|
1
|
Ye T, Ma T, Chen Y, Liu C, Jiao Z, Wang X, Xue H. The role of redox-active small molecules and oxidative protein post-translational modifications in seed aging. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 213:108810. [PMID: 38857563 DOI: 10.1016/j.plaphy.2024.108810] [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: 02/21/2024] [Revised: 05/25/2024] [Accepted: 06/07/2024] [Indexed: 06/12/2024]
Abstract
Seed vigor is a crucial indicator of seed quality. Variations in seed vigor are closely associated with seed properties and storage conditions. The vigor of mature seeds progressively declines during storage, which is called seed deterioration or aging. Seed aging induces a cascade of cellular damage, including impaired subcellular structures and macromolecules, such as lipids, proteins, and DNA. Reactive oxygen species (ROS) act as signaling molecules during seed aging causing oxidative damage and triggering programmed cell death (PCD). Mitochondria are the main site of ROS production and change morphology and function before other organelles during aging. The roles of other small redox-active molecules in regulating cell and seed vigor, such as nitric oxide (NO) and hydrogen sulfide (H2S), were identified later. ROS, NO, and H2S typically regulate protein function through post-translational modifications (PTMs), including carbonylation, S-glutathionylation, S-nitrosylation, and S-sulfhydration. These signaling molecules as well as the PTMs they induce interact to regulate cell fate and seed vigor. This review was conducted to describe the physiological changes and underlying molecular mechanisms that in seed aging and provides a comprehensive view of how ROS, NO, and H2S affect cell death and seed vigor.
Collapse
Affiliation(s)
- Tiantian Ye
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Remediation, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China.
| | - Tianxiao Ma
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Remediation, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China.
| | - Yang Chen
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Remediation, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China.
| | - Chang Liu
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Remediation, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China.
| | - Zhiyuan Jiao
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Remediation, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China.
| | - Xiaofeng Wang
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Remediation, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China.
| | - Hua Xue
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Remediation, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China.
| |
Collapse
|
|
2
|
Li F, Ye H, Wang Y, Zhou J, Zhang G, Liu X, Lu X, Wang F, Chen Q, Chen G, Xiao Y, Tang W, Deng H. Transcriptomic Profiling of Two Rice Thermo-Sensitive Genic Male Sterile Lines with Contrasting Seed Storability after Artificial Accelerated Aging Treatment. PLANTS (BASEL, SWITZERLAND) 2024; 13:945. [PMID: 38611475 PMCID: PMC11013862 DOI: 10.3390/plants13070945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 03/21/2024] [Accepted: 03/22/2024] [Indexed: 04/14/2024]
Abstract
Seed storability has a significant impact on seed vitality and is a crucial genetic factor in maintaining seed value during storage. In this study, RNA sequencing was used to analyze the seed transcriptomes of two rice thermo-sensitive genic male sterile (TGMS) lines, S1146S (storage-tolerant) and SD26S (storage-susceptible), with 0 and 7 days of artificial accelerated aging treatment. In total, 2658 and 1523 differentially expressed genes (DEGs) were identified in S1146S and SD26S, respectively. Among these DEGs, 729 (G1) exhibited similar regulation patterns in both lines, while 1924 DEGs (G2) were specific to S1146S, 789 DEGs (G3) were specific to SD26S, and 5 DEGs (G4) were specific to contrary differential expression levels. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that "translation", "ribosome", "oxidative phosphorylation", "ATP-dependent activity", "intracellular protein transport", and "regulation of DNA-templated transcription" were significantly enriched during seed aging. Several genes, like Os01g0971400, Os01g0937200, Os03g0276500, Os05g0328632, and Os07g0214300, associated with seed storability were identified in G4. Core genes Os03g0100100 (OsPMEI12), Os03g0320900 (V2), Os02g0494000, Os02g0152800, and Os03g0710500 (OsBiP2) were identified in protein-protein interaction (PPI) networks. Seed vitality genes, MKKK62 (Os01g0699600), OsFbx352 (Os10g0127900), FSE6 (Os05g0540000), and RAmy3E (Os08g0473600), related to seed storability were identified. Overall, these results provide novel perspectives for studying the molecular response and related genes of different-storability rice TGMS lines under artificial aging conditions. They also provide new ideas for studying the storability of hybrid rice.
