be necessary for developing such highly salt-tolerant agricultural crops. With this objective, we sequenced the genome of a salt-secreting and extraordinarily salt-tolerant mangrove species, Avicennia marina, that grows optimally in 75% seawater and tolerates >250% seawater. Our reference-grade ~457 Mb genome contains 31 scaffolds corresponding to its chromosomes. We identified 31,477 protein-coding genes and a salinome consisting of 3246 salinity-responsive genes and homologs of 614 experimentally validated salinity tolerance genes. The salinome provides a strong foundation to understand the molecular mechanisms of salinity tolerance in plants and breeding crops suitable for seawater farming.
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Affiliation(s)
- Purushothaman Natarajan
- grid.412742.60000 0004 0635 5080Genomics Laboratory, Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu India
| | - Ashok Kumar Murugesan
- grid.412742.60000 0004 0635 5080Genomics Laboratory, Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu India
| | - Ganesan Govindan
- grid.412742.60000 0004 0635 5080Genomics Laboratory, Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu India
| | - Ayyaru Gopalakrishnan
- grid.411408.80000 0001 2369 7742Centre of Advanced Study in Marine Biology, Faculty of Marine Sciences, Annamalai University, Parangipettai, Tamil Nadu India
| | - Ravichandiran Kumar
- grid.412742.60000 0004 0635 5080Genomics Laboratory, Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu India
| | - Purushothaman Duraisamy
- grid.412742.60000 0004 0635 5080Genomics Laboratory, Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu India
| | - Raju Balaji
- grid.412742.60000 0004 0635 5080Genomics Laboratory, Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu India
| | - Tanuja
- grid.412742.60000 0004 0635 5080Genomics Laboratory, Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu India
| | - Puhan Sushree Shyamli
- grid.418782.00000 0004 0504 0781Institute of Life Sciences, NALCO Square, Bhubaneswar, India
| | - Ajay K. Parida
- grid.418782.00000 0004 0504 0781Institute of Life Sciences, NALCO Square, Bhubaneswar, India
| | - Madasamy Parani
- grid.412742.60000 0004 0635 5080Genomics Laboratory, Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu India
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14
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Bacterial Diversity and Community Structure in the Rhizosphere of Four Halophytes. Curr Microbiol 2021; 78:2720-2732. [PMID: 34023980 DOI: 10.1007/s00284-021-02536-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 05/05/2021] [Indexed: 10/21/2022]
Abstract
The study of the rhizosphere microbial community in salinized soils aids in the elucidation of new and important microbial functional groups, which is of great importance in vegetation restoration and ecological reconstruction of salinized soil. The rhizosphere soil bacterial diversity and community structures of four halophytes, including Kalidium foliatum, Lycium ruthenicum, Karelinia caspia and Phragmites australis, typically distributed in the saline-alkaline land of Southern Xinjiang, China, were studied using an Illumina paired-end sequence platform. The study aims to reveal the alpha diversity, species composition, abundance and the differences of rhizosphere bacteria among the four halophytes, explore their correlation with environmental factors. The results showed that the highest bacterial species diversity was associated with P. communis, followed by K. foliatum, K. caspia, and L. ruthenicum. The species richness was the lowest for L. ruthenicum, while the others showed no significant difference. Firmicutes, Proteobacteria, Actinobacteria and Bacteroidetes were the most dominant phyla. And Bacillus and Halomonas were the most common dominant genera. The bacterial communities associated with K. foliatum and K. caspia were similar, while that of L. ruthenicum was significantly different from other halophytes. Soil total nitrogen and total phosphorus, soil organic matter, soil water content, electronic conductivity and pH were identified as the key factors affecting bacterial abundance associated with the assayed halophytes. These results indicate that the four halophytes evaluated in the present study have a similar rhizosphere bacterial community structure due to their being in the same region. However, the bacterial abundance is different among the plant species, and soil properties are the important factors driving the structures of bacterial communities.
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Barros NLF, Marques DN, Tadaiesky LBA, de Souza CRB. Halophytes and other molecular strategies for the generation of salt-tolerant crops. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 162:581-591. [PMID: 33773233 DOI: 10.1016/j.plaphy.2021.03.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 03/13/2021] [Indexed: 05/27/2023]
Abstract
The current increase in salinity can intensify the disparity between potential and actual crop yields, thus affecting economies and food security. One of the mitigating alternatives is plant breeding via biotechnology, where advances achieved so far are significant. Considering certain aspects when developing studies related to plant breeding can determine the success and accuracy of experimental design. Besides this strategy, halophytes with intrinsic and efficient abilities against salinity can be used as models for improving the response of crops to salinity stress. As crops are mostly glycophytes, it is crucial to point out the molecular differences between these two groups of plants, which may be the key to guiding and optimizing the transformation of glycophytes with halophytic tolerance genes. Therefore, this can broaden perspectives in the trajectory of research towards the cultivation, commercialization, and consumption of salt-tolerant crops on a large scale.
