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Zhao L, Zhao X, Huang L, Liu X, Wang P. Transcriptome analysis of Pennisetum americanum × Pennisetum purpureum and Pennisetum americanum leaves in response to high-phosphorus stress. BMC PLANT BIOLOGY 2024; 24:635. [PMID: 38971717 PMCID: PMC11227232 DOI: 10.1186/s12870-024-05339-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 06/25/2024] [Indexed: 07/08/2024]
Abstract
Excessive phosphorus (P) levels can disrupt nutrient balance in plants, adversely affecting growth. The molecular responses of Pennisetum species to high phosphorus stress remain poorly understood. This study examined two Pennisetum species, Pennisetum americanum × Pennisetum purpureum and Pennisetum americanum, under varying P concentrations (200, 600 and 1000 µmol·L- 1 KH2PO4) to elucidate transcriptomic alterations under high-P conditions. Our findings revealed that P. americanum exhibited stronger adaption to high-P stress compared to P. americanum× P. purpureum. Both species showed an increase in plant height and leaf P content under elevated P levels, with P. americanum demonstrating greater height and higher P content than P. americanum× P. purpureum. Transcriptomic analysis identified significant up- and down-regulation of key genes (e.g. SAUR, GH3, AHP, PIF4, PYL, GST, GPX, GSR, CAT, SOD1, CHS, ANR, P5CS and PsbO) involved in plant hormone signal transduction, glutathione metabolism, peroxisomes, flavonoid biosynthesis, amino acid biosynthesis and photosynthesis pathways. Compared with P. americanum× P. purpureum, P. americanum has more key genes in the KEGG pathway, and some genes have higher expression levels. These results contribute valuable insights into the molecular mechanisms governing high-P stress in Pennisetum species and offer implications for broader plant stress research.
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Affiliation(s)
- Lili Zhao
- College of Animal Science, Guizhou University, Guiyang, 550025, China
| | - Xin Zhao
- College of Animal Science, Guizhou University, Guiyang, 550025, China
| | - Lei Huang
- College of Animal Science, Guizhou University, Guiyang, 550025, China
| | - Xiaoyan Liu
- College of Animal Science, Guizhou University, Guiyang, 550025, China
| | - Puchang Wang
- School of Life Sciences, Guizhou Normal University, Guiyang, 550001, China.
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Maqbool S, Naseer S, Zahra N, Rasool F, Qayyum H, Majeed K, Jahanzaib M, Sajjad M, Fayyaz M, Naeem MK, Khan MR, Zhang H, Rasheed A, Li H. RNAseq of diverse spring wheat cultivars released during last 110 years. Sci Data 2023; 10:884. [PMID: 38065977 PMCID: PMC10709563 DOI: 10.1038/s41597-023-02769-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
Here, we performed RNA-seq based expression analysis of root and leaf tissues of a set of 24 historical spring wheat cultivars representing 110 years of temporal genetic variations. This huge 130 tissues RNAseq dataset was initially used to study expression pattern of 97 genes regulating root growth and development in wheat. Root system architecture (RSA) is an important target for breeding stress-resilient and high-yielding wheat cultivars under climatic fluctuations. However, root transcriptome analysis is usually obscured due to challenges in root research due to their below ground presence. We also validated the dataset by performing correlation analysis between expression of RSA related genes in roots and leaves with 25 root traits analyzed under varying moisture conditions and 10 yield-related traits. The Pearson's correlation coefficients between root phenotypes and expression of root-specific genes varied from -0.72 to 0.78, and strong correlations with genes such as DRO1, TaMOR, ARF4, PIN1 was observed. The presented datasets have multiple uses such as a) studying the change in expression pattern of genes during time, b) differential expression of genes in two very important tissues of wheat i.e., leaf and roots, and c) studying customized expression of genes associated with important phenotypes in diverse wheat cultivars. The initial findings presented here provided key insights into understanding the transcriptomic basis of phenotypic variability of RSA in wheat cultivars.
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Affiliation(s)
- Saman Maqbool
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), CIMMYT-China office, Beijing, China
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Samar Naseer
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Nageen Zahra
- National Institute of Genomics and Advanced Biotechnology (NIGAB), National Agriculture Research Center (NARC), Islamabad, Pakistan
| | - Fatima Rasool
- National Institute of Genomics and Advanced Biotechnology (NIGAB), National Agriculture Research Center (NARC), Islamabad, Pakistan
| | - Humaira Qayyum
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Khawar Majeed
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Muhammad Jahanzaib
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
- Oilseeds Research Program, Crop Sciences Institute (CSI), National Agriculture Research Center (NARC), Islamabad, Pakistan
| | - Muhammad Sajjad
- Department of BioSciences, COMSATS University, Islamabad, Pakistan
| | - Muhammad Fayyaz
- Crop Disease Research Institute, National Agriculture Research Center (NARC), Islamabad, Pakistan
| | - Muhammad Kashif Naeem
- National Institute of Genomics and Advanced Biotechnology (NIGAB), National Agriculture Research Center (NARC), Islamabad, Pakistan
| | - Muhammad Ramzan Khan
- National Institute of Genomics and Advanced Biotechnology (NIGAB), National Agriculture Research Center (NARC), Islamabad, Pakistan
| | - Hao Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), CIMMYT-China office, Beijing, China
- Nanfan Research Institute, CAAS, Sanya, Hainan, China
| | - Awais Rasheed
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), CIMMYT-China office, Beijing, China.
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan.
| | - Huihui Li
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), CIMMYT-China office, Beijing, China.
- Nanfan Research Institute, CAAS, Sanya, Hainan, China.
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Nie Z, Wang L, Zhao P, Wang Z, Shi Q, Liu H. Metabolomics reveals the impact of nitrogen combined with the zinc supply on zinc availability in calcareous soil via root exudates of winter wheat (Triticum aestivum). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 204:108069. [PMID: 37852066 DOI: 10.1016/j.plaphy.2023.108069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 09/25/2023] [Accepted: 09/28/2023] [Indexed: 10/20/2023]
Abstract
A possible mechanism for the improved availability of zinc (Zn) in soil by combining nitrogen (N) with Zn supply was investigated based on the root exudates of winter wheat. N, Zn supply as well as their combination significantly regulated nine root exudates in winter wheat; in which, the secretion of cis-aconitic acid involving in the TCA cycle, C5-branched dibasic acid metabolism, glyoxylate and dicarboxylate metabolism and 2-oxocarboxylic acid metabolism was upregulated by N, Zn supply as well as their combination. N-Zn combination induced the activities of citrate synthase and cis-aconitase in roots and shoots of winter wheat thus to increase the concentrations of citric and aconitic acid; the decrease of isocitric acid concentrations in shoots indicated the inhibited conversion of aconitic acid to isocitric acid by N-Zn combination. It revealed a possible reason for the enhanced secretion of cis-aconitic acid by N-Zn combination. Exogenous addition of 10 μ plant-1 cis-aconitate significantly increased available Zn concentrations in soil and Zn concentrations in winter wheat under N-Zn combination. Thus, the N-Zn combination regulated the metabolism of cis-aconitic acid in winter wheat, thus enhancing the secretion of cis-aconitic acid to increase the bioavailability of Zn in soil.
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Affiliation(s)
- Zhaojun Nie
- Resources and Environment College, Henan Agricultural University, Zhengzhou, 450002, Henan Province, China.
| | - Linglu Wang
- Resources and Environment College, Henan Agricultural University, Zhengzhou, 450002, Henan Province, China.
| | - Peng Zhao
- Resources and Environment College, Henan Agricultural University, Zhengzhou, 450002, Henan Province, China.
| | - Zhenbo Wang
- Resources and Environment College, Henan Agricultural University, Zhengzhou, 450002, Henan Province, China.
| | - Qiuzhe Shi
- Resources and Environment College, Henan Agricultural University, Zhengzhou, 450002, Henan Province, China.
| | - Hongen Liu
- Resources and Environment College, Henan Agricultural University, Zhengzhou, 450002, Henan Province, China.
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Pinit S, Ariyakulkiat L, Chaiwanon J. Rice straw-derived smoke water promotes rice root growth under phosphorus deficiency by modulating oxidative stress and photosynthetic gene expression. Sci Rep 2023; 13:14802. [PMID: 37684292 PMCID: PMC10491667 DOI: 10.1038/s41598-023-41987-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 09/04/2023] [Indexed: 09/10/2023] Open
Abstract
Plant-derived smoke has been shown to promote plant growth and seed germination, but its roles and mechanisms in response to nutrient deficiency stress remain unclear. Plants respond to phosphorus (P) deficiency by undergoing morphological, physiological, and transcriptional changes in order to improve nutrient uptake efficiency. Here, we showed that rice straw-derived smoke water could promote root growth in rice (Oryza sativa cv. Nipponbare) grown under P-sufficient and P-deficient conditions. Transcriptome analysis of the root tissues identified 1309 genes up-regulated and 1311 genes down-regulated by smoke water under P-deficient conditions. The GO terms 'glutathione transferase activity' and 'photosynthesis-light reaction' were found to be significantly enriched among the genes that were up- and down-regulated by smoke water, respectively. Biochemical analysis showed that smoke water reduced P-deficient-induced accumulation of H2O2 and malondialdehyde (MDA), a lipid peroxidation marker, reduced sucrose contents, but increased Fe accumulation. Furthermore, smoke water suppressed the expression of strigolactone biosynthesis genes, which were strongly induced by P deficiency as an adaptive strategy to improve root P uptake. These results revealed a potential mechanism by which smoke water promotes root growth and interacts with P deficiency-induced transcriptional regulation to mitigate P deficiency stress in rice.
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Affiliation(s)
- Sompop Pinit
- Center of Excellence in Environment and Plant Physiology, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Department of Biochemistry, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand
- Center of Excellence in Medical Biotechnology, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand
| | - Lalichat Ariyakulkiat
- Center of Excellence in Environment and Plant Physiology, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Juthamas Chaiwanon
- Center of Excellence in Environment and Plant Physiology, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok, Thailand.
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Prathap V, Kumar S, Tyagi A. Comparative proteome analysis of phosphorus-responsive genotypes reveals the proteins differentially expressed under phosphorous starvation stress in rice. Int J Biol Macromol 2023; 234:123760. [PMID: 36812961 DOI: 10.1016/j.ijbiomac.2023.123760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 02/06/2023] [Accepted: 02/09/2023] [Indexed: 02/23/2023]
Abstract
Phosphorus (P)-deficiency is one of the major nutrient constraints for global rice production. P-deficiency tolerance in rice involves complex regulatory mechanisms. To gain insights into the proteins involved in phosphorus acquisition and use efficiency in rice, proteome analysis of a high-yielding rice cultivar Pusa-44 and its near-isogenic line (NIL)-23 harboring a major phosphorous uptake (Pup1) QTL, grown under control and P-starvation stress, was performed. Comparative proteome profiling of shoot and root tissues from the plants grown hydroponically with P (16 ppm, +P) or without P (0 ppm, -P) resulted in the identification of 681 and 567 differentially expressed proteins (DEPs) in shoot of Pusa-44 and NIL-23, respectively. Similarly, 66 and 93 DEPs were identified in root of Pusa-44 and NIL-23, respectively. These P-starvation responsive DEPs were annotated to be involved in metabolic processes like photosynthesis, starch-, sucrose-, energy-metabolism, transcription factors (mainly ARF, ZFP, HD-ZIP, MYB), and phytohormone signaling. Comparative analysis of the expression patterns observed by proteome analysis with that reported at the transcriptome level indicated the Pup1 QTL-mediated post-transcriptional regulation plays an important role under -P stress. Thus, the present study describes the molecular aspect of the regulatory functions of Pup1 QTL under P-starvation stress in rice, which might help develop an efficient rice cultivar with enhanced P acquisition and assimilation for better performance in P-deficient soil.
