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Islam MS, Ghimire A, Lay L, Khan W, Lee JD, Song Q, Jo H, Kim Y. Identification of Quantitative Trait Loci Controlling Root Morphological Traits in an Interspecific Soybean Population Using 2D Imagery Data. Int J Mol Sci 2024; 25:4687. [PMID: 38731906 PMCID: PMC11083680 DOI: 10.3390/ijms25094687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 04/23/2024] [Accepted: 04/23/2024] [Indexed: 05/13/2024] Open
Abstract
Roots are the hidden and most important part of plants. They serve as stabilizers and channels for uptaking water and nutrients and play a crucial role in the growth and development of plants. Here, two-dimensional image data were used to identify quantitative trait loci (QTL) controlling root traits in an interspecific mapping population derived from a cross between wild soybean 'PI366121' and cultivar 'Williams 82'. A total of 2830 single-nucleotide polymorphisms were used for genotyping, constructing genetic linkage maps, and analyzing QTLs. Forty-two QTLs were identified on twelve chromosomes, twelve of which were identified as major QTLs, with a phenotypic variation range of 36.12% to 39.11% and a logarithm of odds value range of 12.01 to 17.35. Two significant QTL regions for the average diameter, root volume, and link average diameter root traits were detected on chromosomes 3 and 13, and both wild and cultivated soybeans contributed positive alleles. Six candidate genes, Glyma.03G027500 (transketolase/glycoaldehyde transferase), Glyma.03G014500 (dehydrogenases), Glyma.13G341500 (leucine-rich repeat receptor-like protein kinase), Glyma.13G341400 (AGC kinase family protein), Glyma.13G331900 (60S ribosomal protein), and Glyma.13G333100 (aquaporin transporter) showed higher expression in root tissues based on publicly available transcriptome data. These results will help breeders improve soybean genetic components and enhance soybean root morphological traits using desirable alleles from wild soybeans.
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Affiliation(s)
- Mohammad Shafiqul Islam
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea; (M.S.I.); (A.G.); (L.L.); (W.K.); (J.-D.L.); (H.J.)
- Department of Integrative Biology, Kyungpook National University, Daegu 41566, Republic of Korea
- Department of Agriculture, Noakhali Science and Technology University, Noakhali 3814, Bangladesh
| | - Amit Ghimire
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea; (M.S.I.); (A.G.); (L.L.); (W.K.); (J.-D.L.); (H.J.)
- Department of Integrative Biology, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Liny Lay
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea; (M.S.I.); (A.G.); (L.L.); (W.K.); (J.-D.L.); (H.J.)
- Department of Integrative Biology, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Waleed Khan
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea; (M.S.I.); (A.G.); (L.L.); (W.K.); (J.-D.L.); (H.J.)
- Department of Integrative Biology, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Jeong-Dong Lee
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea; (M.S.I.); (A.G.); (L.L.); (W.K.); (J.-D.L.); (H.J.)
- Department of Integrative Biology, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Qijian Song
- Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville Agricultural Research Center, Beltsville, MD 20705, USA;
| | - Hyun Jo
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea; (M.S.I.); (A.G.); (L.L.); (W.K.); (J.-D.L.); (H.J.)
| | - Yoonha Kim
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea; (M.S.I.); (A.G.); (L.L.); (W.K.); (J.-D.L.); (H.J.)
- Department of Integrative Biology, Kyungpook National University, Daegu 41566, Republic of Korea
- Upland Field Machinery Research Center, Kyungpook National University, Daegu 41566, Republic of Korea
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Ding H, Feng X, Yuan Y, Wang B, Wang Y, Zhang J. Genomic investigation of duplication, functional conservation, and divergence in the LRR-RLK Family of Saccharum. BMC Genomics 2024; 25:165. [PMID: 38336615 PMCID: PMC10854099 DOI: 10.1186/s12864-024-10073-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 02/01/2024] [Indexed: 02/12/2024] Open
Abstract
BACKGROUND Sugarcane (Saccharum spp.) holds exceptional global significance as a vital crop, serving as a primary source of sucrose, bioenergy, and various by-products. The optimization of sugarcane breeding by fine-tuning essential traits has become crucial for enhancing crop productivity and stress resilience. Leucine-rich repeat receptor-like kinases (LRR-RLK) genes present promising targets for this purpose, as they are involved in various aspects of plant development and defense processes. RESULTS Here, we present a detailed overview of phylogeny and expression of 288 (495 alleles) and 312 (1365 alleles) LRR-RLK genes from two founding Saccharum species, respectively. Phylogenetic analysis categorized these genes into 15 subfamilies, revealing considerable expansion or reduction in certain LRR-type subfamilies. Compared to other plant species, both Saccharum species had more significant LRR-RLK genes. Examination of cis-acting elements demonstrated that SsLRR-RLK and SoLRR-RLK genes exhibited no significant difference in the types of elements included, primarily involved in four physiological processes. This suggests a broad conservation of LRR-RLK gene function during Saccharum evolution. Synteny analysis indicated that all LRR-RLK genes in both Saccharum species underwent gene duplication, primarily through whole-genome duplication (WGD) or segmental duplication. We identified 28 LRR-RLK genes exhibiting novel expression patterns in response to different tissues, gradient development leaves, and circadian rhythm in the two Saccharum species. Additionally, SoLRR-RLK104, SoLRR-RLK7, SoLRR-RLK113, and SsLRR-RLK134 were identified as candidate genes for sugarcane disease defense response regulators through transcriptome data analysis of two disease stresses. This suggests LRR-RLK genes of sugarcane involvement in regulating various biological processes, including leaf development, plant morphology, photosynthesis, maintenance of circadian rhythm stability, and defense against sugarcane diseases. CONCLUSIONS This investigation into gene duplication, functional conservation, and divergence of LRR-RLK genes in two founding Saccharum species lays the groundwork for a comprehensive genomic analysis of the entire LRR-RLK gene family in Saccharum. The results reveal LRR-RLK gene played a critical role in Saccharum adaptation to diverse conditions, offering valuable insights for targeted breeding and precise phenotypic adjustments.
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Affiliation(s)
- Hongyan Ding
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, 530004, China
| | - Xiaoxi Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, 530004, China
| | - Yuan Yuan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, 530004, China
| | - Baiyu Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, 530004, China
| | - Yuhao Wang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Sugarcane Biology and Genetic Breeding, National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jisen Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, 530004, China.
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Afridi MS, Kumar A, Javed MA, Dubey A, de Medeiros FHV, Santoyo G. Harnessing root exudates for plant microbiome engineering and stress resistance in plants. Microbiol Res 2024; 279:127564. [PMID: 38071833 DOI: 10.1016/j.micres.2023.127564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 11/02/2023] [Accepted: 11/27/2023] [Indexed: 12/23/2023]
Abstract
A wide range of abiotic and biotic stresses adversely affect plant's growth and production. Under stress, one of the main responses of plants is the modulation of exudates excreted in the rhizosphere, which consequently leads to alterations in the resident microbiota. Thus, the exudates discharged into the rhizospheric environment play a preponderant role in the association and formation of plant-microbe interactions. In this review, we aimed to provide a synthesis of the latest and most pertinent literature on the diverse biochemical and structural compositions of plant root exudates. Also, this work investigates into their multifaceted role in microbial nutrition and intricate signaling processes within the rhizosphere, which includes quorum-sensing molecules. Specifically, it explores the contributions of low molecular weight compounds, such as carbohydrates, phenolics, organic acids, amino acids, and secondary metabolites, as well as the significance of high molecular weight compounds, including proteins and polysaccharides. It also discusses the state-of-the-art omics strategies that unveil the vital role of root exudates in plant-microbiome interactions, including defense against pathogens like nematodes and fungi. We propose multiple challenges and perspectives, including exploiting plant root exudates for host-mediated microbiome engineering. In this discourse, root exudates and their derived interactions with the rhizospheric microbiota should receive greater attention due to their positive influence on plant health and stress mitigation.
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Affiliation(s)
- Muhammad Siddique Afridi
- Department of Plant Pathology, Federal University of Lavras, CP3037, 37200-900 Lavras, MG, Brazil.
| | - Ashwani Kumar
- Metagenomics and Secretomics Research Laboratory, Department of Botany, Dr. Harisingh Gour University (A Central University), Sagar 470003, MP, India
| | - Muhammad Ammar Javed
- Institute of Industrial Biotechnology, Government College University, Lahore 54000, Pakistan
| | - Anamika Dubey
- Metagenomics and Secretomics Research Laboratory, Department of Botany, Dr. Harisingh Gour University (A Central University), Sagar 470003, MP, India
| | | | - Gustavo Santoyo
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, 58030 Morelia, Mexico.
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Łabuz J, Banaś AK, Zgłobicki P, Bażant A, Sztatelman O, Giza A, Lasok H, Prochwicz A, Kozłowska-Mroczek A, Jankowska U, Hermanowicz P. Phototropin2 3'UTR overlaps with the AT5G58150 gene encoding an inactive RLK kinase. BMC PLANT BIOLOGY 2024; 24:55. [PMID: 38238701 PMCID: PMC10795372 DOI: 10.1186/s12870-024-04732-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 01/05/2024] [Indexed: 01/22/2024]
Abstract
BACKGROUND This study examines the biological implications of an overlap between two sequences in the Arabidopsis genome, the 3'UTR of the PHOT2 gene and a putative AT5G58150 gene, encoded on the complementary strand. AT5G58150 is a probably inactive protein kinase that belongs to the transmembrane, leucine-rich repeat receptor-like kinase family. Phot2 is a membrane-bound UV/blue light photoreceptor kinase. Thus, both proteins share their cellular localization, on top of the proximity of their loci. RESULTS The extent of the overlap between 3'UTR regions of AT5G58150 and PHOT2 was found to be 66 bp, using RACE PCR. Both the at5g58150 T-DNA SALK_093781C (with insertion in the promoter region) and 35S::AT5G58150-GFP lines overexpress the AT5G58150 gene. A detailed analysis did not reveal any substantial impact of PHOT2 or AT5G58150 on their mutual expression levels in different light and osmotic stress conditions. AT5G58150 is a plasma membrane protein, with no apparent kinase activity, as tested on several potential substrates. It appears not to form homodimers and it does not interact with PHOT2. Lines that overexpress AT5G58150 exhibit a greater reduction in lateral root density due to salt and osmotic stress than wild-type plants, which suggests that AT5G58150 may participate in root elongation and formation of lateral roots. In line with this, mass spectrometry analysis identified proteins with ATPase activity, which are involved in proton transport and cell elongation, as putative interactors of AT5G58150. Membrane kinases, including other members of the LRR RLK family and BSK kinases (positive regulators of brassinosteroid signalling), can also act as partners for AT5G58150. CONCLUSIONS AT5G58150 is a membrane protein that does not exhibit measurable kinase activity, but is involved in signalling through interactions with other proteins. Based on the interactome and root architecture analysis, AT5G58150 may be involved in plant response to salt and osmotic stress and the formation of roots in Arabidopsis.
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Affiliation(s)
- Justyna Łabuz
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387, Kraków, Poland.
| | - Agnieszka Katarzyna Banaś
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland
| | - Piotr Zgłobicki
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland
| | - Aneta Bażant
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland
| | - Olga Sztatelman
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106, Warsaw, Poland
| | - Aleksandra Giza
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387, Kraków, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Łojasiewicza 11, 30-348, Kraków, Poland
| | - Hanna Lasok
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387, Kraków, Poland
| | - Aneta Prochwicz
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387, Kraków, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Łojasiewicza 11, 30-348, Kraków, Poland
| | - Anna Kozłowska-Mroczek
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387, Kraków, Poland
| | - Urszula Jankowska
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387, Kraków, Poland
| | - Paweł Hermanowicz
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387, Kraków, Poland
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Huang R, Jiang S, Dai M, Shi H, Zhu H, Guo Z. Zinc finger transcription factor MtZPT2-2 negatively regulates salt tolerance in Medicago truncatula. PLANT PHYSIOLOGY 2023; 194:564-577. [PMID: 37801609 DOI: 10.1093/plphys/kiad527] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 09/12/2023] [Accepted: 09/13/2023] [Indexed: 10/08/2023]
Abstract
Zinc finger proteins (ZFPs) are transcription factors involved in multiple cellular functions. We identified a C2H2 type ZFP (MtZPT2-2) in Medicago truncatula and demonstrated that it localizes to the nucleus and inhibits the transcription of 2 genes encoding high-affinity potassium transporters (MtHKT1;1 and MtHKT1;2). MtZPT2-2 transcripts were detected in stem, leaf, flower, seeds and roots, with the highest level in the xylem and phloem of roots and stems. MtZPT2-2 transcription in leaves was reduced after salt stress. Compared with the wild-type (WT), transgenic lines overexpressing MtZPT2-2 had decreased salt tolerance, while MtZPT2-2-knockout mutants showed increased salt tolerance. MtHKT1;1 and MtHKT1;2 transcripts and Na+ accumulation in shoots and roots, as well as in the xylem of all genotypes of plants, were increased after salt treatment, with higher levels of MtHKT1;1 and MtHKT1;2 transcripts and Na+ accumulation in MtZPT2-2-knockout mutants and lower levels in MtZPT2-2-overexpressing lines compared with the WT. K+ levels showed no significant difference among plant genotypes under salt stress. Moreover, MtZPT2-2 was demonstrated to bind with the promoter of MtHKT1;1 and MtHKT1;2 to inhibit their expression. Antioxidant enzyme activities and the gene transcript levels were accordingly upregulated in response to salt, with higher levels in MtZPT2-2-knockout mutants and lower levels in MtZPT2-2-overexpressing lines compared with WT. The results suggest that MtZPT2-2 regulates salt tolerance negatively through downregulating MtHKT1;1 and MtHKT1;2 expression directly to reduce Na+ unloading from the xylem and regulates antioxidant defense indirectly.
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Affiliation(s)
- Risheng Huang
- College of Grassland Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Shouzhen Jiang
- College of Grassland Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Mengtong Dai
- College of Grassland Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Haifan Shi
- College of Grassland Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Haifeng Zhu
- College of Grassland Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhenfei Guo
- College of Grassland Science, Nanjing Agricultural University, Nanjing 210095, China
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Szurman-Zubrzycka M, Kurowska M, Till BJ, Szarejko I. Is it the end of TILLING era in plant science? FRONTIERS IN PLANT SCIENCE 2023; 14:1160695. [PMID: 37674734 PMCID: PMC10477672 DOI: 10.3389/fpls.2023.1160695] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 07/19/2023] [Indexed: 09/08/2023]
Abstract
Since its introduction in 2000, the TILLING strategy has been widely used in plant research to create novel genetic diversity. TILLING is based on chemical or physical mutagenesis followed by the rapid identification of mutations within genes of interest. TILLING mutants may be used for functional analysis of genes and being nontransgenic, they may be directly used in pre-breeding programs. Nevertheless, classical mutagenesis is a random process, giving rise to mutations all over the genome. Therefore TILLING mutants carry background mutations, some of which may affect the phenotype and should be eliminated, which is often time-consuming. Recently, new strategies of targeted genome editing, including CRISPR/Cas9-based methods, have been developed and optimized for many plant species. These methods precisely target only genes of interest and produce very few off-targets. Thus, the question arises: is it the end of TILLING era in plant studies? In this review, we recap the basics of the TILLING strategy, summarize the current status of plant TILLING research and present recent TILLING achievements. Based on these reports, we conclude that TILLING still plays an important role in plant research as a valuable tool for generating genetic variation for genomics and breeding projects.
