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Samota MK, Awana M, Krishnan V, Kumar S, Tyagi A, Pandey R, Mithra SVA, Singh A. A novel micronutrients and methyl jasmonate cocktail of elicitors via seed priming improves drought tolerance by mitigating oxidative stress in rice (Oryza sativa L.). PROTOPLASMA 2024; 261:553-570. [PMID: 38159129 DOI: 10.1007/s00709-023-01914-x] [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: 06/15/2023] [Accepted: 12/09/2023] [Indexed: 01/03/2024]
Abstract
Drought is a major limiting factor for rice (Oryza sativa L.) production globally, and a cost-effective seed priming technique using bio-elicitors has been found to have stress mitigating effects. Till date, mostly phytohormones have been preferred as bio-elicitors, but the present study is a novel attempt to demonstrate the favorable role of micronutrients-phytohormone cocktail, i.e., iron (Fe), zinc (Zn), and methyl jasmonate (MJ) via seed priming method in mitigating the deleterious impacts of drought stress through physio-biochemical and molecular manifestations. The effect of cocktail/priming was studied on the relative water content, chlorophyll a/b and carotenoid contents, proline content, abscisic acid (ABA) content, and on the activities of ascorbate peroxidase (APX), superoxide dismutase (SOD), NADPH oxidase (Nox), and catalase (CAT). The expressions of drought-responsive genes OsZn-SOD, OsFe-SOD, and Nox1 were found to be modulated under drought stress in contrasting rice genotypes -N-22 (Nagina-22, drought-tolerant) and PS-5 (Pusa Sugandh-5, drought-sensitive). A progressive rise in carotenoids (10-19%), ABA (18-50%), proline (60-80%), activities of SOD (27-62%), APX (46-61%), CAT (50-80%), Nox (16-30%), and upregulated (0.9-1.6-fold) expressions of OsZn-SOD, OsFe-SOD, and Nox1 genes were found in the primed plants under drought condition. This cocktail would serve as a potential supplement in modern agricultural practices utilizing seed priming technique to mitigate drought stress-induced oxidative burst in food crops.
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Affiliation(s)
- Mahesh Kumar Samota
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi-110012, India
- HCP-Division, ICAR-CIPHET, Abohar, Punjab-152116, India
| | - Monika Awana
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi-110012, India
| | - Veda Krishnan
- 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
| | - Rakesh Pandey
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi-110012, India
| | - S V Amitha Mithra
- ICAR-National Institute for Plant Biotechnology, New Delhi-110012, India
| | - Archana Singh
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi-110012, India.
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Liu J, Qiu S, Xue T, Yuan Y. Physiology and transcriptome of Sapindus mukorossi seeds at different germination stages. Genomics 2024; 116:110822. [PMID: 38471577 DOI: 10.1016/j.ygeno.2024.110822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 03/02/2024] [Accepted: 03/04/2024] [Indexed: 03/14/2024]
Abstract
Sapindus mukorossi has a wide distribution range, high application value, and broad developmental potential. Previous studies have mostly focused on the medicinal and economic value of soapberry; however, few studies have been conducted on its seed germination. This study measured the physiological indicators and hormone content of soapberry seeds at different germination stages and preliminarily determined that abscisic acid (ABA) and indole-3-acetic acid (IAA) are the key hormones that affect the germination of soapberry seeds. Both Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG enrichment) analyses detected hormone transduction pathways, further confirming the key role of plant hormones in the germination process of soapberry seeds. Through transcriptome analysis, we speculated that CYP707A and IPA are key genes in the ABA and IAA synthesis pathways, respectively. This study revealed the close relationship between plant hormones and soapberry seed germination and provided new ideas for further exploration of the germination mechanism of soapberry seeds.
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Affiliation(s)
- Jia Liu
- Department of Civil and Architecture and Engineering, Chuzhou University, Anhui 239000, China
| | - Sumei Qiu
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
| | - Tingting Xue
- Department of Civil and Architecture and Engineering, Chuzhou University, Anhui 239000, China.
| | - Yingdan Yuan
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China.
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Dharni JS, Shi Y, Zhang C, Petersen C, Walia H, Staswick P. Growth and transcriptional response of wheat and rice to the tertiary amine BMVE. FRONTIERS IN PLANT SCIENCE 2024; 14:1273620. [PMID: 38269141 PMCID: PMC10806070 DOI: 10.3389/fpls.2023.1273620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 12/04/2023] [Indexed: 01/26/2024]
Abstract
Introduction Seed vigor is largely a product of sound seed development, maturation processes, genetics, and storage conditions. It is a crucial factor impacting plant growth and crop yield and is negatively affected by unfavorable environmental conditions, which can include drought and heat as well as cold wet conditions. The latter leads to slow germination and increased seedling susceptibility to pathogens. Prior research has shown that a class of plant growth regulators called substituted tertiary amines (STAs) can enhance seed germination, seedling growth, and crop productivity. However, inconsistent benefits have limited STA adoption on a commercial scale. Methods We developed a novel seed treatment protocol to evaluate the efficacy of 2-(N-methyl benzyl aminoethyl)-3-methyl butanoate (BMVE), which has shown promise as a crop seed treatment in field trials. Transcriptomic analysis of rice seedlings 24 h after BMVE treatment was done to identify the molecular basis for the improved seedling growth. The impact of BMVE on seed development was also evaluated by spraying rice panicles shortly after flower fertilization and subsequently monitoring the impact on seed traits. Results BMVE treatment of seeds 24 h after imbibition consistently improved wheat and rice seedling shoot and root growth in lab conditions. Treated wheat seedlings grown to maturity in a greenhouse also resulted in higher biomass than controls, though only under drought conditions. Treated seedlings had increased levels of transcripts involved in reactive oxygen species scavenging and auxin and gibberellic acid signaling. Conversely, several genes associated with increased reactive oxygen species/ROS load, abiotic stress responses, and germination hindering processes were reduced. BMVE spray increased both fresh and mature seed weights relative to the control for plants exposed to 96 h of heat stress. BMVE treatment during seed development also benefited germination and seedling growth in the next generation, under both ambient and heat stress conditions. Discussion The optimized experimental conditions we developed provide convincing evidence that BMVE does indeed have efficacy in plant growth enhancement. The results advance our understanding of how STAs work at the molecular level and provide insights for their practical application to improve crop growth.
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Affiliation(s)
- Jaspinder Singh Dharni
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, United States
| | - Yu Shi
- School of Biological Sciences, University of Nebraska, Lincoln, NE, United States
| | - Chi Zhang
- School of Biological Sciences, University of Nebraska, Lincoln, NE, United States
| | | | - Harkamal Walia
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, United States
| | - Paul Staswick
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, United States
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Ding X, Shi J, Gui J, Zhou H, Yan Y, Zhu X, Xie B, Liu X, He J. Rice Seed Protrusion Quantitative Trait Loci Mapping through Genome-Wide Association Study. PLANTS (BASEL, SWITZERLAND) 2024; 13:134. [PMID: 38202442 PMCID: PMC10780921 DOI: 10.3390/plants13010134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/19/2023] [Accepted: 12/23/2023] [Indexed: 01/12/2024]
Abstract
The germination of seeds is a prerequisite for crop production. Protrusion is important for seed germination, and visible radicle protrusion through seed covering layers is the second phase of the process of seed germination. Analyzing the mechanism of protrusion is important for the cultivation of rice varieties. In this study, 302 microcore germplasm populations were used for the GWAS of the protrusion percentage (PP). The frequency distribution of the PP at 48 h and 72 h is continuous, and six PP-associated QTLs were identified, but only qPP2 was detected repeatedly two times. The candidate gene analysis showed that LOC_Os02g57530 (ETR3), LOC_Os01g57610 (GH3.1) and LOC_Os04g0425 (CTB2) were the candidate genes for qPP2, qPP1 and qPP4, respectively. The haplotype (Hap) analysis revealed that Hap1 of ETR3, Hap1 and 3 of GH3.1 and Hap2 and 5 of CTB2 are elite alleles for the PP. Further validation of the germination phenotype of these candidate genes showed that Hap1 of ETR3 is a favorable allele for the germination percentage; Hap3 of GH3.1 is an elite allele for seed germination; and Hap5 of CTB2 is an elite allele for the PP, the germination percentage and the vigor index. The results of this study identified three putative candidate genes that provide valuable information for understanding the genetic control of seed protrusion in rice.
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Affiliation(s)
| | | | | | | | | | | | | | - Xionglun Liu
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China; (X.D.); (J.S.); (J.G.); (Y.Y.); (X.Z.); (B.X.)
| | - Jiwai He
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China; (X.D.); (J.S.); (J.G.); (Y.Y.); (X.Z.); (B.X.)
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Kim AN, Kim OW, Kim H. A study about factors influencing rice palatability based on changes in sensory and physicochemical properties under different postharvest conditions. Curr Res Food Sci 2023; 7:100625. [PMID: 38021259 PMCID: PMC10660032 DOI: 10.1016/j.crfs.2023.100625] [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: 03/24/2023] [Revised: 09/04/2023] [Accepted: 10/19/2023] [Indexed: 12/01/2023] Open
Abstract
Postharvest management plays a key role in determining the end-use quality of rice; therefore, a practical approach to inhibit quality deterioration is necessary. In this study, the effects of postharvest management-drying delay time (DDT) and moisture content after drying (DM) immediately after harvesting, and storage temperatures (ST) and periods (SP) of dried paddy rice-on the physicochemical, quality, and sensory properties of rice were comprehensively analyzed. Germination rate, seed viability, fat acidity, and sensory quality tended to significantly deteriorate with increasing DDT, DM, ST, and SP. The highest correlation (r = 0.8289) was observed between germination rate and sensory quality, indicating that germination rate can reliably predict sensory quality. Degradation of germination rate and overall sensory quality were analyzed: sensory quality exhibited a more gradual change than germination rate. Lastly, the effects of the postharvest conditions on overall sensory quality were predicted using a regression equation model. DDT, DM, and ST exhibited different patterns of change, which can be used to predict the sensory quality during storage. Germination rate was successfully applied as an influencing factor for the development of a rice-palatability prediction model. The results of this study are useful for maintaining fresh-rice palatability by preventing aging during postharvest storage.
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Affiliation(s)
- Ah-Na Kim
- Research Group of Safety Distribution, Korea Food Research Institute, Wanju-gun, 55365, Republic of Korea
| | - Oui Woung Kim
- Research Group of Safety Distribution, Korea Food Research Institute, Wanju-gun, 55365, Republic of Korea
| | - Hoon Kim
- Research Group of Safety Distribution, Korea Food Research Institute, Wanju-gun, 55365, Republic of Korea
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Niu Y, Wang C, Suo W, Wang G, Zhao J, Wang Z, Zheng Y. Isopropylmalate synthase NtIPMS as a potential molecular marker for seed vigor in tobacco. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2023; 40:43-49. [PMID: 38213928 PMCID: PMC10777126 DOI: 10.5511/plantbiotechnology.23.0118a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 01/18/2023] [Indexed: 01/13/2024]
Abstract
Seed vigor is an important trait for tobacco production. However, the evaluation of seed vigor using molecular biomarkers is scarcely reported in tobacco. In this study, the development of molecular marker isopropylmalate synthase NtIPMS was conducted to detect seed ageing degree and seed priming effect in tobacco. Quantitative real-time PCR (qRT-PCR) analysis showed that the expression of NtIPMS was significantly induced at the initial imbibition stage during seed germination. The NtIPMS expression was positively correlated with the degree of seed ageing in non-pelleted and pelleted seeds. The mRNA level of NtIPMS was gradually increased with the increasing degree of seed ageing. The early best effect of gibberellin priming was observed in 30-h primed seeds, and the highest expression of NtIPMS was observed in 12-h primed seeds. The best stop time-point of seed priming is likely at the time 18 h after the relatively higher NtIPMS expression occurred during seed priming process. The NtIPMS mRNA detection has the potential usage as a potential molecular marker for the evaluation of seed vigor in tobacco.
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Affiliation(s)
- Yongzhi Niu
- Yuxi Zhongyan Seed Company Ltd., Seed Engineering Technology Center of Yunnan Province, Yuxi 653100, China
| | - Chengjing Wang
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Wenlong Suo
- Yuxi Zhongyan Seed Company Ltd., Seed Engineering Technology Center of Yunnan Province, Yuxi 653100, China
| | - Guoping Wang
- Yuxi Zhongyan Seed Company Ltd., Seed Engineering Technology Center of Yunnan Province, Yuxi 653100, China
| | - Jia Zhao
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Zhoufei Wang
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Yunye Zheng
- Yuxi Zhongyan Seed Company Ltd., Seed Engineering Technology Center of Yunnan Province, Yuxi 653100, China
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Chen WQ, Liu DP, Li ZX, Chen K, Luo J, Xu JL. Transcriptome analysis of knockout mutants of rice seed dormancy gene OsVP1 and Sdr4. PLANT CELL REPORTS 2023; 42:309-319. [PMID: 36445461 DOI: 10.1007/s00299-022-02958-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 11/21/2022] [Indexed: 06/16/2023]
Abstract
OsVP1 and Sdr4 play an important role in regulating seed dormancy that involved in multiple metabolism and regulatory pathways. Seed dormancy and germination are critical agricultural traits influencing rice grain yield. Although there are some genes have identified previously, the comprehensive understanding based on transcriptome is still deficient. In this study, we generated mutants of two representative regulators of seed germination, Oryza sativa Viviparous1 (OsVP1) and Seed dormancy 4 (Sdr4), by CRISPR/Cas9 approach and named them cr-osvp1 and cr-sdr4. The weakened dormancy of mutants indicated that the functions of OsVP1 and Sdr4 are required for normal early seed dormancy. There were 4157 and 8285 differentially expressed genes (DEGs) were identified in cr-osvp1 vs. NIP and cr-sdr4 vs. NIP groups, respectively, with a large number of overlapped DEGs between two groups. The gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of common DEGs in two groups showed that genes related to carbohydrate metabolic, nucleoside metabolic, amylase activity and plant hormone signal transduction were involved in the dormancy regulation. These results suggest that OsVP1 and Sdr4 play an important role in regulating seed dormancy by multiple metabolism and regulatory pathways. The systematic analysis of the transcriptional level changes provides theoretical basis for the research of seed dormancy and germination in rice.
