1
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Lv J, Zhou F, Wei Q, Long X, Tian W, Zhai J, Wang J, Zhang Q, Wan D. An alternative 3' splice site of PeuHKT1;3 improves the response to salt stress through enhancing affinity to K + in Populus. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 212:108776. [PMID: 38843683 DOI: 10.1016/j.plaphy.2024.108776] [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: 01/29/2024] [Revised: 04/30/2024] [Accepted: 05/25/2024] [Indexed: 06/17/2024]
Abstract
Alternative splicing (AS) serves as a crucial post-transcriptional regulator in plants that contributes to the resistance to salt stress. However, the underlying mechanism is largely unknown. In this research, we identified an important AS transcript in Populus euphratica, PeuHKT1:3a, generated by alternative 3' splice site splicing mode that resulted in the removal of 252 bases at the 5' end of the first exon in PeuHKT1:3. Protein sequence comparison showed that the site of AS occurred in PeuHKT1:3 is located at a crucial Ser residue within the first pore-loop domain, which leads to inefficient K+ transport in HKT I-type transporters. Expressing PeuHKT1;3a in an axt3 mutant yeast strain can effectively compensate for the lack of intracellular K+, whereas the expression of PeuHKT1;3 cannot yield the effect. Furthermore, in transgenic Arabidopsis and poplar plants, it was observed that lines expressing PeuHKT1;3a exhibited greater salt tolerance compared to those expressing the PeuHKT1;3 strain. Analysis of ion content and flux demonstrated that the transgenic PeuHKT1;3a line exhibited significantly higher K+ content compared to the PeuHKT1;3 line, while there was no significant difference in Na+ content. In conclusion, our findings revealed that AS can give rise to novel variants of HKT I-type proteins in P. euphratica with modified K+ selectivity to keep a higher K+/Na+ ratio to enhanced salt tolerance.
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Affiliation(s)
- Jiaojiao Lv
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China.
| | - Fangfang Zhou
- College of Life and Health, Zhengzhou Technical College, Zhengzhou 450121, China.
| | - Qianqian Wei
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China.
| | - Xiaoqin Long
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China.
| | - Wenjing Tian
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China.
| | - Jiajia Zhai
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China.
| | - Junjie Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China.
| | - Qi Zhang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China.
| | - Dongshi Wan
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China.
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2
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de Oliveira IP, Schaaf C, de Setta N. Drought Responses in Poaceae: Exploring the Core Components of the ABA Signaling Pathway in Setaria italica and Setaria viridis. PLANTS (BASEL, SWITZERLAND) 2024; 13:1451. [PMID: 38891260 PMCID: PMC11174756 DOI: 10.3390/plants13111451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Revised: 05/14/2024] [Accepted: 05/21/2024] [Indexed: 06/21/2024]
Abstract
Drought severely impacts plant development and reproduction, reducing biomass and seed number, and altering flowering patterns. Drought-tolerant Setaria italica and Setaria viridis species have emerged as prominent model species for investigating water deficit responses in the Poaceae family, the most important source of food and biofuel biomass worldwide. In higher plants, abscisic acid (ABA) regulates environmental stress responses, and its signaling entails interactions between PYR/PYL/RCAR receptors and clade A PP2C phosphatases, which in turn modulate SnRK2 kinases via reversible phosphorylation to activate ABA-responsive genes. To compare the diversity of PYR/PYL/RCAR, PP2C, and SnRK2 between S. italica and S. viridis, and their involvement in water deficit responses, we examined gene and regulatory region structures, investigated orthology relationships, and analyzed their gene expression patterns under water stress via a meta-analysis approach. Results showed that coding and regulatory sequences of PYR/PYL/RCARs, PP2Cs, and SnRK2s are highly conserved between Setaria spp., allowing us to propose pairs of orthologous genes for all the loci identified. Phylogenetic relationships indicate which clades of Setaria spp. sequences are homologous to the functionally well-characterized Arabidopsis thaliana PYR/PYL/RCAR, PP2C, and SnRK2 genes. Gene expression analysis showed a general downregulation of PYL genes, contrasting with upregulation of PP2C genes, and variable expression modulation of SnRK2 genes under drought stress. This complex network implies that ABA core signaling is a diverse and multifaceted process. Through our analysis, we identified promising candidate genes for further functional characterization, with great potential as targets for drought resistance studies, ultimately leading to advances in Poaceae biology and crop-breeding strategies.
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Affiliation(s)
| | | | - Nathalia de Setta
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, São Bernardo do Campo 09606-045, SP, Brazil; (I.P.d.O.); (C.S.)
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3
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Uzilday B, Takahashi K, Kobayashi A, Uzilday RO, Fujii N, Takahashi H, Turkan I. Role of Abscisic Acid, Reactive Oxygen Species, and Ca 2+ Signaling in Hydrotropism-Drought Avoidance-Associated Response of Roots. PLANTS (BASEL, SWITZERLAND) 2024; 13:1220. [PMID: 38732435 PMCID: PMC11085316 DOI: 10.3390/plants13091220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 04/23/2024] [Accepted: 04/24/2024] [Indexed: 05/13/2024]
Abstract
Plant roots exert hydrotropism in response to moisture gradients to avoid drought stress. The regulatory mechanism underlying hydrotropism involves novel regulators such as MIZ1 and GNOM/MIZ2 as well as abscisic acid (ABA), reactive oxygen species (ROS), and Ca2+ signaling. ABA, ROS, and Ca2+ signaling are also involved in plant responses to drought stress. Although the mechanism of moisture gradient perception remains largely unknown, the sensory apparatus has been reported to reside in the root elongation zone rather than in the root cap. In Arabidopsis roots, hydrotropism is mediated by the action of MIZ1 and ABA in the cortex of the elongation zone, the accumulation of ROS at the root curvature, and the variation in the cytosolic Ca2+ concentration in the entire root tip including the root cap and stele of the elongation zone. Moreover, root exposure to moisture gradients has been proposed to cause asymmetric ABA distribution or Ca2+ signaling, leading to the induction of the hydrotropic response. A comprehensive and detailed analysis of hydrotropism regulators and their signaling network in relation to the tissues required for their function is apparently crucial for understanding the mechanisms unique to root hydrotropism. Here, referring to studies on plant responses to drought stress, we summarize the recent findings relating to the role of ABA, ROS, and Ca2+ signaling in hydrotropism, discuss their functional sites and plausible networks, and raise some questions that need to be answered in future studies.