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Affiliation(s)
- Miriam Szurman-Zubrzycka
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Marzena Kurowska
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Bradley J. Till
- Veterinary Genetics Laboratory, University of California, Davis, Davis, United States
| | - Iwona Szarejko
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
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Du X, Zhou L, Zhu B, Gu L, Yin H, Wang H. The TabHLH35-TaWAK20-TaSPL5 pathway positively regulates Cd stress in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:153. [PMID: 37310523 DOI: 10.1007/s00122-023-04400-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 06/01/2023] [Indexed: 06/14/2023]
Abstract
KEY MESSAGE Cadmium-induced TaWAK20 regulates the cadmium stress response by phosphorylating TaSPL5 in wheat. Receptor-like kinases (RLKs) are thought to play important roles in responses to abiotic stresses in plants. In this study, we identified a cadmium (Cd)-induced RLK in wheat, TaWAK20, which is a positive regulator of the Cd stress response. TaWAK20 is specifically expressed in root tissue. Overexpression of TaWAK20 significantly improved the tolerance of Cd stress in wheat and decreased Cd accumulation in wheat plants by regulating reactive oxygen species production and scavenging. Yeast one-hybrid assays, electrophoretic mobility shift assays, and firefly luciferase activity analyses demonstrated that the TaWAK20 promoter was bound by the TabHLH35 transcription factor. TaWAK20 interacted with and phosphorylated squamosa promoter binding protein-like 5 (TaSPL5). Furthermore, phosphorylation of TaSPL5 increased its DNA-binding activity. In addition, Arabidopsis-expressing phosphorylated TaSPL5 exhibited greater Cd tolerance than Arabidopsis-expressing unphosphorylated TaSPL5. Taken together, these data identify a TabHLH35-TaWAK20-TaSPL5 module that regulates Cd stress.
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Affiliation(s)
- Xuye Du
- School of Life Sciences, Guizhou Normal University, Guiyang, Guizhou Province, China
| | - Lizhou Zhou
- School of Life Sciences, Guizhou Normal University, Guiyang, Guizhou Province, China
| | - Bin Zhu
- School of Life Sciences, Guizhou Normal University, Guiyang, Guizhou Province, China
| | - Lei Gu
- School of Life Sciences, Guizhou Normal University, Guiyang, Guizhou Province, China.
| | - Huayan Yin
- College of Agronomy, Qingdao Agricultural University, Qingdao, Shandong Province, China.
| | - Hongcheng Wang
- School of Life Sciences, Guizhou Normal University, Guiyang, Guizhou Province, China.
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Sunseri F, Aci MM, Mauceri A, Caldiero C, Puccio G, Mercati F, Abenavoli MR. Short-term transcriptomic analysis at organ scale reveals candidate genes involved in low N responses in NUE-contrasting tomato genotypes. FRONTIERS IN PLANT SCIENCE 2023; 14:1125378. [PMID: 36938018 PMCID: PMC10020590 DOI: 10.3389/fpls.2023.1125378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 02/13/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Understanding the complex regulatory network underlying plant nitrogen (N) responses associated with high Nitrogen Use Efficiency (NUE) is one of the main challenges for sustainable cropping systems. Nitrate (NO3 -), acting as both an N source and a signal molecule, provokes very fast transcriptome reprogramming, allowing plants to adapt to its availability. These changes are genotype- and tissue-specific; thus, the comparison between contrasting genotypes is crucial to uncovering high NUE mechanisms. METHODS Here, we compared, for the first time, the spatio-temporal transcriptome changes in both root and shoot of two NUE contrasting tomato genotypes, Regina Ostuni (high-NUE) and UC82 (low-NUE), in response to short-term (within 24 h) low (LN) and high (HN) NO3 - resupply. RESULTS Using time-series transcriptome data (0, 8, and 24 h), we identified 395 and 482 N-responsive genes differentially expressed (DEGs) between RO and UC82 in shoot and root, respectively. Protein kinase signaling plant hormone signal transduction, and phenylpropanoid biosynthesis were the main enriched metabolic pathways in shoot and root, respectively, and were upregulated in RO compared to UC82. Interestingly, several N transporters belonging to NRT and NPF families, such as NRT2.3, NRT2.4, NPF1.2, and NPF8.3, were found differentially expressed between RO and UC82 genotypes, which might explain the contrasting NUE performances. Transcription factors (TFs) belonging to several families, such as ERF, LOB, GLK, NFYB, ARF, Zinc-finger, and MYB, were differentially expressed between genotypes in response to LN. A complementary Weighted Gene Co-expression Network Analysis (WGCNA) allowed the identification of LN-responsive co-expression modules in RO shoot and root. The regulatory network analysis revealed candidate genes that might have key functions in short-term LN regulation. In particular, an asparagine synthetase (ASNS), a CBL-interacting serine/threonine-protein kinase 1 (CIPK1), a cytokinin riboside 5'-monophosphate phosphoribohydrolase (LOG8), a glycosyltransferase (UGT73C4), and an ERF2 were identified in the shoot, while an LRR receptor-like serine/threonine-protein kinase (FEI1) and two TFs NF-YB5 and LOB37 were identified in the root. DISCUSSION Our results revealed potential candidate genes that independently and/or concurrently may regulate short-term low-N response, suggesting a key role played by cytokinin and ROS balancing in early LN regulation mechanisms adopted by the N-use efficient genotype RO.
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Affiliation(s)
- Francesco Sunseri
- Dipartimento Agraria, Università Mediterranea di Reggio Calabria, Reggio Calabria, Italy
- National Research Council of Italy, Institute of Biosciences and Bioresources (CNR-IBBR), Palermo, Italy
| | - Meriem Miyassa Aci
- Dipartimento Agraria, Università Mediterranea di Reggio Calabria, Reggio Calabria, Italy
| | - Antonio Mauceri
- Dipartimento Agraria, Università Mediterranea di Reggio Calabria, Reggio Calabria, Italy
| | - Ciro Caldiero
- Dipartimento Agraria, Università Mediterranea di Reggio Calabria, Reggio Calabria, Italy
| | - Guglielmo Puccio
- National Research Council of Italy, Institute of Biosciences and Bioresources (CNR-IBBR), Palermo, Italy
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, Viale delle Scienze, Palermo, Italy
| | - Francesco Mercati
- National Research Council of Italy, Institute of Biosciences and Bioresources (CNR-IBBR), Palermo, Italy
| | - Maria Rosa Abenavoli
- Dipartimento Agraria, Università Mediterranea di Reggio Calabria, Reggio Calabria, Italy
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Jiang H, Li Y, Luan M, Huang S, Zhao L, Yang G, Pan G. Single-Molecule Real-Time Sequencing of Full-Length Transcriptome and Identification of Genes Related to Male Development in Cannabis sativa. PLANTS (BASEL, SWITZERLAND) 2022; 11:3559. [PMID: 36559671 PMCID: PMC9782162 DOI: 10.3390/plants11243559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 11/25/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
Female Cannabis sativa plants have important therapeutic properties. The sex ratio of the dioecious cannabis is approximately 1:1. Cultivating homozygous female plants by inducing female plants to produce male flowers is of great practical significance. However, the mechanism underlying cannabis male development remains unclear. In this study, single-molecule real-time (SMRT) sequencing was performed using a mixed sample of female and induced male flowers from the ZYZM1 cannabis variety. A total of 15,241 consensus reads were identified, and 13,657 transcripts were annotated across seven public databases. A total of 48 lncRNAs with an average length of 986.54 bp were identified. In total, 8202 transcripts were annotated as transcription factors, the most common of which were bHLH transcription factors. Moreover, tissue-specific expression pattern analysis showed that 13 MADS transcription factors were highly expressed in male flowers. Furthermore, 232 reads of novel genes were predicted and enriched in lipid metabolism, and qRT-PCR results showed that CER1 may be involved in the development of cannabis male flowers. In addition, 1170 AS events were detected, and two AS events were further validated. Taken together, these results may improve our understanding of the complexity of full-length cannabis transcripts and provide a basis for understanding the molecular mechanism of cannabis male development.
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Affiliation(s)
- Hui Jiang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Science, Changsha 410205, China
| | - Ying Li
- State Key Laboratory Breeding Base of Dao-di Herbs, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Mingbao Luan
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Science, Changsha 410205, China
| | - Siqi Huang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Science, Changsha 410205, China
| | - Lining Zhao
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Science, Changsha 410205, China
| | - Guang Yang
- State Key Laboratory Breeding Base of Dao-di Herbs, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Gen Pan
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Science, Changsha 410205, China
- State Key Laboratory Breeding Base of Dao-di Herbs, China Academy of Chinese Medical Sciences, Beijing 100700, China
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10
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Rehman HM, Chen S, Zhang S, Khalid M, Uzair M, Wilmarth PA, Ahmad S, Lam HM. Membrane Proteomic Profiling of Soybean Leaf and Root Tissues Uncovers Salt-Stress-Responsive Membrane Proteins. Int J Mol Sci 2022; 23:13270. [PMID: 36362058 PMCID: PMC9655375 DOI: 10.3390/ijms232113270] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 10/24/2022] [Accepted: 10/25/2022] [Indexed: 08/13/2023] Open
Abstract
Cultivated soybean (Glycine max (L.)), the world's most important legume crop, has high-to-moderate salt sensitivity. Being the frontier for sensing and controlling solute transport, membrane proteins could be involved in cell signaling, osmoregulation, and stress-sensing mechanisms, but their roles in abiotic stresses are still largely unknown. By analyzing salt-induced membrane proteomic changes in the roots and leaves of salt-sensitive soybean cultivar (C08) seedlings germinated under NaCl, we detected 972 membrane proteins, with those present in both leaves and roots annotated as receptor kinases, calcium-sensing proteins, abscisic acid receptors, cation and anion channel proteins, proton pumps, amide and peptide transporters, and vesicle transport-related proteins etc. Endocytosis, linoleic acid metabolism, and fatty acid biosynthesis pathway-related proteins were enriched in roots whereas phagosome, spliceosome and soluble NSF attachment protein receptor (SNARE) interaction-related proteins were enriched in leaves. Using label-free quantitation, 129 differentially expressed membrane proteins were found in both tissues upon NaCl treatment. Additionally, the 140 NaCl-induced proteins identified in roots and 57 in leaves are vesicle-, mitochondrial-, and chloroplast-associated membrane proteins and those with functions related to ion transport, protein transport, ATP hydrolysis, protein folding, and receptor kinases, etc. Our proteomic results were verified against corresponding gene expression patterns from published C08 RNA-seq data, demonstrating the importance of solute transport and sensing in salt stress responses.
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Affiliation(s)
- Hafiz Mamoon Rehman
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Shengjie Chen
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Shoudong Zhang
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Memoona Khalid
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Muhammad Uzair
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Phillip A. Wilmarth
- Proteomics Shared Resource, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA
| | - Shakeel Ahmad
- Seed Center, Ministry of Environment, Water & Agriculture, Riyadh 14712, Saudi Arabia
| | - Hon-Ming Lam
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
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11
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Yang C, Xie Z, Qian S, Zhang J, Yu Z, Li M, Gu L, Qin S, Zhang Z. Functional analysis of Rehmannia glutinosa key LRR-RLKs during interaction of root exudates with Fusarium oxysporum reveals the roles of immune proteins in formation of replant disease. FRONTIERS IN PLANT SCIENCE 2022; 13:1044070. [PMID: 36388607 PMCID: PMC9660255 DOI: 10.3389/fpls.2022.1044070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 10/13/2022] [Indexed: 06/16/2023]
Abstract
Previous studies have indicated that some Rehmannia glutinosa Leucine-rich repeat receptor-like protein kinases (LRR-RLKs) are involved in the formation of replant disease. However, it remains unclear how the interaction of LRR-RLKs with a key factor, the interaction between root exudates and Fusarium oxysporum, results in formation of replant disease. In this study, the influences of root exudates, F. oxysporum and the interaction of these two factors on expression of nine R. glutinosa LRR-RLKs (RgLRRs) were analyzed. The resulting eight RgLRRs of them were highly expressed at the early stage, and rapidly declined at later stages under mixed treatment of root exudates and F. oxysporum. The functions of nine RgLRRs under root exudates, F. oxysporum and mixed treatment of root exudates and F. oxysporum were preliminarily analyzed using transient overexpression and RNAi experiments. The results showed that high expression of RgLRR19, RgLRR21, RgLRR23 and RgLRR29 could decrease the damage to root cells from the mixed treatment of root exudates and F. oxysporum, but the interference of these genes enhanced the damage levels of root cells. Based on this, stable transgenic R. glutinosa seedlings were acquired. Overexpression of RgLRR29 conferred resistance of R. glutinosa seedlings to root exudates, F. oxysporum and mixed treatment. These results indicated that the continuous proliferation of F. oxysporum supported by root exudates altered the expression patterns of RgLRRs in R. glutinosa, then disordered the growth and development of R. glutinosa, finally leading to the formation of replant disease.
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Affiliation(s)
- Chuyun Yang
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhuomi Xie
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Sheng Qian
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Junyi Zhang
- College of Chemical Engineering, Huaqiao University, Xiamen, China
| | - Zhijian Yu
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mingjie Li
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Li Gu
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shuangshuang Qin
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plant, Nanning, China
| | - Zhongyi Zhang
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou, China
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12
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Zhang X, Sun Y, Qiu X, Lu H, Hwang I, Wang T. Tolerant mechanism of model legume plant Medicago truncatula to drought, salt, and cold stresses. FRONTIERS IN PLANT SCIENCE 2022; 13:847166. [PMID: 36160994 PMCID: PMC9490062 DOI: 10.3389/fpls.2022.847166] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Accepted: 08/15/2022] [Indexed: 06/16/2023]
Abstract
Legume plants produce one-third of the total yield of primary crops and are important food sources for both humans and animals worldwide. Frequent exposure to abiotic stresses, such as drought, salt, and cold, greatly limits the production of legume crops. Several morphological, physiological, and molecular studies have been conducted to characterize the response and adaptation mechanism to abiotic stresses. The tolerant mechanisms of the model legume plant Medicago truncatula to abiotic stresses have been extensively studied. Although many potential genes and integrated networks underlying the M. truncatula in responding to abiotic stresses have been identified and described, a comprehensive summary of the tolerant mechanism is lacking. In this review, we provide a comprehensive summary of the adaptive mechanism by which M. truncatula responds to drought, salt, and cold stress. We also discuss future research that need to be explored to improve the abiotic tolerance of legume plants.