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Affiliation(s)
- Wen-Qiang Chen
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/College of Agriculture, Yangtze University, Jingzhou, 434025, Hubei, China
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China
| | - Da-Pu Liu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhi-Xin Li
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/College of Agriculture, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Kai Chen
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, Guangdong, China
| | - Ju Luo
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China.
| | - Jian-Long Xu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, Guangdong, China.
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Huang P, Hameed R, Abbas M, Balooch S, Alharthi B, Du Y, Abbas A, Younas A, Du D. Integrated omic techniques and their genomic features for invasive weeds. Funct Integr Genomics 2023; 23:44. [PMID: 36680630 DOI: 10.1007/s10142-023-00971-y] [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: 12/08/2022] [Revised: 01/01/2023] [Accepted: 01/11/2023] [Indexed: 01/22/2023]
Abstract
Many emerging invasive weeds display rapid adaptation against different stressful environments compared to their natives. Rapid adaptation and dispersal habits helped invasive populations have strong diversity within the population compared to their natives. Advances in molecular marker techniques may lead to an in-depth understanding of the genetic diversity of invasive weeds. The use of molecular techniques is rapidly growing, and their implications in invasive weed studies are considered powerful tools for genome purposes. Here, we review different approach used multi-omics by invasive weed studies to understand the functional structural and genomic changes in these species under different environmental fluctuations, particularly, to check the accessibility of advance-sequencing techniques used by researchers in genome sequence projects. In this review-based study, we also examine the importance and efficiency of different molecular techniques in identifying and characterizing different genes, associated markers, proteins, metabolites, and key metabolic pathways in invasive and native weeds. Use of these techniques could help weed scientists to further reduce the knowledge gaps in understanding invasive weeds traits. Although these techniques can provide robust insights about the molecular functioning, employing a single omics platform can rarely elucidate the gene-level regulation and the associated real-time expression of weedy traits due to the complex and overlapping nature of biological interactions. We conclude that different multi-omic techniques will provide long-term benefits in launching new genome projects to enhance the understanding of invasive weeds' invasion process.
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Affiliation(s)
- Ping Huang
- Institute of Environment and Ecology, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, People's Republic of China
| | - Rashida Hameed
- Institute of Environment and Ecology, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, People's Republic of China
| | - Manzer Abbas
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, 644000, Sichuan Province, People's Republic of China
| | - Sidra Balooch
- Institute of Botany, Bahauddin Zakariya University, Multan, Punjab, Pakistan
| | - Badr Alharthi
- Department of Biology, University College of Al Khurmah, Taif University, PO. Box 11099, Taif, 21944, Saudi Arabia
| | - Yizhou Du
- Faculty of Engineering, School of Computer Science, University of Sydney, Sydney, New South Wales, Australia
| | - Adeel Abbas
- Institute of Environment and Ecology, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, People's Republic of China.
| | - Afifa Younas
- Department of Botany, Lahore College for Women University, Lahore, Pakistan
| | - Daolin Du
- Institute of Environment and Ecology, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, People's Republic of China.
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He Y, Chen S, Liu K, Chen Y, Cheng Y, Zeng P, Zhu P, Xie T, Chen S, Zhang H, Cheng J. OsHIPL1, a hedgehog-interacting protein-like 1 protein, increases seed vigour in rice. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1346-1362. [PMID: 35315188 PMCID: PMC9241377 DOI: 10.1111/pbi.13812] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 02/19/2022] [Accepted: 03/09/2022] [Indexed: 06/14/2023]
Abstract
The cultivation of rice varieties with high seed vigour is vital for the direct seeding of rice, and the molecular basis of regulation of seed vigour remains elusive. Here, we cloned a new gene OsHIPL1, which encodes hedgehog-interacting protein-like 1 protein as a causal gene of the major QTL qSV3 for rice seed vigour. OsHIPL1 was mainly localized in the plasma membrane and nucleus. RNA sequencing (RNA-seq) revealed that the ABA-related genes were involved in the OsHIPL1 regulation of seed vigour in rice. The higher levels of endogenous ABA were measured in germinating seeds of OsHIPL1 mutants and NIL-qsv3 line compared to IR26 plants, with two up-regulated ABA biosynthesis genes (OsZEP and OsNCED4) and one down-regulated ABA catabolism gene OsABA8ox3. The expression of abscisic acid-insensitive 3 (OsABI3), OsABI4 and OsABI5 was significantly up-regulated in germinating seeds of OsHIPL1 mutants and NIL-qsv3 line compared to IR26 plants. These results indicate that the regulation of seed vigour of OsHIPL1 may be through modulating endogenous ABA levels and altering OsABIs expression during seed germination in rice. Meanwhile, we found that OsHIPL1 interacted with the aquaporin OsPIP1;1, then affected water uptake to promote rice seed germination. Based on analysis of single-nucleotide polymorphism data of rice accessions, we identified a Hap1 haplotype of OsHIPL1 that was positively correlated with seed germination. Our findings showed novel insights into the molecular mechanism of OsHIPL1 on seed vigour.
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Affiliation(s)
- Ying He
- State Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionJiangsu Province Engineering Research Center of Seed Industry Science and TechnologyCyrus Tang Innovation Center for Seed IndustryNanjing Agricultural UniversityNanjingChina
| | - Shanshan Chen
- State Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionJiangsu Province Engineering Research Center of Seed Industry Science and TechnologyCyrus Tang Innovation Center for Seed IndustryNanjing Agricultural UniversityNanjingChina
| | - Kexin Liu
- State Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionJiangsu Province Engineering Research Center of Seed Industry Science and TechnologyCyrus Tang Innovation Center for Seed IndustryNanjing Agricultural UniversityNanjingChina
| | - Yongji Chen
- State Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionJiangsu Province Engineering Research Center of Seed Industry Science and TechnologyCyrus Tang Innovation Center for Seed IndustryNanjing Agricultural UniversityNanjingChina
| | - Yanhao Cheng
- State Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionJiangsu Province Engineering Research Center of Seed Industry Science and TechnologyCyrus Tang Innovation Center for Seed IndustryNanjing Agricultural UniversityNanjingChina
| | - Peng Zeng
- State Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionJiangsu Province Engineering Research Center of Seed Industry Science and TechnologyCyrus Tang Innovation Center for Seed IndustryNanjing Agricultural UniversityNanjingChina
| | - Peiwen Zhu
- State Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionJiangsu Province Engineering Research Center of Seed Industry Science and TechnologyCyrus Tang Innovation Center for Seed IndustryNanjing Agricultural UniversityNanjingChina
| | - Ting Xie
- State Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionJiangsu Province Engineering Research Center of Seed Industry Science and TechnologyCyrus Tang Innovation Center for Seed IndustryNanjing Agricultural UniversityNanjingChina
| | - Sunlu Chen
- State Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionJiangsu Province Engineering Research Center of Seed Industry Science and TechnologyCyrus Tang Innovation Center for Seed IndustryNanjing Agricultural UniversityNanjingChina
| | - Hongsheng Zhang
- State Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionJiangsu Province Engineering Research Center of Seed Industry Science and TechnologyCyrus Tang Innovation Center for Seed IndustryNanjing Agricultural UniversityNanjingChina
| | - Jinping Cheng
- State Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionJiangsu Province Engineering Research Center of Seed Industry Science and TechnologyCyrus Tang Innovation Center for Seed IndustryNanjing Agricultural UniversityNanjingChina
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Sano N, Lounifi I, Cueff G, Collet B, Clément G, Balzergue S, Huguet S, Valot B, Galland M, Rajjou L. Multi-Omics Approaches Unravel Specific Features of Embryo and Endosperm in Rice Seed Germination. FRONTIERS IN PLANT SCIENCE 2022; 13:867263. [PMID: 35755645 PMCID: PMC9225960 DOI: 10.3389/fpls.2022.867263] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 04/29/2022] [Indexed: 06/15/2023]
Abstract
Seed germination and subsequent seedling growth affect the final yield and quality of the crop. Seed germination is defined as a series of processes that begins with water uptake by a quiescent dry seed and ends with the elongation of embryonic axis. Rice is an important cereal crop species, and during seed germination, two tissues function in a different manner; the embryo grows into a seedling as the next generation and the endosperm is responsible for nutritional supply. Toward understanding the integrated roles of each tissue at the transcriptional, translational, and metabolic production levels during germination, an exhaustive "multi-omics" analysis was performed by combining transcriptomics, label-free shotgun proteomics, and metabolomics on rice germinating embryo and endosperm, independently. Time-course analyses of the transcriptome and metabolome in germinating seeds revealed a major turning point in the early phase of germination in both embryo and endosperm, suggesting that dramatic changes begin immediately after water imbibition in the rice germination program at least at the mRNA and metabolite levels. In endosperm, protein profiles mostly showed abundant decreases corresponding to 90% of the differentially accumulated proteins. An ontological classification revealed the shift from the maturation to the germination process where over-represented classes belonged to embryonic development and cellular amino acid biosynthetic processes. In the embryo, 19% of the detected proteins are differentially accumulated during germination. Stress response, carbohydrate, fatty acid metabolism, and transport are the main functional classes representing embryo proteome change. Moreover, proteins specific to the germinated state were detected by both transcriptomic and proteomic approaches and a major change in the network operating during rice germination was uncovered. In particular, concomitant changes of hormonal metabolism-related proteins (GID1L2 and CNX1) implicated in GAs and ABA metabolism, signaling proteins, and protein turnover events emphasized the importance of such biological networks in rice seeds. Using metabolomics, we highlighted the importance of an energetic supply in rice seeds during germination. In both embryo and endosperm, starch degradation, glycolysis, and subsequent pathways related to these cascades, such as the aspartate-family pathway, are activated during germination. A relevant number of accumulated proteins and metabolites, especially in embryos, testifies the pivotal role of energetic supply in the preparation of plant growth. This article summarizes the key genetic pathways in embryo and endosperm during rice seed germination at the transcriptional, translational, and metabolite levels and thereby, emphasizes the value of combined multi-omics approaches to uncover the specific feature of tissues during germination.
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Affiliation(s)
- Naoto Sano
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
| | - Imen Lounifi
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
- MBCC Group, Master Builders Construction Chemical, Singapore, Singapore
| | - Gwendal Cueff
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
| | - Boris Collet
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
| | - Gilles Clément
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
| | - Sandrine Balzergue
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, Beaucouzé, France
| | - Stéphanie Huguet
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
| | - Benoît Valot
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, PAPPSO, Plateforme d'Analyse de Proteomique Paris-Sud-Ouest, Gif-sur-Yvette, France
- Chrono-Environnement Research Team UMR/CNRS-6249, Bourgogne-Franche-Comté University, Besançon, France
| | - Marc Galland
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Loïc Rajjou
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
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11
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Yang B, Chen M, Zhan C, Liu K, Cheng Y, Xie T, Zhu P, He Y, Zeng P, Tang H, Tsugama D, Chen S, Zhang H, Cheng J. Identification of OsPK5 involved in rice glycolytic metabolism and GA/ABA balance for improving seed germination via genome-wide association study. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:3446-3461. [PMID: 35191960 PMCID: PMC9162179 DOI: 10.1093/jxb/erac071] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 02/19/2022] [Indexed: 06/12/2023]
Abstract
Seed germination plays a pivotal role in the plant life cycle, and its precise regulatory mechanisms are not clear. In this study, 19 quantitative trait loci (QTLs) associated with rice seed germination were identified through genome-wide association studies (GWAS) of the following traits in 2016 and 2017: germination rate (GR) at 3, 5, and 7 days after imbibition (DAI) and germination index (GI). Two major stable QTLs, qSG4 and qSG11.1, were found to be associated with GR and GI over 2 continuous years. Furthermore, OsPK5, encoding a pyruvate kinase, was shown to be a crucial regulator of seed germination in rice, and might be a causal gene of the key QTL qSG11.1, on chromosome 11. Natural variation in OsPK5 function altered the activity of pyruvate kinase. The disruption of OsPK5 function resulted in slow germination and seedling growth during seed germination, blocked glycolytic metabolism, caused glucose accumulation, decreased energy levels, and affected the GA/ABA balance. Taken together, our results provide novel insights into the roles of OsPK5 in seed germination, and facilitate its application in rice breeding to improve seed vigour.