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Affiliation(s)
- Baris Uzilday
- Department of Biology, Faculty of Science, Ege University, Bornova 35100, Izmir, Turkey
| | - Kaori Takahashi
- Graduate School of Life Sciences, Tohoku University, Katahira, Sendai 980-8577, Japan
| | - Akie Kobayashi
- Graduate School of Life Sciences, Tohoku University, Katahira, Sendai 980-8577, Japan
| | - Rengin Ozgur Uzilday
- Department of Biology, Faculty of Science, Ege University, Bornova 35100, Izmir, Turkey
| | - Nobuharu Fujii
- Graduate School of Life Sciences, Tohoku University, Katahira, Sendai 980-8577, Japan
| | - Hideyuki Takahashi
- Graduate School of Life Sciences, Tohoku University, Katahira, Sendai 980-8577, Japan
- Research Center for Space Agriculture and Horticulture, Graduate School of Horticulture, Chiba University, Matsudo, Chiba 271-8510, Japan
| | - Ismail Turkan
- Department of Biology, Faculty of Science, Ege University, Bornova 35100, Izmir, Turkey
- Graduate School of Life Sciences, Tohoku University, Katahira, Sendai 980-8577, Japan
- Faculty of Agricultural Sciences and Technologies, Yasar University, University Street, No. 37-39, Bornova 35100, Izmir, Turkey
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4
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Liu M, Li C, Li Y, An Y, Ruan X, Guo Y, Dong X, Ruan Y. Genome-Wide Identification and Characterization of the VQ Motif-Containing Gene Family Based on Their Evolution and Expression Analysis under Abiotic Stress and Hormone Treatments in Foxtail Millet ( Setaria italica L.). Genes (Basel) 2023; 14:genes14051032. [PMID: 37239391 DOI: 10.3390/genes14051032] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 04/20/2023] [Accepted: 04/25/2023] [Indexed: 05/28/2023] Open
Abstract
Valine-glutamine (VQ) motif-containing proteins are transcriptional regulatory cofactors that play critical roles in plant growth and response to biotic and abiotic stresses. However, information on the VQ gene family in foxtail millet (Setaria italica L.) is currently limited. In this study, a total of 32 SiVQ genes were identified in foxtail millet and classified into seven groups (I-VII), based on the constructed phylogenetic relationships; the protein-conserved motif showed high similarity within each group. Gene structure analysis showed that most SiVQs had no introns. Whole-genome duplication analysis revealed that segmental duplications contributed to the expansion of the SiVQ gene family. The cis-element analysis demonstrated that growth and development, stress response, and hormone-response-related cis-elements were all widely distributed in the promoters of the SiVQs. Gene expression analysis demonstrated that the expression of most SiVQ genes was induced by abiotic stress and phytohormone treatments, and seven SiVQ genes showed significant upregulation under both abiotic stress and phytohormone treatments. A potential interaction network between SiVQs and SiWRKYs was predicted. This research provides a basis to further investigate the molecular function of VQs in plant growth and abiotic stress responses.
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Affiliation(s)
- Meiling Liu
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
| | - Cong Li
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
| | - Yuntong Li
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
| | - Yingtai An
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
| | - Xiaoxi Ruan
- School of Materials Science and Engineering, Northeastern University, Shenyang 110819, China
| | - Yicheng Guo
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
| | - Xiaomei Dong
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
| | - Yanye Ruan
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
- Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang Agricultural University, Shenyang 110866, China
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5
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Amy Lyu MJ, Tang Q, Wang Y, Essemine J, Chen F, Ni X, Chen G, Zhu XG. Evolution of gene regulatory network of C 4 photosynthesis in the genus Flaveria reveals the evolutionary status of C 3-C 4 intermediate species. PLANT COMMUNICATIONS 2023; 4:100426. [PMID: 35986514 PMCID: PMC9860191 DOI: 10.1016/j.xplc.2022.100426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/16/2022] [Accepted: 08/11/2022] [Indexed: 06/15/2023]
Abstract
C4 photosynthesis evolved from ancestral C3 photosynthesis by recruiting pre-existing genes to fulfill new functions. The enzymes and transporters required for the C4 metabolic pathway have been intensively studied and well documented; however, the transcription factors (TFs) that regulate these C4 metabolic genes are not yet well understood. In particular, how the TF regulatory network of C4 metabolic genes was rewired during the evolutionary process is unclear. Here, we constructed gene regulatory networks (GRNs) for four closely evolutionarily related species from the genus Flaveria, which represent four different evolutionary stages of C4 photosynthesis: C3 (F. robusta), type I C3-C4 (F. sonorensis), type II C3-C4 (F. ramosissima), and C4 (F. trinervia). Our results show that more than half of the co-regulatory relationships between TFs and core C4 metabolic genes are species specific. The counterparts of the C4 genes in C3 species were already co-regulated with photosynthesis-related genes, whereas the required TFs for C4 photosynthesis were recruited later. The TFs involved in C4 photosynthesis were widely recruited in the type I C3-C4 species; nevertheless, type II C3-C4 species showed a divergent GRN from C4 species. In line with these findings, a 13CO2 pulse-labeling experiment showed that the CO2 initially fixed into C4 acid was not directly released to the Calvin-Benson-Bassham cycle in the type II C3-C4 species. Therefore, our study uncovered dynamic changes in C4 genes and TF co-regulation during the evolutionary process; furthermore, we showed that the metabolic pathway of the type II C3-C4 species F. ramosissima represents an alternative evolutionary solution to the ammonia imbalance in C3-C4 intermediate species.
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Affiliation(s)
- Ming-Ju Amy Lyu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Qiming Tang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences
| | - Yanjie Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences
| | - Jemaa Essemine
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Faming Chen
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Xiaoxiang Ni
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences
| | - Genyun Chen
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Xin-Guang Zhu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.