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Affiliation(s)
- V Prathap
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Suresh Kumar
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India.
| | - Aruna Tyagi
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India.
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Transcriptomics Insights into Phosphorus Stress Response of Myriophyllum aquaticum. Int J Mol Sci 2023; 24:ijms24054874. [PMID: 36902302 PMCID: PMC10003231 DOI: 10.3390/ijms24054874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/31/2023] [Accepted: 02/07/2023] [Indexed: 03/06/2023] Open
Abstract
Through excellent absorption and transformation, the macrophyte Myriophyllum (M.) aquaticum can considerably remove phosphorus from wastewater. The results of changes in growth rate, chlorophyll content, and roots number and length showed that M. aquaticum could cope better with high phosphorus stress compared with low phosphorus stress. Transcriptome and differentially expressed genes (DEGs) analyses revealed that, when exposed to phosphorus stresses at various concentrations, the roots were more active than the leaves, with more DEGs regulated. M. aquaticum also showed different gene expression and pathway regulatory patterns when exposed to low phosphorus and high phosphorus stresses. M. aquaticum's capacity to cope with phosphorus stress was maybe due to its improved ability to regulate metabolic pathways such as photosynthesis, oxidative stress reduction, phosphorus metabolism, signal transduction, secondary metabolites biosynthesis, and energy metabolism. In general, M. aquaticum has a complex and interconnected regulatory network that deals efficiently with phosphorus stress to varying degrees. This is the first time that the mechanisms of M. aquaticum in sustaining phosphorus stress have been fully examined at the transcriptome level using high-throughput sequencing analysis, which may indicate the direction of follow-up research and have some guiding value for its future applications.
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Zhao X, Chen KK, Wang LT, Zhao LL, Wang PC. Transcriptome analysis provides insights into the response of Lotus corniculatus roots to low-phosphorus stress. FRONTIERS IN PLANT SCIENCE 2023; 14:1089380. [PMID: 36938008 PMCID: PMC10014540 DOI: 10.3389/fpls.2023.1089380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 02/17/2023] [Indexed: 06/18/2023]
Abstract
INTRODUCTION A lack of soil phosphorus (P) is a principal factor restricting the normal growth of Lotus corniculatus in the karst area of Guizhou Province, China, but the response mechanism of L. corniculatus under low-phosphorus stress remains unclear. METHODS Therefore, we treated two selected L. corniculatus lines (low-P-intolerant line 08518 and low-P-tolerant line 01549) from 13 L. corniculatus lines with normal phosphorus (0.5 mmol/L KH2PO4, NP) and low phosphorus (0.005 mmol/L KH2PO4, LP) concentrations to study changes in morphological, physiological and transcriptome data under low-phosphorus stress. RESULTS The low-P-tolerant line 01549 exhibited better performance under low-phosphorus stress. Compared with the NP treatment, all root morphological indicators of the low-P-tolerant line 01549 increased, and those of the low-P-intolerant line 08518 decreased under low-P stress. Compared with the NP treatment, acid phosphatase (ACP), catalase (CAT), superoxide dismutase (SOD), and peroxidase (POD) activities, and the malondialdehyde (MDA), soluble sugar (SS), soluble protein (SP) and proline (Pro) contents of the two L. corniculatus lines increased under low-P stress. A transcriptome analysis of L. corniculatus showed that a total of 656 and 2243 differentially expressed genes (DEGs) were identified in line 01549 and line 08518, respectively. Meanwhile, the main pathways, such as carbohydrate metabolism, acid phosphatases, phosphate transporters and biosynthesis of secondary metabolites, as well as related genes were also screened by performing a KEGG enrichment analysis. DISCUSSION The findings provide an essential point of reference for studying the physiological and molecular mechanism of the response to low-P stress in L. corniculatus.
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Affiliation(s)
- Xin Zhao
- College of Animal Science, Guizhou University, Guiyang, China
| | - Ke-ke Chen
- College of Animal Science, Guizhou University, Guiyang, China
| | - Lei-ting Wang
- College of Animal Science, Guizhou University, Guiyang, China
| | - Li-Li Zhao
- College of Animal Science, Guizhou University, Guiyang, China
| | - Pu-Chang Wang
- School of Life Sciences, Guizhou Normal University, Guiyang, China
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Iqbal A, Qiang D, Xiangru W, Huiping G, Hengheng Z, Xiling Z, Meizhen S. Integrative physiological, transcriptome and metabolome analysis reveals the involvement of carbon and flavonoid biosynthesis in low phosphorus tolerance in cotton. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 196:302-317. [PMID: 36738510 DOI: 10.1016/j.plaphy.2023.01.042] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 01/12/2023] [Accepted: 01/19/2023] [Indexed: 06/18/2023]
Abstract
Phosphorus (P) is an essential nutrient controlling plant growth and development through the regulation of basic metabolic processes; however, the molecular details of these pathways remain largely unknown. In this study, physiological, transcriptome, and metabolome analysis were compared for two cotton genotypes with different low P tolerance under P starvation and resupply. The results showed that the glucose, fructose, sucrose, and starch contents increased by 18.2%, 20.4%, 20.2%, and 14.3% in the roots and 18.3%, 23.3%, 11.0%, and 13.6% in the shoot of Jimian169 than DES926, respectively. Moreover, the activities of enzymes related to carbon and phosphorus metabolism were higher in the roots and shoots of Jimian169 than DES926. In addition, transcriptome analysis revealed that the number of differentially expressed genes (DEGs) was higher in both roots (830) and shoots (730) under P starvation and the DEGs drastically reduced upon P resupply. The KEGG analysis indicated that DEGs were mainly enriched in phenylpropanoid biosynthesis, carbon metabolism, and photosynthesis. The metabolome analysis showed the enrichment of phenylpropanoid, organic acids and derivatives, and lipids in all the pairs at a given time point. The combined transcriptome and metabolome analysis revealed that carbon metabolism and flavonoid biosynthesis are involved in the P starvation response in cotton. Moreover, co-expression network analysis identified 3 hub genes in the roots and shoots that regulate the pathways involved in the P starvation response. This study provides the foundation for understanding the mechanisms of low P tolerance and the hub genes as a potential target for the development of low P tolerant genotypes.
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Affiliation(s)
- Asif Iqbal
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Zhengzhou Research Base, School of Agricultural Sciences, Zhengzhou University, Anyang, Henan, 455000, PR China
| | - Dong Qiang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Zhengzhou Research Base, School of Agricultural Sciences, Zhengzhou University, Anyang, Henan, 455000, PR China
| | - Wang Xiangru
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Zhengzhou Research Base, School of Agricultural Sciences, Zhengzhou University, Anyang, Henan, 455000, PR China; Western Agricultural Research Center of Chinese Academy of Agricultural Sciences, Changji, 831100, Xinjiang, PR China
| | - Gui Huiping
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Zhengzhou Research Base, School of Agricultural Sciences, Zhengzhou University, Anyang, Henan, 455000, PR China
| | - Zhang Hengheng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Zhengzhou Research Base, School of Agricultural Sciences, Zhengzhou University, Anyang, Henan, 455000, PR China
| | - Zhang Xiling
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Zhengzhou Research Base, School of Agricultural Sciences, Zhengzhou University, Anyang, Henan, 455000, PR China; Western Agricultural Research Center of Chinese Academy of Agricultural Sciences, Changji, 831100, Xinjiang, PR China.
| | - Song Meizhen
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Zhengzhou Research Base, School of Agricultural Sciences, Zhengzhou University, Anyang, Henan, 455000, PR China; Western Agricultural Research Center of Chinese Academy of Agricultural Sciences, Changji, 831100, Xinjiang, PR China.
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Lu L, Chen S, Yang W, Wu Y, Liu Y, Yin X, Yang Y, Yang Y. Integrated transcriptomic and metabolomic analyses reveal key metabolic pathways in response to potassium deficiency in coconut ( Cocos nucifera L.) seedlings. FRONTIERS IN PLANT SCIENCE 2023; 14:1112264. [PMID: 36860901 PMCID: PMC9968814 DOI: 10.3389/fpls.2023.1112264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
Potassium ions (K+) are important for plant growth and crop yield. However, the effects of K+ deficiency on the biomass of coconut seedlings and the mechanism by which K+ deficiency regulates plant growth remain largely unknown. Therefore, in this study, we compared the physiological, transcriptome, and metabolite profiles of coconut seedling leaves under K+-deficient and K+-sufficient conditions using pot hydroponic experiments, RNA-sequencing, and metabolomics technologies. K+ deficiency stress significantly reduced the plant height, biomass, and soil and plant analyzer development value, as well as K content, soluble protein, crude fat, and soluble sugar contents of coconut seedlings. Under K+ deficiency, the leaf malondialdehyde content of coconut seedlings were significantly increased, whereas the proline (Pro) content was significantly reduced. Superoxide dismutase, peroxidase, and catalase activities were significantly reduced. The contents of endogenous hormones such as auxin, gibberellin, and zeatin were significantly decreased, whereas abscisic acid content was significantly increased. RNA-sequencing revealed that compared to the control, there were 1003 differentially expressed genes (DEGs) in the leaves of coconut seedlings under K+ deficiency. Gene Ontology analysis revealed that these DEGs were mainly related to "integral component of membrane," "plasma membrane," "nucleus", "transcription factor activity," "sequence-specific DNA binding," and "protein kinase activity." Kyoto Encyclopedia of Genes and Genomes pathway analysis indicated that the DEGs were mainly involved in "MAPK signaling pathway-plant," "plant hormone signal transduction," "starch and sucrose metabolism," "plant-pathogen interaction," "ABC transporters," and "glycerophospholipid metabolism." Metabolomic analysis showed that metabolites related to fatty acids, lipidol, amines, organic acids, amino acids, and flavonoids were generally down-regulated in coconut seedlings under K+ deficiency, whereas metabolites related to phenolic acids, nucleic acids, sugars, and alkaloids were mostly up-regulated. Therefore, coconut seedlings respond to K+ deficiency stress by regulating signal transduction pathways, primary and secondary metabolism, and plant-pathogen interaction. These results confirm the importance of K+ for coconut production, and provide a more in-depth understanding of the response of coconut seedlings to K+ deficiency and a basis for improving K+ utilization efficiency in coconut trees.