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Affiliation(s)
- Xiuxiu Zhang
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciencess, Beijing, China
| | - Yu Sun
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciencess, Changchun, China
| | - Xiao Qiu
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Hai Lu
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Inhwan Hwang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, South Korea
| | - Tianzuo Wang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciencess, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
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13
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Lee SB, Kim GJ, Shin JD, Chung W, Park SK, Choi GH, Park SW, Park YJ. Genome-Scale Profiling and High-Throughput Analyses Unravel the Genetic Basis of Arsenic Content Variation in Rice. FRONTIERS IN PLANT SCIENCE 2022; 13:905842. [PMID: 35958208 PMCID: PMC9361212 DOI: 10.3389/fpls.2022.905842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 06/15/2022] [Indexed: 06/15/2023]
Abstract
Ionomics, the study of the composition of mineral nutrients and trace elements in organisms that represent the inorganic component of cells and tissues, has been widely studied to explore to unravel the molecular mechanism regulating the elemental composition of plants. However, the genetic factors of rice subspecies in the interaction between arsenic and functional ions have not yet been explained. Here, the correlation between As and eight essential ions in a rice core collection was analyzed, taking into account growing condition and genetic factors. The results demonstrated that the correlation between As and essential ions was affected by genetic factors and growing condition, but it was confirmed that the genetic factor was slightly larger with the heritability for arsenic content at 53%. In particular, the cluster coefficient of japonica (0.428) was larger than that of indica (0.414) in the co-expression network analysis for 23 arsenic genes, and it was confirmed that the distance between genes involved in As induction and detoxification of japonica was far than that of indica. These findings provide evidence that japonica populations could accumulate more As than indica populations. In addition, the cis-eQTLs of AIR2 (arsenic-induced RING finger protein) were isolated through transcriptome-wide association studies, and it was confirmed that AIR2 expression levels of indica were lower than those of japonica. This was consistent with the functional haplotype results for the genome sequence of AIR2, and finally, eight rice varieties with low AIR2 expression and arsenic content were selected. In addition, As-related QTLs were identified on chromosomes 5 and 6 under flooded and intermittently flooded conditions through genome-scale profiling. Taken together, these results might assist in developing markers and breeding plans to reduce toxic element content and breeding high-quality rice varieties in future.
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Affiliation(s)
- Sang-Beom Lee
- Crop Foundation Research Division, National Institute of Crop Science, Wanju, South Korea
| | - Gyeong-Jin Kim
- Residual Agrochemical Assessment Division, National Institute of Agriculture Science, Wanju, South Korea
| | - Jung-Du Shin
- Bio-Technology of Multidisciplinary Sciences Co., Wanju, South Korea
| | - Woojin Chung
- Department of Environmental Energy Engineering, Kyonggi University, Suwon, South Korea
| | - Soo-Kwon Park
- Crop Foundation Research Division, National Institute of Crop Science, Wanju, South Korea
| | - Geun-Hyoung Choi
- Residual Agrochemical Assessment Division, National Institute of Agriculture Science, Wanju, South Korea
| | - Sang-Won Park
- Reserch Policy Bureau, Rural Development Administration, Wanju, South Korea
| | - Yong-Jin Park
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan, South Korea
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14
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Chakraborty S, Harris JM. At the Crossroads of Salinity and Rhizobium-Legume Symbiosis. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:540-553. [PMID: 35297650 DOI: 10.1094/mpmi-09-21-0231-fi] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Legume roots interact with soil bacteria rhizobia to develop nodules, de novo symbiotic root organs that host these rhizobia and are mini factories of atmospheric nitrogen fixation. Nodulation is a sophisticated developmental process and is sensitive to several abiotic factors, salinity being one of them. While salinity influences both the free-living partners, symbiosis is more vulnerable than other aspects of plant and microbe physiology, and the symbiotic interaction is strongly impaired even under moderate salinity. In this review, we tease apart the various known components of rhizobium-legume symbiosis and how they interact with salt stress. We focus primarily on the initial stages of symbiosis since we have a greater mechanistic understanding of the interaction at these stages.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Sanhita Chakraborty
- Department of Plant Biology, University of Vermont, Burlington, VT 05405, U.S.A
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, U.S.A
| | - Jeanne M Harris
- Department of Plant Biology, University of Vermont, Burlington, VT 05405, U.S.A
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15
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Singh P, Kumar K, Jha AK, Yadava P, Pal M, Rakshit S, Singh I. Global gene expression profiling under nitrogen stress identifies key genes involved in nitrogen stress adaptation in maize (Zea mays L.). Sci Rep 2022; 12:4211. [PMID: 35273237 PMCID: PMC8913646 DOI: 10.1038/s41598-022-07709-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 02/14/2022] [Indexed: 11/25/2022] Open
Abstract
Maize is a heavy consumer of fertilizer nitrogen (N) which not only results in the high cost of cultivation but may also lead to environmental pollution. Therefore, there is a need to develop N-use efficient genotypes, a prerequisite for which is a greater understanding of N-deficiency stress adaptation. In this study, comparative transcriptome analysis was performed using leaf and root tissues from contrasting inbred lines, viz., DMI 56 (tolerant to N stress) and DMI 81 (susceptible to N stress) to delineate the differentially expressed genes (DEGs) under low-N stress. The contrasting lines were grown hydroponically in modified Hoagland solution having either sufficient- or deficient-N, followed by high-throughput RNA-sequencing. A total of 8 sequencing libraries were prepared and 88–97% of the sequenced raw reads were mapped to the reference B73 maize genome. Genes with a p value ≤ 0.05 and fold change of ≥ 2.0 or ≤ − 2 were considered as DEGs in various combinations performed between susceptible and tolerant genotypes. DEGs were further classified into different functional categories and pathways according to their putative functions. Gene Ontology based annotation of these DEGs identified three different functional categories: biological processes, molecular function, and cellular component. The KEGG and Mapman based analysis revealed that most of the DEGs fall into various metabolic pathways, biosynthesis of secondary metabolites, signal transduction, amino acid metabolism, N-assimilation and metabolism, and starch metabolism. Some of the key genes involved in N uptake (high-affinity nitrate transporter 2.2 and 2.5), N assimilation and metabolism (glutamine synthetase, asparagine synthetase), redox homeostasis (SOD, POX), and transcription factors (MYB36, AP2-EREBP) were found to be highly expressed in the tolerant genotype compared to susceptible one. The candidate genes identified in the present study might be playing a pivotal role in low-N stress adaptation in maize and hence could be useful in augmenting further research on N metabolism and development of N-deficiency tolerant maize cultivars.
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Affiliation(s)
- Prabha Singh
- Indian Council of Agricultural Research-Indian Institute of Maize Research, Pusa Campus, New Delhi, 110012, India.,Indian Council of Agricultural Research-Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110012, India.,Indian Council of Agricultural Research-Indian Grassland and Fodder Research Institute, Jhansi, 284003, India
| | - Krishan Kumar
- Indian Council of Agricultural Research-Indian Institute of Maize Research, Pusa Campus, New Delhi, 110012, India
| | - Abhishek Kumar Jha
- Indian Council of Agricultural Research-Indian Institute of Maize Research, Pusa Campus, New Delhi, 110012, India
| | - Pranjal Yadava
- Indian Council of Agricultural Research-Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110012, India
| | - Madan Pal
- Indian Council of Agricultural Research-Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110012, India
| | - Sujay Rakshit
- Indian Council of Agricultural Research-Indian Institute of Maize Research, Pusa Campus, New Delhi, 110012, India
| | - Ishwar Singh
- Indian Council of Agricultural Research-Indian Institute of Maize Research, Pusa Campus, New Delhi, 110012, India.
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16
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Zhang Z, Zhong H, Nan B, Xiao B. Global identification and integrated analysis of heat-responsive long non-coding RNAs in contrasting rice cultivars. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:833-852. [PMID: 34846546 DOI: 10.1007/s00122-021-04001-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 11/15/2021] [Indexed: 06/13/2023]
Abstract
Identified 2743 rice lncRNAs LncRNAs in response to heat stress Function prediction of HRLs Network among HRLs, genes and miRNAs co-localization of HRLs with QTLs Significant motifs in HRL sequences Long non-coding RNAs (lncRNAs) play vital roles in plant responses to environmental challenges. A better understanding of the gene regulation mediated by lncRNAs and their systematic identification would provide great benefits for modern agriculture. In this study, we performed strand-specific RNA sequencing for two rice varieties, heat-tolerant ZS97B and heat-susceptible SYD2 under heat stress. In total, 2743 putative lncRNAs were identified, and their expression profiles in response to heat treatments were established. We identified 231 differentially expressed lncRNAs (DELs) under heat stress, including 31 DELs common to both varieties and 103 and 97 specific to ZS97B and SYD2, respectively, all defined as heat-responsive lncRNAs (HRLs). The target-coding genes of HRLs were predicted, and GO and KEGG annotations of HRL targets revealed functions in which HRLs might be involved. The interaction network between HRLs, target genes and relevant miRNAs was constructed. The HRLs and their targets were compared with publicly available QTLs for rice seedling growth under heat stimulus. Ten HRLs and twelve target genes were linked with five heat stress-relevant QTLs. Sequence analysis revealed several motifs significantly enriched within the 231 HRL sequences. Our findings provide a valuable resource for further characterization of lncRNAs in terms of heat response and plant heat tolerance improvement.
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Affiliation(s)
- Zhengfeng Zhang
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, 430079, China
| | - Huahua Zhong
- College of Plant Science and Technology, Hua Zhong Agricultural University, Wuhan, 430070, China
| | - Bo Nan
- College of Plant Science and Technology, Hua Zhong Agricultural University, Wuhan, 430070, China
| | - Benze Xiao
- College of Plant Science and Technology, Hua Zhong Agricultural University, Wuhan, 430070, China.
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17
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Wang CF, Han GL, Yang ZR, Li YX, Wang BS. Plant Salinity Sensors: Current Understanding and Future Directions. FRONTIERS IN PLANT SCIENCE 2022; 13:859224. [PMID: 35463402 PMCID: PMC9022007 DOI: 10.3389/fpls.2022.859224] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 03/14/2022] [Indexed: 05/07/2023]
Abstract
Salt stress is a major limiting factor for plant growth and crop yield. High salinity causes osmotic stress followed by ionic stress, both of which disturb plant growth and metabolism. Understanding how plants perceive salt stress will help efforts to improve salt tolerance and ameliorate the effect of salt stress on crop growth. Various sensors and receptors in plants recognize osmotic and ionic stresses and initiate signal transduction and adaptation responses. In the past decade, much progress has been made in identifying the sensors involved in salt stress. Here, we review current knowledge of osmotic sensors and Na+ sensors and their signal transduction pathways, focusing on plant roots under salt stress. Based on bioinformatic analyses, we also discuss possible structures and mechanisms of the candidate sensors. With the rapid decline of arable land, studies on salt-stress sensors and receptors in plants are critical for the future of sustainable agriculture in saline soils. These studies also broadly inform our overall understanding of stress signaling in plants.
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18
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Nagar P, Sharma N, Jain M, Sharma G, Prasad M, Mustafiz A. OsPSKR15, a phytosulfokine receptor from rice enhances abscisic acid response and drought stress tolerance. PHYSIOLOGIA PLANTARUM 2022; 174:e13569. [PMID: 34549425 DOI: 10.1111/ppl.13569] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 09/06/2021] [Accepted: 09/20/2021] [Indexed: 06/13/2023]
Abstract
Abscisic acid (ABA) is a major phytohormone that acts as stimuli and plays an important role in plant growth, development, and environmental stress responses. Membrane-localized receptor-like kinases (RLKs) help to detect extracellular stimuli and activate downstream signaling responses to modulate a variety of biological processes. Phytosulfokine receptor (PSKR), a Leu-rich repeat (LRR)-RLK, has been characterized for its role in growth, development and biotic stress. Here, we observed that OsPSKR15, a rice PSKR, was upregulated by ABA in Oryza sativa. We demonstrated OsPSKR15 is a positive regulator in plant response to ABA. Ectopic expression of OsPSKR15 in Arabidopsis thaliana increased the sensitivity to ABA during germination, growth and stomatal closure. Consistently, the expression of ABA-inducible genes was significantly upregulated in these plants. OsPSKR15 also regulated reactive oxygen species (ROS)-mediated ABA signaling in guard cells, thereby governing stomatal closure. Furthermore, the constitutive expression of OsPSKR15 enhanced drought tolerance by reducing the transpirational water loss in Arabidopsis. We also reported that OsPSKR15 directly interacts with AtPYL9 and its orthologue OsPYL11 of rice through its kinase domain in the plasma membrane and nucleus. Altogether, these results reveal an important role of OsPSKR15 in plant response toward abiotic stress in an ABA-dependent manner.
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Affiliation(s)
- Preeti Nagar
- Plant Molecular Biology Laboratory, Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi, India
| | - Namisha Sharma
- National Institute of Plant Genome Research, New Delhi, India
| | - Muskan Jain
- Plant Molecular Biology Laboratory, Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi, India
| | - Gauri Sharma
- Plant Molecular Biology Laboratory, Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi, India
| | - Manoj Prasad
- National Institute of Plant Genome Research, New Delhi, India
| | - Ananda Mustafiz
- Plant Molecular Biology Laboratory, Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi, India
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19
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Liang T, Qing C, Liu P, Zou C, Yuan G, Pan G, Shen Y, Ma L. Joint GWAS and WGCNA uncover the genetic control of calcium accumulation under salt treatment in maize seedlings. PHYSIOLOGIA PLANTARUM 2022; 174:e13606. [PMID: 34837237 DOI: 10.1111/ppl.13606] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 11/16/2021] [Accepted: 11/23/2021] [Indexed: 05/28/2023]
Abstract
Soil salinization is an important factor threatening the yield and quality of maize. Ca2+ plays a considerable role in regulating plant growth under salt stress. Herein, we examined the shoot Ca2+ concentrations, root Ca2+ concentrations, and transport coefficients of seedlings in an association panel composed of 305 maize inbred lines under normal and salt conditions. A genome-wide association study was conducted by using the investigated phenotypes and 46,408 single-nucleotide polymorphisms of the panel. As a result, 53 significant SNPs were specifically detected under salt treatment, and 544 genes were identified in the linkage disequilibrium regions of these SNPs. According to the expression data of the 544 genes, we carried out a weighted coexpression network analysis. Combining the enrichment analyses and functional annotations, four hub genes (GRMZM2G051032, GRMZM2G004314, GRMZM2G421669, and GRMZM2G123314) were finally determined, which were then used to evaluate the genetic variation effects by gene-based association analysis. Only GRMZM2G123314, which encodes a pentatricopeptide repeat protein, was significantly associated with Ca2+ transport and the haplotype G-CT was identified as the superior haplotype. Our study brings novel insights into the genetic and molecular mechanisms of salt stress response and contributes to the development of salt-tolerant varieties in maize.