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Affiliation(s)
| | | | | | - Kexin Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Cyrus Tang Innovation Center for Seed Industry, Nanjing Agricultural University, Nanjing 210095, China
| | - Yanhao Cheng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Cyrus Tang Innovation Center for Seed Industry, Nanjing Agricultural University, Nanjing 210095, China
| | - Ting Xie
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Cyrus Tang Innovation Center for Seed Industry, Nanjing Agricultural University, Nanjing 210095, China
| | - Peiwen Zhu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Cyrus Tang Innovation Center for Seed Industry, Nanjing Agricultural University, Nanjing 210095, China
| | - Ying He
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Cyrus Tang Innovation Center for Seed Industry, Nanjing Agricultural University, Nanjing 210095, China
| | - Peng Zeng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Cyrus Tang Innovation Center for Seed Industry, Nanjing Agricultural University, Nanjing 210095, China
| | - Haijuan Tang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Cyrus Tang Innovation Center for Seed Industry, Nanjing Agricultural University, Nanjing 210095, China
| | - Daisuke Tsugama
- Asian Natural Environmental Science Center (ANESC), The University of Tokyo, 1-1-1 Midori-cho, Nishitokyo-shi, Tokyo 188-0002, Japan
| | - Sunlu Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Cyrus Tang Innovation Center for Seed Industry, Nanjing Agricultural University, Nanjing 210095, China
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12
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Li R, Wu L, Shao Y, Hu Q, Zhang H. Melatonin alleviates copper stress to promote rice seed germination and seedling growth via crosstalk among various defensive response pathways. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 179:65-77. [PMID: 35316694 DOI: 10.1016/j.plaphy.2022.03.016] [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: 12/14/2021] [Revised: 02/24/2022] [Accepted: 03/14/2022] [Indexed: 06/14/2023]
Abstract
Copper (Cu) contamination dramatically affects crop growth and thus threatens crop production; while applications of melatonin (MT) serve as an effective way to tolerate Cu stress for plant development, the underlying mechanism remains largely unknown in rice. Here, we found that Cu toxicity remarkably decreased germination rates and seedling growth compared to the untreated control (CK), while seed priming with a solution of 100 μM MT significantly alleviated the adverse effects on Cu-stressed seeds. In addition, the MT treatment decreased the accumulation of Cu in seedlings at 7 days after imbibition (DAI), possibly through enhanced Cu sequestration, and improved reserve mobilization through the promoted activity of α-amylase and protease in seeds under Cu stress. Interestingly, gibberellin (GA) synthesis was restored to or even exceeded the CK levels in the MT presoaking treatment, while the abscisic acid (ABA) content decreased compared to those of the Cu-stressed seeds, suggesting crosstalk between MT and other phytohormones, e.g., GA and ABA. More importantly, MT pretreatment also significantly promoted the growth of postgermination seedlings. This was largely ascribed to the MT-ameliorated antioxidant system, which consequently reduced the accumulation of Cu stress-induced oxidative products, e.g., hydrogen peroxide (H2O2), malondialdehyde (MDA), and superoxide (O2·_). Collectively, these results demonstrate that seed priming with MT could greatly mitigate the adverse effects of Cu stress on seed germination and subsequent postgermination growth through crosstalk among various defensive response pathways. This study provides vital guidance for applications of MT in agronomic production.
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Affiliation(s)
- Ruiqing Li
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, PR China
| | - Liquan Wu
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, PR China
| | - Yafang Shao
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 311400, PR China
| | - Qunwen Hu
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, PR China
| | - Huali Zhang
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 311400, PR China.
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13
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Ling LZ, Zhang SD. Comparative proteomic analysis between mature and germinating seeds in Paris polyphylla var. yunnanensis. PeerJ 2022; 10:e13304. [PMID: 35578673 PMCID: PMC9107301 DOI: 10.7717/peerj.13304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 03/29/2022] [Indexed: 01/13/2023] Open
Abstract
The long dormancy period of Paris polyphylla var. yunnanensis seeds affects the supply of this scarce plant, which is used as an important traditional Chinese medicine. Mature seeds with a globular embryo and germinating seeds with developed embryo were used to explore the mechanisms of seed germination in this species. The protein profiles between the mature and germinating seeds were compared using the isobaric tags for relative and absolute quantification (iTRAQ) approach. Of the 4,488 proteins identified, a total of 1,305 differentially expressed proteins (DEPs) were detected. A Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of these DEPs indicated that metabolic pathways and the biosynthesis of secondary metabolites were the two top pathways. Additionally, phytohormone quantification shows that the abscisic acid (ABA) level significantly decreased, whereas the GA3 level dramatically increased among nine endogenous gibberellins (GAs), resulting in a significant increase of the GA3/ABA ratio in germinating seeds. The biosynthesis pathways of carotenoid as a precursor for ABA production and GA were further analyzed, and showed that proteinic expressions of the candidate genes in the two pathways did not correlate with the transcriptional abundances. However, 9-cis-epoxycarotenoid dioxygenase (NCED), a rate limited enzyme for ABA biosynthesis, was significantly decreased in mRNA levels in germinating seeds. By contrast, gibberellin 20-oxidase (GA20ox), a key enzyme GA biosynthesis, exhibited the major increase in one copy and a slight decrease in three others at the protentional level in germinating seeds. Gibberellin 2-oxidase (GA2ox), an inactivate enzyme in bioactive GAs, has the tendency to down-regulate in mRNA or at the proteinic level in germinating seeds. Altogether, these results suggested that the analyses of ABA and GA levels, the GA3/ABA ratio, and the expressional patterns of their regulatory genes may provide a novel mechanistic understanding of how phytohormones regulate seed germination in P. polyphylla var. yunnanensis.
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14
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Xiong M, Yu J, Wang J, Gao Q, Huang L, Chen C, Zhang C, Fan X, Zhao D, Liu QQ, Li QF. Brassinosteroids regulate rice seed germination through the BZR1-RAmy3D transcriptional module. PLANT PHYSIOLOGY 2022; 189:402-418. [PMID: 35139229 PMCID: PMC9070845 DOI: 10.1093/plphys/kiac043] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 01/07/2022] [Indexed: 05/03/2023]
Abstract
Seed dormancy and germination, two physiological processes unique to seed-bearing plants, are critical for plant growth and crop production. The phytohormone brassinosteroid (BR) regulates many aspects of plant growth and development, including seed germination. The molecular mechanisms underlying BR control of rice (Oryza sativa) seed germination are mostly unknown. We investigated the molecular regulatory cascade of BR in promoting rice seed germination and post-germination growth. Physiological assays indicated that blocking BR signaling, including introducing defects into the BR-insensitive 1 (BRI1) receptor or overexpressing the glycogen synthase kinase 2 (GSK2) kinase delayed seed germination and suppressed embryo growth. Our results also indicated that brassinazole-resistant 1 (BZR1) is the key downstream transcription factor that mediates BR regulation of seed germination by binding to the alpha-Amylase 3D (RAmy3D) promoter, which affects α-amylase expression and activity and the degradation of starch in the endosperm. The BZR1-RAmy3D module functions independently from the established Gibberellin MYB-alpha-amylase 1A (RAmy1A) module of the gibberellin (GA) pathway. We demonstrate that the BZR1-RAmy3D module also functions in embryo-related tissues. Moreover, RNA-sequencing (RNA-seq) analysis identified more potential BZR1-responsive genes, including those involved in starch and sucrose metabolism. Our study successfully identified the role of the BZR1-RAmy3D transcriptional module in regulating rice seed germination.
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Affiliation(s)
| | | | | | - Qiang Gao
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology/Sate Key Laboratory of Hybrid Rice, College of Agriculture, Yangzhou University, Yangzhou 225009, Jiangsu, China
| | - Lichun Huang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology/Sate Key Laboratory of Hybrid Rice, College of Agriculture, Yangzhou University, Yangzhou 225009, Jiangsu, China
- Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, Jiangsu, China
| | - Chen Chen
- Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, Jiangsu, China
| | - Changquan Zhang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology/Sate Key Laboratory of Hybrid Rice, College of Agriculture, Yangzhou University, Yangzhou 225009, Jiangsu, China
- Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, Jiangsu, China
| | - Xiaolei Fan
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology/Sate Key Laboratory of Hybrid Rice, College of Agriculture, Yangzhou University, Yangzhou 225009, Jiangsu, China
- Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, Jiangsu, China
| | - Dongsheng Zhao
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology/Sate Key Laboratory of Hybrid Rice, College of Agriculture, Yangzhou University, Yangzhou 225009, Jiangsu, China
- Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, Jiangsu, China
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15
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Li H, Li X, Wang G, Zhang J, Wang G. Analysis of gene expression in early seed germination of rice: landscape and genetic regulation. BMC PLANT BIOLOGY 2022; 22:70. [PMID: 35176996 PMCID: PMC8851807 DOI: 10.1186/s12870-022-03458-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 02/09/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Seed germination is a crucial process, which determines the initiation of seed plant life cycle. The early events during this important life cycle transition that called early seed germination is defined as initially water uptake plus radicle growing out of the covering seed layers. However, a specific genome-wide analysis of early seed germination in rice is still obscure. RESULTS In this study, the physiological characteristics of rice seed during seed germination are determined to define key points of early seed germination. Transcriptome analyses of early phase of seed germination provided deeper insight into the genetic regulation landscape. Many genes involved in starch-to-sucrose transition were differentially expressed, especially alpha-amylase 1b and beta-amylase 2, which were predominantly expressed. Differential exon usage (DEU) genes were identified, which were significantly enriched in the pathway of starch and sucrose metabolism, indicating that DEU events were critical for starch-to-sucrose transition at early seed germination. Transcription factors (TFs) were also dramatic expressed, including the abscisic acid (ABA) responsive gene, OsABI5, and gibberellic acid (GA) responsive genes, GAI. Moreover, GAI transactivated GA responsive gene, GAMYB in vivo, indicating a potential pathway involved in early seed germination process. In addition, CBL-interacting protein kinase (CIPK) genes, such as CIPK13, CIPK14 and CIPK17 were potentially interacted with other proteins, indicating its pivotal role at early seed germination. CONCLUSION Taken together, gene regulation of early seed germination in rice was complex and protein-to-gene or protein-to-protein interactions were indispensable.
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Affiliation(s)
- Haoxuan Li
- Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong, China
| | - Xiaozheng Li
- Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Guanjie Wang
- College of Life Sciences, Jilin Agricultural University, Jilin, China
| | - Jianhua Zhang
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong, China.
| | - Guanqun Wang
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
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16
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Liu X, Quan W, Bartels D. Stress memory responses and seed priming correlate with drought tolerance in plants: an overview. PLANTA 2022; 255:45. [PMID: 35066685 PMCID: PMC8784359 DOI: 10.1007/s00425-022-03828-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 01/08/2022] [Indexed: 05/08/2023]
Abstract
Environmental-friendly techniques based on plant stress memory, cross-stress tolerance, and seed priming help sustainable agriculture by mitigating negative effects of dehydration stress. The frequently uneven rainfall distribution caused by global warming will lead to more irregular and multiple abiotic stresses, such as heat stress, dehydration stress, cold stress or the combination of these stresses. Dehydration stress is one of the major environmental factors affecting the survival rate and productivity of plants. Hence, there is an urgent need to develop improved resilient varieties. Presently, technologies based on plant stress memory, cross-stress tolerance and priming of seeds represent fruitful and promising areas of future research and applied agricultural science. In this review, we will provide an overview of plant drought stress memory from physiological, biochemical, molecular and epigenetic perspectives. Drought priming-induced cross-stress tolerance to cold and heat stress will be discussed and the application of seed priming will be illustrated for different species.
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Affiliation(s)
- Xun Liu
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Kirschallee 1, 53115, Bonn, Germany
- College of Bioengineering, Sichuan University of Science & Engineering, Zigong, 643000, China
| | - Wenli Quan
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Kirschallee 1, 53115, Bonn, Germany
- Key Laboratory for Quality Control of Characteristic Fruits and Vegetables of Hubei Province, College of Life Science and Technology, Hubei Engineering University, Xiaogan, 432000, Hubei, China
| | - Dorothea Bartels
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Kirschallee 1, 53115, Bonn, Germany.
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17
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Matilla AJ. The Orthodox Dry Seeds Are Alive: A Clear Example of Desiccation Tolerance. PLANTS (BASEL, SWITZERLAND) 2021; 11:plants11010020. [PMID: 35009023 PMCID: PMC8747232 DOI: 10.3390/plants11010020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 12/07/2021] [Accepted: 12/20/2021] [Indexed: 05/17/2023]
Abstract
To survive in the dry state, orthodox seeds acquire desiccation tolerance. As maturation progresses, the seeds gradually acquire longevity, which is the total timespan during which the dry seeds remain viable. The desiccation-tolerance mechanism(s) allow seeds to remain dry without losing their ability to germinate. This adaptive trait has played a key role in the evolution of land plants. Understanding the mechanisms for seed survival after desiccation is one of the central goals still unsolved. That is, the cellular protection during dry state and cell repair during rewatering involves a not entirely known molecular network(s). Although desiccation tolerance is retained in seeds of higher plants, resurrection plants belonging to different plant lineages keep the ability to survive desiccation in vegetative tissue. Abscisic acid (ABA) is involved in desiccation tolerance through tight control of the synthesis of unstructured late embryogenesis abundant (LEA) proteins, heat shock thermostable proteins (sHSPs), and non-reducing oligosaccharides. During seed maturation, the progressive loss of water induces the formation of a so-called cellular "glass state". This glassy matrix consists of soluble sugars, which immobilize macromolecules offering protection to membranes and proteins. In this way, the secondary structure of proteins in dry viable seeds is very stable and remains preserved. ABA insensitive-3 (ABI3), highly conserved from bryophytes to Angiosperms, is essential for seed maturation and is the only transcription factor (TF) required for the acquisition of desiccation tolerance and its re-induction in germinated seeds. It is noteworthy that chlorophyll breakdown during the last step of seed maturation is controlled by ABI3. This update contains some current results directly related to the physiological, genetic, and molecular mechanisms involved in survival to desiccation in orthodox seeds. In other words, the mechanisms that facilitate that an orthodox dry seed is a living entity.