Collapse
Affiliation(s)
- Fan Li
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China; (F.L.); (H.Y.); (Y.W.); (J.Z.); (G.Z.); (X.L.); (X.L.); (F.W.); (Q.C.); (G.C.); (Y.X.)
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410128, China
| | - Hongbing Ye
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China; (F.L.); (H.Y.); (Y.W.); (J.Z.); (G.Z.); (X.L.); (X.L.); (F.W.); (Q.C.); (G.C.); (Y.X.)
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410128, China
| | - Yingfeng Wang
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China; (F.L.); (H.Y.); (Y.W.); (J.Z.); (G.Z.); (X.L.); (X.L.); (F.W.); (Q.C.); (G.C.); (Y.X.)
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410128, China
| | - Jieqiang Zhou
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China; (F.L.); (H.Y.); (Y.W.); (J.Z.); (G.Z.); (X.L.); (X.L.); (F.W.); (Q.C.); (G.C.); (Y.X.)
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410128, China
| | - Guilian Zhang
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China; (F.L.); (H.Y.); (Y.W.); (J.Z.); (G.Z.); (X.L.); (X.L.); (F.W.); (Q.C.); (G.C.); (Y.X.)
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410128, China
| | - Xiong Liu
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China; (F.L.); (H.Y.); (Y.W.); (J.Z.); (G.Z.); (X.L.); (X.L.); (F.W.); (Q.C.); (G.C.); (Y.X.)
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410128, China
| | - Xuedan Lu
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China; (F.L.); (H.Y.); (Y.W.); (J.Z.); (G.Z.); (X.L.); (X.L.); (F.W.); (Q.C.); (G.C.); (Y.X.)
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410128, China
| | - Feng Wang
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China; (F.L.); (H.Y.); (Y.W.); (J.Z.); (G.Z.); (X.L.); (X.L.); (F.W.); (Q.C.); (G.C.); (Y.X.)
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410128, China
| | - Qiuhong Chen
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China; (F.L.); (H.Y.); (Y.W.); (J.Z.); (G.Z.); (X.L.); (X.L.); (F.W.); (Q.C.); (G.C.); (Y.X.)
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410128, China
| | - Guihua Chen
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China; (F.L.); (H.Y.); (Y.W.); (J.Z.); (G.Z.); (X.L.); (X.L.); (F.W.); (Q.C.); (G.C.); (Y.X.)
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410128, China
| | - Yunhua Xiao
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China; (F.L.); (H.Y.); (Y.W.); (J.Z.); (G.Z.); (X.L.); (X.L.); (F.W.); (Q.C.); (G.C.); (Y.X.)
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410128, China
| | - Wenbang Tang
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China; (F.L.); (H.Y.); (Y.W.); (J.Z.); (G.Z.); (X.L.); (X.L.); (F.W.); (Q.C.); (G.C.); (Y.X.)
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410128, China
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha 410128, China
| | - Huabing Deng
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China; (F.L.); (H.Y.); (Y.W.); (J.Z.); (G.Z.); (X.L.); (X.L.); (F.W.); (Q.C.); (G.C.); (Y.X.)
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, Changsha 410128, China
| |
Collapse
|
|
3
|
Zhou BJ, Li J, Ma CL, Wang YJ, Zhang JL, Chen HH, Lao QX, Wu JD, Duan RM. Metabolomics analysis of the nutraceutical diversity and physiological quality of Torreya yunnanensis seeds during cold storage. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 206:108183. [PMID: 38016368 DOI: 10.1016/j.plaphy.2023.108183] [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: 04/11/2023] [Revised: 09/24/2023] [Accepted: 11/07/2023] [Indexed: 11/30/2023]
Abstract
This study investigated how cold storage affects the nutraceutical diversity and physiological quality of Torreya yunnanensis seeds, using a widely targeted UPLC-MS/MS-based metabolomics analysis. The 373 identified metabolites were divided into nine categories: lipids, phenolic acids, amino acids and derivatives, organic acids, nucleotides, saccharides, vitamins and alcohols. Among them, 49 metabolites showed significant changes after 3 months of cold storage, affecting 28 metabolic pathways. The content of amino acid-related metabolites significantly increased, while the content of sugar-related metabolites decreased during storage. Notably, the content of proline acid, shikimic acid, α-linolenic acid and branched-chain amino acids showed significant changes, indicating their potential role in seed storage. This study deepens our understanding of the nutraceutical diversity and physiological quality of T. yunnanensis seeds during storage, providing insight for conservation efforts and habitat restoration.