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Affiliation(s)
- Tianhu Liang
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Chunyan Qing
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Peng Liu
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Chaoying Zou
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Guangsheng Yuan
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Guangtang Pan
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yaou Shen
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Langlang Ma
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, China
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20
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Bano N, Fakhrah S, Nayak SP, Bag SK, Mohanty CS. Identification of miRNA and their target genes in Cestrum nocturnum L. and Cestrum diurnum L. in stress responses. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:31-49. [PMID: 35221570 PMCID: PMC8847519 DOI: 10.1007/s12298-022-01127-1] [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: 07/23/2021] [Revised: 12/14/2021] [Accepted: 01/07/2022] [Indexed: 06/14/2023]
Abstract
UNLABELLED MicroRNAs (miRNAs) are small, highly conserved non-coding RNA molecules and products of primary miRNAs that regulate the target gene expression. Homology-based approaches were employed to identify miRNAs and their targets in Cestrum nocturnum L. and Cestrum diurnum L. A total of 32 and 12 miRNA candidates were identified in C. nocturnum and C. diurnum. These miRNAs belong to 26 and 10 miRNA families and regulate 1024 and 1007 target genes in C. nocturnum, and C. diurnum, respectively. The functional roles of these miRNAs have not been earlier elucidated in Cestrum. MiR815a, miR849, miR1089 and miR172 have a strong propensity to target genes controlling phytochrome-interacting factor 1 (PIF1), ubiquitin-specific protease 12 (UBP12), leucine-rich repeat (LRR) protein kinase and GAI, RGA, SCR (GRAS) family transcription factor in C. nocturnum. While miR5205a, miR1436 and miR530 regulate PATATIN-like protein 6 (PLP6), PHD finger transcription factor and myb domain protein 48 (MYB48) in C. diurnum. Overall, these miRNAs have regulatory responses in biotic and abiotic stresses in both plant species. Eight putative miRNAs and their target genes were selected for qRT-PCR validation. The validated results suggested the importance of miR815a, miR849, miR5205a, miR1089, miR172, miR1436, and miR530 in exerting control over stress responses in C. nocturnum and C. diurnum. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-022-01127-1.
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Affiliation(s)
- Nasreen Bano
- CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001 India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001 India
| | - Shafquat Fakhrah
- CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001 India
- Department of Botany, University of Lucknow, Lucknow, Uttar Pradesh 226007 India
| | - Sagar Prasad Nayak
- CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001 India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001 India
| | - Sumit Kumar Bag
- CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001 India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001 India
- Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute, Lucknow, India
| | - Chandra Sekhar Mohanty
- CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001 India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001 India
- Plant Genetic Resources and Improvement Division, CSIR-National Botanical Research Institute, Lucknow, India
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21
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Geng B, Wang Q, Huang R, Liu Y, Guo Z, Lu S. A novel LRR-RLK (CTLK) confers cold tolerance through regulation on the C-repeat-binding factor pathway, antioxidants, and proline accumulation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:1679-1689. [PMID: 34626033 DOI: 10.1111/tpj.15535] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 09/26/2021] [Accepted: 10/04/2021] [Indexed: 06/13/2023]
Abstract
Leucine-rich repeat-receptor-like kinase (LRR-RLK) is a large subfamily of plant RLKs; however, its role in cold tolerance is still unknown. A novel cold tolerance LRR-RLK gene (MtCTLK1) in Medicago truncatula was identified using the transgenic lines overexpressing MtCTLK1 (MtCTLK1-OE) and mtctlk1 lines with Tnt1 retrotransposon insertion. Compared with the wild-type, MtCTLK1-OE lines had increased cold tolerance and mtctlk1 showed decreased cold tolerance. The impaired cold tolerance in mtctlk1 could be complemented by the transgenic expression of MtCTLK1 or its homolog MfCTLK1 from Medicago falcata. Antioxidant enzyme activities and proline accumulation as well as transcript levels of the associated genes were increased in response to cold, with higher levels in MtCTLK1-OE or lower levels in mtctlk1 lines as compared with wild type. C-Repeat-Binding Factors (CBFs) and CBF-dependent cold-responsive genes were also induced in response to cold, and higher transcript levels of CBFs and CBF-dependent cold-responsive genes were observed in MtCTLK1-OE lines whereas lower levels in mtctlk1 mutants. The results validate the role of MtCTLK1 or MfCTLK1 in the regulation of cold tolerance through the CBF pathway, antioxidant defense system and proline accumulation. It also provides a valuable gene for the molecular breeding program to improve cold tolerance in crops.
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Affiliation(s)
- Bohao Geng
- College of Grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Qi Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Engineering Research Center for Grassland Science, College of Life Sciences, South China Agricultural University, Guangzhou, China
- College of Biological Engineering, Henan University of Technology, Zhengzhou, 450001, China
| | - Risheng Huang
- College of Grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Yajie Liu
- College of Grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Zhenfei Guo
- College of Grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Shaoyun Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Engineering Research Center for Grassland Science, College of Life Sciences, South China Agricultural University, Guangzhou, China
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22
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Yang M, Wang L, Chen C, Guo X, Lin C, Huang W, Chen L. Genome-wide analysis of autophagy-related genes in Medicago truncatula highlights their roles in seed development and response to drought stress. Sci Rep 2021; 11:22933. [PMID: 34824334 PMCID: PMC8616919 DOI: 10.1038/s41598-021-02239-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 11/08/2021] [Indexed: 01/15/2023] Open
Abstract
Autophagy is a highly conserved process of degradation of cytoplasmic constituents in eukaryotes. It is involved in the growth and development of plants, as well as in biotic and abiotic stress response. Although autophagy-related (ATG) genes have been identified and characterized in many plant species, little is known about this process in Medicago truncatula. In this study, 39 ATGs were identified, and their gene structures and conserved domains were systematically characterized in M. truncatula. Many cis-elements, related to hormone and stress responsiveness, were identified in the promoters of MtATGs. Phylogenetic and interaction network analyses suggested that the function of MtATGs is evolutionarily conserved in Arabidopsis and M. truncatula. The expression of MtATGs, at varied levels, was detected in all examined tissues. In addition, most of the MtATGs were highly induced during seed development and drought stress, which indicates that autophagy plays an important role in seed development and responses to drought stress in M. truncatula. In conclusion, this study gives a comprehensive overview of MtATGs and provides important clues for further functional analysis of autophagy in M. truncatula.
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Affiliation(s)
- Mingkang Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Liping Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Chumin Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Xu Guo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Chuanglie Lin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Wei Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.
| | - Liang Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.
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23
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Wang Z, Li N, Yu Q, Wang H. Genome-Wide Characterization of Salt-Responsive miRNAs, circRNAs and Associated ceRNA Networks in Tomatoes. Int J Mol Sci 2021; 22:12238. [PMID: 34830118 PMCID: PMC8625345 DOI: 10.3390/ijms222212238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 11/08/2021] [Accepted: 11/08/2021] [Indexed: 11/28/2022] Open
Abstract
Soil salinization is a major environmental stress that causes crop yield reductions worldwide. Therefore, the cultivation of salt-tolerant crops is an effective way to sustain crop yield. Tomatoes are one of the vegetable crops that are moderately sensitive to salt stress. Global market demand for tomatoes is huge and growing. In recent years, the mechanisms of salt tolerance in tomatoes have been extensively investigated; however, the molecular mechanism through which non-coding RNAs (ncRNAs) respond to salt stress is not well understood. In this study, we utilized small RNA sequencing and whole transcriptome sequencing technology to identify salt-responsive microRNAs (miRNAs), messenger RNAs (mRNAs), and circular RNAs (circRNAs) in roots of M82 cultivated tomato and Solanum pennellii (S. pennellii) wild tomato under salt stress. Based on the theory of competitive endogenous RNA (ceRNA), we also established several salt-responsive ceRNA networks. The results showed that circRNAs could act as miRNA sponges in the regulation of target mRNAs of miRNAs, thus participating in the response to salt stress. This study provides insights into the mechanisms of salt tolerance in tomatoes and serves as an effective reference for improving the salt tolerance of salt-sensitive cultivars.
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Affiliation(s)
- Zhongyu Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
| | - Ning Li
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China;
- Key Laboratory of Horticulture Crop Genomics and Genetic Improvement in Xinjiang, Urumqi 830091, China
- College of Horticulture, Xinjiang Agricultural University, Urumqi 830052, China
| | - Qinghui Yu
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China;
| | - Huan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
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24
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Gupta A, Shaw BP, Sahu BB. Post-translational regulation of the membrane transporters contributing to salt tolerance in plants. FUNCTIONAL PLANT BIOLOGY : FPB 2021; 48:1199-1212. [PMID: 34665998 DOI: 10.1071/fp21153] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 08/07/2021] [Indexed: 06/13/2023]
Abstract
This review article summarises the role of membrane transporters and their regulatory kinases in minimising the toxicity of Na+ in the plant under salt stress. The salt-tolerant plants keep their cytosolic level of Na+ up to 10-50mM. The first line of action in this context is the generation of proton motive force by the plasma membrane H+-ATPase. The generated proton motive force repolarises the membrane that gets depolarised due to passive uptake of Na+ under salt stress. The proton motive force generated also drives the plasma membrane Na+/H+ antiporter, SOS1 that effluxes the cytosolic Na+ back into the environment. At the intracellular level, Na+ is sequestered by the vacuole. Vacuolar Na+ uptake is mediated by Na+/H+ antiporter, NHX, driven by the electrochemical gradient for H+, generated by tonoplast H+ pumps, both H+ATPase and PPase. However, it is the expression of the regulatory kinases that make these transporters active through post-translational modification enabling them to effectively manage the cytosolic level of Na+, which is essential for tolerance to salinity in plants. Yet our knowledge of the expression and functioning of the regulatory kinases in plant species differing in tolerance to salinity is scant. Bioinformatics-based identification of the kinases like OsCIPK24 in crop plants, which are mostly salt-sensitive, may enable biotechnological intervention in making the crop cultivar more salt-tolerant, and effectively increasing its annual yield.
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Affiliation(s)
- Amber Gupta
- Abiotic Stress and Agro-Biotechnology Laboratory, Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha, 751023, India; and Regional Centre for Biotechnology, Faridabad, Haryana, 121001, India
| | - Birendra Prasad Shaw
- Abiotic Stress and Agro-Biotechnology Laboratory, Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha, 751023, India; and Regional Centre for Biotechnology, Faridabad, Haryana, 121001, India
| | - Binod Bihari Sahu
- Department of Life Science, NIT Rourkela, Rourkela, Odisha, 769008, India
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25
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Lin W, Wang Y, Liu X, Shang JX, Zhao L. OsWAK112, A Wall-Associated Kinase, Negatively Regulates Salt Stress Responses by Inhibiting Ethylene Production. FRONTIERS IN PLANT SCIENCE 2021; 12:751965. [PMID: 34675955 PMCID: PMC8523997 DOI: 10.3389/fpls.2021.751965] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 09/06/2021] [Indexed: 05/27/2023]
Abstract
The wall-associated kinase (WAK) multigene family plays critical roles in various cellular processes and stress responses in plants, however, whether WAKs are involved in salt tolerance is obscure. Herein, we report the functional characterization of a rice WAK, WAK112, whose expression is suppressed by salt. Overexpression of OsWAK112 in rice and heterologous expression of OsWAK112 in Arabidopsis significantly decreased plant survival under conditions of salt stress, while knocking down the OsWAK112 in rice increased plant survival under salt stress. OsWAK112 is universally expressed in plant and associated with cell wall. Meanwhile, in vitro kinase assays and salt tolerance analyses showed that OsWAK112 possesses kinase activity and that it plays a negative role in the response of plants to salt stress. In addition, OsWAK112 interacts with S-adenosyl-L-methionine synthetase (SAMS) 1/2/3, which catalyzes SAM synthesis from ATP and L-methionine, and promotes OsSAMS1 degradation under salt stress. Furthermore, in OsWAK112-overexpressing plants, there is a decreased SAMS content and a decreased ethylene content under salt stress. These results indicate that OsWAK112 negatively regulates plant salt responses by inhibiting ethylene production, possibly via direct binding with OsSAMS1/2/3.
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Affiliation(s)
| | | | | | | | - Liqun Zhao
- *Correspondence: Liqun Zhao, ; orcid.org/0000-0001-6718-8130
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26
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Chakraborty S, Driscoll HE, Abrahante JE, Zhang F, Fisher RF, Harris JM. Salt Stress Enhances Early Symbiotic Gene Expression in Medicago truncatula and Induces a Stress-Specific Set of Rhizobium-Responsive Genes. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:904-921. [PMID: 33819071 PMCID: PMC8578154 DOI: 10.1094/mpmi-01-21-0019-r] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Salt stress is a major agricultural concern inhibiting not only plant growth but also the symbiotic association between legume roots and the soil bacteria rhizobia. This symbiotic association is initiated by a molecular dialogue between the two partners, leading to the activation of a signaling cascade in the legume host and, ultimately, the formation of nitrogen-fixing root nodules. Here, we show that a moderate salt stress increases the responsiveness of early symbiotic genes in Medicago truncatula to its symbiotic partner, Sinorhizobium meliloti while, conversely, inoculation with S. meliloti counteracts salt-regulated gene expression, restoring one-third to control levels. Our analysis of early nodulin 11 (ENOD11) shows that salt-induced expression is dynamic, Nod-factor dependent, and requires the ionic but not the osmotic component of salt. We demonstrate that salt stimulation of rhizobium-induced gene expression requires NSP2, which functions as a node to integrate the abiotic and biotic signals. In addition, our work reveals that inoculation with S. meliloti succinoglycan mutants also hyperinduces ENOD11 expression in the presence or absence of salt, suggesting a possible link between rhizobial exopolysaccharide and the plant response to salt stress. Finally, we identify an accessory set of genes that are induced by rhizobium only under conditions of salt stress and have not been previously identified as being nodulation-related genes. Our data suggest that interplay of core nodulation genes with different accessory sets, specific for different abiotic conditions, functions to establish the symbiosis. Together, our findings reveal a complex and dynamic interaction between plant, microbe, and environment.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Sanhita Chakraborty
- Department of Plant Biology, University of Vermont, Burlington, VT 05405, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Heather E. Driscoll
- Vermont Biomedical Research Network (VBRN), Department of Biology, Norwich University, Northfield, Vermont 05663, USA
| | - Juan E. Abrahante
- University of Minnesota Informatics Institute (UMII) (CCRB 1-210C), 2231 6th Street SE, Minneapolis, MN 55455, USA
| | - Fan Zhang
- Vermont Biomedical Research Network (VBRN), Department of Biology, University of Vermont, Burlington, Vermont 05405, USA
- Institute for Translational Research and Department of family medicine, University of North Texas Health Science Center, Fort Worth, TX, 76107
| | - Robert F. Fisher
- Stanford University, Department of Biology, 371 Serra Mall, Stanford, California 94305-5020, USA
| | - Jeanne M. Harris
- Department of Plant Biology, University of Vermont, Burlington, VT 05405, USA
- Corresponding author: Jeanne M. Harris ()
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27
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Ambachew D, Blair MW. Genome Wide Association Mapping of Root Traits in the Andean Genepool of Common Bean ( Phaseolus vulgaris L.) Grown With and Without Aluminum Toxicity. FRONTIERS IN PLANT SCIENCE 2021; 12:628687. [PMID: 34249030 PMCID: PMC8269929 DOI: 10.3389/fpls.2021.628687] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 04/13/2021] [Indexed: 06/13/2023]
Abstract
Common bean is one of the most important grain legumes for human diets but is produced on marginal lands with unfavorable soil conditions; among which Aluminum (Al) toxicity is a serious and widespread problem. Under low pH, stable forms of Al dissolve into the soil solution and as phytotoxic ions inhibit the growth and function of roots through injury to the root apex. This results in a smaller root system that detrimentally effects yield. The goal of this study was to evaluate 227 genotypes from an Andean diversity panel (ADP) of common bean and determine the level of Al toxicity tolerance and candidate genes for this abiotic stress tolerance through root trait analysis and marker association studies. Plants were grown as seedlings in hydroponic tanks at a pH of 4.5 with a treatment of high Al concentration (50 μM) compared to a control (0 μM). The roots were harvested and scanned to determine average root diameter, root volume, root surface area, number of root links, number of root tips, and total root length. Percent reduction or increase was calculated for each trait by comparing treatments. Genome wide association study (GWAS) was conducted by testing phenotypic data against single nucleotide polymorphism (SNP) marker genotyping data for the panel. Principal components and a kinship matrix were included in the mixed linear model to correct for population structure. Analyses of variance indicated the presence of significant difference between genotypes. The heritability of traits ranged from 0.67 to 0.92 in Al-treated and reached similar values in non-treated plants. GWAS revealed significant associations between root traits and genetic markers on chromosomes Pv01, Pv04, Pv05, Pv06, and Pv11 with some SNPs contributing to more than one trait. Candidate genes near these loci were analyzed to explain the detected association and included an Al activated malate transporter gene and a multidrug and toxic compound extrusion gene. This study showed that polygenic inheritance was critical to aluminum toxicity tolerance in common beans roots. Candidate genes found suggested that exudation of malate and citrate as organic acids would be important for Al tolerance. Possible cross-talk between mechanisms of aluminum tolerance and resistance to other abiotic stresses are discussed.