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Affiliation(s)
- Lilan Lu
- Hainan Key Laboratory of Tropical Oil Crops Biology, Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, China
| | - Siting Chen
- Hainan Key Laboratory of Tropical Oil Crops Biology, Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, China
| | - Weibo Yang
- Hainan Key Laboratory of Tropical Oil Crops Biology, Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, China
| | - Yi Wu
- Hainan Key Laboratory of Tropical Oil Crops Biology, Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, China
| | - Yingying Liu
- School of Earth Sciences, China University of Geosciences, Wuhan, Hubei, China
| | - Xinxing Yin
- Hainan Key Laboratory of Tropical Oil Crops Biology, Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, China
| | - Yaodong Yang
- Hainan Key Laboratory of Tropical Oil Crops Biology, Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, China
| | - Yanfang Yang
- Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
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Zhang J, Zhang H, Wang P, Chen J, Cao Y. Gene Expression, Hormone Signaling, and Nutrient Uptake in the Root Regermination of Grafted Watermelon Plants with Different Pumpkin Rootstocks. JOURNAL OF PLANT GROWTH REGULATION 2023; 42:1051-1066. [PMID: 0 DOI: 10.1007/s00344-022-10613-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 01/19/2022] [Indexed: 05/20/2023]
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Guo F, Chen D, Zong Z, Wu W, Mo C, Zheng Z, Li J, Zhang X, Xiong D. Comprehensive analysis of aberrantly expressed circRNAs, mRNAs and lncRNAs in patients with nasopharyngeal carcinoma. J Clin Lab Anal 2023; 37:e24836. [PMID: 36597889 PMCID: PMC9937882 DOI: 10.1002/jcla.24836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 12/28/2022] [Accepted: 12/28/2022] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND The location of nasopharyngeal cancer is hidden, so it is difficult to diagnose at an early stage. In this study, we aimed to investigate the expression profiles of circRNAs, mRNAs and IncRNAs and to provide some basis for further studies. METHODS Expression profiles of circRNAs, mRNAs, and lncRNAs were analyzed using microarray techniques. The differentially expressed ncRNA was calculated by bioinformatics. RESULTS A total of 3048 circRNAs, 2179 lncRNAs, and 2015 mRNAs were detected to be significantly differentially expressed in NPC. The most upregulated circRNAs, lncRNAs, and mRNAs were hsa-circ-0067562, NONHSAT232922.1, and HOXB13, respectively. And, the most downregulated circRNAs, lncRNAs, and mRNAs were hsa_circ_0078837, lnc-TTC8-4:3, and LTF, respectively. The number of upregulated DE lncRNAs was more than twice than those downregulated. Our data showed that 80.44% of pairs of lncRNAs and cis-mRNAs demonstrated positive correlations. For lncRNAs and trans-mRNAs pairs, 53.7% of pairs showed positive correlation. LncRNA-mediated cis regulation is a prevalent regulatory mode in the development of nasopharyngeal carcinoma. CR1, LRMP and SORBS2 are predicted to be mediated not only by cis-acting lncRNA modes of action, but also by trans-acting lncRNA mechanisms. Additionally, we constructed a diagnostic prediction model with a high sensitivity and specificity. CONCLUSION Our study characterized the landscape of circRNAs, mRNAs and lncRNAs in NPC tissue and provided novel insights into the molecular mechanisms of NPC.
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Affiliation(s)
- Feifan Guo
- School of MedicineAnhui University of Science and TechnologyHuainanChina,Medical Laboratory of the Third Affiliated Hospital of Shenzhen UniversityShenzhenChina
| | - Dayang Chen
- Medical Laboratory of the Third Affiliated Hospital of Shenzhen UniversityShenzhenChina
| | - Zengyan Zong
- School of MedicineAnhui University of Science and TechnologyHuainanChina,Medical Laboratory of the Third Affiliated Hospital of Shenzhen UniversityShenzhenChina
| | - Wei Wu
- Medical Laboratory of the Third Affiliated Hospital of Shenzhen UniversityShenzhenChina
| | - Chan Mo
- Medical Laboratory of the Third Affiliated Hospital of Shenzhen UniversityShenzhenChina
| | - Zhou Zheng
- Medical Laboratory of the Third Affiliated Hospital of Shenzhen UniversityShenzhenChina
| | - Jian Li
- Department of Otolaryngology, The First Affiliated HospitalSun Yat‐sen UniversityGuangzhouChina,Guangzhou Key Laboratory of OtorhinolaryngologyGuangzhouChina
| | - Xiuming Zhang
- School of MedicineAnhui University of Science and TechnologyHuainanChina,Medical Laboratory of the Third Affiliated Hospital of Shenzhen UniversityShenzhenChina
| | - Dan Xiong
- School of MedicineAnhui University of Science and TechnologyHuainanChina,Medical Laboratory of the Third Affiliated Hospital of Shenzhen UniversityShenzhenChina
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12
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Ren S, Wang Y. Protoplast Isolation for Plant Single-Cell RNA-seq. Methods Mol Biol 2023; 2686:301-305. [PMID: 37540365 DOI: 10.1007/978-1-0716-3299-4_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
The growth and development of plants depends on diversified gene expression in different cell types. Compared to traditional bulk RNA sequencing, droplet-based single-cell RNA sequencing (scRNA-seq) allows for transcriptome profiling of individual cells within heterogeneous tissues. scRNA-seq provides a high-resolution atlas of cellular characterization and vastly improves our understandings of the interactions between individual cells and the microenvironment. However, the difficulty in protoplast isolation has limited the application of single-cell sequencing technology in plant research. Here we describe a high-efficiency protoplast isolation protocol for scRNA-seq.
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Affiliation(s)
- Shulin Ren
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Ying Wang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
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13
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Imran M, Shafiq S, Tang X. CRISPR-Cas9-mediated editing of BADH2 gene triggered fragrance revolution in rice. PHYSIOLOGIA PLANTARUM 2023; 175:e13871. [PMID: 36748269 DOI: 10.1111/ppl.13871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 12/26/2022] [Accepted: 02/01/2023] [Indexed: 06/18/2023]
Abstract
Fragrance is one of the most important quality traits for breeding in rice. The natural aroma substance 2-acetyl-1-pyrroline (2-AP) is a key fragrance compound among over 200 volatiles identified in fragrant rice. In addition to rice, there are other plant species that contain a germplasm that naturally produces a fragrant aroma. These other plant species all have lower activity levels of the enzyme BETAINE ALDEHYDE DEHYDROGENASE 2 (BADH2). Therefore, improving fragrance efficiency has been a focus of intensive research. Recent studies have engineered BADH2 gene, which is responsible for fragrance trait in non-fragrant cultivars of rice, using CRISPR-Cas9. Although engineering rice BADH2 can be useful for upregulating 2-AP, there are still a lot of restrictions on how it can be applied in practice. In this review article, we discuss the recent developments in BADH2 editing and propose potential future strategies to effectively target BADH2 for transcriptional regulation, with the goal of producing a better fragrance.
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Affiliation(s)
- Muhammad Imran
- Department of Crop Science and Technology, College of Agriculture, South China Agricultural University, Guangzhou, China
- Scientific Observing and Experimental Station of Crop Cultivation in South China, Ministry of Agriculture, Guangzhou, China
- Yingdong College of Biology and Agriculture, Shaoguan University, Shaoguan, China
| | - Sarfraz Shafiq
- Department of Anatomy and Cell Biology, University of Western Ontario, London, Ontario, Canada
| | - Xiangru Tang
- Department of Crop Science and Technology, College of Agriculture, South China Agricultural University, Guangzhou, China
- Scientific Observing and Experimental Station of Crop Cultivation in South China, Ministry of Agriculture, Guangzhou, China
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14
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Li P, Yu J, Feng N, Weng J, Rehman A, Huang J, Tu S, Niu Q. Physiological and Transcriptomic Analyses Uncover the Reason for the Inhibition of Photosynthesis by Phosphate Deficiency in Cucumis melo L. Int J Mol Sci 2022; 23:ijms232012073. [PMID: 36292929 PMCID: PMC9603772 DOI: 10.3390/ijms232012073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 09/05/2022] [Accepted: 10/05/2022] [Indexed: 11/23/2022] Open
Abstract
Phosphate (Pi) deficiency is a common phenomenon in agricultural production and limits plant growth. Recent work showed that long-term Pi deficiency caused the inhibition of photosynthesis and inefficient electron transport. However, the underlying mechanisms are still unknown. In this study, we used the physiological, histochemical, and transcriptomic methods to investigate the effect of low-Pi stress on photosynthetic gas exchange parameters, cell membrane lipid, chloroplast ultrastructure, and transcriptional regulation of key genes in melon seedlings. The results showed that Pi deficiency significantly downregulated the expression of aquaporin genes, induced an increase in ABA levels, and reduced the water content and free water content of melon leaves, which caused physiological drought in melon leaves. Therefore, gas exchange was disturbed. Pi deficiency also reduced the phospholipid contents in leaf cell membranes, caused the peroxidation of membrane lipids, and destroyed the ultrastructure of chloroplasts. The transcriptomic analysis showed that 822 differentially expressed genes (DEGs) were upregulated and 1254 downregulated by Pi deficiency in leaves. GO and KEGG enrichment analysis showed that DEGs significantly enriched in chloroplast thylakoid membrane composition (GO:0009535), photosynthesis-antenna proteins (map00196), and photosynthesis pathways (map00195) were downregulated by Pi deficiency. It indicated that Pi deficiency regulated photosynthesis-related genes at the transcriptional level, thereby affecting the histochemical properties and physiological functions, and consequently causing the reduced light assimilation ability and photosynthesis efficiency. It enriches the mechanism of photosynthesis inhibition by Pi deficiency.
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15
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Wang R, Chen Y, Kaur G, Wu X, Nguyen HT, Shen R, Pandey AK, Lan P. Differentially reset transcriptomes and genome bias response orchestrate wheat response to phosphate deficiency. PHYSIOLOGIA PLANTARUM 2022; 174:e13767. [PMID: 36281840 DOI: 10.1111/ppl.13767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 08/11/2022] [Accepted: 08/15/2022] [Indexed: 06/16/2023]
Abstract
Phosphorus (P) is an essential macronutrient for all organisms. Phosphate (Pi) deficiency reduces grain yield and quality in wheat. Understanding how wheat responds to Pi deficiency at the global transcriptional level remains limited. We revisited the available RNA-seq transcriptome from Pi-starved wheat roots and shoots subjected to Pi starvation. Genome-wide transcriptome resetting was observed under Pi starvation, with a total of 917 and 2338 genes being differentially expressed in roots and shoots, respectively. Chromosomal distribution analysis of the gene triplets and differentially expressed genes (DEGs) revealed that the D genome displayed genome induction bias and, specifically, the chromosome 2D might be a key contributor to Pi-limiting triggered gene expression response. Alterations in multiple metabolic pathways pertaining to secondary metabolites, transcription factors and Pi uptake-related genes were evidenced. This study provides genomic insight and the dynamic landscape of the transcriptional changes contributing to the hexaploid wheat during Pi starvation. The outcomes of this study and the follow-up experiments have the potential to assist the development of Pi-efficient wheat cultivars.
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Affiliation(s)
- Ruonan Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yinglong Chen
- UWA Institute of Agriculture, and School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
| | - Gazaldeep Kaur
- Department of Biotechnology, National Agri-Food Biotechnology Institute, Mohali, Punjab, India
| | - Xiaoba Wu
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Henry T Nguyen
- Division of Plant Sciences, College of Agriculture, Food and Natural Resources, University of Missouri, Columbia, Missouri, USA
| | - Renfang Shen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Ajay Kumar Pandey
- Department of Biotechnology, National Agri-Food Biotechnology Institute, Mohali, Punjab, India
| | - Ping Lan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
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16
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Li Y, Yang X, Liu H, Wang W, Wang C, Ding G, Xu F, Wang S, Cai H, Hammond JP, White PJ, Shabala S, Yu M, Shi L. Local and systemic responses conferring acclimation of Brassica napus roots to low phosphorus conditions. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4753-4777. [PMID: 35511123 DOI: 10.1093/jxb/erac177] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 04/27/2022] [Indexed: 06/14/2023]
Abstract
Due to the non-uniform distribution of inorganic phosphate (Pi) in the soil, plants modify their root architecture to improve acquisition of this nutrient. In this study, a split-root system was employed to assess the nature of local and systemic signals that modulate root architecture of Brassica napus grown with non-uniform Pi availability. Lateral root (LR) growth was regulated systemically by non-uniform Pi distribution, by increasing the second-order LR (2°LR) density in compartments with high Pi supply but decreasing it in compartments with low Pi availability. Transcriptomic profiling identified groups of genes regulated, both locally and systemically, by Pi starvation. The number of systemically induced genes was greater than the number of genes locally induced, and included genes related to abscisic acid (ABA) and jasmonic acid (JA) signalling pathways, reactive oxygen species (ROS) metabolism, sucrose, and starch metabolism. Physiological studies confirmed the involvement of ABA, JA, sugars, and ROS in the systemic Pi starvation response. Our results reveal the mechanistic basis of local and systemic responses of B. napus to Pi starvation and provide new insights into the molecular and physiological basis of root plasticity.