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Affiliation(s)
| | - Deyvid Novaes Marques
- Departamento de Genética, Universidade de São Paulo, Escola Superior de Agricultura "Luiz de Queiroz", Piracicaba, SP, CEP 13418-900, Brazil
| | - Lorene Bianca Araújo Tadaiesky
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, CEP 66075-110, Brazil; Programa de Pós-Graduação em Agronomia, Universidade Federal Rural da Amazônia, Belém, PA, CEP 66077-530, Brazil
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16
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Ganie SA, Wani SH, Henry R, Hensel G. Improving rice salt tolerance by precision breeding in a new era. CURRENT OPINION IN PLANT BIOLOGY 2021; 60:101996. [PMID: 33444976 DOI: 10.1016/j.pbi.2020.101996] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/16/2020] [Accepted: 12/19/2020] [Indexed: 05/03/2023]
Abstract
Rice is a premier staple food that constitutes the bulk of the daily diet of the majority of people in Asia. Agricultural productivity must be boosted to support this huge demand for rice. However, production is jeopardized by soil salinity. Advances in whole-genome sequencing, marker-assisted breeding strategies, and targeted mutagenesis have substantially improved the toolbox of today's breeders. Given that salinity has a major influence on rice at both the seedling and reproductive stages, understanding and manipulating this trait will have an enormous impact on sustainable production. This article summarizes recent developments in the understanding of the mechanisms of salt tolerance and how state-of-the-art tools such as RNA guided CRISPR endonuclease technology including targeted mutagenesis or base and prime editing can help in gene discovery and functional analysis as well as in transferring favorable alleles into elite breeding material to speed the breeding of salt-tolerant rice cultivars.
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Affiliation(s)
- Showkat Ahmad Ganie
- Department of Biotechnology, Visva-Bharati, Santiniketan 731235, West Bengal, India.
| | - Shabir Hussain Wani
- Mountain Research Centre for Field Crops, Khudwani - 192101, Sher-e-Kashmir University of Agricultural Sciences and Technology, Kashmir, J&K, India
| | - Robert Henry
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Goetz Hensel
- Centre for Plant Genome Engineering, Institute of Plant Biochemistry, Heinrich-Heine-University, Universitätsstraße 1, 40225 Düsseldorf, Germany; Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstraße 3, OT Gatersleben, 06466 Seeland, Germany; Division of Molecular Biology, Centre of Region Haná for Biotechnological and Agriculture Research, Czech Advanced Technology and Research Institute, Palacký University, Olomouc, Czech Republic.
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17
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Xu K, Zhao Y, Zhao S, Liu H, Wang W, Zhang S, Yang X. Genome-Wide Identification and Low Temperature Responsive Pattern of Actin Depolymerizing Factor (ADF) Gene Family in Wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2021; 12:618984. [PMID: 33719289 PMCID: PMC7943747 DOI: 10.3389/fpls.2021.618984] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 02/05/2021] [Indexed: 05/07/2023]
Abstract
The actin depolymerizing factor (ADF) gene family, which is conserved in eukaryotes, is important for plant development, growth, and stress responses. Cold stress restricts wheat growth, development, and distribution. However, genome-wide identification and functional analysis of the ADF family in wheat is limited. Further, because of the promising role of ADF genes in cold response, there is need for an understanding of the function of this family on wheat under cold stress. In this study, 25 ADF genes (TaADFs) were identified in the wheat genome and they are distributed on 15 chromosomes. The TaADF gene structures, duplication events, encoded conversed motifs, and cis-acting elements were investigated. Expression profiles derived from RNA-seq data and real-time quantitative PCR analysis revealed the tissue- and temporal-specific TaADF expression patterns. In addition, the expression levels of TaADF13/16/17/18/20/21/22 were significantly affected by cold acclimation or freezing conditions. Overexpression of TaADF16 increased the freezing tolerance of transgenic Arabidopsis, possibly because of enhanced ROS scavenging and changes to the osmotic regulation in cells. The expression levels of seven cold-responsive genes were up-regulated in the transgenic Arabidopsis plants, regardless of whether the plants were exposed to low temperature. These findings provide fundamental information about the wheat ADF genes and may help to elucidate the regulatory effects of the encoded proteins on plant development and responses to low-temperature stress.
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Affiliation(s)
- Ke Xu
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
| | - Yong Zhao
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
| | - Sihang Zhao
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
| | - Haodong Liu
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
| | - Weiwei Wang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
- Cangzhou Academy of Agriculture and Forestry Sciences, Cangzhou, China
| | - Shuhua Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
| | - Xueju Yang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
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18
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Cao H, Amin R, Niu L, Song Z, Dong B, Li H, Wang L, Meng D, Yang Q, Fu Y. Multidimensional analysis of actin depolymerising factor family in pigeon pea under different environmental stress revealed specific response genes in each subgroup. FUNCTIONAL PLANT BIOLOGY : FPB 2021; 48:180-194. [PMID: 32970987 DOI: 10.1071/fp20190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 08/15/2020] [Indexed: 06/11/2023]
Abstract
Actin depolymerising factor (ADF) is an actin binding protein that is ubiquitous in animal and plant cells. It plays an important role in plant growth and development, as well as resistance to biotic and abiotic stress. The research of plant ADF family has been restricted to Arabidopsis thaliana (L.) Heynh. and some herb crops, but no woody cash crops have been reported to date. All members of the Cajanus cajan (L.) Millsp. ADF (CcADF) family were identified from the pigeon pea genome, and distributed among the four subfamilies by phylogenetic analysis. CcADFs were relatively conservative in gene structure evolution, protein structure and functional expression, and different CcADFs showed specific expression patterns under different treatments. The expression characteristics of several key CcADFs were revealed by analysing the stress response pattern of CcADFs and the time series RNA-seq of aluminium stress. Among them, CcADF9 in the first subgroup specifically responded to aluminium stress in the roots; CcADF3 in the second subgroup intensively responded to fungal infection in the leaves; and CcADF2 in the fourth subgroup positively responded to various stress treatments in different tissues. This study extended the relationship between plant ADF family and aluminium tolerance, as well as adding to the understanding of CcADF family in woody crops.