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28
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Arefian M, Bhagya N, Prasad TSK. Phosphorylation-mediated signalling in flowering: prospects and retrospects of phosphoproteomics in crops. Biol Rev Camb Philos Soc 2021; 96:2164-2191. [PMID: 34047006 DOI: 10.1111/brv.12748] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 05/11/2021] [Accepted: 05/13/2021] [Indexed: 12/18/2022]
Abstract
Protein phosphorylation is a major post-translational modification, regulating protein function, stability, and subcellular localization. To date, annotated phosphorylation data are available mainly for model organisms and humans, despite the economic importance of crop species and their large kinomes. Our understanding of the phospho-regulation of flowering in relation to the biology and interaction between the pollen and pistil is still significantly lagging, limiting our knowledge on kinase signalling and its potential applications to crop production. To address this gap, we bring together relevant literature that were previously disconnected to present an overview of the roles of phosphoproteomic signalling pathways in modulating molecular and cellular regulation within specific tissues at different morphological stages of flowering. This review is intended to stimulate research, with the potential to increase crop productivity by providing a platform for novel molecular tools.
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Affiliation(s)
- Mohammad Arefian
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - N Bhagya
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - T S Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore, 575018, India
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29
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Moin M, Saha A, Bakshi A, Madhav MS, Kirti PB. Constitutive expression of Ribosomal Protein L6 modulates salt tolerance in rice transgenic plants. Gene 2021; 789:145670. [PMID: 33892070 DOI: 10.1016/j.gene.2021.145670] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 03/14/2021] [Accepted: 04/15/2021] [Indexed: 12/17/2022]
Abstract
We have functionally characterized the RPL6, a Ribosomal Protein Large subunit gene for salt stress tolerance in rice. The overexpression of RPL6 resulted in tolerance to moderate (150 mM) to high (200 mM) levels of salt (NaCl). The transgenic rice plants expressing RPL6 constitutively showed better phenotypic and physiological responses with high quantum efficiency, accumulation of higher chlorophyll and proline contents, and an overall increase in seed yield compared with the wild type in salt stress treatments. An iTRAQ-based comparative proteomic analysis revealed the high expression of about 333 proteins among the 4378 DAPs in a selected overexpression line of RPL6 treated with 200 mM of NaCl. The functional analysis showed that these highly accumulated proteins (HAPs) are involved in photosynthesis, ribosome and chloroplast biogenesis, ion transportation, transcription and translation regulation, phytohormone and secondary metabolite signal transduction. An in silico network analysis of HAPs predicted that RPL6 binds with translation-related proteins and helicases, which coordinately affect the activities of a comprehensive signaling network, thereby inducing tolerance and promoting growth and productivity in response to salt stress. Our overall findings identified a novel candidate, RPL6, whose characterization contributed to the existing knowledge on the complexity of salt tolerance mechanism in plants.
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Affiliation(s)
- Mazahar Moin
- Biotechnology Division, ICAR-Indian Institute of Rice Research (IIRR), Hyderabad 500030, India.
| | - Anusree Saha
- Department of Plant Sciences, University of Hyderabad, Hyderabad 500046, India
| | - Achala Bakshi
- Biotechnology Division, ICAR-Indian Institute of Rice Research (IIRR), Hyderabad 500030, India
| | - M S Madhav
- Biotechnology Division, ICAR-Indian Institute of Rice Research (IIRR), Hyderabad 500030, India
| | - P B Kirti
- Department of Plant Sciences, University of Hyderabad, Hyderabad 500046, India; Agri-Biotech Foundation, PJTS Agricultural University, Hyderabad 500030, India
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30
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Shao A, Wang W, Fan S, Xu X, Yin Y, Erick A, Li X, Wang G, Wang H, Fu J. Comprehensive transcriptional analysis reveals salt stress-regulated key pathways, hub genes and time-specific responsive gene categories in common bermudagrass (Cynodon dactylon (L.) Pers.) roots. BMC PLANT BIOLOGY 2021; 21:175. [PMID: 33838660 PMCID: PMC8035780 DOI: 10.1186/s12870-021-02939-1] [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: 07/09/2020] [Accepted: 03/25/2021] [Indexed: 06/02/2023]
Abstract
BACKGROUND Despite its good salt-tolerance level, key genes and pathways involved with temporal salt response of common bermudagrass (Cynodon dactylon (L.) Pers.) have not been explored. Therefore, in this study, to understand the underlying regulatory mechanism following the different period of salt exposure, a comprehensive transcriptome analysis of the bermudagrass roots was conducted. RESULTS The transcripts regulated after 1 h, 6 h, or 24 h of hydroponic exposure to 200 mM NaCl in the roots of bermudagrass were investigated. Dataset series analysis revealed 16 distinct temporal salt-responsive expression profiles. Enrichment analysis identified potentially important salt responsive genes belonging to specific categories, such as hormonal metabolism, secondary metabolism, misc., cell wall, transcription factors and genes encoded a series of transporters. Weighted gene co-expression network analysis (WGCNA) revealed that lavenderblush2 and brown4 modules were significantly positively correlated with the proline content and peroxidase activity and hub genes within these two modules were further determined. Besides, after 1 h of salt treatment, genes belonging to categories such as signalling receptor kinase, transcription factors, tetrapyrrole synthesis and lipid metabolism were immediately and exclusively up-enriched compared to the subsequent time points, which indicated fast-acting and immediate physiological responses. Genes involved in secondary metabolite biosynthesis such as simple phenols, glucosinolates, isoflavones and tocopherol biosynthesis were exclusively up-regulated after 24 h of salt treatment, suggesting a slightly slower reaction of metabolic adjustment. CONCLUSION Here, we revealed salt-responsive genes belonging to categories that were commonly or differentially expressed in short-term salt stress, suggesting possible adaptive salt response mechanisms in roots. Also, the distinctive salt-response pathways and potential salt-tolerant hub genes investigated can provide useful future references to explore the molecular mechanisms of bermudagrass.
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Affiliation(s)
- An Shao
- Coastal Salinity Tolerant Grass Engineering and Technology Research Center, Ludong University, Yantai, Shandong, People's Republic of China
| | - Wei Wang
- Coastal Salinity Tolerant Grass Engineering and Technology Research Center, Ludong University, Yantai, Shandong, People's Republic of China
| | - Shugao Fan
- Coastal Salinity Tolerant Grass Engineering and Technology Research Center, Ludong University, Yantai, Shandong, People's Republic of China
| | - Xiao Xu
- Coastal Salinity Tolerant Grass Engineering and Technology Research Center, Ludong University, Yantai, Shandong, People's Republic of China
| | - Yanling Yin
- Coastal Salinity Tolerant Grass Engineering and Technology Research Center, Ludong University, Yantai, Shandong, People's Republic of China
| | - Amombo Erick
- Coastal Salinity Tolerant Grass Engineering and Technology Research Center, Ludong University, Yantai, Shandong, People's Republic of China
| | - Xiaoning Li
- Coastal Salinity Tolerant Grass Engineering and Technology Research Center, Ludong University, Yantai, Shandong, People's Republic of China
| | - Guangyang Wang
- Coastal Salinity Tolerant Grass Engineering and Technology Research Center, Ludong University, Yantai, Shandong, People's Republic of China
| | - Hongli Wang
- Coastal Salinity Tolerant Grass Engineering and Technology Research Center, Ludong University, Yantai, Shandong, People's Republic of China
| | - Jinmin Fu
- Coastal Salinity Tolerant Grass Engineering and Technology Research Center, Ludong University, Yantai, Shandong, People's Republic of China.
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Liu ZY, Li XP, Zhang TQ, Wang YY, Wang C, Gao CQ. Overexpression of ThMYB8 mediates salt stress tolerance by directly activating stress-responsive gene expression. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 302:110668. [PMID: 33288032 DOI: 10.1016/j.plantsci.2020.110668] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 08/05/2020] [Accepted: 09/05/2020] [Indexed: 05/02/2023]
Abstract
MYB transcription factors are important in abiotic stress responses; however, the detailed mechanisms are unclear. Tamarix hispida contains multiple MYB genes. The present study characterized T. hispida MYB8 (ThMYB8) during salt stress using transgenic T. hispida and Arabidopsis assays. ThMYB8 overexpression and ThMYB8 RNAi analysis demonstrated that ThMYB8 enhanced the salt stress tolerance. Transgenic Arabidopsis ectopic expression of ThMYB8 significantly increased root growth, fresh weight, and seed germination rate compared with that of the wild-type under salt stress. Physiological parameters analysis in T. hispida and Arabidopsis showed that ThMYB8 overexpressing plants had the lowest levels of O2, H2O2, cell death, malondialdehyde, and electrolyte leakage. Overexpression of ThMYB8 regulated Na+ and K+ concentrations in plant tissues while maintaining K+/Na+ homeostasis. Analysis using qRT-PCR and ChIP-PCR identified possible downstream ThMYB8-regulated genes. ThMYB8 regulated the expression of ThCYP450-2 (cytochrome p450-2), Thltk (leucine-rich repeat transmembrane protein kinase), and ThTIP (aquaporin TIP) by binding to the MBSI motif ('CAACTG') in their promoters. The results indicated that ThMYB8 enhanced salt stress tolerance in T. hispida by regulating gene expression related to the activation of stress-associated physiological changes, such as enhanced reactive oxygen species scavenging capability, maintaining K+/Na+ homeostasis, and decreasing the malondialdehyde content and lipid peroxidation cell membranes.
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Affiliation(s)
- Zhong-Yuan Liu
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin 150040, China
| | - Xin-Ping Li
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin 150040, China
| | - Teng-Qian Zhang
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin 150040, China
| | - Yuan-Yuan Wang
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin 150040, China
| | - Chao Wang
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin 150040, China
| | - Cai-Qiu Gao
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin 150040, China.
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Lin F, Li S, Wang K, Tian H, Gao J, Zhao Q, Du C. A leucine-rich repeat receptor-like kinase, OsSTLK, modulates salt tolerance in rice. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 296:110465. [PMID: 32540023 DOI: 10.1016/j.plantsci.2020.110465] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Revised: 02/24/2020] [Accepted: 03/08/2020] [Indexed: 05/23/2023]
Abstract
Leucine-rich repeat receptor-like kinases (LRR-RLKs) have been widely associated with plant abiotic stress responses. However, the functions of the majority of LRR-RLKs has not been well defined. Here, we identified a novel rice LRR-RLK member involved in salt tolerance and designated as OsSTLK (Oryza sativa L. Salt-Tolerance LRR-RLK). Transcript analysis showed that OsSTLK was significantly induced in response to salt stress in rice shoot and root in a time and dosage-dependent fashion. Phenotypic observations indicated that OsSTLK overexpression exhibited reduced salt sensitivity, and improved salt stress tolerance. Further physiological analysis showed that OsSTLK overexpression remarkably reduced electrolyte leakage, malondialdehyde (MDA) content, reactive oxygen species (ROS) accumulation under salt stress conditions by up-regulating ROS-scavenging activities and modifying stomatal patterning. Moreover, Na+/K+ ratio and MAPK phosphorylation level were also reduced in OsSTLK-overexpression transgenic rice plants compared with WT control. Taken together, our findings suggested that OsSTLK as an important positive regulator of salt stress tolerance perhaps through regulating ROS scavenging system, Na+/K+ ratio and MAPK signal pathway.
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Affiliation(s)
- Faming Lin
- Collaborative Innovation Center of Henan Grain Crops, Rice Engineer Center in Henan Province, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Shen Li
- Collaborative Innovation Center of Henan Grain Crops, Rice Engineer Center in Henan Province, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Ke Wang
- Collaborative Innovation Center of Henan Grain Crops, Rice Engineer Center in Henan Province, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Haoran Tian
- Collaborative Innovation Center of Henan Grain Crops, Rice Engineer Center in Henan Province, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Junfeng Gao
- Collaborative Innovation Center of Henan Grain Crops, Rice Engineer Center in Henan Province, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Quanzhi Zhao
- Collaborative Innovation Center of Henan Grain Crops, Rice Engineer Center in Henan Province, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China.
| | - Changqing Du
- Collaborative Innovation Center of Henan Grain Crops, Rice Engineer Center in Henan Province, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China.
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Sun X, Zhu J, Li X, Li Z, Han L, Luo H. AsHSP26.8a, a creeping bentgrass small heat shock protein integrates different signaling pathways to modulate plant abiotic stress response. BMC PLANT BIOLOGY 2020; 20:184. [PMID: 32345221 PMCID: PMC7189581 DOI: 10.1186/s12870-020-02369-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 03/29/2020] [Indexed: 05/24/2023]
Abstract
BACKGROUND Small heat shock proteins (sHSPs) are critical for plant response to biotic and abiotic stresses, especially heat stress. They have also been implicated in various aspects of plant development. However, the acting mechanisms of the sHSPs in plants, especially in perennial grass species, remain largely elusive. RESULTS In this study, AsHSP26.8a, a novel chloroplast-localized sHSP gene from creeping bentgrass (Agrostis stolonifera L.) was cloned and its role in plant response to environmental stress was studied. AsHSP26.8a encodes a protein of 26.8 kDa. Its expression was strongly induced in both leaf and root tissues by heat stress. Transgenic Arabidopsis plants overexpressing AsHSP26.8a displayed reduced tolerance to heat stress. Furthermore, overexpression of AsHSP26.8a resulted in hypersensitivity to hormone ABA and salinity stress. Global gene expression analysis revealed AsHSP26.8a-modulated expression of heat-shock transcription factor gene, and the involvement of AsHSP26.8a in ABA-dependent and -independent as well as other stress signaling pathways. CONCLUSIONS Our results suggest that AsHSP26.8a may negatively regulate plant response to various abiotic stresses through modulating ABA and other stress signaling pathways.