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6
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Evolutionary Analysis of StSnRK2 Family Genes and Their Overexpression in Transgenic Tobacco Improve Drought Tolerance. Int J Mol Sci 2023; 24:ijms24021000. [PMID: 36674521 PMCID: PMC9861535 DOI: 10.3390/ijms24021000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 12/31/2022] [Accepted: 01/03/2023] [Indexed: 01/06/2023] Open
Abstract
Sucrose non-ferment 1-related protein kinase 2 (SnRK2) is a highly conserved protein kinase in plants that plays an important role in regulating plant response to drought stress. Although it has been reported in some plants, the evolutionary relationship of potato SnRK2s and their function in drought resistance have not been systematically analyzed. In this study, molecular characteristic analysis showed that 8 StSnRK2s were distributed on six chromosomes, coding proteins were divided into three subgroups, and StSnRK2s clustered in the same subgroup had similar conserved motifs and domains. In addition, StSnRK2 has a wide range of replication events in some species, making it closer to dicots in the process of evolution. In addition, the average nonsynonymous substitution rate/synonymous substitution rate (Ka/Ks) value of SnRK2s in monocots was higher than that of dicots. The codon usage index showed that SnRK2s prefer to use cytosine 3 (C3s), guanine 3 (G3s) and GC content (GC3s) in monocots, whereas thymine 3 (T3s) and adenine 3 (A3s) are preferred in dicots. Furthermore, stress response analysis showed that the expression of StSnRK2s under different degrees of drought stress significantly correlated with one or more stress-related physiological indices, such as proline and malondialdehyde (MDA) content, superoxide dismutase (SOD) and catalase (CAT) activity, ion leakage (IL) etc. The drought resistance of StSnRK2 transgenic plants was determined to occur in the order of StSnRK2.1/2.8 > StSnRK2.2/2.5 > StSnRK2.4/2.6 > StSnRK2.3 > StSnRK2.7, was attributed to not only lower IL but also higher proline, soluble sugar contents and stress-related genes in transgenic plants compared to wild type (WT). In conclusion, this study provides useful insights into the evolution and function of StSnRK2s and lays a foundation for further study on the molecular mechanism of StSnRK2s regulating potato drought resistance.
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7
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Chen J, Zhang J, Liu Q, Wang X, Wen J, Sun Y, Dong S. Mining for genes related to pistil abortion in Prunus sibirica L. PeerJ 2022; 10:e14366. [PMID: 36405023 PMCID: PMC9673769 DOI: 10.7717/peerj.14366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 10/19/2022] [Indexed: 11/16/2022] Open
Abstract
In Prunus sibirica, the phenomenon of pistil abortion is very common and seriously affects its fruit quality and yield; however, the molecular mechanisms of pistil abortion remains unclear. In this study, we identified differentially expressed genes (DEGs) and pathways associated with pistil abortion using transcriptome sequencing. After comparative analysis, a total of 1,950 DEGs were identified, of which 1,000 were upregulated, and 950 were downregulated. Gene Ontology (GO) functional enrichment analysis of DEGs showed that metabolic process, cellular process, single-organism process, membrane, membrane part, cell, binding, catalytic activity, and transporter activity contained the largest number of DEGs. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis showed that the plant-pathogen interaction, starch and sucrose metabolism, and plant hormone signal transduction pathways contained the largest number of DEGs. The NAC, bHLH, and B3 transcription factor families contained the largest number of DEGs. qRT-PCR detection confirmed that the gene expression levels were consistent with the transcriptome sequencing results. This study provides a theoretical basis and scientific basis for further research on the molecular mechanisms of P. sibirica pistil abortion.
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Affiliation(s)
- Jianhua Chen
- College of Forestry, Shenyang Agricultural University, Shenyang, China
| | - Jian Zhang
- College of Forestry, Shenyang Agricultural University, Shenyang, China
| | - Quangang Liu
- College of Forestry, Shenyang Agricultural University, Shenyang, China
| | - Xinxin Wang
- College of Forestry, Shenyang Agricultural University, Shenyang, China
| | - Jiaxing Wen
- College of Forestry, Shenyang Agricultural University, Shenyang, China
| | - Yongqiang Sun
- College of Forestry, Shenyang Agricultural University, Shenyang, China
| | - Shengjun Dong
- College of Forestry, Shenyang Agricultural University, Shenyang, China
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8
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Aggarwal PR, Pramitha L, Choudhary P, Singh RK, Shukla P, Prasad M, Muthamilarasan M. Multi-omics intervention in Setaria to dissect climate-resilient traits: Progress and prospects. FRONTIERS IN PLANT SCIENCE 2022; 13:892736. [PMID: 36119586 PMCID: PMC9470963 DOI: 10.3389/fpls.2022.892736] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 08/05/2022] [Indexed: 06/15/2023]
Abstract
Millets constitute a significant proportion of underutilized grasses and are well known for their climate resilience as well as excellent nutritional profiles. Among millets, foxtail millet (Setaria italica) and its wild relative green foxtail (S. viridis) are collectively regarded as models for studying broad-spectrum traits, including abiotic stress tolerance, C4 photosynthesis, biofuel, and nutritional traits. Since the genome sequence release, the crop has seen an exponential increase in omics studies to dissect agronomic, nutritional, biofuel, and climate-resilience traits. These studies have provided first-hand information on the structure, organization, evolution, and expression of several genes; however, knowledge of the precise roles of such genes and their products remains elusive. Several open-access databases have also been instituted to enable advanced scientific research on these important crops. In this context, the current review enumerates the contemporary trend of research on understanding the climate resilience and other essential traits in Setaria, the knowledge gap, and how the information could be translated for the crop improvement of related millets, biofuel crops, and cereals. Also, the review provides a roadmap for studying other underutilized crop species using Setaria as a model.
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Affiliation(s)
- Pooja Rani Aggarwal
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Lydia Pramitha
- School of Agriculture and Biosciences, Karunya Institute of Technology and Sciences, Coimbatore, Tamil Nadu, India
| | - Pooja Choudhary
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | | | - Pooja Shukla
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Manoj Prasad
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
- National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Mehanathan Muthamilarasan
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
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9
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Suguiyama VF, Rodriguez JDP, Dos Santos TCN, Lira BS, de Haro LA, Silva JPN, Borba EL, Purgatto E, da Silva EA, Bellora N, Carrari F, Centeno DDC, Bermúdez LF, Rossi M, de Setta N. Regulatory mechanisms behind the phenotypic plasticity associated with Setaria italica water deficit tolerance. PLANT MOLECULAR BIOLOGY 2022; 109:761-780. [PMID: 35524936 DOI: 10.1007/s11103-022-01273-w] [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: 12/20/2021] [Accepted: 04/11/2022] [Indexed: 06/14/2023]
Abstract
Drought is one of the main environmental stresses that negatively impacts vegetative and reproductive yield. Water deficit responses are determined by the duration and intensity of the stress, which, together with plant genotype, will define the chances of plant survival. The metabolic adjustments in response to water deficit are complex and involve gene expression modulation regulated by DNA-binding proteins and epigenetic modifications. This last mechanism may also regulate the activity of transposable elements, which in turn impact the expression of nearby loci. Setaria italica plants submitted to five water deficit regimes were analyzed through a phenotypical approach, including growth, physiological, RNA-seq and sRNA-seq analyses. The results showed a progressive reduction in yield as a function of water deficit intensity associated with signaling pathway modulation and metabolic adjustments. We identified a group of loci that were consistently associated with drought responses, some of which were related to water deficit perception, signaling and regulation. Finally, an analysis of the transcriptome and sRNAome allowed us to identify genes putatively regulated by TE- and sRNA-related mechanisms and an intriguing positive correlation between transcript levels and sRNA accumulation in gene body regions. These findings shed light on the processes that allow S. italica to overcome drought and survive under water restrictive conditions.