Collapse
Affiliation(s)
- Bing-Jiang Zhou
- Southwest Research Center for Engineering Technology of Landscape Architecture (State Forestry and Grassland Administration), College of Landscape Architecture and Horticulture Sciences, Southwest Forestry University, Kunming 650224, China; Experimental Center of Tropical Forestry, Chinese Academy of Forestry, Pingxiang 532600, China
| | - Jing Li
- School of Life Science, Southwest Forestry University, Kunming 650224, China
| | - Chang-Le Ma
- Southwest Research Center for Engineering Technology of Landscape Architecture (State Forestry and Grassland Administration), College of Landscape Architecture and Horticulture Sciences, Southwest Forestry University, Kunming 650224, China.
| | - Yu-Jie Wang
- School of Geography and Ecotourism, Southwest Forestry University, Kunming 650224, China
| | - Jin-Li Zhang
- Southwest Research Center for Engineering Technology of Landscape Architecture (State Forestry and Grassland Administration), College of Landscape Architecture and Horticulture Sciences, Southwest Forestry University, Kunming 650224, China
| | - Hong-Hui Chen
- Experimental Center of Tropical Forestry, Chinese Academy of Forestry, Pingxiang 532600, China
| | - Qing-Xiang Lao
- Experimental Center of Tropical Forestry, Chinese Academy of Forestry, Pingxiang 532600, China
| | - Jun-Duo Wu
- Experimental Center of Tropical Forestry, Chinese Academy of Forestry, Pingxiang 532600, China
| | - Run-Mei Duan
- Experimental Center of Tropical Forestry, Chinese Academy of Forestry, Pingxiang 532600, China
| |
Collapse
|
|
4
|
Yi K, Yue J, Yang S, Jiang Y, Hong L, Zeng H, Wei K, Mao P, Sun Y, Dou L, Li M. Germination of aged oat seeds associated with changes in antioxidant enzyme activity and storage compounds mobilization. PHYSIOLOGIA PLANTARUM 2023; 175:e14020. [PMID: 37882312 DOI: 10.1111/ppl.14020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 08/26/2023] [Accepted: 08/29/2023] [Indexed: 10/27/2023]
Abstract
Germination of aged seeds may be associated with specific metabolic changes. The objective of this study was to examine physiological and metabolic alterations before and after germination of control and aged oat (Avena sativa) seeds. The activity of antioxidant enzymes and the level of storage compounds were measured in the embryo and endosperm at 0, 4, 16, and 32 h of imbibition for control seeds and 0, 4, 16, 32, and 60 h of imbibition for medium vigor seeds after artificially accelerated aging; metabolomic changes were determined in embryos at 16 and 32 h of seed imbibition. In aged oat seeds, superoxide dismutase activity and catalase activity increased in the late imbibition stage. The content of soluble sugars decreased significantly in the later stages of imbibition, while the content of proteins increased in 32 h of seed imbibition eventually producing mannitol and proline. The mobilization of fat in deteriorated seeds was mainly through the sphingolipid metabolic pathway generated by cell growth-promoting dihydrosphingosine-1-phosphate. Ascorbic acid, avenanthramide and proline levels increased significantly at 60 h of imbibition, playing an important role in the germination of aged oat seeds.