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Affiliation(s)
- Xinbo Sun
- Key Laboratory of Crop Growth Regulation of Hebei Province, College of Agronomy, Hebei Agricultural University, Baoding, Hebei, 071001, People's Republic of China
- Department of Genetics and Biochemistry, Clemson University, 110 Biosystems Research Complex, Clemson, SC, 29634, USA
| | - Junfei Zhu
- Key Laboratory of Crop Growth Regulation of Hebei Province, College of Agronomy, Hebei Agricultural University, Baoding, Hebei, 071001, People's Republic of China
| | - Xin Li
- Key Laboratory of Crop Growth Regulation of Hebei Province, College of Agronomy, Hebei Agricultural University, Baoding, Hebei, 071001, People's Republic of China
| | - Zhigang Li
- Department of Genetics and Biochemistry, Clemson University, 110 Biosystems Research Complex, Clemson, SC, 29634, USA
| | - Liebao Han
- Turfgrass Research Institute, Beijing Forestry University, Beijing, 100083, People's Republic of China.
| | - Hong Luo
- Department of Genetics and Biochemistry, Clemson University, 110 Biosystems Research Complex, Clemson, SC, 29634, USA.
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Li Q, Qin Y, Hu X, Li G, Ding H, Xiong X, Wang W. Transcriptome analysis uncovers the gene expression profile of salt-stressed potato (Solanum tuberosum L.). Sci Rep 2020; 10:5411. [PMID: 32214109 PMCID: PMC7096413 DOI: 10.1038/s41598-020-62057-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 03/05/2020] [Indexed: 12/14/2022] Open
Abstract
Potato (Solanum tuberosum L.) is an important staple food worldwide. However, its growth has been heavily suppressed by salt stress. The molecular mechanisms of salt tolerance in potato remain unclear. It has been shown that the tetraploid potato Longshu No. 5 is a salt-tolerant genotype. Therefore, in this study we conducted research to identify salt stress response genes in Longshu No. 5 using a NaCl treatment and time-course RNA sequencing. The total number of differentially expressed genes (DEGs) in response to salt stress was 5508. Based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, it was found that DEGs were significantly enriched in the categories of nucleic acid binding, transporter activity, ion or molecule transport, ion binding, kinase activity and oxidative phosphorylation. Particularly, the significant differential expression of encoding ion transport signaling genes suggests that this signaling pathway plays a vital role in salt stress response in potato. Finally, the DEGs in the salt response pathway were verified by Quantitative real-time PCR (qRT-PCR). These results provide valuable information on the salt tolerance of molecular mechanisms in potatoes, and establish a basis for breeding salt-tolerant cultivars.
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Affiliation(s)
- Qing Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Root and Tuber Crops, Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
- College of Horticulture, Hunan Agricultural University/Hunan Provincial Engineering Research Center for Potatoes/Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Changsha, 410128, China
| | - Yuzhi Qin
- College of Horticulture, Hunan Agricultural University/Hunan Provincial Engineering Research Center for Potatoes/Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Changsha, 410128, China
| | - Xinxi Hu
- College of Horticulture, Hunan Agricultural University/Hunan Provincial Engineering Research Center for Potatoes/Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Changsha, 410128, China
| | - Guangcun Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Root and Tuber Crops, Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
| | - Hongying Ding
- College of Horticulture, Hunan Agricultural University/Hunan Provincial Engineering Research Center for Potatoes/Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Changsha, 410128, China
| | - Xingyao Xiong
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Root and Tuber Crops, Ministry of Agriculture and Rural Affairs, Beijing, 100081, China.
- College of Horticulture, Hunan Agricultural University/Hunan Provincial Engineering Research Center for Potatoes/Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Changsha, 410128, China.
| | - Wanxing Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Root and Tuber Crops, Ministry of Agriculture and Rural Affairs, Beijing, 100081, China.
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Nongpiur RC, Singla-Pareek SL, Pareek A. The quest for osmosensors in plants. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:595-607. [PMID: 31145792 DOI: 10.1093/jxb/erz263] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 05/22/2019] [Indexed: 05/20/2023]
Abstract
Osmotic stress has severe effects on crop productivity. Since climate change is predicted to exacerbate this problem, the development of new crops that are tolerant to osmotic stresses, especially drought and salinity stress, is required. However, only limited success has been achieved to date, primarily because of the lack of a clear understanding of the mechanisms that facilitate osmosensing. Here, we discuss the potential mechanisms of osmosensing in plants. We highlight the roles of proteins such as receptor-like kinases, which sense stress-induced cell wall damage, mechanosensitive calcium channels, which initiate a calcium-induced stress response, and phospholipase C, a membrane-bound enzyme that is integral to osmotic stress perception. We also discuss the roles of aquaporins and membrane-bound histidine kinases, which could potentially detect changes in extracellular osmolarity in plants, as they do in prokaryotes and lower eukaryotes. These putative osmosensors have the potential to serve as master regulators of the osmotic stress response in plants and could prove to be useful targets for the selection of osmotic stress-tolerant crops.
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Affiliation(s)
- Ramsong Chantre Nongpiur
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Sneh Lata Singla-Pareek
- 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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Cruz MV, Mori GM, Oh DH, Dassanayake M, Zucchi MI, Oliveira RS, Souza APD. Molecular responses to freshwater limitation in the mangrove tree Avicennia germinans (Acanthaceae). Mol Ecol 2019; 29:344-362. [PMID: 31834961 DOI: 10.1111/mec.15330] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 11/27/2019] [Accepted: 11/28/2019] [Indexed: 12/31/2022]
Abstract
Environmental variation along the geographical space can shape populations by natural selection. In the context of global warming and changing precipitation regimes, it is crucial to understand the role of environmental heterogeneity in tropical trees adaptation, given their disproportional contribution to water and carbon biogeochemical cycles. Here, we investigated how heterogeneity in freshwater availability along tropical wetlands has influenced molecular variations of the black mangrove (Avicennia germinans). A total of 57 trees were sampled at seven sites differing markedly in precipitation regime and riverine freshwater inputs. Using 2,297 genome-wide single nucleotide polymorphic markers, we found signatures of natural selection by the association between variations in allele frequencies and environmental variables, including the precipitation of the warmest quarter and the annual precipitation. Additionally, we found candidate loci for selection based on statistical deviations from neutral expectations of interpopulation differentiation. Most candidate loci within transcribed sequences were functionally associated with central aspects of drought tolerance or plant response to drought. Moreover, our results suggest the occurrence of the rapid evolution of a population, probably in response to sudden and persistent limitations in plant access to soil water, following a road construction in 1974. Observations supporting rapid evolution included the reduction in tree size and changes in allele frequencies and in transcript expression associated with increased drought tolerance through the accumulation of osmoprotectants and antioxidants, biosynthesis of cuticles, protection against protein degradation, stomatal closure, photorespiration and photosynthesis. We describe a major role of spatial heterogeneity in freshwater availability in the specialization of this typically tropical tree.
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Affiliation(s)
- Mariana Vargas Cruz
- Department of Plant Biology, Institute of Biology, University of Campinas (Unicamp), Campinas, Brazil
| | | | - Dong-Ha Oh
- Department of Biological Sciences, Louisiana State University (LSU), Louisiana, LA, USA
| | - Maheshi Dassanayake
- Department of Biological Sciences, Louisiana State University (LSU), Louisiana, LA, USA
| | | | - Rafael Silva Oliveira
- Department of Plant Biology, Institute of Biology, University of Campinas (Unicamp), Campinas, Brazil
| | - Anete Pereira de Souza
- Department of Plant Biology, Institute of Biology, University of Campinas (Unicamp), Campinas, Brazil
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Nanda AK, El Habti A, Hocart CH, Masle J. ERECTA receptor-kinases play a key role in the appropriate timing of seed germination under changing salinity. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:6417-6435. [PMID: 31504732 PMCID: PMC6859730 DOI: 10.1093/jxb/erz385] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 08/15/2019] [Indexed: 05/21/2023]
Abstract
Appropriate timing of seed germination is crucial for the survival and propagation of plants, and for crop yield, especially in environments prone to salinity or drought. However, the exact mechanisms by which seeds perceive changes in soil conditions and integrate them to trigger germination remain elusive, especially once the seeds are non-dormant. In this study, we determined that the Arabidopsis ERECTA (ER), ERECTA-LIKE1 (ERL1), and ERECTA-LIKE2 (ERL2) leucine-rich-repeat receptor-like kinases regulate seed germination and its sensitivity to changes in salt and osmotic stress levels. Loss of ER alone, or in combination with ERL1 and/or ERL2, slows down the initiation of germination and its progression to completion, or arrests it altogether under saline conditions, until better conditions return. This function is maternally controlled via the tissues surrounding the embryo, with a primary role being played by the properties of the seed coat and its mucilage. These relate to both seed-coat expansion and subsequent differentiation and to salinity-dependent interactions between the mucilage, subtending seed coat layers and seed interior in the germinating seed. Salt-hypersensitive er105, er105 erl1.2, er105 erl2.1 and triple-mutant seeds also exhibit increased sensitivity to exogenous ABA during germination, and under salinity show an enhanced up-regulation of the germination repressors and inducers of dormancy ABA-insensitive-3, ABA-insensitive-5, DELLA-encoding RGL2, and Delay-Of-Germination-1. These findings reveal a novel role of the ERECTA receptor-kinases in the sensing of conditions at the seed surface and the integration of developmental, dormancy and stress signalling pathways in seeds. They also open novel avenues for the genetic improvement of plant adaptation to changing drought and salinity patterns.
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Affiliation(s)
- Amrit K Nanda
- Research School of Biology, The Australian National University, Canberra ACT, Australia
| | - Abdeljalil El Habti
- Research School of Biology, The Australian National University, Canberra ACT, Australia
| | - Charles H Hocart
- Research School of Biology, The Australian National University, Canberra ACT, Australia
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Zeng A, Chen P, Korth KL, Ping J, Thomas J, Wu C, Srivastava S, Pereira A, Hancock F, Brye K, Ma J. RNA sequencing analysis of salt tolerance in soybean (Glycine max). Genomics 2019; 111:629-635. [PMID: 29626511 DOI: 10.1016/j.ygeno.2018.03.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Revised: 03/07/2018] [Accepted: 03/26/2018] [Indexed: 01/13/2023]
Abstract
Salt stress causes foliar chlorosis and scorch, plant stunting, and eventually yield reduction in soybean. There are differential responses, namely tolerance (excluder) and intolerance (includer), among soybean germplasm. However, the genetic and physiological mechanisms for salt tolerance is complex and not clear yet. Based on the results from the screening of the RA-452 x Osage mapping population, two F4:6 lines with extreme responses, most tolerant and most sensitive, were selected for a time-course gene expression study in which the 250 mM NaCl treatment was initially imposed at the V1 stage and continued for 24 h (hrs). Total RNA was isolated from the leaves harvested at 0, 6, 12, 24 h after the initiation of salt treatment, respectively. The RNA-Seq analysis was conducted to compare the salt tolerant genotype with salt sensitive genotype at each time point using RNA-Seq pipeline method. A total of 2374, 998, 1746, and 630 differentially expressed genes (DEGs) between salt-tolerant line and salt-sensitive line, were found at 0, 6, 12, and 24 h, respectively. The expression patterns of 154 common DEGs among all the time points were investigated, of which, six common DEGs were upregulated and seven common DEGs were downregulated in salt-tolerant line. Moreover, 13 common DEGs were dramatically expressed at all the time points. Based on Log2 (fold change) of expression level of salt-tolerant line to salt-sensitive line and gene annotation, Glyma.02G228100, Glyma.03G226000, Glyma.03G031000, Glyma.03G031400, Glyma.04G180300, Glyma.04G180400, Glyma.05 g204600, Glyma.08G189600, Glyma.13G042200, and Glyma.17G173200, were considered to be the key potential genes involving in the salt-tolerance mechanism in the soybean salt-tolerant line.
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Affiliation(s)
- Ailan Zeng
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR 72701, USA; Monsanto Company, 700 Chesterfield Pkwy W, Chesterfield, MO 63017, USA
| | - Pengyin Chen
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR 72701, USA; Fisher Delta Research Center, University of Missouri, 147 State Hwy T, Portageville, MO 63873, USA.
| | - Ken L Korth
- Department of Plant Pathology, University of Arkansas, Fayetteville, AR 72701, USA
| | - Jieqing Ping
- Department of Agronomy, Purdue University, West Lafayette, IN 47907, USA
| | - Julie Thomas
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR 72701, USA
| | - Chengjun Wu
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR 72701, USA
| | - Subodh Srivastava
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
| | - Andy Pereira
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR 72701, USA
| | - Floyd Hancock
- Former Monsanto Soybean Breeder, 2711 Blacks Ferry Road, Pocahontas, AR 72455, USA
| | - Kristofor Brye
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR 72701, USA
| | - Jianxin Ma
- Department of Agronomy, Purdue University, West Lafayette, IN 47907, USA
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Zhang R, Chen H, Duan M, Zhu F, Wen J, Dong J, Wang T. Medicago falcata MfSTMIR, an E3 ligase of endoplasmic reticulum-associated degradation, is involved in salt stress response. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 98:680-696. [PMID: 30712282 PMCID: PMC6849540 DOI: 10.1111/tpj.14265] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 01/22/2019] [Accepted: 01/23/2019] [Indexed: 05/28/2023]
Abstract
Recent studies on E3 of endoplasmic reticulum (ER)-associated degradation (ERAD) in plants have revealed homologs in yeast and animals. However, it remains unknown whether the plant ERAD system contains a plant-specific E3 ligase. Here, we report that MfSTMIR, which encodes an ER-membrane-localized RING E3 ligase that is highly conserved in leguminous plants, plays essential roles in the response of ER and salt stress in Medicago. MfSTMIR expression was induced by salt and tunicamycin (Tm). mtstmir loss-of-function mutants displayed impaired induction of the ER stress-responsive genes BiP1/2 and BiP3 under Tm treatment and sensitivity to salt stress. MfSTMIR promoted the degradation of a known ERAD substrate, CPY*. MfSTMIR interacted with the ERAD-associated ubiquitin-conjugating enzyme MtUBC32 and Sec61-translocon subunit MtSec61γ. MfSTMIR did not affect MtSec61γ protein stability. Our results suggest that the plant-specific E3 ligase MfSTMIR participates in the ERAD pathway by interacting with MtUBC32 and MtSec61γ to relieve ER stress during salt stress.