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Affiliation(s)
- Vanessa Fuentes Suguiyama
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, São Bernardo do Campo, SP, Brazil
| | | | | | - Bruno Silvestre Lira
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Luis Alejandro de Haro
- Departament of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - João Paulo Naldi Silva
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, São Bernardo do Campo, SP, Brazil
| | - Eduardo Leite Borba
- Departamento de Botânica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Eduardo Purgatto
- Departamento de Alimentos e Nutrição Experimental, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Emerson Alves da Silva
- Instituto de Botânica da Secretaria do Meio Ambiente do Estado de São Paulo, São Paulo, SP, Brazil
| | - Nicolas Bellora
- Institute of Nuclear Technologies for Health (Intecnus), National Scientific and Technical Research Council (CONICET), 8400, Bariloche, Argentina
| | - Fernando Carrari
- Instituto de Agrobiotecnología Y Biología Molecular (IABIMO), CICVYA, INTA-CONICET, Hurlingham, Argentina
- Cátedra de Genética, Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Danilo da Cruz Centeno
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, São Bernardo do Campo, SP, Brazil
| | - Luisa Fernanda Bermúdez
- Instituto de Agrobiotecnología Y Biología Molecular (IABIMO), CICVYA, INTA-CONICET, Hurlingham, Argentina
- Cátedra de Genética, Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Magdalena Rossi
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Nathalia de Setta
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, São Bernardo do Campo, SP, Brazil.
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10
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Jin R, Yu T, Guo P, Liu M, Pan J, Zhao P, Zhang Q, Zhu X, Wang J, Zhang A, Cao Q, Tang Z. Comparative Transcriptome and Interaction Protein Analysis Reveals the Mechanism of IbMPK3-Overexpressing Transgenic Sweet Potato Response to Low-Temperature Stress. Genes (Basel) 2022; 13:genes13071247. [PMID: 35886030 PMCID: PMC9317282 DOI: 10.3390/genes13071247] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 06/20/2022] [Accepted: 07/06/2022] [Indexed: 02/04/2023] Open
Abstract
The sweet potato is very sensitive to low temperature. Our previous study revealed that IbMPK3-overexpressing transgenic sweet potato (M3) plants showed stronger low-temperature stress tolerance than wild-type plants (WT). However, the mechanism of M3 plants in response to low-temperature stress is unclear. To further analyze how IbMPK3 mediates low-temperature stress in sweet potato, WT and M3 plants were exposed to low-temperature stress for 2 h and 12 h for RNA-seq analysis, whereas normal conditions were used as a control (CK). In total, 3436 and 8718 differentially expressed genes (DEGs) were identified in WT at 2 h (vs. CK) and 12 h (vs. CK) under low-temperature stress, respectively, whereas 1450 and 9291 DEGs were detected in M3 plants, respectively. Many common and unique DEGs were analyzed in WT and M3 plants. DEGs related to low temperature were involved in Ca2+ signaling, MAPK cascades, the reactive oxygen species (ROS) signaling pathway, hormone transduction pathway, encoding transcription factor families (bHLH, NAC, and WRKY), and downstream stress-related genes. Additionally, more upregulated genes were associated with the MAPK pathway in M3 plants during short-term low-temperature stress (CK vs. 2 h), and more upregulated genes were involved in secondary metabolic synthesis in M3 plants than in the WT during the long-time low-temperature stress treatment (CK vs. 12 h), such as fatty acid biosynthesis and elongation, glutathione metabolism, flavonoid biosynthesis, carotenoid biosynthesis, and zeatin biosynthesis. Moreover, the interaction proteins of IbMPK3 related to photosynthesis, or encoding CaM, NAC, and ribosomal proteins, were identified using yeast two-hybrid (Y2H). This study may provide a valuable resource for elucidating the sweet potato low-temperature stress resistance mechanism, as well as data to support molecular-assisted breeding with the IbMPK3 gene.
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Affiliation(s)
- Rong Jin
- Xuzhou Sweet Potato Research Center, Xuzhou Institute of Agricultural Sciences Jiangsu, China/Key Laboratory of Sweet Potato Biology and Genetic Breeding, Ministry of Agriculture/National Agricultural Experimental Station for Soil Quality, Xuzhou 221000, China; (R.J.); (P.G.); (M.L.); (P.Z.); (Q.Z.); (X.Z.); (J.W.); (A.Z.); (Q.C.)
| | - Tao Yu
- Tube Division, Crop Research Institute, Liaoning Academy of Agricultural Sciences, Shenyang 110000, China; (T.Y.); (J.P.)
| | - Pengyu Guo
- Xuzhou Sweet Potato Research Center, Xuzhou Institute of Agricultural Sciences Jiangsu, China/Key Laboratory of Sweet Potato Biology and Genetic Breeding, Ministry of Agriculture/National Agricultural Experimental Station for Soil Quality, Xuzhou 221000, China; (R.J.); (P.G.); (M.L.); (P.Z.); (Q.Z.); (X.Z.); (J.W.); (A.Z.); (Q.C.)
| | - Ming Liu
- Xuzhou Sweet Potato Research Center, Xuzhou Institute of Agricultural Sciences Jiangsu, China/Key Laboratory of Sweet Potato Biology and Genetic Breeding, Ministry of Agriculture/National Agricultural Experimental Station for Soil Quality, Xuzhou 221000, China; (R.J.); (P.G.); (M.L.); (P.Z.); (Q.Z.); (X.Z.); (J.W.); (A.Z.); (Q.C.)
| | - Jiaquan Pan
- Tube Division, Crop Research Institute, Liaoning Academy of Agricultural Sciences, Shenyang 110000, China; (T.Y.); (J.P.)
| | - Peng Zhao
- Xuzhou Sweet Potato Research Center, Xuzhou Institute of Agricultural Sciences Jiangsu, China/Key Laboratory of Sweet Potato Biology and Genetic Breeding, Ministry of Agriculture/National Agricultural Experimental Station for Soil Quality, Xuzhou 221000, China; (R.J.); (P.G.); (M.L.); (P.Z.); (Q.Z.); (X.Z.); (J.W.); (A.Z.); (Q.C.)
| | - Qiangqiang Zhang
- Xuzhou Sweet Potato Research Center, Xuzhou Institute of Agricultural Sciences Jiangsu, China/Key Laboratory of Sweet Potato Biology and Genetic Breeding, Ministry of Agriculture/National Agricultural Experimental Station for Soil Quality, Xuzhou 221000, China; (R.J.); (P.G.); (M.L.); (P.Z.); (Q.Z.); (X.Z.); (J.W.); (A.Z.); (Q.C.)