Collapse
Affiliation(s)
- Kun Yi
- Forage Seed Laboratory, College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Jiaming Yue
- Forage Seed Laboratory, College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Shuangfeng Yang
- Forage Seed Laboratory, College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Yiwei Jiang
- Department of Agronomy, Purdue University, West Lafayette, Indiana, USA
| | - Liu Hong
- Forage Seed Laboratory, College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Hanguo Zeng
- Forage Seed Laboratory, College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Kai Wei
- Forage Seed Laboratory, College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Peisheng Mao
- Forage Seed Laboratory, College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Yan Sun
- Forage Seed Laboratory, College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Liru Dou
- Forage Seed Laboratory, College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Manli Li
- Forage Seed Laboratory, College of Grassland Science and Technology, China Agricultural University, Beijing, China
| |
Collapse
|
|
5
|
Pagano A, Macovei A, Balestrazzi A. Molecular dynamics of seed priming at the crossroads between basic and applied research. PLANT CELL REPORTS 2023; 42:657-688. [PMID: 36780009 PMCID: PMC9924218 DOI: 10.1007/s00299-023-02988-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
The potential of seed priming is still not fully exploited. Our limited knowledge of the molecular dynamics of seed pre-germinative metabolism is the main hindrance to more effective new-generation techniques. Climate change and other recent global crises are disrupting food security. To cope with the current demand for increased food, feed, and biofuel production, while preserving sustainability, continuous technological innovation should be provided to the agri-food sector. Seed priming, a pre-sowing technique used to increase seed vigor, has become a valuable tool due to its potential to enhance germination and stress resilience under changing environments. Successful priming protocols result from the ability to properly act on the seed pre-germinative metabolism and stimulate events that are crucial for seed quality. However, the technique still requires constant optimization, and researchers are committed to addressing some key open questions to overcome such drawbacks. In this review, an update of the current scientific and technical knowledge related to seed priming is provided. The rehydration-dehydration cycle associated with priming treatments can be described in terms of metabolic pathways that are triggered, modulated, or turned off, depending on the seed physiological stage. Understanding the ways seed priming affects, either positively or negatively, such metabolic pathways and impacts gene expression and protein/metabolite accumulation/depletion represents an essential step toward the identification of novel seed quality hallmarks. The need to expand the basic knowledge on the molecular mechanisms ruling the seed response to priming is underlined along with the strong potential of applied research on primed seeds as a source of seed quality hallmarks. This route will hasten the implementation of seed priming techniques needed to support sustainable agriculture systems.
Collapse
Affiliation(s)
- Andrea Pagano
- Department of Biology and Biotechnology 'L. Spallanzani', Via Ferrata 1, 27100, Pavia, Italy
| | - Anca Macovei
- Department of Biology and Biotechnology 'L. Spallanzani', Via Ferrata 1, 27100, Pavia, Italy
- National Biodiversity Future Center (NBFC), 90133, Palermo, Italy
| | - Alma Balestrazzi
- Department of Biology and Biotechnology 'L. Spallanzani', Via Ferrata 1, 27100, Pavia, Italy.
- National Biodiversity Future Center (NBFC), 90133, Palermo, Italy.
| |
Collapse
|
|
6
|
Sanyal R, Kumar S, Pattanayak A, Kar A, Bishi SK. Optimizing raffinose family oligosaccharides content in plants: A tightrope walk. FRONTIERS IN PLANT SCIENCE 2023; 14:1134754. [PMID: 37056499 PMCID: PMC10088399 DOI: 10.3389/fpls.2023.1134754] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 03/08/2023] [Indexed: 06/19/2023]
Abstract
Plants synthesize various compounds for their growth, metabolism, and stress mitigation, and one such group of compounds is the raffinose family of oligosaccharides (RFOs). RFOs are non-reducing oligosaccharides having galactose residues attached to a sucrose moiety. They act as carbohydrate reserves in plants, assisting in seed germination, desiccation tolerance, and biotic/abiotic stress tolerance. Although legumes are among the richest sources of dietary proteins, the direct consumption of legumes is hindered by an excess of RFOs in the edible parts of the plant, which causes flatulence in humans and monogastric animals. These opposing characteristics make RFOs manipulation a complicated tradeoff. An in-depth knowledge of the chemical composition, distribution pattern, tissue mobilization, and metabolism is required to optimize the levels of RFOs. The most recent developments in our understanding of RFOs distribution, physiological function, genetic regulation of their biosynthesis, transport, and degradation in food crops have been covered in this review. Additionally, we have suggested a few strategies that can sustainably reduce RFOs in order to solve the flatulence issue in animals. The comprehensive information in this review can be a tool for researchers to precisely control the level of RFOs in crops and create low antinutrient, nutritious food with wider consumer acceptability.