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Affiliation(s)
- Yalin Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Microelement Research Center/Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
| | - Xinyu Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Microelement Research Center/Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
| | - HaiJiang Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Microelement Research Center/Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
| | - Wei Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Microelement Research Center/Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
| | - Chuang Wang
- Microelement Research Center/Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
| | - Guangda Ding
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Microelement Research Center/Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
| | - Fangsen Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Microelement Research Center/Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
| | - Sheliang Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Microelement Research Center/Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
| | - Hongmei Cai
- Microelement Research Center/Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
| | - John P Hammond
- School of Agriculture, Policy and Development, University of Reading, Reading, UK
| | - Philip J White
- Microelement Research Center/Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
- The James Hutton Institute, Invergowrie, Dundee, UK
| | - Sergey Shabala
- Tasmanian Institute of Agriculture, College of Science and Engineering, University of Tasmania, Hobart, Tas, Australia
- International Research Center for Environmental Membrane Biology & Department of Horticulture, Foshan University, Foshan, China
| | - Min Yu
- International Research Center for Environmental Membrane Biology & Department of Horticulture, Foshan University, Foshan, China
| | - Lei Shi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Microelement Research Center/Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
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17
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Rasool F, Khan MR, Schneider M, Uzair M, Aqeel M, Ajmal W, Léon J, Naz AA. Transcriptome unveiled the gene expression patterns of root architecture in drought-tolerant and sensitive wheat genotypes. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 178:20-30. [PMID: 35247694 DOI: 10.1016/j.plaphy.2022.02.025] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 01/26/2022] [Accepted: 02/27/2022] [Indexed: 06/14/2023]
Abstract
Drought is a big challenge for agricultural production. Root attributes are the important target traits for breeding high-yielding sustainable wheat varieties against ever changing climatic conditions. However, the transcriptomic of wheat concerning root architecture remained obscure. Here, we explored RNA-Seq based transcriptome to dissect putative genes involved in root system variations in naturally occurring six genotypes (drought-tolerant and sensitive) of wheat. Global RNA-Seq based root transcriptome analysis revealed single nucleotide polymorphisms (SNPs) variations and differentially expressed genes. Putative 56 SNPs were identified related to 15 genes involved in root architecture. Enrichment of these genes using GO terms demonstrated that differentially expressed genes (DEGs) are divided into sub-categories implicated in molecular functions, cellular components and biological processes. The KEGG analysis of DEGs in each comparison of genotype include metabolic, biosynthesis of secondary metabolites, microbial metabolism in diverse environments and biosynthesis of antibiotics. A deeper insight into DEGs unveiled various pathways involved in drought response and positive gravitropism. These genes belong to various transcription factor families such as DOF, C3H, MYB, and NAC involved in root developmental and stress-related pathways. Local White and UZ-11-CWA-8, which are drought-tolerant genotypes, harbor over-representation of most of DEGs or transcription factors. Notably, a microtubule-associated protein MAPRE1 belonging to RP/EB family recruited in positive gravitropism was enriched. Real-time PCR analysis revealed expression of MAPRE1 and PAL genes is consistent with RNA-seq data. The presented data and genetic resources seem valuable for providing genes involved in the root system architecture of drought-tolerant and susceptible genotypes.
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Affiliation(s)
- Fatima Rasool
- Genome Editing & Sequencing Lab, National Centre for Bioinformatics, Quaid-i-Azam University, Islamabad, 45320, Pakistan; National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Park Road, Islamabad, 45500, Pakistan
| | - Muhammad Ramzan Khan
- Genome Editing & Sequencing Lab, National Centre for Bioinformatics, Quaid-i-Azam University, Islamabad, 45320, Pakistan; National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Park Road, Islamabad, 45500, Pakistan.
| | - Michael Schneider
- Institute of Crop Science and Resource Conservation (INRES), Department of Crop Genetics and Biotechnology, Rheinische Friedrich-Wilhelms University of Bonn, Germany
| | - Muhammad Uzair
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Park Road, Islamabad, 45500, Pakistan
| | - Muhammad Aqeel
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Park Road, Islamabad, 45500, Pakistan
| | - Wajya Ajmal
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Park Road, Islamabad, 45500, Pakistan
| | - Jens Léon
- Institute of Crop Science and Resource Conservation (INRES), Department of Crop Genetics and Biotechnology, Rheinische Friedrich-Wilhelms University of Bonn, Germany
| | - Ali Ahmed Naz
- Institute of Crop Science and Resource Conservation (INRES), Department of Crop Genetics and Biotechnology, Rheinische Friedrich-Wilhelms University of Bonn, Germany.
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18
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Kumar S, Agrawal A, Seem K, Kumar S, Vinod KK, Mohapatra T. Transcriptome analysis of a near-isogenic line and its recurrent parent reveals the role of Pup1 QTL in phosphorus deficiency tolerance of rice at tillering stage. PLANT MOLECULAR BIOLOGY 2022; 109:29-50. [PMID: 35275352 DOI: 10.1007/s11103-022-01254-z] [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] [Received: 10/17/2021] [Accepted: 02/15/2022] [Indexed: 05/20/2023]
Abstract
Phosphorus (P) is essential for cellular processes like respiration, photosynthesis, biosynthesis of membrane phospholipids, etc. To cope with P deficiency stress, plants adopt reprograming of the expression of genes involved in different metabolic/signaling pathways for survival, growth, and development. Plants use transcriptional, post-transcriptional, and/or post-translational machinery to achieve P homeostasis. Several transcription factors (TFs), miRNAs, and P transporters play important roles in P deficiency tolerance; however, the underlying mechanisms responsible for P deficiency tolerance remain poorly understood. Studies on P starvation/deficiency responses in plants at early (seedling) stage of growth have been reported but only a few of them focused on molecular responses of the plant at advanced (tillering or reproductive) stage of growth. To decipher the strategies adopted by rice at tillering stage under P deficiency stress, a pair of contrasting genotypes [Pusa-44 (a high-yielding, P deficiency sensitive cultivar) and its near-isogenic line (NIL-23, P deficiency tolerant) for Pup1 QTL] was used for morphophysiological, biochemical, and molecular analyses. Comparative analyses of shoot and root tissues from 45-day-old plants grown hydroponically under P sufficient (16 ppm) or P deficient (4 ppm) medium confirmed some of the known morphophysiological responses. Moreover, RNA-seq analysis revealed the important roles of phosphate transporters, TFs, auxin-responsive proteins, modulation in the cell wall, fatty acid metabolism, and chromatin architecture/epigenetic modifications in providing P deficiency tolerance to NIL-23, which were brought in due to the introgression of the Pup1 QTL in Pusa-44. This study provides insights into the molecular functions of Pup1 for P deficiency tolerance, which might be utilized to improve P-use efficiency of rice for better productivity in P deficient soils. KEY MESSAGE: Introgression of Pup1 QTL in high-yielding rice cultivar modulates mainly phosphate transporters, TFs, auxin-responsive proteins, cell wall structure, fatty acid metabolism, and chromatin architecture/epigenetic modifications at tillering stage of growth under phosphorus deficiency stress.
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Affiliation(s)
- Suresh Kumar
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
| | - Anuradha Agrawal
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Karishma Seem
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | | | - K K Vinod
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
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19
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Role of Wheat Phosphorus Starvation Tolerance 1 Genes in Phosphorus Acquisition and Root Architecture. Genes (Basel) 2022; 13:genes13030487. [PMID: 35328041 PMCID: PMC8950872 DOI: 10.3390/genes13030487] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 03/03/2022] [Accepted: 03/07/2022] [Indexed: 12/04/2022] Open
Abstract
The wheat plant requires elevated phosphorus levels for its normal growth and yield, but continuously depleting non-renewable phosphorus reserves in the soil is one of the biggest challenges in agricultural production worldwide. The Phosphorus Starvation Tolerance 1 (PSTOL1) gene has been reported to play a key role in efficient P uptake, deeper rooting, and high yield in rice. However, the function of the PSTOL1 gene in wheat is still unclear. In this study, a total of 22 PSTOL1 orthologs were identified in the wheat genome, and found that wheat PSTOL1 orthologs are unevenly distributed on chromosomes, and these genes were under strong purifying selection. Under different phosphorus regimes, wheat PSTOL1 genes showed differential expression patterns in different tissues. These results strengthen the classification of Pakistan-13 as a P-efficient cultivar and Shafaq-06 as a P-inefficient cultivar. Phenotypic characterization demonstrated that Pakistan-13 wheat cultivar has significantly increased P uptake, root length, root volume, and root surface area compared to Shafaq-06. Some wheat PSTOL1 orthologs are co-localized with phosphorus starvation’s related quantitative trait loci (QTLs), suggesting their potential role in phosphorus use efficiency. Altogether, these results highlight the role of the wheat PSTOL1 genes in wheat P uptake, root architecture, and efficient plant growth. This comprehensive study will be helpful for devising sustainable strategies for wheat crop production and adaptation to phosphorus insufficiency.
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20
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Yadav MR, Choudhary M, Singh J, Lal MK, Jha PK, Udawat P, Gupta NK, Rajput VD, Garg NK, Maheshwari C, Hasan M, Gupta S, Jatwa TK, Kumar R, Yadav AK, Prasad PVV. Impacts, Tolerance, Adaptation, and Mitigation of Heat Stress on Wheat under Changing Climates. Int J Mol Sci 2022; 23:ijms23052838. [PMID: 35269980 PMCID: PMC8911405 DOI: 10.3390/ijms23052838] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 02/21/2022] [Accepted: 02/25/2022] [Indexed: 12/14/2022] Open
Abstract
Heat stress (HS) is one of the major abiotic stresses affecting the production and quality of wheat. Rising temperatures are particularly threatening to wheat production. A detailed overview of morpho-physio-biochemical responses of wheat to HS is critical to identify various tolerance mechanisms and their use in identifying strategies to safeguard wheat production under changing climates. The development of thermotolerant wheat cultivars using conventional or molecular breeding and transgenic approaches is promising. Over the last decade, different omics approaches have revolutionized the way plant breeders and biotechnologists investigate underlying stress tolerance mechanisms and cellular homeostasis. Therefore, developing genomics, transcriptomics, proteomics, and metabolomics data sets and a deeper understanding of HS tolerance mechanisms of different wheat cultivars are needed. The most reliable method to improve plant resilience to HS must include agronomic management strategies, such as the adoption of climate-smart cultivation practices and use of osmoprotectants and cultured soil microbes. However, looking at the complex nature of HS, the adoption of a holistic approach integrating outcomes of breeding, physiological, agronomical, and biotechnological options is required. Our review aims to provide insights concerning morpho-physiological and molecular impacts, tolerance mechanisms, and adaptation strategies of HS in wheat. This review will help scientific communities in the identification, development, and promotion of thermotolerant wheat cultivars and management strategies to minimize negative impacts of HS.