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Affiliation(s)
- Rongxue Zhang
- State Key Laboratory of AgrobiotechnologyCollege of Biological SciencesChina Agricultural UniversityBeijing100193China
- Crop Research Institute of Tianjin Academy of Agricultural SciencesTianjin300384China
| | - Hong Chen
- State Key Laboratory of AgrobiotechnologyCollege of Biological SciencesChina Agricultural UniversityBeijing100193China
| | - Mei Duan
- State Key Laboratory of AgrobiotechnologyCollege of Biological SciencesChina Agricultural UniversityBeijing100193China
| | - Fugui Zhu
- State Key Laboratory of AgrobiotechnologyCollege of Biological SciencesChina Agricultural UniversityBeijing100193China
| | - Jiangqi Wen
- Plant Biology DivisionSamuel Roberts Noble Research InstituteArdmoreOklahoma73401USA
| | - Jiangli Dong
- State Key Laboratory of AgrobiotechnologyCollege of Biological SciencesChina Agricultural UniversityBeijing100193China
| | - Tao Wang
- State Key Laboratory of AgrobiotechnologyCollege of Biological SciencesChina Agricultural UniversityBeijing100193China
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Zaman MSU, Malik AI, Erskine W, Kaur P. Changes in gene expression during germination reveal pea genotypes with either "quiescence" or "escape" mechanisms of waterlogging tolerance. PLANT, CELL & ENVIRONMENT 2019; 42:245-258. [PMID: 29761495 DOI: 10.1111/pce.13338] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 05/01/2018] [Accepted: 05/01/2018] [Indexed: 05/12/2023]
Abstract
Waterlogging causes germination failure in pea (Pisum sativum L.). Three genotypes (BARI Motorshuti-3, Natore local-2 [NL-2], and Kaspa) contrasting in ability to germinate in waterlogged soil were exposed to different durations of waterlogging. Whole genome RNAseq was employed to capture differentially expressing genes. The ability to germinate in waterlogged soil was associated with testa colour and testa membrane integrity as confirmed by electrical conductivity measurements. Genotypes Kaspa and NL-2 displayed different mechanisms of tolerance. In Kaspa, an energy conserving strategy was indicated by a strong upregulation of tyrosine protein kinsase and down regulation of linoleate 9S-lipoxygenase 5, a fat metabolism gene. In contrast, a faster energy utilization strategy was suggested in NL-2 by the marked upregulation of a subtilase family protein and peroxisomal adenine nucleotide carrier 2, a fat metabolizing gene. Waterlogging susceptibility in germinating seeds of genotype BARI Motorshuti-3 was linked to upregulation of a kunitz-type trypsin/protease inhibitor that blocks protein metabolism and may lead to excessive lipid metabolism and the membrane leakage associated with waterlogging damage. Pathway analyses based on gene ontologies showed seed storage protein metabolism as upregulated in tolerant genotypes and downregulated in the sensitive genotype. Understanding the tolerance mechanism provides a platform to breed for adaptation to waterlogging stress at germination in pea.
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Affiliation(s)
- Md Shahin Uz Zaman
- Centre for Plant Genetics and Breeding, UWA School of Agriculture and Environment, The University of Western Australia, Crawley, Western Australia, 6009, Australia
- Institute of Agriculture, The University of Western Australia, Crawley, Western Australia, 6009, Australia
| | - Al Imran Malik
- Centre for Plant Genetics and Breeding, UWA School of Agriculture and Environment, The University of Western Australia, Crawley, Western Australia, 6009, Australia
| | - William Erskine
- Centre for Plant Genetics and Breeding, UWA School of Agriculture and Environment, The University of Western Australia, Crawley, Western Australia, 6009, Australia
- Institute of Agriculture, The University of Western Australia, Crawley, Western Australia, 6009, Australia
| | - Parwinder Kaur
- Centre for Plant Genetics and Breeding, UWA School of Agriculture and Environment, The University of Western Australia, Crawley, Western Australia, 6009, Australia
- Institute of Agriculture, The University of Western Australia, Crawley, Western Australia, 6009, Australia
- Telethon Kids Institute, Subiaco, Western Australia, 6008, Australia
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Yuan N, Rai KM, Balasubramanian VK, Upadhyay SK, Luo H, Mendu V. Genome-wide identification and characterization of LRR-RLKs reveal functional conservation of the SIF subfamily in cotton (Gossypium hirsutum). BMC PLANT BIOLOGY 2018; 18:185. [PMID: 30189845 PMCID: PMC6128003 DOI: 10.1186/s12870-018-1395-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 08/27/2018] [Indexed: 05/12/2023]
Abstract
BACKGROUND As one of the largest subfamilies of the receptor-like protein kinases (RLKs) in plants, Leucine Rich Repeats-RLKs (LRR-RLKs) are involved in many critical biological processes including growth, development and stress responses in addition to various physiological roles. Arabidopsis contains 234 LRR-RLKs, and four members of Stress Induced Factor (SIF) subfamily (AtSIF1-AtSIF4) which are involved in abiotic and biotic stress responses. Herein, we aimed at identification and functional characterization of SIF subfamily in cultivated tetraploid cotton Gossypium hirsutum. RESULTS Genome-wide analysis of cotton LRR-RLK gene family identified 543 members and phylogenetic analysis led to the identification of 6 cotton LRR-RLKs with high homology to Arabidopsis SIFs. Of the six SIF homologs, GhSIF1 is highly conserved exhibiting 46-47% of homology with AtSIF subfamily in amino acid sequence. The GhSIF1 was transiently silenced using Virus-Induced Gene Silencing system specifically targeting the 3' Untranslated Region. The transiently silenced cotton seedlings showed enhanced salt tolerance compared to the control plants. Further, the transiently silenced plants showed better growth, lower electrolyte leakage, and higher chlorophyll and biomass contents. CONCLUSIONS Overall, 543 LRR-RLK genes were identified using genome-wide analysis in cultivated tetraploid cotton G. hirsutum. The present investigation also demonstrated the conserved salt tolerance function of SIF family member in cotton. The GhSIF1 gene can be knocked out using genome editing technologies to improve salt tolerance in cotton.
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Affiliation(s)
- Ning Yuan
- Fiber and Biopolymer Research Institute (FBRI), Department of Plant and Soil Science, Texas Tech University, Lubbock, TX 79409 USA
| | - Krishan Mohan Rai
- Fiber and Biopolymer Research Institute (FBRI), Department of Plant and Soil Science, Texas Tech University, Lubbock, TX 79409 USA
| | - Vimal Kumar Balasubramanian
- Fiber and Biopolymer Research Institute (FBRI), Department of Plant and Soil Science, Texas Tech University, Lubbock, TX 79409 USA
| | | | - Hong Luo
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634 USA
| | - Venugopal Mendu
- Fiber and Biopolymer Research Institute (FBRI), Department of Plant and Soil Science, Texas Tech University, Lubbock, TX 79409 USA
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Hu L, Ye M, Kuai P, Ye M, Erb M, Lou Y. OsLRR-RLK1, an early responsive leucine-rich repeat receptor-like kinase, initiates rice defense responses against a chewing herbivore. THE NEW PHYTOLOGIST 2018; 219:1097-1111. [PMID: 29878383 DOI: 10.1111/nph.15247] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 05/01/2018] [Indexed: 05/20/2023]
Abstract
Plants are constantly exposed to a variety of environmental stresses, including herbivory. How plants perceive herbivores on a molecular level is poorly understood. Leucine-rich repeat receptor-like kinases (LRR-RLKs), the largest subfamily of RLKs, are essential for plants to detect external stress signals, and may therefore also be involved in herbivore perception. Here, we employed RNA interference silencing, phytohormone profiling and complementation, as well as herbivore resistance assays, to investigate the requirement of an LRR-RLK for the initiation of rice (Oryza sativa) defenses against the chewing herbivore striped stem borer (SSB) Chilo suppressalis. We discovered a plasma membrane-localized LRR-RLK, OsLRR-RLK1, whose transcription is strongly up-regulated by SSB attack and treatment with oral secretions of Spodoptera frugiperda. OsLRR-RLK1 acts upstream of mitogen-activated protein kinase (MPK) cascades, and positively regulates defense-related MPKs and WRKY transcription factors. Moreover, OsLRR-RLK1 is a positive regulator of SSB-elicited, but not wound-elicited, levels of jasmonic acid and ethylene, trypsin protease inhibitor activity and plant resistance towards SSB. OsLRR-RLK1 therefore plays an important role in herbivory-induced defenses of rice. Given the well-documented role of LRR-RLKs in the perception of stress-related molecules, we speculate that OsLRR-RLK1 may be involved in the perception of herbivory-associated molecular patterns.
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Affiliation(s)
- Lingfei Hu
- State Key Laboratory of Rice Biology & Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, 310058, Hangzhou, China
- Institute of Plant Sciences, University of Bern, 3013, Bern, Switzerland
| | - Meng Ye
- State Key Laboratory of Rice Biology & Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, 310058, Hangzhou, China
- Institute of Plant Sciences, University of Bern, 3013, Bern, Switzerland
| | - Peng Kuai
- State Key Laboratory of Rice Biology & Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, 310058, Hangzhou, China
| | - Miaofen Ye
- State Key Laboratory of Rice Biology & Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, 310058, Hangzhou, China
| | - Matthias Erb
- Institute of Plant Sciences, University of Bern, 3013, Bern, Switzerland
| | - Yonggen Lou
- State Key Laboratory of Rice Biology & Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, 310058, Hangzhou, China
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Quantitative proteomic analysis using iTRAQ to identify salt-responsive proteins during the germination stage of two Medicago species. Sci Rep 2018; 8:9553. [PMID: 29934583 PMCID: PMC6015060 DOI: 10.1038/s41598-018-27935-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 06/12/2018] [Indexed: 01/01/2023] Open
Abstract
Salt stress is one of the primary abiotic stresses responsible for decreasing crop yields worldwide. Germinating seeds can be greatly influenced by saline conditions. In this study, the physiological and phenotypic changes induced by salt treatments (10–50 mM NaCl and Na2SO4 mixtures) were analysed for Zhongmu-3 (Medicago sativa) and R108 (Medicago truncatula) seedlings. Our observations indicated that Zhongmu-3 was more salt-tolerant than R108. To characterize the protein expression profiles of these two Medicago species in response to salt stress, an iTRAQ-based quantitative proteomic analysis was applied to examine salt-responsive proteins. We identified 254 differentially changed salt-responsive proteins. Compared with control levels, the abundance of 121 proteins increased and 44 proteins decreased in salt-treated Zhongmu-3 seedlings, while 119 proteins increased and 18 proteins decreased in R108 seedlings. Moreover, 48 differentially changed proteins were common to Zhongmu-3 and R108 seedlings. A subsequent functional annotation indicated these proteins influenced diverse processes, such as catalytic activity, binding, and antioxidant activity. Furthermore, the corresponding transcript levels of 15 differentially changed proteins were quantified by qRT-PCR. The data presented herein provide new insights into salt-responsive proteins, with potential implications for enhancing the salt tolerance of Medicago species.
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Yuan N, Yuan S, Li Z, Zhou M, Wu P, Hu Q, Mendu V, Wang L, Luo H. STRESS INDUCED FACTOR 2, a Leucine-Rich Repeat Kinase Regulates Basal Plant Pathogen Defense. PLANT PHYSIOLOGY 2018; 176:3062-3080. [PMID: 29463771 PMCID: PMC5884590 DOI: 10.1104/pp.17.01266] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 02/07/2018] [Indexed: 05/22/2023]
Abstract
Protein kinases play fundamental roles in plant development and environmental stress responses. Here, we identified the STRESS INDUCED FACTOR (SIF) gene family, which encodes four leucine-rich repeat receptor-like protein kinases in Arabidopsis (Arabidopsis thaliana). The four genes, SIF1 to SIF4, are clustered in the genome and highly conserved, but they have temporally and spatially distinct expression patterns. We employed Arabidopsis SIF knockout mutants and overexpression transgenics to examine SIF involvement during plant pathogen defense. SIF genes are rapidly induced by biotic or abiotic stresses, and SIF proteins localize to the plasma membrane. Simultaneous knockout of SIF1 and SIF2 led to improved plant salt tolerance, whereas SIF2 overexpression enhanced PAMP-triggered immunity and prompted basal plant defenses, significantly improving pathogen resistance. Furthermore, SIF2 overexpression plants exhibited up-regulated expression of the defense-related genes WRKY53 and flg22-INDUCED RECEPTOR-LIKE KINASE1 as well as enhanced MPK3/MPK6 phosphorylation upon pathogen and elicitor treatments. The expression of the calcium signaling-related gene PHOSPHATE-INDUCED1 also was enhanced in the SIF2-overexpressing lines upon pathogen inoculation but repressed in the sif2 mutants. Bimolecular fluorescence complementation demonstrates that the BRI1-ASSOCIATED RECEPTOR KINASE1 protein is a coreceptor of the SIF2 kinase in the signal transduction pathway during pathogen invasion. These findings characterize a stress-responsive protein kinase family and illustrate how SIF2 modulates signal transduction for effective plant pathogenic defense.
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Affiliation(s)
- Ning Yuan
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina 29634-0318
| | - Shuangrong Yuan
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina 29634-0318
| | - Zhigang Li
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina 29634-0318
| | - Man Zhou
- College of Natural, Applied, and Health Sciences, Wenzhou Kean University, Wenzhou, Zhejiang, China 325035
| | - Peipei Wu
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina 29634-0318
| | - Qian Hu
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina 29634-0318
| | - Venugopal Mendu
- Fiber and Biopolymer Research Institute, Department of Plant and Soil Science, Texas Tech University, Lubbock, Texas 79409-2122
| | - Liangjiang Wang
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina 29634-0318
| | - Hong Luo
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina 29634-0318
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Li B, Tunc-Ozdemir M, Urano D, Jia H, Werth EG, Mowrey DD, Hicks LM, Dokholyan NV, Torres MP, Jones AM. Tyrosine phosphorylation switching of a G protein. J Biol Chem 2018; 293:4752-4766. [PMID: 29382719 DOI: 10.1074/jbc.ra117.000163] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 01/26/2018] [Indexed: 01/08/2023] Open
Abstract
Heterotrimeric G protein complexes are molecular switches relaying extracellular signals sensed by G protein-coupled receptors (GPCRs) to downstream targets in the cytoplasm, which effect cellular responses. In the plant heterotrimeric GTPase cycle, GTP hydrolysis, rather than nucleotide exchange, is the rate-limiting reaction and is accelerated by a receptor-like regulator of G signaling (RGS) protein. We hypothesized that posttranslational modification of the Gα subunit in the G protein complex regulates the RGS-dependent GTPase cycle. Our structural analyses identified an invariant phosphorylated tyrosine residue (Tyr166 in the Arabidopsis Gα subunit AtGPA1) located in the intramolecular domain interface where nucleotide binding and hydrolysis occur. We also identified a receptor-like kinase that phosphorylates AtGPA1 in a Tyr166-dependent manner. Discrete molecular dynamics simulations predicted that phosphorylated Tyr166 forms a salt bridge in this interface and potentially affects the RGS protein-accelerated GTPase cycle. Using a Tyr166 phosphomimetic substitution, we found that the cognate RGS protein binds more tightly to the GDP-bound Gα substrate, consequently reducing its ability to accelerate GTPase activity. In conclusion, we propose that phosphorylation of Tyr166 in AtGPA1 changes the binding pattern with AtRGS1 and thereby attenuates the steady-state rate of the GTPase cycle. We coin this newly identified mechanism "substrate phosphoswitching."