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Affiliation(s)
- Hongyan Cao
- State Forestry and Grassland Administration Key Laboratory of Forest Resources and Environmental Management, Beijing Forestry University, Beijing 100083, PR China
| | - Rohul Amin
- State Forestry and Grassland Administration Key Laboratory of Forest Resources and Environmental Management, Beijing Forestry University, Beijing 100083, PR China
| | - Lili Niu
- Beijing Advanced Innovation Centre for Tree Breeding by Molecular Design, Beijing 100083, PR China
| | - Zhihua Song
- State Forestry and Grassland Administration Key Laboratory of Forest Resources and Environmental Management, Beijing Forestry University, Beijing 100083, PR China
| | - Biying Dong
- State Forestry and Grassland Administration Key Laboratory of Forest Resources and Environmental Management, Beijing Forestry University, Beijing 100083, PR China
| | - Hanghang Li
- State Forestry and Grassland Administration Key Laboratory of Forest Resources and Environmental Management, Beijing Forestry University, Beijing 100083, PR China
| | - Litao Wang
- State Forestry and Grassland Administration Key Laboratory of Forest Resources and Environmental Management, Beijing Forestry University, Beijing 100083, PR China
| | - Dong Meng
- State Forestry and Grassland Administration Key Laboratory of Forest Resources and Environmental Management, Beijing Forestry University, Beijing 100083, PR China; and Beijing Advanced Innovation Centre for Tree Breeding by Molecular Design, Beijing 100083, PR China
| | - Qing Yang
- State Forestry and Grassland Administration Key Laboratory of Forest Resources and Environmental Management, Beijing Forestry University, Beijing 100083, PR China; and Corresponding authors. ;
| | - Yujie Fu
- State Forestry and Grassland Administration Key Laboratory of Forest Resources and Environmental Management, Beijing Forestry University, Beijing 100083, PR China; and Beijing Advanced Innovation Centre for Tree Breeding by Molecular Design, Beijing 100083, PR China; and Key Laboratory of Forestry Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, China; and Corresponding authors. ;
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Wungrampha S, Joshi R, Rathore RS, Singla-Pareek SL, Pareek A. CO 2 uptake and chlorophyll a fluorescence of Suaeda fruticosa grown under diurnal rhythm and after transfer to continuous dark. PHOTOSYNTHESIS RESEARCH 2019; 142:211-227. [PMID: 31317383 DOI: 10.1007/s11120-019-00659-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 07/04/2019] [Indexed: 05/15/2023]
Abstract
Although only 2-4% of absorbed light is emitted as chlorophyll (Chl) a fluorescence, its measurement provides valuable information on photosynthesis of the plant, particularly of Photosystem II (PSII) and Photosystem I (PSI). In this paper, we have examined photosynthetic parameters of Suaeda fruticosa L. (family: Amaranthaceae), surviving under extreme xerohalophytic conditions, as influenced by diurnal rhythm or continuous dark condition. We report here CO2 gas exchange and the kinetics of Chl a fluorescence of S. fruticosa, made every 3 hours (hrs) for 3 days, using a portable infra-red gas analyzer and a Handy PEA fluorimeter. Our measurements on CO2 gas exchange show the maximum rate of photosynthesis to be at 08:00 hrs under diurnal condition and at 05:00 hrs under continuous dark. From the OJIP phase of Chl a fluorescence transient, we have inferred that the maximum quantum yield of PSII photochemistry must have increased during the night under diurnal rhythm, and between 11:00 and 17:00 hrs under constant dark. Overall, our study has revealed novel insights into how photosynthetic reactions are affected by the photoperiodic cycles in S. fruticosa under high salinity. This study has further revealed a unique strategy operating in this xero-halophyte where the repair mechanism for damaged PSII operates during the dark, which, we suggest, contributes to its ecological adaptation and ability to survive and reproduce under extreme saline, high light, and drought conditions. We expect these investigations to help in identifying key genes and pathways for raising crops for saline and dry areas.
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Affiliation(s)
- Silas Wungrampha
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Rohit Joshi
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Ray S Rathore
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| | - Sneh L Singla-Pareek
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| | - Ashwani Pareek
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India.
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