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Affiliation(s)
- Malu Ram Yadav
- Division of Agronomy, Rajasthan Agricultural Research Institute, Sri Karan Narendra Agriculture University, Jobner, Jaipur 303329, India; (M.R.Y.); (J.S.); (N.K.G.); (N.K.G.); (S.G.); (T.K.J.); (A.K.Y.)
| | - Mukesh Choudhary
- School of Agriculture and Environment, The University of Western Australia, Perth 6009, Australia;
| | - Jogendra Singh
- Division of Agronomy, Rajasthan Agricultural Research Institute, Sri Karan Narendra Agriculture University, Jobner, Jaipur 303329, India; (M.R.Y.); (J.S.); (N.K.G.); (N.K.G.); (S.G.); (T.K.J.); (A.K.Y.)
| | - Milan Kumar Lal
- Division of Crop Physiology, Biochemistry and Post-Harvest Technology, Indian Council of Agricultural Research (ICAR)-Central Potato Research Institute, Shimla 171001, India;
| | - Prakash Kumar Jha
- Feed the Future Innovation Lab for Collaborative Research on Sustainable Intensification, Kansas State University, Manhattan, KS 66506, USA;
- Correspondence: ; Tel.: +1-(517)-944-4698
| | - Pushpika Udawat
- Janardan Rai Nagar Rajasthan Vidyapeeth, Udaipur 313001, India;
| | - Narendra Kumar Gupta
- Division of Agronomy, Rajasthan Agricultural Research Institute, Sri Karan Narendra Agriculture University, Jobner, Jaipur 303329, India; (M.R.Y.); (J.S.); (N.K.G.); (N.K.G.); (S.G.); (T.K.J.); (A.K.Y.)
| | - Vishnu D. Rajput
- Academy of Biology and Biotechnology, Southern Federal University, 344090 Rostov-on-Don, Russia;
| | - Nitin Kumar Garg
- Division of Agronomy, Rajasthan Agricultural Research Institute, Sri Karan Narendra Agriculture University, Jobner, Jaipur 303329, India; (M.R.Y.); (J.S.); (N.K.G.); (N.K.G.); (S.G.); (T.K.J.); (A.K.Y.)
| | - Chirag Maheshwari
- Division of Biochemistry, Indian Council of Agricultural Research, Indian Agricultural Research Institute, New Delhi 110012, India;
| | - Muzaffar Hasan
- Division of Agro Produce Processing, Central Institute of Agricultural Engineering, Bhopal 462038, India;
| | - Sunita Gupta
- Division of Agronomy, Rajasthan Agricultural Research Institute, Sri Karan Narendra Agriculture University, Jobner, Jaipur 303329, India; (M.R.Y.); (J.S.); (N.K.G.); (N.K.G.); (S.G.); (T.K.J.); (A.K.Y.)
| | - Tarun Kumar Jatwa
- Division of Agronomy, Rajasthan Agricultural Research Institute, Sri Karan Narendra Agriculture University, Jobner, Jaipur 303329, India; (M.R.Y.); (J.S.); (N.K.G.); (N.K.G.); (S.G.); (T.K.J.); (A.K.Y.)
| | - Rakesh Kumar
- Division of Agronomy, Indian Council of Agricultural Research, National Dairy Research Institute, Karnal 132001, India;
| | - Arvind Kumar Yadav
- Division of Agronomy, Rajasthan Agricultural Research Institute, Sri Karan Narendra Agriculture University, Jobner, Jaipur 303329, India; (M.R.Y.); (J.S.); (N.K.G.); (N.K.G.); (S.G.); (T.K.J.); (A.K.Y.)
| | - P. V. Vara Prasad
- Feed the Future Innovation Lab for Collaborative Research on Sustainable Intensification, Kansas State University, Manhattan, KS 66506, USA;
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA
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21
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Hibbert L, Taylor G. Improving phosphate use efficiency in the aquatic crop watercress (Nasturtium officinale). HORTICULTURE RESEARCH 2022; 9:uhac011. [PMID: 35147194 PMCID: PMC8969064 DOI: 10.1093/hr/uhac011] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 11/30/2021] [Indexed: 06/14/2023]
Abstract
Watercress is a nutrient-dense leafy green crop, traditionally grown in aquatic outdoor systems and increasingly seen as well-suited for indoor hydroponic systems. However, there is concern that this crop has a detrimental impact on the environment through direct phosphate additions causing environmental pollution. Phosphate-based fertilisers are supplied to enhanced crop yield, but their use may contribute to eutrophication of waterways downstream of traditional watercress farms. One option is to develop a more phosphate use efficient (PUE) crop. This review identifies the key traits for this aquatic crop (the ideotype), for future selection, marker development and breeding. Traits identified as important for PUE are (i) increased root surface area through prolific root branching and adventitious root formation, (ii) aerenchyma formation and root hair growth. Functional genomic traits for improved PUE are (iii) efficacious phosphate remobilisation and scavenging strategies and (iv) the use of alternative metabolic pathways. Key genomic targets for this aquatic crop are identified as: PHT phosphate transporter genes, global transcriptional regulators such as those of the SPX family and genes involved in galactolipid and sulfolipid biosynthesis such as MGD2/3, PECP1, PSR2, PLDζ1/2 and SQD2. Breeding for enhanced PUE in watercress will be accelerated by improved molecular genetic resources such as a full reference genome sequence that is currently in development.
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Affiliation(s)
- Lauren Hibbert
- School of Biological Sciences, University of Southampton, Southampton, Hampshire, SO17 1BJ, UK
- Department of Plant Sciences, UC Davis, Davis, CA, 95616, USA
| | - Gail Taylor
- School of Biological Sciences, University of Southampton, Southampton, Hampshire, SO17 1BJ, UK
- Department of Plant Sciences, UC Davis, Davis, CA, 95616, USA
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22
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Li S, Cai TT, Li H. Transfer Learning for High-Dimensional Linear Regression: Prediction, Estimation and Minimax Optimality. J R Stat Soc Series B Stat Methodol 2022; 84:149-173. [PMID: 35210933 PMCID: PMC8863181 DOI: 10.1111/rssb.12479] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
This paper considers estimation and prediction of a high-dimensional linear regression in the setting of transfer learning where, in addition to observations from the target model, auxiliary samples from different but possibly related regression models are available. When the set of informative auxiliary studies is known, an estimator and a predictor are proposed and their optimality is established. The optimal rates of convergence for prediction and estimation are faster than the corresponding rates without using the auxiliary samples. This implies that knowledge from the informative auxiliary samples can be transferred to improve the learning performance of the target problem. When the set of informative auxiliary samples is unknown, we propose a data-driven procedure for transfer learning, called Trans-Lasso, and show its robustness to non-informative auxiliary samples and its efficiency in knowledge transfer. The proposed procedures are demonstrated in numerical studies and are applied to a dataset concerning the associations among gene expressions. It is shown that Trans-Lasso leads to improved performance in gene expression prediction in a target tissue by incorporating data from multiple different tissues as auxiliary samples.
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Affiliation(s)
- Sai Li
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennvania, Philadelphia, PA 19104
| | - T. Tony Cai
- Department of Statistics, The Wharton School, University of Pennsylvania, Philadelphia, PA 19104
| | - Hongzhe Li
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
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23
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Li Z, Hu J, Wu Y, Wang J, Song H, Chai M, Cong L, Miao F, Ma L, Tang W, Yang C, Tao Q, Zhong S, Zhao Y, Liu H, Yang G, Wang Z, Sun J. Integrative analysis of the metabolome and transcriptome reveal the phosphate deficiency response pathways of alfalfa. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 170:49-63. [PMID: 34847401 DOI: 10.1016/j.plaphy.2021.11.039] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/23/2021] [Accepted: 11/23/2021] [Indexed: 06/13/2023]
Abstract
Understanding the mechanisms underlying the responses to inorganic phosphate (Pi) deficiency in alfalfa will help enhance Pi acquisition efficiency and the sustainable use of phosphorous resources. Integrated global metabolomic and transcriptomic analyses of mid-vegetative alfalfa seedlings under 12-day Pi deficiency were conducted. Limited seedling growth were found, including 13.24%, 16.85% and 33.36% decreases in height, root length and photosynthesis, and a 24.10% increase in root-to-shoot ratio on day 12. A total of 322 and 448 differentially abundant metabolites and 1199 and 1061 differentially expressed genes were identified in roots and shoots. Increased (>3.68-fold) inorganic phosphate transporter 1;4 and SPX proteins levels in the roots (>2.15-fold) and shoots (>2.50-fold) were related to Pi absorption and translocation. The levels of phospholipids and Pi-binding carbohydrates and nucleosides were decreased, while those of phosphatases and pyrophosphatases in whole seedlings were induced under reduced Pi. In addition, nitrogen assimilation was affected by inhibiting high-affinity nitrate transporters (NRT2.1 and NRT3.1), and nitrate reductase. Increased delphinidin-3-glucoside might contribute to the gray-green leaves induced by Pi limitation. Stress-induced MYB, WRKY and ERF transcription factors were identified. The responses of alfalfa to Pi deficiency were summarized as local systemic signaling pathways, including root growth, stress-related responses consisting of enzymatic and nonenzymatic systems, and hormone signaling and systemic signaling pathways including Pi recycling and Pi sensing in the whole plant, as well as Pi recovery, and nitrate and metal absorption in the roots. This study provides important information on the molecular mechanism of the response to Pi deficiency in alfalfa.
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Affiliation(s)
- Zhenyi Li
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Jingyun Hu
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Yao Wu
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Jixiang Wang
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Hui Song
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Maofeng Chai
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Lili Cong
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Fuhong Miao
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Lichao Ma
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Wei Tang
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Chao Yang
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Qibo Tao
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Shangzhi Zhong
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Yiran Zhao
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Hongqing Liu
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Guofeng Yang
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Zengyu Wang
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Juan Sun
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China.
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24
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Kaur S, Kumari A, Sharma N, Pandey AK, Garg M. Physiological and molecular response of colored wheat seedlings against phosphate deficiency is linked to accumulation of distinct anthocyanins. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 170:338-349. [PMID: 34959054 DOI: 10.1016/j.plaphy.2021.12.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 12/16/2021] [Accepted: 12/17/2021] [Indexed: 06/14/2023]
Abstract
Anthocyanin rich colored wheat with additional health benefits has created interest among breeders, consumers and policy makers to address the prevailing malnutrition in the vulnerable population. Researchers are exploring how colored wheat could perform under different nutrient conditions for the maintenance of growth and development. The present study was aimed to investigate the differential response of phosphorous (Pi) deficiency at the seedling stage using hydroponics. Our results showed that Pi-deficiency triggered typical response in the wheat along with the changes in the plant root morphology, total biomass, micronutrient concentration and distinct anthocyanin accumulation. Our physiological and biochemical data revealed that these parameters were positively altered under stress in the colored wheat and the adaptation followed the trend of white < blue <purple < black. Our results also confirmed that stress induced accumulation of distinct anthocyanins including derivatives of cyanidin, delphinidin and peonidin in a genotype dependent manner. Differential expression pattern visualized for the transcripts encoding phosphate transporters, anthocyanin biosynthesis, putative transporters and regulators may be one of the underlying factors. Altogether, our data showed that the black wheat genotype with highest anthocyanin content could able to adapt better with the P stress. This study will help in identifying suitable colored wheat adapting the stress condition and have potential for influence on the future agricultural cultivation practices.
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Affiliation(s)
- Satveer Kaur
- National Agri-Food Biotechnology Institute, Mohali, Punjab, India, 140306; Department of Biotechnology, Panjab University, Chandigarh, India
| | - Anita Kumari
- National Agri-Food Biotechnology Institute, Mohali, Punjab, India, 140306; University Institute of Engineering and Technology, Panjab University, Chandigarh, India
| | - Natasha Sharma
- National Agri-Food Biotechnology Institute, Mohali, Punjab, India, 140306
| | - Ajay K Pandey
- National Agri-Food Biotechnology Institute, Mohali, Punjab, India, 140306.
| | - Monika Garg
- National Agri-Food Biotechnology Institute, Mohali, Punjab, India, 140306.
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25
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Liu H, Wu J, Su Y, Li Y, Zuo D, Liu H, Liu Y, Mei X, Huang H, Yang M, Zhu S. Allyl Isothiocyanate in the Volatiles of Brassica juncea Inhibits the Growth of Root Rot Pathogens of Panax notoginseng by Inducing the Accumulation of ROS. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:13713-13723. [PMID: 34780155 DOI: 10.1021/acs.jafc.1c05225] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The cultivation of Panax notoginseng is often seriously hindered by root rot disease caused by the accumulation of soil-borne pathogens. Here, the inhibitory activity of Brassica juncea volatiles on P. notoginseng root rot pathogens was assessed and compounds in volatiles were identified. Furthermore, the antimicrobial activity and mechanism of allyl isothiocyanate (AITC) were deciphered by integrated transcriptome and metabolome analyses. The volatiles of B. juncea showed dose-dependent antimicrobial activity against root rot pathogens. AITC, identified as the main volatile compound, not only significantly inhibited pathogen growth in vitro but also suppressed root rot disease in the field. Integrated transcriptomic and metabolomics analysis revealed that AITC inhibited Fusarium solani by interfering with energy production and induced the accumulation of ROS by decreasing the content of glutathione (GSH). In summary, B. juncea releases AITC to inhibit soil-borne pathogens and could be used as a rotation crop or soil fumigant to alleviate root rot disease.