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Affiliation(s)
- Bo Li
- Departments of Biology, Chapel Hill, North Carolina 27599
| | | | - Daisuke Urano
- Departments of Biology, Chapel Hill, North Carolina 27599; Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604, Singapore
| | - Haiyan Jia
- Departments of Biology, Chapel Hill, North Carolina 27599
| | - Emily G Werth
- Department of Chemistry, Chapel Hill, North Carolina 27599
| | - David D Mowrey
- Biochemistry/Biophysics, Chapel Hill, North Carolina 27599
| | - Leslie M Hicks
- Department of Chemistry, Chapel Hill, North Carolina 27599
| | | | - Matthew P Torres
- Department of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332
| | - Alan M Jones
- Departments of Biology, Chapel Hill, North Carolina 27599; Pharmacology, University of North Carolina, Chapel Hill, North Carolina 27599.
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Oh ES, Lee Y, Chae WB, Rameneni JJ, Park YS, Lim YP, Oh MH. Biochemical Analysis of the Role of Leucine-Rich Repeat Receptor-Like Kinases and the Carboxy-Terminus of Receptor Kinases in Regulating Kinase Activity in Arabidopsis thaliana and Brassica oleracea. Molecules 2018; 23:molecules23010236. [PMID: 29361797 PMCID: PMC6017770 DOI: 10.3390/molecules23010236] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 01/08/2018] [Accepted: 01/15/2018] [Indexed: 12/28/2022] Open
Abstract
Protein post-translational modification by phosphorylation is essential for the activity and stability of proteins in higher plants and underlies their responses to diverse stimuli. There are more than 300 leucine-rich repeat receptor-like kinases (LRR-RLKs), a major group of receptor-like kinases (RLKs) that plays an important role in growth, development, and biotic stress responses in higher plants. To analyze auto- and transphosphorylation patterns and kinase activities in vitro, 43 full-length complementary DNA (cDNA) sequences were cloned from genes encoding LRR-RLKs. Autophosphorylation activity was found in the cytoplasmic domains (CDs) of 18 LRR-RLKs; 13 of these LRR-RLKs with autophosphorylation activity showed transphosphorylation in Escherichia coli. BRI1-Associated Receptor Kinase (BAK1), which is critically involved in the brassinosteroid and plant innate immunity signal transduction pathways, showed strong auto- and transphosphorylation with multi-specific kinase activity within 2 h of induction of Brassica oleraceae BAK1-CD (BoBAK1-CD) in E. coli; moreover, the carboxy-terminus of LRR-RLKs regulated phosphorylation and kinase activity in Arabidopsis thaliana and vegetative crops.
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Affiliation(s)
- Eun-Seok Oh
- Department of Biological Sciences, College of Biological Sciences and Biotechnology, Chungnam National University, Daejeon 34134, Korea.
| | - Yeon Lee
- Department of Biological Sciences, College of Biological Sciences and Biotechnology, Chungnam National University, Daejeon 34134, Korea.
| | - Won Byoung Chae
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, RDA, Wanju 55365, Korea.
| | - Jana Jeevan Rameneni
- Department of Horticulture, College of Agriculture and Life Science, Chungnam National University, Daejeon 34134, Korea.
| | - Yong-Soon Park
- Department of Biological Sciences, College of Biological Sciences and Biotechnology, Chungnam National University, Daejeon 34134, Korea.
| | - Yong Pyo Lim
- Department of Horticulture, College of Agriculture and Life Science, Chungnam National University, Daejeon 34134, Korea.
| | - Man-Ho Oh
- Department of Biological Sciences, College of Biological Sciences and Biotechnology, Chungnam National University, Daejeon 34134, Korea.
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Abstract
Many researchers have sought along the last two decades a legume species that could serve as a model system for genetic studies to resolve specific developmental or metabolic processes that cannot be studied in other model plants. Nitrogen fixation, nodulation, compound leaf, inflorescence and plant architecture, floral development, pod formation, secondary metabolite biosynthesis, and other developmental and metabolic aspects are legume-specific or show important differences with those described in Arabidopsis thaliana, the most studied model plant. Mainly Medicago truncatula and Lotus japonicus were proposed in the 1990s as model systems due to their key attributes, diploid genome, autogamous nature, short generation times, small genome sizes, and both species can be readily transformed. After more than decade-long, the genome sequences of both species are essentially complete, and a series of functional genomics tools have been successfully developed and applied. Mutagens that cause insertions or deletions are being used in these model systems because these kinds of DNA rearrangements are expected to assist in the isolation of the corresponding genes by Target-Induced Local Lesions IN Genomes (TILLING) approaches. Different M. truncatula mutants have been obtained following γ-irradiation or fast neutron bombardment (FNB), ethyl-nitrosourea (ENU) or ethyl-methanesulfonate (EMS) treatments, T-DNA and activation tagging, use of the tobacco retrotransposon Tnt1 to produce insertional mutants, gene silencing by RNAi, and transient post-transcriptional gene silencing by virus-induced gene silencing (VIGS). Emerging technologies of targeted mutagenesis and gene editing, such as the CRISPR-Cas9 system, could open a new era in this field. Functional genomics tools and phenotypic analyses of several mutants generated in M. truncatula have been essential to better understand differential aspects of legumes development and metabolism.
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Affiliation(s)
- Luis A Cañas
- CSIC-UPV, Institute for Plant Cell and Molecular Biology (IBMCP), Valencia, Spain.
| | - José Pío Beltrán
- CSIC-UPV, Institute for Plant Cell and Molecular Biology (IBMCP), Valencia, Spain
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Hao J, Yang J, Dong J, Fei SZ. Characterization of BdCBF genes and genome-wide transcriptome profiling of BdCBF3-dependent and -independent cold stress responses in Brachypodium distachyon. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 262:52-61. [PMID: 28716420 DOI: 10.1016/j.plantsci.2017.06.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 06/02/2017] [Indexed: 05/23/2023]
Abstract
Freezing stress substantially reduces crop yields and limits plant distribution. The identification of genes critical for cold acclimation is thus of great importance. C-repeat binding factors (CBFs) are transcription factors that play key regulatory roles in the cold acclimation process, which dramatically increases freezing tolerance in plants. We report here that B. distachyon can successfully cold acclimate and we identified a CBF gene family consisting of eight genes in a tandem array and are designated as BdCBF1-8. Expression analysis indicated that all the eight BdCBF genes are induced by cold. Freezing tolerance experiments showed that the knockdown of BdCBF3 gene in RNAi cbf3 mutant plants results in a significant reduction in survival after an exposure to freezing temperatures. RNA-seq transcriptomic analysis was conducted using the wild type and cbf3 mutant plants under both normal and cold conditions. We identified 460, 3213, 2839 and 1871 differentially expressed genes exhibiting different expression levels by pairwise comparisons of cbf3 (23°C) vs. WT (23°C), WT (23°C) vs. WT (4°C), cbf3 (23°C) vs. cbf3 (4°C), and cbf3 (4°C) vs. WT (4°C), respectively. These differentially expressed genes were enriched in several biological pathways. Combined analyses of differentially expressed genes in some of the enriched pathways provide insights into mechanisms of plant response to cold in the BdCBF3-dependent, -independent or -compensatory categories.
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Affiliation(s)
- Jingjie Hao
- Interdepartmental Graduate Major in Genetics, Iowa State University, Ames, IA 50011, USA
| | - Jinliang Yang
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Jiangli Dong
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100094, China
| | - Shui-Zhang Fei
- Interdepartmental Graduate Major in Genetics, Iowa State University, Ames, IA 50011, USA; Department of Horticulture, Iowa State University, Ames, IA 50011, USA.
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Wang J, Liu S, Li C, Wang T, Zhang P, Chen K. PnLRR-RLK27, a novel leucine-rich repeats receptor-like protein kinase from the Antarctic moss Pohlia nutans, positively regulates salinity and oxidation-stress tolerance. PLoS One 2017; 12:e0172869. [PMID: 28241081 PMCID: PMC5328275 DOI: 10.1371/journal.pone.0172869] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2016] [Accepted: 02/11/2017] [Indexed: 11/17/2022] Open
Abstract
Leucine-rich repeats receptor-like kinases (LRR-RLKs) play important roles in plant growth and development as well as stress responses. Here, 56 LRR-RLK genes were identified in the Antarctic moss Pohlia nutans transcriptome, which were further classified into 11 subgroups based on their extracellular domain. Of them, PnLRR-RLK27 belongs to the LRR II subgroup and its expression was significantly induced by abiotic stresses. Subcellular localization analysis showed that PnLRR-RLK27 was a plasma membrane protein. The overexpression of PnLRR-RLK27 in Physcomitrella significantly enhanced the salinity and ABA tolerance in their gametophyte growth. Similarly, PnLRR-RLK27 heterologous expression in Arabidopsis increased the salinity and ABA tolerance in their seed germination and early root growth as well as the tolerance to oxidative stress. PnLRR-RLK27 overproduction in these transgenic plants increased the expression of salt stress/ABA-related genes. Furthermore, PnLRR-RLK27 increased the activities of reactive oxygen species (ROS) scavengers and reduced the levels of malondialdehyde (MDA) and ROS. Taken together, these results suggested that PnLRR-RLK27 as a signaling regulator confer abiotic stress response associated with the regulation of the stress- and ABA-mediated signaling network.
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Affiliation(s)
- Jing Wang
- School of Life Science and National Glycoengineering Research Center, Shandong University, Jinan, China
| | - Shenghao Liu
- Marine Ecology Research Center, The First Institute of Oceanography, State Oceanic Administration, Qingdao, China
| | - Chengcheng Li
- School of Life Science and National Glycoengineering Research Center, Shandong University, Jinan, China
| | - Tailin Wang
- School of Life Science and National Glycoengineering Research Center, Shandong University, Jinan, China
| | - Pengying Zhang
- School of Life Science and National Glycoengineering Research Center, Shandong University, Jinan, China
- Shandong Provincial Key Laboratory of Carbohydrate Chemistry and Glycobiology, Jinan, China
| | - Kaoshan Chen
- School of Life Science and National Glycoengineering Research Center, Shandong University, Jinan, China
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Meena KK, Sorty AM, Bitla UM, Choudhary K, Gupta P, Pareek A, Singh DP, Prabha R, Sahu PK, Gupta VK, Singh HB, Krishanani KK, Minhas PS. Abiotic Stress Responses and Microbe-Mediated Mitigation in Plants: The Omics Strategies. FRONTIERS IN PLANT SCIENCE 2017; 8:172. [PMID: 28232845 PMCID: PMC5299014 DOI: 10.3389/fpls.2017.00172] [Citation(s) in RCA: 250] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 01/27/2017] [Indexed: 05/19/2023]
Abstract
Abiotic stresses are the foremost limiting factors for agricultural productivity. Crop plants need to cope up adverse external pressure created by environmental and edaphic conditions with their intrinsic biological mechanisms, failing which their growth, development, and productivity suffer. Microorganisms, the most natural inhabitants of diverse environments exhibit enormous metabolic capabilities to mitigate abiotic stresses. Since microbial interactions with plants are an integral part of the living ecosystem, they are believed to be the natural partners that modulate local and systemic mechanisms in plants to offer defense under adverse external conditions. Plant-microbe interactions comprise complex mechanisms within the plant cellular system. Biochemical, molecular and physiological studies are paving the way in understanding the complex but integrated cellular processes. Under the continuous pressure of increasing climatic alterations, it now becomes more imperative to define and interpret plant-microbe relationships in terms of protection against abiotic stresses. At the same time, it also becomes essential to generate deeper insights into the stress-mitigating mechanisms in crop plants for their translation in higher productivity. Multi-omics approaches comprising genomics, transcriptomics, proteomics, metabolomics and phenomics integrate studies on the interaction of plants with microbes and their external environment and generate multi-layered information that can answer what is happening in real-time within the cells. Integration, analysis and decipherization of the big-data can lead to a massive outcome that has significant chance for implementation in the fields. This review summarizes abiotic stresses responses in plants in-terms of biochemical and molecular mechanisms followed by the microbe-mediated stress mitigation phenomenon. We describe the role of multi-omics approaches in generating multi-pronged information to provide a better understanding of plant-microbe interactions that modulate cellular mechanisms in plants under extreme external conditions and help to optimize abiotic stresses. Vigilant amalgamation of these high-throughput approaches supports a higher level of knowledge generation about root-level mechanisms involved in the alleviation of abiotic stresses in organisms.
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Affiliation(s)
- Kamlesh K. Meena
- Department of Microbiology, School of Edaphic Stress Management, National Institute of Abiotic Stress Management, Indian Council of Agricultural ResearchBaramati, India
| | - Ajay M. Sorty
- Department of Microbiology, School of Edaphic Stress Management, National Institute of Abiotic Stress Management, Indian Council of Agricultural ResearchBaramati, India
| | - Utkarsh M. Bitla
- Department of Microbiology, School of Edaphic Stress Management, National Institute of Abiotic Stress Management, Indian Council of Agricultural ResearchBaramati, India
| | - Khushboo Choudhary
- Department of Microbiology, School of Edaphic Stress Management, National Institute of Abiotic Stress Management, Indian Council of Agricultural ResearchBaramati, India
| | - Priyanka Gupta
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru UniversityNew Delhi, India
| | - Ashwani Pareek
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru UniversityNew Delhi, India
| | - Dhananjaya P. Singh
- Department of Biotechnology, National Bureau of Agriculturally Important Microorganisms, Indian Council of Agricultural ResearchKushmaur, India
| | - Ratna Prabha
- Department of Biotechnology, National Bureau of Agriculturally Important Microorganisms, Indian Council of Agricultural ResearchKushmaur, India
| | - Pramod K. Sahu
- Department of Biotechnology, National Bureau of Agriculturally Important Microorganisms, Indian Council of Agricultural ResearchKushmaur, India
| | - Vijai K. Gupta
- Molecular Glyco-Biotechnology Group, Discipline of Biochemistry, School of Natural Sciences, National University of Ireland GalwayGalway, Ireland
- Department of Chemistry and Biotechnology, ERA Chair of Green Chemistry, School of Science, Tallinn University of TechnologyTallinn, Estonia
| | - Harikesh B. Singh
- Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu UniversityVaranasi, India
| | - Kishor K. Krishanani
- Department of Microbiology, School of Edaphic Stress Management, National Institute of Abiotic Stress Management, Indian Council of Agricultural ResearchBaramati, India
| | - Paramjit S. Minhas
- Department of Microbiology, School of Edaphic Stress Management, National Institute of Abiotic Stress Management, Indian Council of Agricultural ResearchBaramati, India
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