| | - Xiaoya Zhu
- Xuzhou Sweet Potato Research Center, Xuzhou Institute of Agricultural Sciences Jiangsu, China/Key Laboratory of Sweet Potato Biology and Genetic Breeding, Ministry of Agriculture/National Agricultural Experimental Station for Soil Quality, Xuzhou 221000, China; (R.J.); (P.G.); (M.L.); (P.Z.); (Q.Z.); (X.Z.); (J.W.); (A.Z.); (Q.C.)
| | - Jing Wang
- Xuzhou Sweet Potato Research Center, Xuzhou Institute of Agricultural Sciences Jiangsu, China/Key Laboratory of Sweet Potato Biology and Genetic Breeding, Ministry of Agriculture/National Agricultural Experimental Station for Soil Quality, Xuzhou 221000, China; (R.J.); (P.G.); (M.L.); (P.Z.); (Q.Z.); (X.Z.); (J.W.); (A.Z.); (Q.C.)
| | - Aijun Zhang
- Xuzhou Sweet Potato Research Center, Xuzhou Institute of Agricultural Sciences Jiangsu, China/Key Laboratory of Sweet Potato Biology and Genetic Breeding, Ministry of Agriculture/National Agricultural Experimental Station for Soil Quality, Xuzhou 221000, China; (R.J.); (P.G.); (M.L.); (P.Z.); (Q.Z.); (X.Z.); (J.W.); (A.Z.); (Q.C.)
| | - Qinghe Cao
- Xuzhou Sweet Potato Research Center, Xuzhou Institute of Agricultural Sciences Jiangsu, China/Key Laboratory of Sweet Potato Biology and Genetic Breeding, Ministry of Agriculture/National Agricultural Experimental Station for Soil Quality, Xuzhou 221000, China; (R.J.); (P.G.); (M.L.); (P.Z.); (Q.Z.); (X.Z.); (J.W.); (A.Z.); (Q.C.)
| | - Zhonghou Tang
- Xuzhou Sweet Potato Research Center, Xuzhou Institute of Agricultural Sciences Jiangsu, China/Key Laboratory of Sweet Potato Biology and Genetic Breeding, Ministry of Agriculture/National Agricultural Experimental Station for Soil Quality, Xuzhou 221000, China; (R.J.); (P.G.); (M.L.); (P.Z.); (Q.Z.); (X.Z.); (J.W.); (A.Z.); (Q.C.)
- Correspondence: ; Tel.: +86-0516-82189235
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11
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Travassos-Lins J, de Oliveira Rocha CC, de Souza Rodrigues T, Alves-Ferreira M. Evaluation of the molecular and physiological response to dehydration of two accessions of the model plant Setaria viridis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 169:211-223. [PMID: 34808464 DOI: 10.1016/j.plaphy.2021.11.015] [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: 10/13/2021] [Accepted: 11/11/2021] [Indexed: 06/13/2023]
Abstract
Water deficits are responsible for countless agricultural losses. Among the affected crops, C4 plants are of special interest due to their high water and nitrogen use efficiency. Two accessions of Setaria viridis (Ast-1 and A10.1) with contrasting responses to water deficit were used in the current work to better understand the mechanisms behind drought tolerance in C4 species. Our results showed that although the A10.1 accession exhibited a reduced size and lower Rfd values in comparison to Ast-1, it had overall higher Fv/Fm and lower NPQ values in well-watered conditions. The water deficit induction was performed with PEG-8000 at the grain-filling stage using dehydration cycles. Analysis of physiological measurements showed the A10.1 accession as being more tolerant to multiple water deficit exposures. In addition, PCA identified a clear difference in the pattern of drought response of the accessions. Four drought marker genes previously described in the literature were chosen to evaluate the response at the molecular level: SvP5CS2, SvDHN1, SvNAC6, and SvWRKY1. Besides confirming that Ast-1 is a more sensitive accession, the expression analysis revealed that SvNAC1 might better monitor drought stress, while SvWRKY1 was able to differentiate the two accessions. Distinct evolutionary histories of each accession may be behind their differences in response to water deficits.
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Affiliation(s)
- João Travassos-Lins
- Laboratory of Plant Molecular Genetics and Biotechnology, Federal University of Rio de Janeiro, Biology Institute, Dept. of Genetics, Av. Carlos Chagas Filho, 373 - Ilha do Fundão, 21941-902, Rio de Janeiro, RJ, Brazil
| | - Caio César de Oliveira Rocha
- Laboratory of Plant Molecular Genetics and Biotechnology, Federal University of Rio de Janeiro, Biology Institute, Dept. of Genetics, Av. Carlos Chagas Filho, 373 - Ilha do Fundão, 21941-902, Rio de Janeiro, RJ, Brazil
| | - Tamires de Souza Rodrigues
- Laboratory of Plant Molecular Genetics and Biotechnology, Federal University of Rio de Janeiro, Biology Institute, Dept. of Genetics, Av. Carlos Chagas Filho, 373 - Ilha do Fundão, 21941-902, Rio de Janeiro, RJ, Brazil
| | - Marcio Alves-Ferreira
- Laboratory of Plant Molecular Genetics and Biotechnology, Federal University of Rio de Janeiro, Biology Institute, Dept. of Genetics, Av. Carlos Chagas Filho, 373 - Ilha do Fundão, 21941-902, Rio de Janeiro, RJ, Brazil.
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12
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Ruiz-Partida R, Rosario SM, Lozano-Juste J. An Update on Crop ABA Receptors. PLANTS 2021; 10:plants10061087. [PMID: 34071543 PMCID: PMC8229007 DOI: 10.3390/plants10061087] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 05/06/2021] [Accepted: 05/13/2021] [Indexed: 11/19/2022]
Abstract
The hormone abscisic acid (ABA) orchestrates the plant stress response and regulates sophisticated metabolic and physiological mechanisms essential for survival in a changing environment. Plant ABA receptors were described more than 10 years ago, and a considerable amount of information is available for the model plant Arabidopsis thaliana. Unfortunately, this knowledge is still very limited in crops that hold the key to feeding a growing population. In this review, we summarize genomic, genetic and structural data obtained in crop ABA receptors. We also provide an update on ABA perception in major food crops, highlighting specific and common features of crop ABA receptors.