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Affiliation(s)
- Haijiao Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
- Key Laboratory for Agro-Biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Jiaqing Wu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
- Key Laboratory for Agro-Biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Yingwei Su
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
- Key Laboratory for Agro-Biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Yingbin Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
- Key Laboratory for Agro-Biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Denghong Zuo
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
- Key Laboratory for Agro-Biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Hongbin Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
- Key Laboratory for Agro-Biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Yixiang Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
- Key Laboratory for Agro-Biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Xinyue Mei
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
- Key Laboratory for Agro-Biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Huichuan Huang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
- Key Laboratory for Agro-Biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Min Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
- Key Laboratory for Agro-Biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Shusheng Zhu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
- Key Laboratory for Agro-Biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
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26
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Zhu Q, Yuan Y, Yan B, Zhou J, Zuo J, Bai L. A new biomimetic nanozyme of hemin/graphdiyne oxide with superior peroxidase-like activity for colorimetric bioassays. Analyst 2021; 146:7284-7293. [PMID: 34749389 DOI: 10.1039/d1an01456k] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Graphdiyne oxide (GDYO) is a novel type of two-dimensional carbon allotrope nanomaterial consisting of a large conjugated system and excellent chemical stability. To date, application of GDYO as a nanozyme in biosensing has been rarely reported. In this study, a novel ultrasensitive colorimetric bioassay was constructed using a hemin/GDYO nanocomposite (H/GDYO) as a new nanozyme with superior peroxidase-like activity for the detection of H2O2 and glucose. It was discovered that H/GDYO exhibited 6-fold higher peroxidase-like activity than pure hemin. Catalytic kinetic analysis showed that H/GDYO had a much higher affinity for H2O2 and glucose than that of hemin. The designed colorimetric bioassay displayed excellent sensitivity for H2O2 and glucose detection with a wide linear range of 0.015-0.5 mM and 0.1-10 mM, respectively, while the limit of detection (LOD) was as low as 4.39 μM and 38 μM, respectively. Moreover, it was successfully applied for the analysis of H2O2 in milk and glucose in real human serum samples with acceptable recoveries. Importantly, the developed colorimetric bioassay shows good agreement with the results obtained from a commercial blood glucose meter. We believe that the proposed method could provide a promising prospect for medical diagnosis and biotechnology.
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Affiliation(s)
- Qiqi Zhu
- Chongqing Research Center for Pharmaceutical Engineering, College of Pharmacy, Chongqing Medical University, Chongqing 400016, PR China.
| | - Yonghua Yuan
- Research Center for Pharmacodynamic Evaluation Engineering Technology of Chongqing, College of Pharmacy, Chongqing Medical University, Chongqing 400016, PR China
| | - Bin Yan
- The Eighth Middle School of Chongqing, Chongqing 400030, PR China
| | - Jing Zhou
- Chongqing Research Center for Pharmaceutical Engineering, College of Pharmacy, Chongqing Medical University, Chongqing 400016, PR China.
| | - Jianli Zuo
- Research Center for Pharmacodynamic Evaluation Engineering Technology of Chongqing, College of Pharmacy, Chongqing Medical University, Chongqing 400016, PR China
| | - Lijuan Bai
- Chongqing Research Center for Pharmaceutical Engineering, College of Pharmacy, Chongqing Medical University, Chongqing 400016, PR China.
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27
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Payne JA, Barnes RA, Downey AX, Freeman DA, Johnson LR, Rodriguez RA, Sloan MA, Valdez CM, Voorhees WB, Whitmore JN. Temperature Dynamics in Rat Brains Exposed to Near-Field Waveguide Outputs at 2.8 GHz. Bioelectromagnetics 2021; 43:14-24. [PMID: 34719046 DOI: 10.1002/bem.22377] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 07/29/2021] [Accepted: 10/10/2021] [Indexed: 01/07/2023]
Abstract
Biological effects in the microwave band of the radiofrequency (RF) spectrum are thermally mediated. For acute high-power microwave exposures, these effects will depend on transient time-temperature histories within the tissue. In this article, we summarize the transient temperature response of rats exposed to RF energy emanating from an open-ended rectangular waveguide. These exposures produced specific absorption rates of approximately 36 and 203 W/kg in the whole body and brain, respectively. We then use the experimentally measured thermal data to infer the baseline perfusion rate in the brain and modify a custom thermal modeling tool based upon these findings. Finally, we compare multi-physics simulations of rat brain temperature against empirical measurements in both live and euthanized subjects and find close agreement between model and experimentation. This research revealed that baseline brain perfusion rates in rat subjects could be larger than previously assumed in the RF thermal modeling literature, and plays a significant role in the transient thermal response to high-power microwave exposures. © 2021 Bioelectromagnetics Society.
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Affiliation(s)
- Jason A Payne
- Air Force Research Laboratory, 711th Human Performance Wing, Airman Systems Directorate, Bioeffects Division, JBSA Fort Sam Houston, TX
| | - Ronald A Barnes
- Air Force Research Laboratory, 711th Human Performance Wing, Airman Systems Directorate, Bioeffects Division, JBSA Fort Sam Houston, TX
| | | | - David A Freeman
- General Dynamics Information Technology, JBSA Fort Sam Houston, TX
| | - Leland R Johnson
- Air Force Research Laboratory, 711th Human Performance Wing, Airman Systems Directorate, Bioeffects Division, JBSA Fort Sam Houston, TX
| | | | - Mark A Sloan
- General Dynamics Information Technology, JBSA Fort Sam Houston, TX
| | - Christopher M Valdez
- Air Force Research Laboratory, 711th Human Performance Wing, Airman Systems Directorate, Bioeffects Division, JBSA Fort Sam Houston, TX
| | - William B Voorhees
- Air Force Research Laboratory, 711th Human Performance Wing, Airman Systems Directorate, Bioeffects Division, JBSA Fort Sam Houston, TX
| | - Jeffrey N Whitmore
- Air Force Research Laboratory, 711th Human Performance Wing, Airman Systems Directorate, Bioeffects Division, JBSA Fort Sam Houston, TX
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28
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Artur MAS, Kajala K. Convergent evolution of gene regulatory networks underlying plant adaptations to dry environments. PLANT, CELL & ENVIRONMENT 2021; 44:3211-3222. [PMID: 34196969 PMCID: PMC8518057 DOI: 10.1111/pce.14143] [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: 09/15/2020] [Accepted: 06/25/2021] [Indexed: 05/21/2023]
Abstract
Plants transitioned from an aquatic to a terrestrial lifestyle during their evolution. On land, fluctuations on water availability in the environment became one of the major problems they encountered. The appearance of morpho-physiological adaptations to cope with and tolerate water loss from the cells was undeniably useful to survive on dry land. Some of these adaptations, such as carbon concentrating mechanisms (CCMs), desiccation tolerance (DT) and root impermeabilization, appeared in multiple plant lineages. Despite being crucial for evolution on land, it has been unclear how these adaptations convergently evolved in the various plant lineages. Recent advances on whole genome and transcriptome sequencing are revealing that co-option of genes and gene regulatory networks (GRNs) is a common feature underlying the convergent evolution of these adaptations. In this review, we address how the study of CCMs and DT has provided insight into convergent evolution of GRNs underlying plant adaptation to dry environments, and how these insights could be applied to currently emerging understanding of evolution of root impermeabilization through different barrier cell types. We discuss examples of co-option, conservation and innovation of genes and GRNs at the cell, tissue and organ levels revealed by recent phylogenomic (comparative genomic) and comparative transcriptomic studies.
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Affiliation(s)
- Mariana A. S. Artur
- Laboratory of Plant PhysiologyWageningen UniversityWageningenThe Netherlands
- Plant Ecophysiology, Institute of Environmental BiologyUtrecht UniversityUtrechtThe Netherlands
| | - Kaisa Kajala
- Plant Ecophysiology, Institute of Environmental BiologyUtrecht UniversityUtrechtThe Netherlands
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29
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Sun T, Zhang J, Zhang Q, Li X, Li M, Yang Y, Zhou J, Wei Q, Zhou B. Transcriptome and metabolome analyses revealed the response mechanism of apple to different phosphorus stresses. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 167:639-650. [PMID: 34481154 DOI: 10.1016/j.plaphy.2021.08.040] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 08/22/2021] [Accepted: 08/25/2021] [Indexed: 06/13/2023]
Abstract
Phosphorus (P) is an important element in numerous metabolic reactions and signalling pathways, but the molecular details of these pathways remain largely unknown. In this study, physiological, transcriptome and metabolite analyses of apple leaves and roots were compared under different P conditions. The results showed that different P stresses influenced phenotypic characteristics, soil plant analytical development (SPAD) values and the contents of flavonoids and anthocyanins in apple seedlings. The contents of hydrogen peroxide (H2O2) and malondialdehyde (MDA) and the activities of superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), acid phosphatase (ACP) and purple acid phosphatase (PAP) were also affected by different P stresses. In addition, RNA sequencing (RNA-seq) was used to characterize the influence of different P stresses on apple seedlings. Compared with control apple plants, there were 1246 and 1183 differentially expressed genes (DEGs) in leaves and roots under the low-P treatment and 60 and 1030 DEGs in leaves and roots under the high-P treatment, respectively. Gene Ontology (GO) analysis indicated that apple trees might change their responses to metabolic processes, cell proliferation, regulation of biological processes, reactive oxygen species metabolic processes and flavonoid metabolic processes under P stress. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis further indicated that DEGs act on the mitogen-activated protein kinase (MAPK) signalling pathway, flavonoid biosynthesis, phenylpropanoid biosynthesis, and ATP-binding cassette (ABC) transporters. The metabolome analysis revealed that the levels of most amino acids and their derivatives, organic acids and flavonoids in roots treated with low-P stress were higher than those in roots of apple seedlings under control growth conditions. Apple seedlings regulate the flavonoid pathway to respond to different phosphorus environments. The results provide a framework for understanding the metabolic processes underlying different P responses and provide a foundation for improving the utilization efficiency of P in apple trees.