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Affiliation(s)
- Angel J Matilla
- Departamento de Biología Funcional (Área Fisiología Vegetal), Facultad de Farmacia, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
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18
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Sun L, Yuan Z, Wang D, Li J, Shi J, Hu Y, Yu J, Chen X, Chen S, Liang W, Zhang D. Carbon Starved Anther modulates sugar and ABA metabolism to protect rice seed germination and seedling fitness. PLANT PHYSIOLOGY 2021; 187:2405-2418. [PMID: 34618084 PMCID: PMC8644061 DOI: 10.1093/plphys/kiab391] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 07/26/2021] [Indexed: 06/13/2023]
Abstract
Seed germination is critical for plant survival and agricultural production, which is affected by both internal seed factors and external environmental conditions. However, the genetic basis and underlying molecular mechanisms of early seed germination in crops remain largely unclear. Here, we report that R2R3 MYB transcription factor Carbon Starved Anther (CSA) is expressed specifically in Oryza sativa embryo and aleurone in response to seed imbibition, peaking at 3-6 h and undetectable by 24-h post-imbibition. CSA seeds germinated more quickly than wild-type rice seeds and had higher levels of amylase activity, glucose, and inactive abscisic acid-glucose ester (ABA-GE), but lower levels of ABA. Through analyzing the CSA-associated transcriptome and CSA binding to downstream target genes, we identified two glycolytic genes as direct CSA targets. CSA inhibits Amylase 3A expression to limit glucose production from starch and activates Os3BGlu6 expression to promote de-conjugation of ABA-GE to ABA; these functions serve to slow germination and improve seedling resilience to abiotic stress in the first 3 weeks of growth. Therefore, this study unveils a protection mechanism conferred by CSA during early seed germination by balancing glucose and ABA metabolism to optimize seed germination and stress response fitness.
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Affiliation(s)
- Linlin Sun
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zheng Yuan
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Key Laboratory of Crop Marker-Assisted Breeding of Huaian Municipality, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environmental Protection, Huaian 223300, China
| | - Duoxiang Wang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jingbin Li
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jin Shi
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yangyang Hu
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jing Yu
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaofei Chen
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Sixue Chen
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, Florida 32610, USA
| | - Wanqi Liang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Key Laboratory of Crop Marker-Assisted Breeding of Huaian Municipality, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environmental Protection, Huaian 223300, China
- School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, South Australia 5064, Australia
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19
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Song Y, Gao X, Wu Y. Key Metabolite Differences Between Korean Pine ( Pinus koraiensis) Seeds With Primary Physiological Dormancy and No-Dormancy. FRONTIERS IN PLANT SCIENCE 2021; 12:767108. [PMID: 34880891 PMCID: PMC8647843 DOI: 10.3389/fpls.2021.767108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 10/14/2021] [Indexed: 06/13/2023]
Abstract
Pinus Koraiensis seeds have physiological dormancy. Cold stratification releases seed dormancy. The changes in metabolite profiles of dormant seeds and cold stratified seeds during shorter incubation time in a favorable condition for seed germination have been studied. However, a more-long-term detection of the changes in metabolites in dormant seeds can identify the real metabolic pathways responsible for dormancy. Metabolite composition was investigated in embryo and megagametophyte of primary physiological dormant seeds (DS) of P. Koraiensis collected at 0, 1, 2, 4, and 6 weeks of incubation and of non-primary physiological dormant seeds (NDS) sampled at 0 and 1 week of incubation, seed coat rupture stage, and radicle protrusion stage. Embryos contained higher levels of most metabolites than megagametophyte. Strong accumulation of most metabolites in DS occurred at 1 and 4 weeks of incubation. A larger reduction in the relative levels of most phosphorylated sugars and amino acids in NDS was found between 1-week-incubation and seed coat rupture stage. The relative levels of metabolites involved in carbohydrate metabolism, especially the pentose phosphate pathway (PPP) and tricarboxylic acid (TCA) cycle, were higher in the embryos of 4-week-incubated DS, but the relative contents of intermediate metabolites of most amino acid metabolism were lower compared to 1-week-incubated NDS. We suggested that the disturbed carbohydrate metabolism and amino acid metabolism in the embryos of DS after 4 weeks of incubation maybe related to primary dormancy. Our study provides information for a better understanding of the mechanism of seed dormancy.
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Affiliation(s)
- Yuan Song
- College of Eco-Environmental Engineering, Guizhou Minzu University, Guiyang, China
- Karst Environmental Geological Hazard Prevention Laboratory of Guizhou Minzu University, Guiyang, China
| | - Xiaoye Gao
- College of Eco-Environmental Engineering, Guizhou Minzu University, Guiyang, China
| | - Yunjie Wu
- College of Eco-Environmental Engineering, Guizhou Minzu University, Guiyang, China
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20
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Metabolic Changes in Seed Embryos of Hypoxia-Tolerant Rice and Hypoxia-Sensitive Barley at the Onset of Germination. PLANTS 2021; 10:plants10112456. [PMID: 34834819 PMCID: PMC8622212 DOI: 10.3390/plants10112456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/03/2021] [Accepted: 11/11/2021] [Indexed: 11/29/2022]
Abstract
Rice (Oryza sativa L.) and barley (Hordeum vulgare L.) are the cereal species differing in tolerance to oxygen deficiency. To understand metabolic differences determining the sensitivity to low oxygen, we germinated rice and barley seeds and studied changes in the levels of reactive oxygen species (ROS) and reactive nitrogen species (RNS), activities of the enzymes involved in their scavenging, and measured cell damage parameters. The results show that alcohol dehydrogenase activity was higher in rice than in barley embryos providing efficient anaerobic fermentation. Nitric oxide (NO) levels were also higher in rice embryos indicating higher NO turnover. Both fermentation and NO turnover can explain higher ATP/ADP ratio values in rice embryos as compared to barley. Rice embryos were characterized by higher activity of S-nitrosoglutathione reductase than in barley and a higher level of free thiols in proteins. The activities of antioxidant enzymes (superoxide dismutase, ascorbate peroxidase, monodehydroascorbate reductase, dehydroascorbate reductase) in imbibed embryos were higher in rice than in barley, which corresponded to the reduced levels of ROS, malonic dialdehyde and electrolyte leakage. The observed differences in metabolic changes in embryos of the two cereal species differing in tolerance to hypoxia can partly explain the adaptation of rice to low oxygen environments.
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21
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Seed Dormancy and Pre-Harvest Sprouting in Rice-An Updated Overview. Int J Mol Sci 2021; 22:ijms222111804. [PMID: 34769234 PMCID: PMC8583970 DOI: 10.3390/ijms222111804] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 10/27/2021] [Accepted: 10/28/2021] [Indexed: 12/14/2022] Open
Abstract
Pre-harvest sprouting is a critical phenomenon involving the germination of seeds in the mother plant before harvest under relative humid conditions and reduced dormancy. As it results in reduced grain yield and quality, it is a common problem for the farmers who have cultivated the rice and wheat across the globe. Crop yields need to be steadily increased to improve the people’s ability to adapt to risks as the world’s population grows and natural disasters become more frequent. To improve the quality of grain and to avoid pre-harvest sprouting, a clear understanding of the crops should be known with the use of molecular omics approaches. Meanwhile, pre-harvest sprouting is a complicated phenomenon, especially in rice, and physiological, hormonal, and genetic changes should be monitored, which can be modified by high-throughput metabolic engineering techniques. The integration of these data allows the creation of tailored breeding lines suitable for various demands and regions, and it is crucial for increasing the crop yields and economic benefits. In this review, we have provided an overview of seed dormancy and its regulation, the major causes of pre-harvest sprouting, and also unraveled the novel avenues to battle pre-harvest sprouting in cereals with special reference to rice using genomics and transcriptomic approaches.
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Li W, Yang B, Xu J, Peng L, Sun S, Huang Z, Jiang X, He Y, Wang Z. A genome-wide association study reveals that the 2-oxoglutarate/malate translocator mediates seed vigor in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:478-491. [PMID: 34376020 DOI: 10.1111/tpj.15455] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 08/01/2021] [Accepted: 08/05/2021] [Indexed: 05/25/2023]
Abstract
Seed vigor is an important trait for the direct seeding of rice (Oryza sativa L.). In this study, we examined the genetic architecture of variation in the germination rate using a diverse panel of rice accessions. Four quantitative trait loci for germination rate were identified using a genome-wide association study during early germination. One candidate gene, encoding the 2-oxoglutarate/malate translocator (OsOMT), was validated for qGR11. Disruption of this gene (Osomt mutants) reduced seed vigor, including seed germination and seedling growth, in rice. Functional analysis revealed that OsOMT influences seed vigor mainly by modulating amino acid levels and glycolysis and tricarboxylic acid cycle processes. The levels of most amino acids, including the Glu family (Glu, Pro, Arg, and GABA), Asp family (Asp, Thr, Lys, Ile, and Met), Ser family (Ser, Gly, and Cys), and others (His, Ala, Leu, and Val), were significantly reduced in the mature grains and the early germinating seeds of Osomt mutants compared to wild type (WT). The glucose and soluble sugar contents, as well as adenosine triphosphate levels, were significantly decreased in germinating seeds of Osomt mutants compared to WT. These results provide important insights into the role of OsOMT in seed vigor in rice.
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Affiliation(s)
- Wenjun Li
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Bin Yang
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Jiangyu Xu
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Liling Peng
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Shan Sun
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Zhibo Huang
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Xiuhua Jiang
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Yongqi He
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Zhoufei Wang
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
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Gonu H, Wanapu C, Withayagiat U. The Correlation of Free and Bound Phenolic Acid with Antioxidant Activity Accelerated by Germination Period and Temperature. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2021. [DOI: 10.1080/03610470.2021.1966287] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Hellie Gonu
- Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Chatuchak, Bangkok, Thailand
| | - Chokchai Wanapu
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Ulaiwan Withayagiat
- Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Chatuchak, Bangkok, Thailand
- Fermentation Technology Research Center, Faculty of Agro-Industry, Kasetsart University, Chatuchak, Bangkok, Thailand
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24
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Kim H, Lee YH. Spatiotemporal Assembly of Bacterial and Fungal Communities of Seed-Seedling-Adult in Rice. Front Microbiol 2021; 12:708475. [PMID: 34421867 PMCID: PMC8375405 DOI: 10.3389/fmicb.2021.708475] [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: 05/12/2021] [Accepted: 07/19/2021] [Indexed: 01/04/2023] Open
Abstract
Seeds harbor not only genetic information about plants but also microbial communities affecting plants’ vigor. Knowledge on the movement and formation of seed microbial communities during plant development remains insufficient. Here, we address this knowledge gap by investigating endophytic bacterial and fungal communities of seeds, seedlings, and adult rice plants. We found that seed coats act as microbial niches for seed bacterial and fungal communities. The presence or absence of the seed coat affected taxonomic composition and diversity of bacterial and fungal communities associated with seeds and seedlings. Ordination analysis showed that niche differentiation between above- and belowground compartments leads to compositional differences in endophytic bacterial and fungal communities originating from seeds. Longitudinal tracking of the composition of microbial communities from field-grown rice revealed that bacterial and fungal communities originating from seeds persist in the leaf, stem, and root endospheres throughout the life cycle. Our study provides ecological insights into the assembly of the initial endophytic microbial communities of plants from seeds.
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Affiliation(s)
- Hyun Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
| | - Yong-Hwan Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea.,Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea.,Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, South Korea.,Center for Fungal Genetic Resources, Seoul National University, Seoul, South Korea.,Plant Genomics and Breeding Institute, Seoul National University, Seoul, South Korea.,Plant Immunity Research Center, Seoul National University, Seoul, South Korea
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25
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Guha T, Das H, Mukherjee A, Kundu R. Elucidating ROS signaling networks and physiological changes involved in nanoscale zero valent iron primed rice seed germination sensu stricto. Free Radic Biol Med 2021; 171:11-25. [PMID: 33965567 DOI: 10.1016/j.freeradbiomed.2021.05.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 05/02/2021] [Accepted: 05/03/2021] [Indexed: 01/05/2023]
Abstract
Reactive oxygen species (ROS) play pivotal roles during seed dormancy and germination. Metabolically active cells of seeds generate ROS and successful germination is governed by internal ROS contents, maintained within an optimum "oxidative window" by several ROS scavengers. Although ROS was previously considered hazardous, optimum ROS generation in seeds can mediate early seed germination by acting as messengers for cell signaling involved in endosperm weakening, stored food mobilization, etc. Recent reports suggest that nanopriming can expedite seed germination rates and enhance seed quality and crop performances. However, nanoparticle-driven signal cascades involved during seed germination are still unknown. The present study is aimed to explore molecular mechanisms for promoting germination in nanoprimed seeds and to investigate the plausible role of nanoparticle-mediated ROS generation in this process. Here rice seeds were primed with 20 mg L -1nanoscale zero valent iron (nZVI) for 72 h and several biochemical and physiological changes were monitored at different time points (5, 10, 20, 40, 60, and 80 h). To gain insight into roles of ROS in germination rate enhancement, intercellular ROS inhibitor, diphenyleneiodonium (DPI) was taken as another priming agent. Seed priming with DPI impaired seed germination percentage, hydrolytic enzyme activities due to ROS imbalance. On the contrary, seeds primed with both DPI and nZVI could recover from deleterious consequences of DPI treatment. Although DPI impaired intercellular ROS generation, nZVI can generate ROS independently which was confirmed from ROS localization assay. In both nZVI and the DPI and nZVI co-primed sets, significant up-regulation in genes like OsGA3Ox2, OsGAMYB were observed which are responsible for regulating the activity of several hydrolases and mediates efficient mobilization of storage food reserves of seeds. Thus, nZVI priming has potential to regulate intracellular ROS levels and orchestrate all the metabolic activities which eventually up-regulates seed germination rate and seed vigour.