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Affiliation(s)
- Rafael Ruiz-Partida
- Consejo Superior de Investigaciones Científicas (CSIC), Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universitat Politècnica de València (UPV), Calle Ingeniero Fausto Elio s/n, Edificio 8E, 46022 Valencia, Spain; (R.R.-P.); (S.M.R.)
| | - Sttefany M. Rosario
- Consejo Superior de Investigaciones Científicas (CSIC), Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universitat Politècnica de València (UPV), Calle Ingeniero Fausto Elio s/n, Edificio 8E, 46022 Valencia, Spain; (R.R.-P.); (S.M.R.)
- Laboratorio de Biología Molecular, Facultad de Ciencias Agronómicas y Veterinarias, Universidad Autónoma de Santo Domingo (UASD), Camino de Engombe, Santo Domingo 10904, Dominican Republic
| | - Jorge Lozano-Juste
- Consejo Superior de Investigaciones Científicas (CSIC), Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universitat Politècnica de València (UPV), Calle Ingeniero Fausto Elio s/n, Edificio 8E, 46022 Valencia, Spain; (R.R.-P.); (S.M.R.)
- Correspondence:
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13
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Francesconi S, Harfouche A, Maesano M, Balestra GM. UAV-Based Thermal, RGB Imaging and Gene Expression Analysis Allowed Detection of Fusarium Head Blight and Gave New Insights Into the Physiological Responses to the Disease in Durum Wheat. FRONTIERS IN PLANT SCIENCE 2021; 12:628575. [PMID: 33868331 PMCID: PMC8047627 DOI: 10.3389/fpls.2021.628575] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 03/12/2021] [Indexed: 05/24/2023]
Abstract
Wheat is one of the world's most economically important cereal crop, grown on 220 million hectares. Fusarium head blight (FHB) disease is considered a major threat to durum (Triticum turgidum subsp. durum (Desfontaines) Husnache) and bread wheat (T. aestivum L.) cultivars and is mainly managed by the application of fungicides at anthesis. However, fungicides are applied when FHB symptoms are clearly visible and the spikes are almost entirely bleached (% of diseased spikelets > 80%), by when it is too late to control FHB disease. For this reason, farmers often react by performing repeated fungicide treatments that, however, due to the advanced state of the infection, cause a waste of money and pose significant risks to the environment and non-target organisms. In the present study, we used unmanned aerial vehicle (UAV)-based thermal infrared (TIR) and red-green-blue (RGB) imaging for FHB detection in T. turgidum (cv. Marco Aurelio) under natural field conditions. TIR and RGB data coupled with ground-based measurements such as spike's temperature, photosynthetic efficiency and molecular identification of FHB pathogens, detected FHB at anthesis half-way (Zadoks stage 65, ZS 65), when the percentage (%) of diseased spikelets ranged between 20% and 60%. Moreover, in greenhouse experiments the transcripts of the key genes involved in stomatal closure were mostly up-regulated in F. graminearum-inoculated plants, demonstrating that the physiological mechanism behind the spike's temperature increase and photosynthetic efficiency decrease could be attributed to the closure of the guard cells in response to F. graminearum. In addition, preliminary analysis revealed that there is differential regulation of genes between drought-stressed and F. graminearum-inoculated plants, suggesting that there might be a possibility to discriminate between water stress and FHB infection. This study shows the potential of UAV-based TIR and RGB imaging for field phenotyping of wheat and other cereal crop species in response to environmental stresses. This is anticipated to have enormous promise for the detection of FHB disease and tremendous implications for optimizing the application of fungicides, since global food crop demand is to be met with minimal environmental impacts.
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Affiliation(s)
- Sara Francesconi
- Department of Agriculture and Forest Sciences (DAFNE), University of Tuscia, Viterbo, Italy
| | - Antoine Harfouche
- Department for Innovation in Biological, Agro-Food and Forest Systems (DIBAF), University of Tuscia, Viterbo, Italy
| | - Mauro Maesano
- Department for Innovation in Biological, Agro-Food and Forest Systems (DIBAF), University of Tuscia, Viterbo, Italy
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14
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Mendes Bezerra AC, da Cunha Valença D, da Gama Junqueira NE, Moll Hüther C, Borella J, Ferreira de Pinho C, Alves Ferreira M, Oliveira Medici L, Ortiz-Silva B, Reinert F. Potassium supply promotes the mitigation of NaCl-induced effects on leaf photochemistry, metabolism and morphology of Setaria viridis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 160:193-210. [PMID: 33513466 DOI: 10.1016/j.plaphy.2021.01.021] [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: 12/20/2020] [Accepted: 01/15/2021] [Indexed: 06/12/2023]
Abstract
Soil salinity has the potential to severely affect crop performance. To maintain cell functioning and improve salt tolerance, the maintenance of K+ homeostasis is crucial in several plant metabolism processes. Besides, potassium fertilization can efficiently alleviate the perilous effects of salinity. We characterized impacts in Setaria viridis exposed to NaCl and KCl to underlying photochemistry mechanisms, K+ and Na+ shoot contents, enzymatic activity, electrolytic leakage, and morphological responses focusing on non-stomatal limitation of photosynthesis. Plants were exposed to sodium chloride (NaCl; 0, 150 and 250 mM) and potassium chloride (KCl; 0, 5, 9 mM). The exposure to NaCl affected S. viridis leaves morphological and physiologically. Plants submitted to 150 mM showed reductions in performance indexes (PIabs and PItotal; JIP-test), and the presence of positive K- and L-bands. Plants exposed to 250 mM exhibited blockage in electron flow further than QA within 48h and permanent photoinhibition at 96 h. The presence of 9 and 5 mM of KCl counteracted the effects of NaCl on plants submitted to 150 mM, concomitant with increases in K+ accumulation and cell turgidity conservation, causing positive effects in plant growth and metabolism. Neither KCl concentrations were effective in reducing NaCl-induced effects on plants exposed to 250 mM of NaCl. Our results support the conclusion that greater availability of K+ alleviates the harmful effects of salinity in S. viridis under moderate stress and that application of KCl as means of lightning saline stress has a concentration and a salt level limit that must be experimentally determined.