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Affiliation(s)
- Tingting Sun
- Beijing Academy of Agriculture and Forestry Sciences, Institute of Forestry and Pomology, Beijing Academy of Forestry and Pomology Sciences, Beijing Engineering Research Center for Deciduous Fruit Trees, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, Beijing, 100093, China; School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, Inner Mongolia, China
| | - Junke Zhang
- Beijing Academy of Agriculture and Forestry Sciences, Institute of Forestry and Pomology, Beijing Academy of Forestry and Pomology Sciences, Beijing Engineering Research Center for Deciduous Fruit Trees, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, Beijing, 100093, China
| | - Qiang Zhang
- Beijing Academy of Agriculture and Forestry Sciences, Institute of Forestry and Pomology, Beijing Academy of Forestry and Pomology Sciences, Beijing Engineering Research Center for Deciduous Fruit Trees, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, Beijing, 100093, China
| | - Xingliang Li
- Beijing Academy of Agriculture and Forestry Sciences, Institute of Forestry and Pomology, Beijing Academy of Forestry and Pomology Sciences, Beijing Engineering Research Center for Deciduous Fruit Trees, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, Beijing, 100093, China
| | - Minji Li
- Beijing Academy of Agriculture and Forestry Sciences, Institute of Forestry and Pomology, Beijing Academy of Forestry and Pomology Sciences, Beijing Engineering Research Center for Deciduous Fruit Trees, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, Beijing, 100093, China
| | - Yuzhang Yang
- Beijing Academy of Agriculture and Forestry Sciences, Institute of Forestry and Pomology, Beijing Academy of Forestry and Pomology Sciences, Beijing Engineering Research Center for Deciduous Fruit Trees, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, Beijing, 100093, China
| | - Jia Zhou
- Beijing Academy of Agriculture and Forestry Sciences, Institute of Forestry and Pomology, Beijing Academy of Forestry and Pomology Sciences, Beijing Engineering Research Center for Deciduous Fruit Trees, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, Beijing, 100093, China
| | - Qinping Wei
- Beijing Academy of Agriculture and Forestry Sciences, Institute of Forestry and Pomology, Beijing Academy of Forestry and Pomology Sciences, Beijing Engineering Research Center for Deciduous Fruit Trees, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, Beijing, 100093, China
| | - Beibei Zhou
- Beijing Academy of Agriculture and Forestry Sciences, Institute of Forestry and Pomology, Beijing Academy of Forestry and Pomology Sciences, Beijing Engineering Research Center for Deciduous Fruit Trees, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, Beijing, 100093, China.
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30
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Mahapatra S, Sahu SS. ANOVA-particle swarm optimization-based feature selection and gradient boosting machine classifier for improved protein-protein interaction prediction. Proteins 2021; 90:443-454. [PMID: 34528291 DOI: 10.1002/prot.26236] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Revised: 08/09/2021] [Accepted: 09/03/2021] [Indexed: 01/22/2023]
Abstract
Feature fusion and selection strategies have been applied to improve accuracy in the prediction of protein-protein interaction (PPI). In this paper, an embedded feature selection framework is developed by integrating a cost function based on analysis of variance (ANOVA) with the particle swarm optimization (PSO), termed AVPSO. Initially, the features of the protein sequences extracted using pseudo-amino acid composition (PseAAC), conjoint triad composition, and local descriptor are fused. Then, AVPSO is employed to select the optimal set of features. The light gradient boosting machine (LGBM) classifier is used to predict the PPIs using the optimal feature subset. On the five-fold cross-validation analysis, the proposed model (AVPSO-LGBM) achieved an average accuracy of 97.12% and 95.09%, respectively, on the intraspecies PPI datasets Saccharomyces cerevisiae and Helicobacter pylori. On the interspecies, PPI datasets of the Human-Bacillus and Human-Yersinia, an average accuracy of 95.20% and 93.44%, are achieved. Results obtained on independent test datasets, and network datasets show that the prediction accuracy of the AVPSO-LGBM is better than the existing methods, demonstrating its generalization ability. The improved prediction performance obtained by the proposed model makes it a reliable and effective PPI prediction model.
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Affiliation(s)
- Satyajit Mahapatra
- Department of Electronics and Communication Engineering, Birla Institute of Technology, Ranchi, India
| | - Sitanshu Sekhar Sahu
- Department of Electronics and Communication Engineering, Birla Institute of Technology, Ranchi, India
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31
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Nefissi Ouertani R, Arasappan D, Abid G, Ben Chikha M, Jardak R, Mahmoudi H, Mejri S, Ghorbel A, Ruhlman TA, Jansen RK. Transcriptomic Analysis of Salt-Stress-Responsive Genes in Barley Roots and Leaves. Int J Mol Sci 2021; 22:8155. [PMID: 34360920 PMCID: PMC8348758 DOI: 10.3390/ijms22158155] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 07/22/2021] [Accepted: 07/23/2021] [Indexed: 12/03/2022] Open
Abstract
Barley is characterized by a rich genetic diversity, making it an important model for studies of salinity response with great potential for crop improvement. Moreover, salt stress severely affects barley growth and development, leading to substantial yield loss. Leaf and root transcriptomes of a salt-tolerant Tunisian landrace (Boulifa) exposed to 2, 8, and 24 h salt stress were compared with pre-exposure plants to identify candidate genes and pathways underlying barley's response. Expression of 3585 genes was upregulated and 5586 downregulated in leaves, while expression of 13,200 genes was upregulated and 10,575 downregulated in roots. Regulation of gene expression was severely impacted in roots, highlighting the complexity of salt stress response mechanisms in this tissue. Functional analyses in both tissues indicated that response to salt stress is mainly achieved through sensing and signaling pathways, strong transcriptional reprograming, hormone osmolyte and ion homeostasis stabilization, increased reactive oxygen scavenging, and activation of transport and photosynthesis systems. A number of candidate genes involved in hormone and kinase signaling pathways, as well as several transcription factor families and transporters, were identified. This study provides valuable information on early salt-stress-responsive genes in roots and leaves of barley and identifies several important players in salt tolerance.
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Affiliation(s)
- Rim Nefissi Ouertani
- Laboratory of Plant Molecular Physiology, Center of Biotechnology of Borj Cedria, B.P. 901, Hammam-Lif 2050, Tunisia; (R.N.O.); (M.B.C.); (R.J.); (S.M.); (A.G.)
| | - Dhivya Arasappan
- Center for Biomedical Research Support, University of Texas at Austin, Austin, TX 78712, USA;
| | - Ghassen Abid
- Laboratory of Legumes and Sustainable Agrosystems, Center of Biotechnology of Borj Cedria, B.P. 901, Hammam-Lif 2050, Tunisia;
| | - Mariem Ben Chikha
- Laboratory of Plant Molecular Physiology, Center of Biotechnology of Borj Cedria, B.P. 901, Hammam-Lif 2050, Tunisia; (R.N.O.); (M.B.C.); (R.J.); (S.M.); (A.G.)
| | - Rahma Jardak
- Laboratory of Plant Molecular Physiology, Center of Biotechnology of Borj Cedria, B.P. 901, Hammam-Lif 2050, Tunisia; (R.N.O.); (M.B.C.); (R.J.); (S.M.); (A.G.)
| | - Henda Mahmoudi
- International Center for Biosaline Agriculture, Dubai 00000, United Arab Emirates;
| | - Samiha Mejri
- Laboratory of Plant Molecular Physiology, Center of Biotechnology of Borj Cedria, B.P. 901, Hammam-Lif 2050, Tunisia; (R.N.O.); (M.B.C.); (R.J.); (S.M.); (A.G.)
| | - Abdelwahed Ghorbel
- Laboratory of Plant Molecular Physiology, Center of Biotechnology of Borj Cedria, B.P. 901, Hammam-Lif 2050, Tunisia; (R.N.O.); (M.B.C.); (R.J.); (S.M.); (A.G.)
| | - Tracey A. Ruhlman
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA;
| | - Robert K. Jansen
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA;
- Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah 21589, Saudi Arabia
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Di Tomo P, Alessio N, Falone S, Pietrangelo L, Lanuti P, Cordone V, Santini SJ, Di Pietrantonio N, Marchisio M, Protasi F, Di Pietro N, Formoso G, Amicarelli F, Galderisi U, Pandolfi A. Endothelial cells from umbilical cord of women affected by gestational diabetes: A suitable in vitro model to study mechanisms of early vascular senescence in diabetes. FASEB J 2021; 35:e21662. [PMID: 34046935 DOI: 10.1096/fj.202002072rr] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 04/26/2021] [Accepted: 04/28/2021] [Indexed: 12/16/2022]
Abstract
Human umbilical cord endothelial cells (HUVECs) obtained from women affected by gestational diabetes (GD-HUVECs) display durable pro-atherogenic modifications and might be considered a valid in vitro model for studying chronic hyperglycemia effects on early endothelial senescence. Here, we demonstrated that GD- compared to C-HUVECs (controls) exhibited oxidative stress, altered both mitochondrial membrane potential and antioxidant response, significant increase of senescent cells characterized by a reduced NAD-dependent deacetylase sirtuin-1 (SIRT1) activity together with an increase in cyclin-dependent kinase inhibitor-2A (P16), cyclin-dependent kinase inhibitor-1 (P21), and tumor protein p53 (P53) acetylation. This was associated with the p300 activation, and its silencing significantly reduced the GD-HUVECs increased protein levels of P300 and Ac-P53 thus indicating a persistent endothelial senescence via SIRT1/P300/P53/P21 pathway. Overall, our data suggest that GD-HUVECs can represent an "endothelial hyperglycemic memory" model to investigate in vitro the early endothelium senescence in cells chronically exposed to hyperglycemia in vivo.
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Affiliation(s)
- Pamela Di Tomo
- Department of Medical and Oral Sciences and Biotechnologies, University "G. d'Annunzio" of Chieti-Pescara, Chieti, Italy.,Center for Advanced Studies and Technology - CAST (ex CeSI-MeT), University "G. d'Annunzio" of Chieti-Pescara, Italy
| | - Nicola Alessio
- Department of Experimental Medicine, University of Campania "L. Vanvitelli", Napoli, Italy
| | - Stefano Falone
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - Laura Pietrangelo
- Center for Advanced Studies and Technology - CAST (ex CeSI-MeT), University "G. d'Annunzio" of Chieti-Pescara, Italy.,Department of Medicine and Aging Sciences, University "G. d'Annunzio" of Chieti-Pescara, Chieti, Italy
| | - Paola Lanuti
- Center for Advanced Studies and Technology - CAST (ex CeSI-MeT), University "G. d'Annunzio" of Chieti-Pescara, Italy.,Department of Medicine and Aging Sciences, University "G. d'Annunzio" of Chieti-Pescara, Chieti, Italy
| | - Valeria Cordone
- Department of Biomedical and Specialist Surgical Sciences, University of Ferrara, Ferrara, Italy
| | - Silvano Junior Santini
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - Nadia Di Pietrantonio
- Department of Medical and Oral Sciences and Biotechnologies, University "G. d'Annunzio" of Chieti-Pescara, Chieti, Italy.,Center for Advanced Studies and Technology - CAST (ex CeSI-MeT), University "G. d'Annunzio" of Chieti-Pescara, Italy
| | - Marco Marchisio
- Center for Advanced Studies and Technology - CAST (ex CeSI-MeT), University "G. d'Annunzio" of Chieti-Pescara, Italy.,Department of Medicine and Aging Sciences, University "G. d'Annunzio" of Chieti-Pescara, Chieti, Italy
| | - Feliciano Protasi
- Center for Advanced Studies and Technology - CAST (ex CeSI-MeT), University "G. d'Annunzio" of Chieti-Pescara, Italy.,Department of Medicine and Aging Sciences, University "G. d'Annunzio" of Chieti-Pescara, Chieti, Italy
| | - Natalia Di Pietro
- Department of Medical and Oral Sciences and Biotechnologies, University "G. d'Annunzio" of Chieti-Pescara, Chieti, Italy.,Center for Advanced Studies and Technology - CAST (ex CeSI-MeT), University "G. d'Annunzio" of Chieti-Pescara, Italy
| | - Gloria Formoso
- Center for Advanced Studies and Technology - CAST (ex CeSI-MeT), University "G. d'Annunzio" of Chieti-Pescara, Italy.,Department of Medicine and Aging Sciences, University "G. d'Annunzio" of Chieti-Pescara, Chieti, Italy
| | - Fernanda Amicarelli
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - Umberto Galderisi
- Department of Experimental Medicine, University of Campania "L. Vanvitelli", Napoli, Italy
| | - Assunta Pandolfi
- Department of Medical and Oral Sciences and Biotechnologies, University "G. d'Annunzio" of Chieti-Pescara, Chieti, Italy.,Center for Advanced Studies and Technology - CAST (ex CeSI-MeT), University "G. d'Annunzio" of Chieti-Pescara, Italy
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Kumar S, Chugh C, Seem K, Kumar S, Vinod KK, Mohapatra T. Characterization of contrasting rice (Oryza sativa L.) genotypes reveals the Pi-efficient schema for phosphate starvation tolerance. BMC PLANT BIOLOGY 2021; 21:282. [PMID: 34154533 PMCID: PMC8215752 DOI: 10.1186/s12870-021-03015-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 05/05/2021] [Indexed: 05/10/2023]
Abstract
BACKGROUND Phosphorus (P), being one of the essential components of nucleic acids, cell membranes and enzymes, indispensable for diverse cellular processes like photosynthesis/carbohydrate metabolism, energy production, redox homeostasis and signaling. Crop yield is severely affected due to Phosphate (Pi) deficiency; and to cope with Pi-deficiency, plants have evolved several strategies. Some rice genotypes are compatible with low Pi availability, whereas others are sensitive to Pi deficiency. However, the underlying molecular mechanism for low Pi tolerance remains largely unexplored. RESULT Several studies were carried out to understand Pi-deficiency responses in rice at seedling stage, but few of them targeted molecular aspects/responses of Pi-starvation at the advanced stage of growth. To delineate the molecular mechanisms for low Pi tolerance, a pair of contrasting rice (Oryza sativa L.) genotypes [viz. Pusa-44 (Pi-deficiency sensitive) and its near isogenic line (NIL-23, Pi-deficiency tolerant) harboring Phosphorus uptake 1 (Pup1) QTL from an aus landrace Kasalath] were used. Comparative morphological, physiological, and biochemical analyses confirmed some of the well-known findings. Transcriptome analysis of shoot and root tissues from 45-day-old rice plants grown hydroponically under P-sufficient (16 ppm Pi) or P-starved (0 ppm Pi) medium revealed that Pi-starvation stress causes global transcriptional reprogramming affecting several transcription factors, signaling pathways and other regulatory genes. We could identify several significantly up-regulated genes in roots of NIL-23 under Pi-starvation which might be responsible for the Pi starvation tolerance. Pathway enrichment analysis indicated significant role of certain phosphatases, transporters, transcription factors, carbohydrate metabolism, hormone-signaling, and epigenetic processes in improving P-starvation stress tolerance in NIL-23. CONCLUSION We report the important candidate mechanisms for Pi acquisition/solubilization, recycling, remobilization/transport, sensing/signalling, genetic/epigenetic regulation, and cell wall structural changes to be responsible for P-starvation tolerance in NIL-23. The study provides some of the novel information useful for improving phosphorus-use efficiency in rice cultivars.