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Affiliation(s)
- Titir Guha
- Centre of Advanced Study, Department of Botany, Calcutta University, 35, Ballygange Circular Road, Kolkata-19, India
| | - Hrimeeka Das
- Centre of Advanced Study, Department of Botany, Calcutta University, 35, Ballygange Circular Road, Kolkata-19, India
| | - Amitava Mukherjee
- Centre for Nanobiotechnology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India
| | - Rita Kundu
- Centre of Advanced Study, Department of Botany, Calcutta University, 35, Ballygange Circular Road, Kolkata-19, India.
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26
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Xu Q, Liu Q, Chen Z, Yue Y, Liu Y, Zhao Y, Zhou DX. Histone deacetylases control lysine acetylation of ribosomal proteins in rice. Nucleic Acids Res 2021; 49:4613-4628. [PMID: 33836077 PMCID: PMC8096213 DOI: 10.1093/nar/gkab244] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 03/21/2021] [Accepted: 04/08/2021] [Indexed: 01/04/2023] Open
Abstract
Lysine acetylation (Kac) is well known to occur in histones for chromatin function and epigenetic regulation. In addition to histones, Kac is also detected in a large number of proteins with diverse biological functions. However, Kac function and regulatory mechanism for most proteins are unclear. In this work, we studied mutation effects of rice genes encoding cytoplasm-localized histone deacetylases (HDAC) on protein acetylome and found that the HDAC protein HDA714 was a major deacetylase of the rice non-histone proteins including many ribosomal proteins (r-proteins) and translation factors that were extensively acetylated. HDA714 loss-of-function mutations increased Kac levels but reduced abundance of r-proteins. In vitro and in vivo experiments showed that HDA714 interacted with r-proteins and reduced their Kac. Substitutions of lysine by arginine (depleting Kac) in several r-proteins enhance, while mutations of lysine to glutamine (mimicking Kac) decrease their stability in transient expression system. Ribo-seq analysis revealed that the hda714 mutations resulted in increased ribosome stalling frequency. Collectively, the results uncover Kac as a functional posttranslational modification of r-proteins which is controlled by histone deacetylases, extending the role of Kac in gene expression to protein translational regulation.
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Affiliation(s)
- Qiutao Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China
| | - Qian Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China
| | - Zhengting Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China
| | - Yaping Yue
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China
| | - Yuan Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China
| | - Yu Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China
| | - Dao-Xiu Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China.,Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRAE, University Paris-Saclay, 91405 Orsay, France
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27
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Castano-Duque L, Ghosal S, Quilloy FA, Mitchell-Olds T, Dixit S. An epigenetic pathway in rice connects genetic variation to anaerobic germination and seedling establishment. PLANT PHYSIOLOGY 2021; 186:1042-1059. [PMID: 33638990 PMCID: PMC8195528 DOI: 10.1093/plphys/kiab100] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 02/09/2021] [Indexed: 06/12/2023]
Abstract
Rice production is shifting from transplanting seedlings to direct sowing of seeds. Following heavy rains, directly sown seeds may need to germinate under anaerobic environments, but most rice (Oryza sativa) genotypes cannot survive these conditions. To identify the genetic architecture of complex traits, we quantified percentage anaerobic germination (AG) in 2,700 (wet-season) and 1,500 (dry-season) sequenced rice genotypes and performed genome-wide association studies (GWAS) using 693,502 single nucleotide polymorphisms. This was followed by post-GWAS analysis with a generalized SNP-to-gene set analysis, meta-analysis, and network analysis. We determined that percentage AG is intermediate-to-high among indica subpopulations, and AG is a polygenic trait associated with transcription factors linked to ethylene responses or genes involved in metabolic processes that are known to be associated with AG. Our post-GWAS analysis identified several genes involved in a wide variety of metabolic processes. We subsequently performed functional analysis focused on the small RNA and methylation pathways. We selected CLASSY 1 (CLSY1), a gene involved in the RNA-directed DNA methylation (RdDm) pathway, for further analyses under AG and found several lines of evidence that CLSY1 influences AG. We propose that the RdDm pathway plays a role in rice responses to water status during germination and seedling establishment developmental stages.
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Affiliation(s)
| | - Sharmistha Ghosal
- Rice Breeding Platform, International Rice Research Institute. Pili Drive, Los Baños, Laguna 4031, Philippines
| | - Fergie A Quilloy
- Rice Breeding Platform, International Rice Research Institute. Pili Drive, Los Baños, Laguna 4031, Philippines
| | | | - Shalabh Dixit
- Rice Breeding Platform, International Rice Research Institute. Pili Drive, Los Baños, Laguna 4031, Philippines
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28
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Tappiban P, Ying Y, Xu F, Bao J. Proteomics and Post-Translational Modifications of Starch Biosynthesis-Related Proteins in Developing Seeds of Rice. Int J Mol Sci 2021; 22:5901. [PMID: 34072759 PMCID: PMC8199009 DOI: 10.3390/ijms22115901] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/26/2021] [Accepted: 05/28/2021] [Indexed: 12/25/2022] Open
Abstract
Rice (Oryza sativa L.) is a foremost staple food for approximately half the world's population. The components of rice starch, amylose, and amylopectin are synthesized by a series of enzymes, which are responsible for rice starch properties and functionality, and then affect rice cooking and eating quality. Recently, proteomics technology has been applied to the establishment of the differentially expressed starch biosynthesis-related proteins and the identification of posttranslational modifications (PTMs) target starch biosynthesis proteins as well. It is necessary to summarize the recent studies in proteomics and PTMs in rice endosperm to deepen our understanding of starch biosynthesis protein expression and regulation, which will provide useful information to rice breeding programs and industrial starch applications. The review provides a comprehensive summary of proteins and PTMs involved in starch biosynthesis based on proteomic studies of rice developing seeds. Starch biosynthesis proteins in rice seeds were differentially expressed in the developing seeds at different developmental stages. All the proteins involving in starch biosynthesis were identified using proteomics methods. Most starch biosynthesis-related proteins are basically increased at 6-20 days after flowering (DAF) and decreased upon the high-temperature conditions. A total of 10, 14, 2, 17, and 7 starch biosynthesis related proteins were identified to be targeted by phosphorylation, lysine acetylation, succinylation, lysine 2-hydroxyisobutyrylation, and malonylation, respectively. The phosphoglucomutase is commonly targeted by five PTMs types. Research on the function of phosphorylation in multiple enzyme complex formation in endosperm starch biosynthesis is underway, while the functions of other PTMs in starch biosynthesis are necessary to be conducted in the near future.
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Affiliation(s)
- Piengtawan Tappiban
- Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Zhejiang Province, Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China; (P.T.); (Y.Y.); (F.X.)
| | - Yining Ying
- Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Zhejiang Province, Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China; (P.T.); (Y.Y.); (F.X.)
| | - Feifei Xu
- Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Zhejiang Province, Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China; (P.T.); (Y.Y.); (F.X.)
| | - Jinsong Bao
- Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Zhejiang Province, Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China; (P.T.); (Y.Y.); (F.X.)
- Hainan Institute of Zhejiang University, Yazhou Bay Science and Technology City, Yazhou District, Sanya 572025, China
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29
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Cavite HJM, Mactal AG, Evangelista EV, Cruz JA. Biochemical characteristics and inoculation effects of multi-trait plant growth-promoting rhizobacteria on upland rice (Oryza sativa L. cv PSB Rc23) seedling growth. Arch Microbiol 2021; 203:3533-3540. [PMID: 33938971 DOI: 10.1007/s00203-021-02337-z] [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: 09/21/2020] [Revised: 04/13/2021] [Accepted: 04/17/2021] [Indexed: 10/21/2022]
Abstract
Plant growth-promoting rhizobacteria (PGPR) are known to stimulate plant growth because of their versatility in nutrient transformation. However, the success of PGPR inoculation depends not only on their ability to promote plant growth but also on their capacity to metabolize substrates that can be used as energy for the development and survival of the crops. Given the important influence of seed germination and vigor on crop yield, this study investigated the biochemical characteristics and effectiveness of multi-trait PGPR isolates in enhancing upland rice seedling growth and vigor. Biochemical identification was done using Biolog GEN III Microbial Identification System. Isolates were characterized based on their ability to metabolize all major classes of biochemicals in the carbon source utilization and chemical sensitivity assays. Identified rhizobacterial isolates were tested in vitro to evaluate their inoculation effects on the growth of PSB Rc23 upland rice seedlings. Biochemical identification results showed that rhizobacterial isolates have extensive metabolic activities in a wide range of carbon sources. Inoculation effects revealed that isolate IBBw1a was the most effective in enhancing root length and vigor index of rice seedlings in vitro, yielding a significant increase of 60% and 53%, respectively, over the uninoculated control. This study suggests that rhizobacterial isolates from upland rice may have commercial significance to improve seedling growth and vigor. These isolates will undergo a further assessment of their effectiveness in actual upland rice field conditions as they were already proven effective growth promoters in laboratory and screenhouse conditions. Such future activity can uncover their efficacy as potential biofertilizers in the actual soil environment.
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Affiliation(s)
- Harry Jay M Cavite
- Faculty of Agricultural Technology, King Mongkut's Institute of Technology Ladkrabang, Bangkok, 10520, Thailand. .,College of Agriculture, Central Luzon State University, 3120, Science City of Muñoz, Nueva Ecija, Philippines.
| | - Ariel G Mactal
- College of Agriculture, Central Luzon State University, 3120, Science City of Muñoz, Nueva Ecija, Philippines
| | - Editha V Evangelista
- Agronomy, Soils and Plant Physiology Division, Philippine Rice Research Institute, 3119, Science City of Muñoz, Nueva Ecija, Philippines
| | - Jayvee A Cruz
- Agronomy, Soils and Plant Physiology Division, Philippine Rice Research Institute, 3119, Science City of Muñoz, Nueva Ecija, Philippines
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Kantayos V, Kim JS, Baek SH. Alteration of resveratrol-dependent glycosyltransferase activity by elicitation in DJ-526 rice. GM CROPS & FOOD 2021; 12:242-250. [PMID: 33393843 PMCID: PMC7801123 DOI: 10.1080/21645698.2020.1859314] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Since the successful creation of DJ-526, a resveratrol-enriched rice cultivar, research has focused on resveratrol production because of its great potential in pharmaceutical applications. However, the utilization of resveratrol in DJ-526 is limited by glycosylation, which converts resveratrol to its glucoside (piceid), in a process driven by glycosyltransferase. The verification of resveratrol-dependent glycosyltransferase activity is an essential strategy for improving resveratrol production in DJ-526 rice. In this study, 27 candidate glycosyltransferases were evaluated in germinated seeds. Among the candidates, only R12 exhibited upregulation related to increased resveratrol and piceid content during seed germination, whereas various effects on the activity of glycosyltransferase were observed by the presence of a bio-elicitor. Yeast extract tended to enhance glycosyltransferase activity by seven candidates, and a specific peak for an unknown compound production was identified. Conversely, chitosan acted as a glycosyltransferase inhibitor. Our results suggested that R12 and R19 are the most relevant candidate resveratrol-dependent glycosyltransferases in DJ-526 seeds during germination and elicitation. Future research should assess the possibility of silencing these candidate genes in an effort to improve resveratrol levels in DJ-526 rice.
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Affiliation(s)
- Vipada Kantayos
- Department of Well-being Resources, Sunchon National University , Suncheon, Korea
| | - Jin-Suk Kim
- Department of Well-being Resources, Sunchon National University , Suncheon, Korea
| | - So-Hyeon Baek
- Department of Well-being Resources, Sunchon National University , Suncheon, Korea
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31
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Zhao J, He Y, Huang S, Wang Z. Advances in the Identification of Quantitative Trait Loci and Genes Involved in Seed Vigor in Rice. FRONTIERS IN PLANT SCIENCE 2021; 12:659307. [PMID: 34335643 PMCID: PMC8316977 DOI: 10.3389/fpls.2021.659307] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 03/22/2021] [Indexed: 05/08/2023]
Abstract
Seed vigor is a complex trait, including the seed germination, seedling emergence, and growth, as well as seed storability and stress tolerance, which is important for direct seeding in rice. Seed vigor is established during seed development, and its level is decreased during seed storage. Seed vigor is influenced by genetic and environmental factors during seed development, storage, and germination stages. A lot of factors, such as nutrient reserves, seed dying, seed dormancy, seed deterioration, stress conditions, and seed treatments, will influence seed vigor during seed development to germination stages. This review highlights the current advances on the identification of quantitative trait loci (QTLs) and regulatory genes involved in seed vigor at seed development, storage, and germination stages in rice. These identified QTLs and regulatory genes will contribute to the improvement of seed vigor by breeding, biotechnological, and treatment approaches.