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Affiliation(s)
- Ana Carolina Mendes Bezerra
- Universidade Federal Do Rio de Janeiro/IB -Dept. of Botany, Av. Carlos Chagas Filho, 373 - Ilha Do Fundão -21941-902, Rio de Janeiro, RJ, Brazil.
| | - David da Cunha Valença
- Universidade Federal Do Rio de Janeiro/IB -Dept. of Botany, Av. Carlos Chagas Filho, 373 - Ilha Do Fundão -21941-902, Rio de Janeiro, RJ, Brazil.
| | - Nicia Eloísa da Gama Junqueira
- Universidade Federal Do Rio de Janeiro/IB -Dept. of Botany, Av. Carlos Chagas Filho, 373 - Ilha Do Fundão -21941-902, Rio de Janeiro, RJ, Brazil.
| | - Cristina Moll Hüther
- Universidade Federal Fluminense - Dept. of Agricultural and Environmental Engineering, R. Passo da Pátria 156, São Domingos - 24210-240 - Niterói, RJ, Brazil.
| | - Junior Borella
- Universidade Federal Do Rio Grande - Institute of Biological Sciences, Av. Itália, Km 8, Bairro Carreiros - 96203-900 - Rio Grande, RS, Brazil.
| | - Camila Ferreira de Pinho
- Universidade Federal Rural Do Rio de Janeiro - Dept. of Plant Sciences, Rod. BR 465, Km 7 - 23897-000, Seropédica, RJ, Brazil.
| | - Marcio Alves Ferreira
- Universidade Federal Do Rio de Janeiro/IB - Dept. of Genetics, Av. Carlos Chagas Filho, 373 - Ilha Do Fundão - 21941-902, Rio de Janeiro, RJ, Brazil.
| | - Leonardo Oliveira Medici
- Universidade Federal Rural Do Rio de Janeiro - Dept. of Physiological Sciences, Rod. BR 465, Km 7 - 23897-000, Seropédica, RJ, Brazil.
| | - Bianca Ortiz-Silva
- Universidade Federal Do Rio de Janeiro- NUMPEX-Bio, Estrada de Xerém, 27- Duque de Caxias - 25245-390, Rio de Janeiro, RJ, Brazil.
| | - Fernanda Reinert
- Universidade Federal Do Rio de Janeiro/IB -Dept. of Botany, Av. Carlos Chagas Filho, 373 - Ilha Do Fundão -21941-902, Rio de Janeiro, RJ, Brazil.
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15
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Wang X, Liu H, Siddique KHM, Yan G. Transcriptomic profiling of wheat near-isogenic lines reveals candidate genes on chromosome 3A for pre-harvest sprouting resistance. BMC PLANT BIOLOGY 2021; 21:53. [PMID: 33478384 PMCID: PMC7818928 DOI: 10.1186/s12870-021-02824-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 01/05/2021] [Indexed: 05/24/2023]
Abstract
BACKGROUND Pre-harvest sprouting (PHS) in wheat can cause severe damage to both grain yield and quality. Resistance to PHS is a quantitative trait controlled by many genes located across all 21 wheat chromosomes. The study targeted a large-effect quantitative trait locus (QTL) QPhs.ccsu-3A.1 for PHS resistance using several sets previously developed near-isogenic lines (NILs). Two pairs of NILs with highly significant phenotypic differences between the isolines were examined by RNA sequencing for their transcriptomic profiles on developing seeds at 15, 25 and 35 days after pollination (DAP) to identify candidate genes underlying the QTL and elucidate gene effects on PHS resistance. At each DAP, differentially expressed genes (DEGs) between the isolines were investigated. RESULTS Gene ontology and KEGG pathway enrichment analyses of key DEGs suggested that six candidate genes underlie QPhs.ccsu-3A.1 responsible for PHS resistance in wheat. Candidate gene expression was further validated by quantitative RT-PCR. Within the targeted QTL interval, 16 genetic variants including five single nucleotide polymorphisms (SNPs) and 11 indels showed consistent polymorphism between resistant and susceptible isolines. CONCLUSIONS The targeted QTL is confirmed to harbor core genes related to hormone signaling pathways that can be exploited as a key genomic region for marker-assisted selection. The candidate genes and SNP/indel markers detected in this study are valuable resources for understanding the mechanism of PHS resistance and for marker-assisted breeding of the trait in wheat.
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Affiliation(s)
- Xingyi Wang
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, 6009, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
| | - Hui Liu
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, 6009, Australia.
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia.
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
| | - Guijun Yan
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, 6009, Australia.
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia.
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16
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Ohanenye IC, Tsopmo A, Ejike CE, Udenigwe CC. Germination as a bioprocess for enhancing the quality and nutritional prospects of legume proteins. Trends Food Sci Technol 2020. [DOI: 10.1016/j.tifs.2020.05.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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17
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Matilla AJ. Auxin: Hormonal Signal Required for Seed Development and Dormancy. PLANTS (BASEL, SWITZERLAND) 2020; 9:E705. [PMID: 32492815 PMCID: PMC7356396 DOI: 10.3390/plants9060705] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 05/27/2020] [Accepted: 05/27/2020] [Indexed: 12/11/2022]
Abstract
The production of viable seeds is a key event in the life cycle of higher plants. Historically, abscisic acid (ABA) and gibberellin (GAs) were considered the main hormones that regulate seed formation. However, auxin has recently emerged as an essential player that modulates, in conjunction with ABA, different cellular processes involved in seed development as well as the induction, regulation and maintenance of primary dormancy (PD). This review examines and discusses the key role of auxin as a signaling molecule that coordinates seed life. The cellular machinery involved in the synthesis and transport of auxin, as well as their cellular and tissue compartmentalization, is crucial for the development of the endosperm and seed-coat. Thus, auxin is an essential compound involved in integuments development, and its transport from endosperm is regulated by AGAMOUS-LIKE62 (AGL62) whose transcript is specifically expressed in the endosperm. In addition, recent biochemical and genetic evidence supports the involvement of auxins in PD. In this process, the participation of the transcriptional regulator ABA INSENSITIVE3 (ABI3) is critical, revealing a cross-talk between auxin and ABA signaling. Future experimental aimed at advancing knowledge of the role of auxins in seed development and PD are also discussed.
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Affiliation(s)
- Angel J Matilla
- Departamento de Biología Funcional (Área Fisiología Vegetal), Facultad de Farmacia, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
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18
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Simões MS, Carvalho GG, Ferreira SS, Hernandes-Lopes J, de Setta N, Cesarino I. Genome-wide characterization of the laccase gene family in Setaria viridis reveals members potentially involved in lignification. PLANTA 2020; 251:46. [PMID: 31915928 DOI: 10.1007/s00425-020-03337-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Accepted: 01/02/2020] [Indexed: 05/23/2023]
Abstract
Five laccase genes are potentially involved in developmental lignification in the model C4 grass Setaria viridis and their different tissue specificities suggest subfunctionalization events. Plant laccases are copper-containing glycoproteins involved in monolignol oxidation and, therefore, their activity is essential for lignin polymerization. Although these enzymes belong to large multigene families with highly redundant members, not all of them are thought to be involved in lignin metabolism. Here, we report on the genome-wide characterization of the laccase gene family in the model C4 grass Setaria viridis and further identification of the members potentially involved in monolignol oxidation. A total of 52 genes encoding laccases (SvLAC1 to SvLAC52) were found in the genome of S. viridis, and phylogenetic analyses showed that these genes were heterogeneously distributed among the characteristic six subclades of the family and are under relaxed selective constraints. The observed expansion in the total number of genes in this species was mainly caused by tandem duplications within subclade V, which accounts for 68% of the whole family. Comparative phylogenetic analyses showed that the expansion of subclade V is specifically observed for the Paniceae tribe within the Panicoideae subfamily in grasses. Five SvLAC genes (SvLAC9, SvLAC13, SvLAC15, SvLAC50, and SvLAC52) fulfilled the criteria established to identify lignin-related candidates: (1) phylogenetic proximity to previously characterized lignin-related laccases from other species, (2) similar expression pattern to that observed for lignin biosynthetic genes in the S. viridis elongating internode, and (3) high expression in S. viridis tissues undergoing active lignification. In addition, in situ hybridization experiments not only confirmed that these selected SvLAC genes were expressed in lignifying cells, but also that their expression showed different tissue specificities, suggesting subfunctionalization events within the family. These five laccase genes are strong candidates to be involved in lignin polymerization in S. viridis and might be good targets for lignin bioengineering strategies.