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Affiliation(s)
- Suresh Kumar
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi , 110012, India.
| | - Chetna Chugh
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi , 110012, India
| | - Karishma Seem
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi , 110012, India
| | | | - K K Vinod
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
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Yi H, Zhang Q, Sun Y, Ma S. Assisted estimation of gene expression graphical models. Genet Epidemiol 2021; 45:372-385. [PMID: 33527531 PMCID: PMC8137544 DOI: 10.1002/gepi.22377] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 12/16/2020] [Accepted: 12/31/2020] [Indexed: 02/02/2023]
Abstract
In the study of gene expression data, network analysis has played a uniquely important role. To accommodate the high dimensionality and low sample size and generate interpretable results, regularized estimation is usually conducted in the construction of gene expression Gaussian Graphical Models (GGM). Here we use GeO-GGM to represent gene-expression-only GGM. Gene expressions are regulated by regulators. gene-expression-regulator GGMs (GeR-GGMs), which accommodate gene expressions as well as their regulators, have been constructed accordingly. In practical data analysis, with a "lack of information" caused by the large number of model parameters, limited sample size, and weak signals, the construction of both GeO-GGMs and GeR-GGMs is often unsatisfactory. In this article, we recognize that with the regulation between gene expressions and regulators, the sparsity structures of a GeO-GGM and its GeR-GGM counterpart can satisfy a hierarchy. Accordingly, we propose a joint estimation which reinforces the hierarchical structure and use the construction of a GeO-GGM to assist that of its GeR-GGM counterpart and vice versa. Consistency properties are rigorously established, and an effective computational algorithm is developed. In simulation, the assisted construction outperforms the separation construction of GeO-GGM and GeR-GGM. Two The Cancer Genome Atlas data sets are analyzed, leading to findings different from the direct competitors.
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Affiliation(s)
- Huangdi Yi
- Department of Biostatistics, Yale University
| | - Qingzhao Zhang
- Department of Statistics, School of Economics; Key Laboratory of Econometrics, Ministry of Education; The Wang Yanan Institute for Studies in Economics, Xiamen University
| | - Yifan Sun
- Center of Applied Statistics, School of Statistics, Renmin University of China
| | - Shuangge Ma
- Department of Biostatistics, Yale University
- Department of Statistics, School of Economics; Key Laboratory of Econometrics, Ministry of Education; The Wang Yanan Institute for Studies in Economics, Xiamen University
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35
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A comparison of shared patterns of differential gene expression and gene ontologies in response to water-stress in roots and leaves of four diverse genotypes of Lolium and Festuca spp. temperate pasture grasses. PLoS One 2021; 16:e0249636. [PMID: 33831050 PMCID: PMC8031407 DOI: 10.1371/journal.pone.0249636] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 03/22/2021] [Indexed: 12/13/2022] Open
Abstract
Ryegrasses (Lolium spp.) and fescues (Festuca spp.) are closely related and widely cultivated perennial forage grasses. As such, resilience in the face of abiotic stresses is an important component of their traits. We have compared patterns of differentially expressed genes (DEGs) in roots and leaves of two perennial ryegrass genotypes and a single genotype of each of a festulolium (predominantly Italian ryegrass) and meadow fescue with the onset of water stress, focussing on overall patterns of DEGs and gene ontology terms (GOs) shared by all four genotypes. Plants were established in a growing medium of vermiculite watered with nutrient solution. Leaf and root material were sampled at 35% (saturation) and, as the medium dried, at 15%, 5% and 1% estimated water contents (EWCs) and RNA extracted. Differential gene expression was evaluated comparing the EWC sampling points from RNAseq data using a combination of analysis methods. For all genotypes, the greatest numbers of DEGs were identified in the 35/1 and 5/1 comparisons in both leaves and roots. In total, 566 leaf and 643 root DEGs were common to all 4 genotypes, though a third of these leaf DEGs were not regulated in the same up/down direction in all 4 genotypes. For roots, the equivalent figure was 1% of the DEGs. GO terms shared by all four genotypes were often enriched by both up- and down-regulated DEGs in the leaf, whereas generally, only by either up- or down-regulated DEGs in the root. Overall, up-regulated leaf DEGs tended to be more genotype-specific than down-regulated leaf DEGs or root DEGs and were also associated with fewer GOs. On average, only 5–15% of the DEGs enriching common GO terms were shared by all 4 genotypes, suggesting considerable variation in DEGs between related genotypes in enacting similar biological processes.
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36
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Soumya PR, Burridge AJ, Singh N, Batra R, Pandey R, Kalia S, Rai V, Edwards KJ. Population structure and genome-wide association studies in bread wheat for phosphorus efficiency traits using 35 K Wheat Breeder's Affymetrix array. Sci Rep 2021; 11:7601. [PMID: 33828173 PMCID: PMC8027818 DOI: 10.1038/s41598-021-87182-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 03/15/2021] [Indexed: 02/02/2023] Open
Abstract
Soil bioavailability of phosphorus (P) is a major concern for crop productivity worldwide. As phosphatic fertilizers are a non-renewable resource associated with economic and environmental issues so, the sustainable option is to develop P use efficient crop varieties. We phenotyped 82 diverse wheat (Triticum aestivum L.) accessions in soil and hydroponics at low and sufficient P. To identify the genic regions for P efficiency traits, the accessions were genotyped using the 35 K-SNP array and genome-wide association study (GWAS) was performed. The high-quality SNPs across the genomes were evenly distributed with polymorphic information content values varying between 0.090 and 0.375. Structure analysis revealed three subpopulations (C1, C2, C3) and the phenotypic responses of these subpopulations were assessed for P efficiency traits. The C2 subpopulation showed the highest genetic variance and heritability values for numerous agronomically important traits as well as strong correlation under both P levels in soil and hydroponics. GWAS revealed 78 marker-trait associations (MTAs) but only 35 MTAs passed Bonferroni Correction. A total of 297 candidate genes were identified for these MTAs and their annotation suggested their involvement in several biological process. Out of 35, nine (9) MTAs were controlling polygenic trait (two controlling four traits, one controlling three traits and six controlling two traits). These multi-trait MTAs (each controlling two or more than two correlated traits) could be utilized for improving bread wheat to tolerate low P stress through marker-assisted selection (MAS).
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Affiliation(s)
- Preman R. Soumya
- grid.418196.30000 0001 2172 0814Mineral Nutrition Laboratory, Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110 012 India ,grid.459442.a0000 0001 2164 6327Present Address: Regional Agricultural Research Station, Kerala Agricultural University, Ambalavayal, Wayanad, 673593 Kerala India
| | - Amanda J. Burridge
- grid.5337.20000 0004 1936 7603Life Sciences, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ UK
| | - Nisha Singh
- grid.418105.90000 0001 0643 7375ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110 012 India
| | - Ritu Batra
- grid.418196.30000 0001 2172 0814Mineral Nutrition Laboratory, Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110 012 India
| | - Renu Pandey
- grid.418196.30000 0001 2172 0814Mineral Nutrition Laboratory, Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110 012 India
| | - Sanjay Kalia
- Department of Biotechnology, C.G.O Complex, Lodhi Road, New Delhi, 110003 India
| | - Vandana Rai
- grid.418105.90000 0001 0643 7375ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110 012 India
| | - Keith J. Edwards
- grid.5337.20000 0004 1936 7603Life Sciences, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ UK
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37
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Removal of superior wheat kernels promotes filling of inferior kernels by changing carbohydrate metabolism and sink strength. ACTA ACUST UNITED AC 2021. [DOI: 10.1016/j.cj.2020.12.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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38
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Ding N, Huertas R, Torres‐Jerez I, Liu W, Watson B, Scheible W, Udvardi M. Transcriptional, metabolic, physiological and developmental responses of switchgrass to phosphorus limitation. PLANT, CELL & ENVIRONMENT 2021; 44:186-202. [PMID: 32822068 PMCID: PMC7821211 DOI: 10.1111/pce.13872] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 08/11/2020] [Accepted: 08/17/2020] [Indexed: 05/10/2023]
Abstract
Knowing how switchgrass (Panicum virgatum L.) responds and adapts to phosphorus (P)-limitation will aid efforts to optimize P acquisition and use in this species for sustainable biomass production. This integrative study investigated the impacts of mild, moderate, and severe P-stress on genome transcription and whole-plant metabolism, physiology and development in switchgrass. P-limitation reduced overall plant growth, increased root/shoot ratio, increased root branching at moderate P-stress, and decreased root diameter with increased density and length of root hairs at severe P-stress. RNA-seq analysis revealed thousands of genes that were differentially expressed under moderate and severe P-stress in roots and/or shoots compared to P-replete plants, with many stress-induced genes involved in transcriptional and other forms of regulation, primary and secondary metabolism, transport, and other processes involved in P-acquisition and homeostasis. Amongst the latter were multiple miRNA399 genes and putative targets of these. Metabolite profiling showed that levels of most sugars and sugar alcohols decreased with increasing P stress, while organic and amino acids increased under mild and moderate P-stress in shoots and roots, although this trend reversed under severe P-stress, especially in shoots.
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Affiliation(s)
- Na Ding
- Noble Research Institute LLCArdmoreOklahomaUSA
| | | | | | - Wei Liu
- Noble Research Institute LLCArdmoreOklahomaUSA
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