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Smolikova G, Gorbach D, Lukasheva E, Mavropolo-Stolyarenko G, Bilova T, Soboleva A, Tsarev A, Romanovskaya E, Podolskaya E, Zhukov V, Tikhonovich I, Medvedev S, Hoehenwarter W, Frolov A. Bringing New Methods to the Seed Proteomics Platform: Challenges and Perspectives. Int J Mol Sci 2020; 21:E9162. [PMID: 33271881 PMCID: PMC7729594 DOI: 10.3390/ijms21239162] [Citation(s) in RCA: 12] [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: 11/10/2020] [Revised: 11/26/2020] [Accepted: 11/27/2020] [Indexed: 12/14/2022] Open
Abstract
For centuries, crop plants have represented the basis of the daily human diet. Among them, cereals and legumes, accumulating oils, proteins, and carbohydrates in their seeds, distinctly dominate modern agriculture, thus play an essential role in food industry and fuel production. Therefore, seeds of crop plants are intensively studied by food chemists, biologists, biochemists, and nutritional physiologists. Accordingly, seed development and germination as well as age- and stress-related alterations in seed vigor, longevity, nutritional value, and safety can be addressed by a broad panel of analytical, biochemical, and physiological methods. Currently, functional genomics is one of the most powerful tools, giving direct access to characteristic metabolic changes accompanying plant development, senescence, and response to biotic or abiotic stress. Among individual post-genomic methodological platforms, proteomics represents one of the most effective ones, giving access to cellular metabolism at the level of proteins. During the recent decades, multiple methodological advances were introduced in different branches of life science, although only some of them were established in seed proteomics so far. Therefore, here we discuss main methodological approaches already employed in seed proteomics, as well as those still waiting for implementation in this field of plant research, with a special emphasis on sample preparation, data acquisition, processing, and post-processing. Thereby, the overall goal of this review is to bring new methodologies emerging in different areas of proteomics research (clinical, food, ecological, microbial, and plant proteomics) to the broad society of seed biologists.
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Affiliation(s)
- Galina Smolikova
- Department of Plant Physiology and Biochemistry, St. Petersburg State University; 199034 St. Petersburg, Russia; (G.S.); (T.B.); (S.M.)
| | - Daria Gorbach
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
| | - Elena Lukasheva
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
| | - Gregory Mavropolo-Stolyarenko
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
| | - Tatiana Bilova
- Department of Plant Physiology and Biochemistry, St. Petersburg State University; 199034 St. Petersburg, Russia; (G.S.); (T.B.); (S.M.)
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry; 06120 Halle (Saale), Germany
| | - Alena Soboleva
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry; 06120 Halle (Saale), Germany
| | - Alexander Tsarev
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry; 06120 Halle (Saale), Germany
| | - Ekaterina Romanovskaya
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
| | - Ekaterina Podolskaya
- Institute of Analytical Instrumentation, Russian Academy of Science; 190103 St. Petersburg, Russia;
- Institute of Toxicology, Russian Federal Medical Agency; 192019 St. Petersburg, Russia
| | - Vladimir Zhukov
- All-Russia Research Institute for Agricultural Microbiology; 196608 St. Petersburg, Russia; (V.Z.); (I.T.)
| | - Igor Tikhonovich
- All-Russia Research Institute for Agricultural Microbiology; 196608 St. Petersburg, Russia; (V.Z.); (I.T.)
- Department of Genetics and Biotechnology, St. Petersburg State University; 199034 St. Petersburg, Russia
| | - Sergei Medvedev
- Department of Plant Physiology and Biochemistry, St. Petersburg State University; 199034 St. Petersburg, Russia; (G.S.); (T.B.); (S.M.)
| | - Wolfgang Hoehenwarter
- Proteome Analytics Research Group, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany;
| | - Andrej Frolov
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry; 06120 Halle (Saale), Germany
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Comparative Physiological and Proteomic Analysis Reveals Different Involvement of Proteins during Artificial Aging of Siberian Wildrye Seeds. PLANTS 2020; 9:plants9101370. [PMID: 33076425 PMCID: PMC7650541 DOI: 10.3390/plants9101370] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 10/13/2020] [Accepted: 10/13/2020] [Indexed: 02/01/2023]
Abstract
Seed aging has an important effect on the germplasm preservation and industrialized production of Siberian wildrye (Elymus sibiricus) in the Qinghai-Tibet Plateau. However, so far its underlying molecular mechanisms still largely remain unknown. To shed light on this topic, one-year stored seeds of E. sibiricus were exposed to artificial aging treatments (AAT), followed by seed vigor characteristics and physiological status monitoring. Then global proteomics analysis was undertaken by the tandem mass tags (TMT) technique, and the proteins were quantified with liquid chromatography-tandem mass spectrometry on three aging time points (0 h, 36 h and 72 h). Finally, we verified the expression of related proteins by parallel reaction monitoring (PRM). Our results demonstrated that the seed vigor decreased remarkably in response to artificial aging, but the relative ion-leakage and malondialdehyde content, superoxide anion and hydrogen peroxide showed the opposite situation. Proteomic results showed that a total of 4169 proteins were identified and quantified. Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated that a series of key pathways including carbohydrate metabolism, lipid metabolism, and antioxidant activity were severely damaged by aging treatments. Numerous key proteins such as glyceraldehyde triphosphate glyceraldehyde dehydrogenase, succinate dehydrogenase, lipoxygenase, peroxidase, glutathione-s-transferase and late embryogenesis abundant proteins were significantly down-regulated. However, the up-regulation of the heat shock protein family has made a positive contribution to oxidative stress resistance in seeds. This study provides a useful catalog of the E. sibiricus proteomes with insights into the future genetic improvement of seed storability.
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Dolui AK, Vijayaraj P. Functional Omics Identifies Serine Hydrolases That Mobilize Storage Lipids during Rice Seed Germination. PLANT PHYSIOLOGY 2020; 184:693-708. [PMID: 32817194 PMCID: PMC7536657 DOI: 10.1104/pp.20.00268] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 08/04/2020] [Indexed: 05/10/2023]
Abstract
Elucidating proteolipidome dynamics is crucial for understanding the roles of these molecules in plant physiology and disease. Sequence-based functional annotation of the protein is inadequate, since protein activities depend on posttranslational modification. In this study, we applied a gel-free activity-based protein profiling approach to unravel the active lipases, including other Serine hydrolases (SHs), expressed during seed germination in rice (Oryza sativa). We successfully mapped the active sites of 43 active SHs encompassing lipases/esterases, GDSL lipases, proteases, Ser carboxypeptidases, ABHD protein, pectin acetylesterase, and other SHs. The mRNA expression levels of those genes encoding the identified SHs were monitored using microarray analysis. The lipidome analysis revealed distinct patterns of molecular species distribution in individual lipid classes and displayed the metabolic connections between lipid mobilization and rice seedling growth. Changes in the mobilization of storage lipids and their molecular species remodeling were correlated with the expression of the identified lipases and their lipase activity in a time-dependent manner. The physiological significance of the identified SHs was explored during biotic stress with Fusarium verticillioides infection. The fungal infection significantly reduced lipase activity and lipid mobilization, thus impairing the rice seedling. Collectively, our data demonstrate application of the functional proteome strategy along with the shotgun lipidome approach for the identification of active SHs, and thus for deciphering the role of lipid homeostasis during rice seed germination.
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Affiliation(s)
- Achintya Kumar Dolui
- Lipid and Nutrition Laboratory, Department of Lipid Science, Council of Scientific and Industrial Research-Central Food Technological Research Institute, Mysore, Karnataka, 570020, India
- Academy of Scientific and Innovative Research, Ghaziabad, 201002, Uttar Pradesh, India
| | - Panneerselvam Vijayaraj
- Lipid and Nutrition Laboratory, Department of Lipid Science, Council of Scientific and Industrial Research-Central Food Technological Research Institute, Mysore, Karnataka, 570020, India
- Academy of Scientific and Innovative Research, Ghaziabad, 201002, Uttar Pradesh, India
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Kim H, Kim OW, Ahn JH, Kim BM, Oh J, Kim HJ. Metabolomic Analysis of Germinated Brown Rice at Different Germination Stages. Foods 2020; 9:E1130. [PMID: 32824423 PMCID: PMC7491196 DOI: 10.3390/foods9081130] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 08/04/2020] [Accepted: 08/13/2020] [Indexed: 11/16/2022] Open
Abstract
Brown rice (BR) is unpolished rice containing many bioactive compounds in addition to the basic nutrients of the rice grain. Herein, BR was germinated for up to 48 h to prepare germinated brown rice (GBR). The physiological and chemical changes in the GBR during germination were analyzed. GBR samples germinated for 48 h were in the radicle-emergence stage, but root formation was not observed. The change in the GBR metabolite profile during germination was analyzed to determine the effect of germination on the chemical profiles of the GBR samples. Twenty-five metabolites including acidic compounds, amino acids, sugars, lipid metabolites, and secondary metabolites were identified as the components that contributed to the variations in the GBR groups germinated for different time periods. Among the metabolites, the carbohydrates associated with energy production and lipid metabolites changed significantly. Based on the identified metabolites, a metabolomic pathway was proposed. Carbohydrate metabolism, citric acid cycle, and lipid metabolism were the main processes that were affected during germination. Although further studies on the relationship between the metabolite profile and nutritional quality of the GBR are needed, these results are useful for understanding the effect of germination on the physiological and chemical changes in BR.
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Affiliation(s)
- Hoon Kim
- Korea Food Research Institute, Research Group of Consumer Safety, 245 Nongsaengmyeong-ro, Iseo-myeon, Wanju-Gun, Jeollabuk-do 55365, Korea; (H.K.); (O.-W.K.); (J.-H.A.)
| | - Oui-Woung Kim
- Korea Food Research Institute, Research Group of Consumer Safety, 245 Nongsaengmyeong-ro, Iseo-myeon, Wanju-Gun, Jeollabuk-do 55365, Korea; (H.K.); (O.-W.K.); (J.-H.A.)
| | - Jae-Hwan Ahn
- Korea Food Research Institute, Research Group of Consumer Safety, 245 Nongsaengmyeong-ro, Iseo-myeon, Wanju-Gun, Jeollabuk-do 55365, Korea; (H.K.); (O.-W.K.); (J.-H.A.)
| | - Bo-Min Kim
- EZmass.Co. Ltd., 501 Jinjudaero, Jinju, Gyeongsangnam-do 52828, Korea; (B.-M.K.); (J.O.)
| | - Juhong Oh
- EZmass.Co. Ltd., 501 Jinjudaero, Jinju, Gyeongsangnam-do 52828, Korea; (B.-M.K.); (J.O.)
| | - Hyun-Jin Kim
- EZmass.Co. Ltd., 501 Jinjudaero, Jinju, Gyeongsangnam-do 52828, Korea; (B.-M.K.); (J.O.)
- Division of Applied Life Sciences (BK21 plus), Department of Food Science and Technology, and Institute of Agriculture and Life Science, Gyeongsang National University, 501 Jinjudaero, Jinju, Gyeongsangnam-do 52828, Korea
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36
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Weckwerth W, Ghatak A, Bellaire A, Chaturvedi P, Varshney RK. PANOMICS meets germplasm. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:1507-1525. [PMID: 32163658 PMCID: PMC7292548 DOI: 10.1111/pbi.13372] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Revised: 02/17/2020] [Accepted: 02/26/2020] [Indexed: 05/14/2023]
Abstract
Genotyping-by-sequencing has enabled approaches for genomic selection to improve yield, stress resistance and nutritional value. More and more resource studies are emerging providing 1000 and more genotypes and millions of SNPs for one species covering a hitherto inaccessible intraspecific genetic variation. The larger the databases are growing, the better statistical approaches for genomic selection will be available. However, there are clear limitations on the statistical but also on the biological part. Intraspecific genetic variation is able to explain a high proportion of the phenotypes, but a large part of phenotypic plasticity also stems from environmentally driven transcriptional, post-transcriptional, translational, post-translational, epigenetic and metabolic regulation. Moreover, regulation of the same gene can have different phenotypic outputs in different environments. Consequently, to explain and understand environment-dependent phenotypic plasticity based on the available genotype variation we have to integrate the analysis of further molecular levels reflecting the complete information flow from the gene to metabolism to phenotype. Interestingly, metabolomics platforms are already more cost-effective than NGS platforms and are decisive for the prediction of nutritional value or stress resistance. Here, we propose three fundamental pillars for future breeding strategies in the framework of Green Systems Biology: (i) combining genome selection with environment-dependent PANOMICS analysis and deep learning to improve prediction accuracy for marker-dependent trait performance; (ii) PANOMICS resolution at subtissue, cellular and subcellular level provides information about fundamental functions of selected markers; (iii) combining PANOMICS with genome editing and speed breeding tools to accelerate and enhance large-scale functional validation of trait-specific precision breeding.
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Affiliation(s)
- Wolfram Weckwerth
- Molecular Systems Biology (MOSYS)Department of Functional and Evolutionary EcologyFaculty of Life SciencesUniversity of ViennaViennaAustria
- Vienna Metabolomics Center (VIME)University of ViennaViennaAustria
| | - Arindam Ghatak
- Molecular Systems Biology (MOSYS)Department of Functional and Evolutionary EcologyFaculty of Life SciencesUniversity of ViennaViennaAustria
| | - Anke Bellaire
- Molecular Systems Biology (MOSYS)Department of Functional and Evolutionary EcologyFaculty of Life SciencesUniversity of ViennaViennaAustria
| | - Palak Chaturvedi
- Molecular Systems Biology (MOSYS)Department of Functional and Evolutionary EcologyFaculty of Life SciencesUniversity of ViennaViennaAustria
| | - Rajeev K. Varshney
- Center of Excellence in Genomics & Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadTelanganaIndia
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37
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Weckwerth W, Ghatak A, Bellaire A, Chaturvedi P, Varshney RK. PANOMICS meets germplasm. PLANT BIOTECHNOLOGY JOURNAL 2020; 18. [PMID: 32163658 PMCID: PMC7292548 DOI: 10.1111/pbi.13372,10.13140/rg.2.1.1233.5760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Genotyping-by-sequencing has enabled approaches for genomic selection to improve yield, stress resistance and nutritional value. More and more resource studies are emerging providing 1000 and more genotypes and millions of SNPs for one species covering a hitherto inaccessible intraspecific genetic variation. The larger the databases are growing, the better statistical approaches for genomic selection will be available. However, there are clear limitations on the statistical but also on the biological part. Intraspecific genetic variation is able to explain a high proportion of the phenotypes, but a large part of phenotypic plasticity also stems from environmentally driven transcriptional, post-transcriptional, translational, post-translational, epigenetic and metabolic regulation. Moreover, regulation of the same gene can have different phenotypic outputs in different environments. Consequently, to explain and understand environment-dependent phenotypic plasticity based on the available genotype variation we have to integrate the analysis of further molecular levels reflecting the complete information flow from the gene to metabolism to phenotype. Interestingly, metabolomics platforms are already more cost-effective than NGS platforms and are decisive for the prediction of nutritional value or stress resistance. Here, we propose three fundamental pillars for future breeding strategies in the framework of Green Systems Biology: (i) combining genome selection with environment-dependent PANOMICS analysis and deep learning to improve prediction accuracy for marker-dependent trait performance; (ii) PANOMICS resolution at subtissue, cellular and subcellular level provides information about fundamental functions of selected markers; (iii) combining PANOMICS with genome editing and speed breeding tools to accelerate and enhance large-scale functional validation of trait-specific precision breeding.