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Affiliation(s)
- Marcella Siqueira Simões
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua Do Matão, 277, São Paulo, 05508-090, Brazil
| | - Gabriel Garon Carvalho
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua Do Matão, 277, São Paulo, 05508-090, Brazil
| | - Sávio Siqueira Ferreira
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua Do Matão, 277, São Paulo, 05508-090, Brazil
| | - José Hernandes-Lopes
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua Do Matão, 277, São Paulo, 05508-090, Brazil
| | - Nathalia de Setta
- Centro de Ciências Naturais E Humanas, Universidade Federal Do ABC, São Bernardo do Campo, São Paulo, 09606-070, Brazil
| | - Igor Cesarino
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua Do Matão, 277, São Paulo, 05508-090, Brazil.
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19
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Transcriptome analysis of Actinidia chinensis in response to Botryosphaeria dothidea infection. PLoS One 2020; 15:e0227303. [PMID: 31914162 PMCID: PMC6948751 DOI: 10.1371/journal.pone.0227303] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 12/16/2019] [Indexed: 11/26/2022] Open
Abstract
Ripe rot caused by Botryosphaeria dothidea causes extensive production losses in kiwifruit (Actinidia chinensis Planch.). Our previous study showed that kiwifruit variety “Jinyan” is resistant to B. dothidea while “Hongyang” is susceptible. For a comparative analysis of the response of these varieties to B. dothidea infection, we performed a transcriptome analysis by RNA sequencing. A total of 305.24 Gb of clean bases were generated from 36 libraries of which 175.76 Gb was from the resistant variety and 129.48 Gb from the susceptible variety. From the libraries generated, we identified 44,656 genes including 39,041 reference genes, 5,615 novel transcripts, and 13,898 differentially expressed genes (DEGs). Among these, 2,373 potentially defense-related genes linked to calcium signaling, mitogen-activated protein kinase (MAPK), cell wall modification, phytoalexin synthesis, transcription factors, pattern-recognition receptors, and pathogenesis-related proteins may regulate kiwifruit resistance to B. dothidea. DEGs involved in calcium signaling, MAPK, and cell wall modification in the resistant variety were induced at an earlier stage and at higher levels compared with the susceptible variety. Thirty DEGs involved in plant defense response were strongly induced in the resistant variety at all three time points. This study allowed the first comprehensive understanding of kiwifruit transcriptome in response to B. dothidea and may help identify key genes required for ripe rot resistance in kiwifruit.
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Chhetri HB, Furches A, Macaya-Sanz D, Walker AR, Kainer D, Jones P, Harman-Ware AE, Tschaplinski TJ, Jacobson D, Tuskan GA, DiFazio SP. Genome-Wide Association Study of Wood Anatomical and Morphological Traits in Populus trichocarpa. FRONTIERS IN PLANT SCIENCE 2020; 11:545748. [PMID: 33013968 PMCID: PMC7509168 DOI: 10.3389/fpls.2020.545748] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 08/21/2020] [Indexed: 05/04/2023]
Abstract
To understand the genetic mechanisms underlying wood anatomical and morphological traits in Populus trichocarpa, we used 869 unrelated genotypes from a common garden in Clatskanie, Oregon that were previously collected from across the distribution range in western North America. Using GEMMA mixed model analysis, we tested for the association of 25 phenotypic traits and nine multitrait combinations with 6.741 million SNPs covering the entire genome. Broad-sense trait heritabilities ranged from 0.117 to 0.477. Most traits were significantly correlated with geoclimatic variables suggesting a role of climate and geography in shaping the variation of this species. Fifty-seven SNPs from single trait GWAS and 11 SNPs from multitrait GWAS passed an FDR threshold of 0.05, leading to the identification of eight and seven nearby candidate genes, respectively. The percentage of phenotypic variance explained (PVE) by the significant SNPs for both single and multitrait GWAS ranged from 0.01% to 6.18%. To further evaluate the potential roles of candidate genes, we used a multi-omic network containing five additional data sets, including leaf and wood metabolite GWAS layers and coexpression and comethylation networks. We also performed a functional enrichment analysis on coexpression nearest neighbors for each gene model identified by the wood anatomical and morphological trait GWAS analyses. Genes affecting cell wall composition and transport related genes were enriched in wood anatomy and stomatal density trait networks. Signaling and metabolism related genes were also common in networks for stomatal density. For leaf morphology traits (leaf dry and wet weight) the networks were significantly enriched for GO terms related to photosynthetic processes as well as cellular homeostasis. The identified genes provide further insights into the genetic control of these traits, which are important determinants of the suitability and sustainability of improved genotypes for lignocellulosic biofuel production.
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Affiliation(s)
- Hari B. Chhetri
- Department of Biology, West Virginia University, Morgantown, WV, United States
| | - Anna Furches
- Biosciences Division, and The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN, United States
| | - David Macaya-Sanz
- Department of Biology, West Virginia University, Morgantown, WV, United States
| | - Alejandro R. Walker
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, United States
| | - David Kainer
- Biosciences Division, and The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Piet Jones
- Biosciences Division, and The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN, United States
| | - Anne E. Harman-Ware
- Biosciences Center, and National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Timothy J. Tschaplinski
- Biosciences Division, and The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Daniel Jacobson
- Biosciences Division, and The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN, United States
| | - Gerald A. Tuskan
- Biosciences Division, and The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Stephen P. DiFazio
- Department of Biology, West Virginia University, Morgantown, WV, United States
- *Correspondence: Stephen P. DiFazio,
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