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Affiliation(s)
- Wolfram Weckwerth
- Molecular Systems Biology (MOSYS)Department of Functional and Evolutionary EcologyFaculty of Life SciencesUniversity of ViennaViennaAustria
- Vienna Metabolomics Center (VIME)University of ViennaViennaAustria
| | - Arindam Ghatak
- Molecular Systems Biology (MOSYS)Department of Functional and Evolutionary EcologyFaculty of Life SciencesUniversity of ViennaViennaAustria
| | - Anke Bellaire
- Molecular Systems Biology (MOSYS)Department of Functional and Evolutionary EcologyFaculty of Life SciencesUniversity of ViennaViennaAustria
| | - Palak Chaturvedi
- Molecular Systems Biology (MOSYS)Department of Functional and Evolutionary EcologyFaculty of Life SciencesUniversity of ViennaViennaAustria
| | - Rajeev K. Varshney
- Center of Excellence in Genomics & Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadTelanganaIndia
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Li X, Fei R, Chen Z, Fan C, Sun X. Plant hormonal changes and differential expression profiling reveal seed dormancy removal process in double dormant plant-herbaceous peony. PLoS One 2020; 15:e0231117. [PMID: 32240252 PMCID: PMC7117732 DOI: 10.1371/journal.pone.0231117] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Accepted: 03/16/2020] [Indexed: 01/10/2023] Open
Abstract
Herbaceous peony (Paeonia lactiflora Pall.) is a popular ornamental and medicinal plant. Taking approximately six to seven months, the seeds germination under natural conditions experiences dual dormancies, which seriously affects horticultural cultivation. Few studies have been conducted on exploring both biological and molecular mechanism that regulates dormancy removal process in hypocotyls double dormant plants. Here, we first measured ABA and GA3 content changes at four key dormancy break stages, and then performed transcriptomic analyses to identify the differentially expressed genes (DEGs) using RNA-seq. We subsequently carried out Quantitative real-time PCR (qRT-PCR) to validate RNA-seq data. ABA content decreased during the whole dormancy removal process and GA3 content exhibited decreasing slightly and then increasing trend. RNA sequencing de novo assembly generated a total of 99,577 unigenes. 20,344 unigenes were differentially expressed in the whole dormancy release process. The qPCR results of 54 selected unigenes were consistent with the FPKM values obtained from RNA-seq. Our results summarize a valuable collection of gene expression profiles characterizing the dormancy release process. The DEGs are candidates for functional analyses of genes affecting the dormancy release, which is a precious resource for the on-going physiological and molecular investigation of seeds dormancy removal in other perennial plants.
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Affiliation(s)
- Xueting Li
- Horticulture College, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Riwen Fei
- Horticulture College, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Zhijing Chen
- Forestry College, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Chuanzhu Fan
- Department of Biological Sciences, Wayne State University, Detroit, MI, United States of America
| | - Xiaomei Sun
- Horticulture College, Shenyang Agricultural University, Shenyang, Liaoning, China
- Forestry College, Shenyang Agricultural University, Shenyang, Liaoning, China
- * E-mail:
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39
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He D, Li M, Damaris RN, Bu C, Xue J, Yang P. Quantitative ubiquitylomics approach for characterizing the dynamic change and extensive modulation of ubiquitylation in rice seed germination. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:1430-1447. [PMID: 31677306 DOI: 10.1111/tpj.14593] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 09/26/2019] [Accepted: 10/16/2019] [Indexed: 05/22/2023]
Abstract
During seed germination, cells embark on extensive post-transcriptional and post-translational modifications (PTM), providing a perfect platform to study these events in embryo rebooting from relative quiescenct to highly active state. PR-619, a deubiquitylase inhibitor, delayed the rice seed germination and resulted in the accumulation of ubiquitylated proteins, which indicated the protein ubiquitylation is involved in this process. Using the K-Ɛ-GG antibody enrichment method integrated with high-resolution mass spectrometry, a list of 2576 lysine ubiquitylated (Kub) sites in 1171 proteins was compiled for rice embryos at 0, 12 and 24 h after imbibition (HAI). Of these, the abundance of 1419 Kub sites in 777 proteins changed significantly. Most of them substantially increased within the first 12 HAI, which is similar to the dynamic state previously observed for protein phosphorylation, implying that the first 12 HAI are essential for subsequent switch during rice seed germination. We also quantitatively analyzed the embryo proteome in these samples. Generally, a specific protein's abundance in the ubiquitylome was uncorrelated to that in the proteome. The differentially ubiquitinated proteins were greatly enriched in the categories of protein processing, DNA and RNA processing/regulation related, signaling, and transport. The DiGly footprint of the Kub sites was significantly reduced on K48, a linkage typically associated with proteasome-mediated degradation. These observations suggest ubiquitylation may modulate the protein function more than providing 26S degradation signals in the early stage of rice seed germination. Revealing this comprehensive ubiquitylome greatly increases our understanding of this critical PTM during seed germination.
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Affiliation(s)
- Dongli He
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Ming Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Rebecca N Damaris
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Chen Bu
- Jingjie PTM BioLab (Hangzhou) Co. Ltd, Hangzhou, 310018, China
| | - Jianyou Xue
- Jingjie PTM BioLab (Hangzhou) Co. Ltd, Hangzhou, 310018, China
| | - Pingfang Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
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The expression pattern of OsDim1 in rice and its proposed function. Sci Rep 2019; 9:18492. [PMID: 31811256 PMCID: PMC6897961 DOI: 10.1038/s41598-019-54898-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 11/19/2019] [Indexed: 11/22/2022] Open
Abstract
Development of plant tissues is dependent on numerous factors, including hormone activity, signaling, cell division, and elongation. In plants, Defective Entry into Mitosis 1 (Dim1) homologs are recognized as pivotal in leaf senescence and progress of normal growth, but their role in rice has not been functionally characterized. The findings presented in this paper suggest that OsDim1 is important in early seedling development, pollen tube elongation, and impacts rice yield components. The gene is expressed in the scutellum, endosperm, embryonic root, shoot, pollen grains and tubes, as well as in several organs of the rice flower. According to the present study findings, RNAi mediated knockdown of OsDim1 resulted in phytohormonal imbalance, reduced amylase activity, affected differentiation of embryonic root elongation zone tissues, suppressed embryonic root and shoot growth, and impaired pollen tube elongation. In contrast, overexpression of OsDim1 showed significant growth in embryonic roots and shoots, while it increased culm length, total number of tillers per plant, seed setting rate, and total number of grains per panicle compared to its wild type line. In summary, we propose OsDim1 plays an important role in seedling growth and pollen tube elongation, and has pleiotropic effects on reproductive tissues.
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Sano N, Takebayashi Y, To A, Mhiri C, Rajjou LC, Nakagami H, Kanekatsu M. Shotgun Proteomic Analysis Highlights the Roles of Long-Lived mRNAs and De Novo Transcribed mRNAs in Rice Seeds upon Imbibition. PLANT & CELL PHYSIOLOGY 2019; 60:2584-2596. [PMID: 31373371 DOI: 10.1093/pcp/pcz152] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 07/27/2019] [Indexed: 05/22/2023]
Abstract
During seed germination, proteins are translated not only from mRNAs newly transcribed upon imbibition but also from long-lived mRNAs that are synthesized during seed maturation and stored in the mature dry seeds. To clarify the distinct roles of proteins translated from long-lived mRNAs and de novo transcribed mRNAs in germinating rice embryos, proteome analysis based on liquid chromatography-tandem mass spectrometry (LC-MS/MS) combining the use of a transcriptional inhibitor was performed. We observed that α-amanitin significantly represses transcription in germinating embryos; nevertheless, the embryos could germinate, albeit slowly. The proteomic analysis revealed that a total of 109 proteins were translated from long-lived mRNAs associated with germination as well as 222 proteins whose expression were dependent on de novo transcription upon imbibition. Transcriptomic datasets available in public databases demonstrated that mRNAs of the 222 proteins notably increased during germination while those of the 109 proteins highly accumulated in dry embryos and constitutively expressed upon imbibition. Gene Ontology enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that many of the 109 proteins from long-lived mRNAs are implicated in energy production such as glycolysis or annotated as nucleotide binding proteins, while the 222 proteins are involved in pathways such as pyruvate metabolism and TCA cycle following glycolysis, and momilactones biosynthesis. We propose that long-lived mRNAs support initial energy production and activation of translational machinery upon imbibition whereas de novo transcription accelerates the energy production after glycolysis, which enables rice seeds to germinate vigorously.
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Affiliation(s)
- Naoto Sano
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Universit� Paris-Saclay, Versailles, France
| | - Yumiko Takebayashi
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
| | - Alexandra To
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Universit� Paris-Saclay, Versailles, France
| | - Corinne Mhiri
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Universit� Paris-Saclay, Versailles, France
| | - Loï C Rajjou
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Universit� Paris-Saclay, Versailles, France
| | - Hirofumi Nakagami
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
- Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, Cologne, Germany
| | - Motoki Kanekatsu
- Department of Plant Production, United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
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Nagaraju M, Reddy PS, Kumar SA, Kumar A, Rajasheker G, Rao DM, Kavi Kishor PB. Genome-wide identification and transcriptional profiling of small heat shock protein gene family under diverse abiotic stress conditions in Sorghum bicolor (L.). Int J Biol Macromol 2019; 142:822-834. [PMID: 31622710 DOI: 10.1016/j.ijbiomac.2019.10.023] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 08/16/2019] [Accepted: 10/02/2019] [Indexed: 11/24/2022]
Abstract
The small heat shock proteins (sHsps/Hsp20s) are the molecular chaperones that maintain proper folding, trafficking and disaggregation of proteins under diverse abiotic stress conditions. In the present investigation, a genome-wide scan revealed the presence of a total of 47 sHsps in Sorghum bicolor (SbsHsps), distributed across 10 subfamilies, the major subfamily being P (plastid) group with 17 genes. Chromosomes 1 and 3 appear as the hot spot regions for SbsHsps, and majority of them were found acidic, hydrophilic, unstable and intron less. Interestingly, promoter analysis indicated that they are associated with both biotic and abiotic stresses, as well as plant development. Sorghum sHsps exhibited 15 paralogous and 20 orthologous duplications. Expression analysis of 15 genes selected from different subfamilies showed high transcript levels in roots and leaves implying that they are likely to participate in the developmental processes. SbsHsp genes were highly induced by diverse abiotic stresses inferring their critical role in mediating the environmental stress responses. Gene expression data revealed that SbsHsp-02 is a candidate gene expressed in all the tissues under varied stress conditions tested. Our results contribute to the understanding of the complexity of SbsHsp genes and help to analyse them further for functional validation.
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Affiliation(s)
- M Nagaraju
- Department of Genetics, Osmania University, Hyderabad 500 007, India; Biochemistry Division, ICMR-National Institute of Nutrition, Hyderabad 500 007, India
| | - Palakolanu Sudhakar Reddy
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad 502 324, India
| | - S Anil Kumar
- Department of Biotechnology, Vignan's Foundation for Science, Technology and Research, Vadlamudi, Guntur, Andhra Pradesh 522 213, India
| | - Anuj Kumar
- Advance Center for Computational & Applied Biotechnology, Uttarakhand Council for Biotechnology (UCB), Dehradun 248 007, India
| | - G Rajasheker
- Department of Genetics, Osmania University, Hyderabad 500 007, India
| | - D Manohar Rao
- Department of Genetics, Osmania University, Hyderabad 500 007, India.
| | - P B Kavi Kishor
- Department of Genetics, Osmania University, Hyderabad 500 007, India.
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KhalKhal E, Rezaei-Tavirani M, Rostamii-Nejad M. Pharmaceutical Advances and Proteomics Researches. IRANIAN JOURNAL OF PHARMACEUTICAL RESEARCH : IJPR 2019; 18:51-67. [PMID: 32802089 PMCID: PMC7393046 DOI: 10.22037/ijpr.2020.112440.13758] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Proteomics enables understanding the composition, structure, function and interactions of the entire protein complement of a cell, a tissue, or an organism under exactly defined conditions. Some factors such as stress or drug effects will change the protein pattern and cause the present or absence of a protein or gradual variation in abundances. The aim of this study is to explore relationship between proteomics application and drug discovery. "proteomics", "Application", and "pharmacology were the main keywords that were searched in PubMed (PubMed Central), Web of Science, and Google Scholar. The titles that were stablished by 2019, were studied and after study of the appreciated abstracts, the full texts of the 118 favor documents were extracted. Changes in the proteome provide a snapshot of the cell activities and physiological processes. Proteomics shows the observed protein changes to the causal effects and generate a complete three-dimensional map of the cell indicating their exact location. Proteomics is used in different biological fields and is applied in medicine, agriculture, food microbiology, industry, and pharmacy and drug discovery. Biomarker discovery, follow up of drug effect on the patients, and in vitro and in vivo proteomic investigation about the drug treated subjects implies close relationship between proteomics advances and application and drug discovery and development. This review overviews and summarizes the applications of proteomics especially in pharmacology and drug discovery.
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Affiliation(s)
- Ensieh KhalKhal
- Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Mostafa Rezaei-Tavirani
- Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Mohammad Rostamii-Nejad
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Transcriptome approach to address low seed germination in Cyclobalanopsis gilva to save forest ecology. BIOCHEM SYST ECOL 2018. [DOI: 10.1016/j.bse.2018.09.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Romero-Rodríguez MC, Jorrín-Novo JV, Castillejo MA. Toward characterizing germination and early growth in the non-orthodox forest tree species Quercus ilex through complementary gel and gel-free proteomic analysis of embryo and seedlings. J Proteomics 2018; 197:60-70. [PMID: 30408563 DOI: 10.1016/j.jprot.2018.11.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Revised: 10/23/2018] [Accepted: 11/04/2018] [Indexed: 11/15/2022]
Abstract
By using two complementary proteomics, gel-based and gel-free (shotgun) approaches, the protein profiles of the non-orthodox forest tree species Quercus ilex seeds during germination and early seedling growth have been compared. Proteins were extracted from embryo axis, radicle and shoot tissues at different developmental stages. Proteins were subjected to one- and two-dimensional gel electrophoresis. A multivariate analysis (PCA) revealed that SDS-PAGE clearly separated germination (0-24 h post-imbibition), postgermination (72-216 h post-imbibition) and early seedling growth stages (2 weeks post-imbibition). Image analysis of the two-dimensional gels revealed a total of 732 spots, 103 of which were significantly variable among developmental stages. After MALDI-TOF/TOF MS analysis, 90 spots were identified, belonging to six main functional categories: carbohydrate, amino acids, energy, and protein metabolism, biosynthesis of secondary metabolites, and redox processes. The gel-based approach disclosed important metabolic changes that occurred in the holm oak seed after the germination. However, few proteins were significantly altered during the germination period (from 0 h to 24 h post imbibition) and, because of that, a further shotgun analysis was therefore used to analyse changes in the protein profile during seed germination. Up to 1250 proteins could be confidently identified, with 153 being variable. They belonged to the main functional categories of carbohydrate, amino acids and secondary metabolism, protein degradation, and responses to abiotic stress. The accumulation of proteases and amino acids metabolism proteins in mature seeds can be reflecting the production of energy from the mobilization of storage proteins to start germination. These results, therefore, corroborate the hypothesis that the mature non-orthodox seeds of Q. ilex have all the machinery necessary for rapidly resuming metabolic activities and starting the germination process, in contrast to that occurs in orthodox seeds, which metabolic activity ceases in mature dry seeds. The use of a genus-specific database combined with the public Viridiplantae database improved the quality and quantity of protein identification in this orphan species. In addition, both proteomics approaches (gel-based and shotgun) were complementary, with shotgun increasing by over two-fold the coverage of the proteome analysed. Both approaches provided similar results and supported the same conclusions on the metabolic switch experienced by the seed upon germination. SIGNIFICANCE: The optimal seed germination is a prerequisite for successful seedling establishment and plant vigour, being of great relevance in the case of crops and commercial woody plants. By using a complementary gel-based and gel-free proteomic strategy we have study the protein profiles of the non-orthodox forest tree species Quercus ilex seeds during germination and early seedling growth. The contribution of this work is of great importance, due to the complemented proteomic approaches giving similar clues to the metabolic state of the mature Q. ilex seed before the germination starts, and the metabolic switch experienced by the imbibed acorn until the seedling is established.
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Affiliation(s)
- María Cristina Romero-Rodríguez
- Agroforestry and Plant Biochemistry, Proteomics, and Systems Biology Research Group, Department of Biochemistry and Molecular Biology- ETSIAM, University of Cordoba, UCO-CeiA3, Spain; Centro Multidisciplinario de Investigaciones Tecnológicas, Dirección General de Investigación Científica y Tecnológica, Universidad Nacional de Asunción, Paraguay; Departamento de Química Biológica, Dirección de Investigaciones, Facultad de Ciencias Químicas, Universidad Nacional de Asunción, Paraguay.
| | - Jesús V Jorrín-Novo
- Agroforestry and Plant Biochemistry, Proteomics, and Systems Biology Research Group, Department of Biochemistry and Molecular Biology- ETSIAM, University of Cordoba, UCO-CeiA3, Spain
| | - María Angeles Castillejo
- Agroforestry and Plant Biochemistry, Proteomics, and Systems Biology Research Group, Department of Biochemistry and Molecular Biology- ETSIAM, University of Cordoba, UCO-CeiA3, Spain.
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Kumar A, Pathak RK, Gayen A, Gupta S, Singh M, Lata C, Sharma H, Roy JK, Gupta SM. Systems biology of seeds: decoding the secret of biochemical seed factories for nutritional security. 3 Biotech 2018; 8:460. [PMID: 30370201 PMCID: PMC6200710 DOI: 10.1007/s13205-018-1483-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 10/16/2018] [Indexed: 11/28/2022] Open
Abstract
Seeds serve as biochemical factories of nutrition, processing, bio-energy and storage related important bio-molecules and act as a delivery system to transmit the genetic information to the next generation. The research pertaining towards delineating the complex system of regulation of genes and pathways related to seed biology and nutrient partitioning is still under infancy. To understand these, it is important to know the genes and pathway(s) involved in the homeostasis of bio-molecules. In recent past with the advent and advancement of modern tools of genomics and genetic engineering, multi-layered 'omics' approaches and high-throughput platforms are being used to discern the genes and proteins involved in various metabolic, and signaling pathways and their regulations for understanding the molecular genetics of biosynthesis and homeostasis of bio-molecules. This can be possible by exploring systems biology approaches via the integration of omics data for understanding the intricacy of seed development and nutrient partitioning. These information can be exploited for the improvement of biologically important chemicals for large-scale production of nutrients and nutraceuticals through pathway engineering and biotechnology. This review article thus describes different omics tools and other branches that are merged to build the most attractive area of research towards establishing the seeds as biochemical factories for human health and nutrition.
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Affiliation(s)
- Anil Kumar
- Rani Lakshmi Bai Central Agricultural University, Jhansi, Uttar Pradesh 284003 India
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
| | - Rajesh Kumar Pathak
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
- Department of Biotechnology, G. B. Pant Institute of Engineering and Technology, Pauri Garhwal, Uttarakhand 246194 India
| | - Aranyadip Gayen
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
| | - Supriya Gupta
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
| | - Manoj Singh
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
| | - Charu Lata
- Council of Scientific and Industrial Research-National Botanical Research Institute, Lucknow, India
| | - Himanshu Sharma
- National Agri-Food Biotechnology Institute, Mohali, Punjab 140306 India
| | - Joy Kumar Roy
- National Agri-Food Biotechnology Institute, Mohali, Punjab 140306 India
| | - Sanjay Mohan Gupta
- Molecular Biology and Genetic Engineering Laboratory, Defence Institute of Bio-Energy Research (DIBER), DRDO, Haldwani, 263139 India
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Liu Y, Han C, Deng X, Liu D, Liu N, Yan Y. Integrated physiology and proteome analysis of embryo and endosperm highlights complex metabolic networks involved in seed germination in wheat (Triticum aestivum L.). JOURNAL OF PLANT PHYSIOLOGY 2018; 229:63-76. [PMID: 30041047 DOI: 10.1016/j.jplph.2018.06.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 06/27/2018] [Accepted: 06/27/2018] [Indexed: 06/08/2023]
Abstract
The aim of this study was to investigate the physiological and proteomic changes in the embryo and endosperm during seed germination in the elite Chinese bread wheat cultivar Zhengmai 366. Upon imbibition, seed size and water content increased rapidly, followed by a series of metabolic changes including increases in soluble sugar content and α-amylase activity, a decrease in starch content, and a rapid increase in plant hormones. In total, 57 and 45 differentially accumulated proteins (DAPs) from the embryo and endosperm, respectively, were identified at five germination stages (0, 6, 12, 18, and 24 h). Principal component analysis revealed a significant proteome difference between embryo and endosperm as well as the different germination stages. The largest proteome changes occurred 24 h after seed imbibition. Embryo DAP spots were mainly involved in energy metabolism, amino acid metabolism, stress/defense, and protein metabolism; those from the endosperm were primarily related to storage protein and carbohydrate metabolism. Protein-protein interaction analysis revealed a complicated interaction network between energy-related proteins and other proteins. Metabolic pathway analysis highlighted complex regulatory networks in the embryo and endosperm that regulate wheat seed germination. These results provide new insights into the molecular mechanisms of seed germination.
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Affiliation(s)
- Yue Liu
- College of Life Science, Capital Normal University, 100048 Beijing, China.
| | - Caixia Han
- College of Life Science, Capital Normal University, 100048 Beijing, China.
| | - Xiong Deng
- College of Life Science, Capital Normal University, 100048 Beijing, China.
| | - Dongmiao Liu
- College of Life Science, Capital Normal University, 100048 Beijing, China.
| | - Nannan Liu
- College of Life Science, Capital Normal University, 100048 Beijing, China.
| | - Yueming Yan
- College of Life Science, Capital Normal University, 100048 Beijing, China; Hubei Collaborative Innovation Center for Grain Industry (HCICGI), Yangtze University, 434025 Jingzhou, China.
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Zhang L, Hu W, Gao Y, Pan H, Zhang Q. A cytosolic class II small heat shock protein, PfHSP17.2, confers resistance to heat, cold, and salt stresses in transgenic Arabidopsis. Genet Mol Biol 2018; 41:649-660. [PMID: 30235397 PMCID: PMC6136373 DOI: 10.1590/1678-4685-gmb-2017-0206] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 01/11/2018] [Indexed: 11/22/2022] Open
Abstract
We cloned and characterized the full-length coding sequence of a small heat shock (sHSP) gene, PfHSP17.2, from Primula forrestii leaves following heat stress treatment. Homology and phylogenetic analysis suggested that PfHSP17.2 is a cytosolic class II sHSP, which was further supported by the cytosolic localization of transient expression of PfHSP17.2 fused with green fluorescent protein reporter. Expression analysis showed that PfHSP17.2 was highly inducible by heat stress in almost all the vegetative and generative tissues and was expressed under salt, cold, and oxidative stress conditions as well. Moreover, the expression of PfHSP17.2 in P. forrestii was detected in certain developmental growth stages. Transgenic Arabidopsis thaliana constitutively expressing PfHSP17.2 displayed increased thermotolerance and higher resistance to salt and cold compared with wild type plants. It is suggested that PfHSP17.2 plays a key role in heat and other abiotic stresses.
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Affiliation(s)
- Lu Zhang
- Department of Landscape Architecture, School of Civil Engineering and Architecture, Zhejiang Sci-Tech University, Hangzhou, Zhejiang Province, China.,College of Landscape Architecture, Beijing Forestry University, China National Engineering Research Center for Floriculture, Beijing, China
| | - Weijuan Hu
- College of Landscape Architecture, Beijing Forestry University, China National Engineering Research Center for Floriculture, Beijing, China
| | - Yike Gao
- College of Landscape Architecture, Beijing Forestry University, China National Engineering Research Center for Floriculture, Beijing, China
| | - Huitang Pan
- College of Landscape Architecture, Beijing Forestry University, China National Engineering Research Center for Floriculture, Beijing, China
| | - Qixiang Zhang
- College of Landscape Architecture, Beijing Forestry University, China National Engineering Research Center for Floriculture, Beijing, China
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MEENA RK, PULLAIAHGARI D, GUDIPALLI P. Proteomic analysis of heterotic seed germination in maize using F1 hybrid DHM 117 and its parental inbreds. Turk J Biol 2018; 42:345-363. [PMID: 30814898 PMCID: PMC6392162 DOI: 10.3906/biy-1803-13] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
A number of differentially expressed proteins (DEPs) were identified in comparative two-dimensional gel electrophoresis analysis of dry and 24-h water-imbibed seeds of maize F1 hybrid DHM 117 (BML 6 × BML 7) and its parental inbreds. Of the DEPs, 53.4% (86/161) in dry seeds and 58% (127/219) in water-imbibed seeds exhibited a nonadditive pattern in the F1 hybrid as compared to parental inbreds. A total of 30 DEPs were categorized into different biological processes, most of which were related to metabolism and energy (34%), followed by storage proteins (27%), stress response (23%), transcription and translation (7%), cell cycle (3%), and hormone biosynthesis (3%). The transcript accumulation pattern of 8 selected genes corresponding to DEPs was examined using qRTPCR. Interestingly, LEA protein Rab28 showed higher accumulation in dry seeds at both protein and transcript levels, whereas indole3-acetaldehyde oxidase showed lower accumulation in water-imbibed seeds of the F1 hybrid than the female parent at the protein level. Thus, the DEPs particularly involved in metabolic and energy processes, as well as hormone biosynthesis in the F 1 hybrid, might be responsible for heterotic seed germination in the F1 hybrid. The DEPs identified in this study provide a scope for improving the seed germination trait of agricultural crops.
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Affiliation(s)
- Rajesh Kumar MEENA
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad
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Gachibowli, Hyderabad, Telangana
,
India
| | - Durgeshwar PULLAIAHGARI
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad
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Gachibowli, Hyderabad, Telangana
,
India
| | - Padmaja GUDIPALLI
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad
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Gachibowli, Hyderabad, Telangana
,
India
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