Collapse
Affiliation(s)
- Rajarshi Sanyal
- School of Genomics and Molecular Breeding, ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, Jharkhand, India
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi, India
| | - Sandeep Kumar
- Automation & Plant Engineering Division, ICAR-National Institute of Secondary Agriculture, Ranchi, Jharkhand, India
| | - Arunava Pattanayak
- School of Genomics and Molecular Breeding, ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, Jharkhand, India
| | - Abhijit Kar
- Automation & Plant Engineering Division, ICAR-National Institute of Secondary Agriculture, Ranchi, Jharkhand, India
| | - Sujit K. Bishi
- School of Genomics and Molecular Breeding, ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, Jharkhand, India
| |
Collapse
|
|
7
|
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.
Collapse
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
| |
Collapse
|
|
8
|
Zhang G, Xu J, Wang Y, Sun X, Huang S, Huang L, Liu Y, Liu H, Sun J. Combined transcriptome and metabolome analyses reveal the mechanisms of ultrasonication improvement of brown rice germination. ULTRASONICS SONOCHEMISTRY 2022; 91:106239. [PMID: 36435087 PMCID: PMC9694063 DOI: 10.1016/j.ultsonch.2022.106239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/12/2022] [Accepted: 11/22/2022] [Indexed: 06/16/2023]
Abstract
This study investigated the effects of ultrasonication treatment on the germination rate of brown rice. Brown rice grains were subjected to ultrasound (40 kHz/30 min) and then incubated for 36 h at 37 °C to germinate the seeds. Ultrasonic treatment increased the germination rate of brown rice by up to ∼28 % at 30 h. Transcriptomic and metabolomic analyses were performed to explore the mechanisms underlying the effect of ultrasonic treatment on the brown rice germination rate. Comparing the treated and control check samples, 867 differentially expressed genes (DEGs) were identified, including 638 upregulated and 229 downregulated), as well as 498 differentially accumulated metabolites (DAMs), including 422 up accumulated and 76 down accumulated. Multi-omics analysis revealed that the germination rate of brown rice was promoted by increased concentrations of low-molecular metabolites (carbohydrates and carbohydrate conjugates, fatty acids, amino acids, peptides, and analogues), and transcription factors (ARR-B, NAC, bHLH and AP2/EREBP families) as well as increased carbon metabolism. These findings provide new insights into the mechanisms of action of ultrasound in improving the brown rice germination rate and candidate DEGs and DAMs responsible for germination have been identified.
Collapse
Affiliation(s)
- Guangchen Zhang
- College of Food Science and Technology, Bohai University, Jinzhou, Liaoning, China
| | - Jiaxin Xu
- College of Food Science and Technology, Bohai University, Jinzhou, Liaoning, China
| | - Yiqiao Wang
- Rice Research Institute, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Xue Sun
- College of Food Science and Technology, Bohai University, Jinzhou, Liaoning, China
| | - Shaosong Huang
- Rice Research Institute, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Lihua Huang
- College of Food Science and Technology, Bohai University, Jinzhou, Liaoning, China
| | - Youhong Liu
- Institute of Crop Cultivation and Tillage, Heilongjiang Academy of Agricultural Sciences/Northeast Branch of National Center of Technology Innovation for Saline-Alkali Tolerant Rice, Harbin, China
| | - He Liu
- College of Food Science and Technology, Bohai University, Jinzhou, Liaoning, China.
| | - Jian Sun
- Rice Research Institute, Shenyang Agricultural University, Shenyang, Liaoning, China; Collaborative Innovation Center for Genetic Improvement and High Quality and Efficiency Production of Northeast Japonica Rice in China, Shenyang Agricultural University, Shenyang, Liaoning, China.
| |
Collapse
|
|
9
|
Zhang Y, Fan F, Zhang Q, Luo Y, Liu Q, Gao J, Liu J, Chen G, Zhang H. Identification and Functional Analysis of Long Non-Coding RNA (lncRNA) in Response to Seed Aging in Rice. PLANTS (BASEL, SWITZERLAND) 2022; 11:3223. [PMID: 36501265 PMCID: PMC9737669 DOI: 10.3390/plants11233223] [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: 09/15/2022] [Revised: 11/11/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
Many lncRNAs have been shown to play a vital role in aging processes. However, how lncRNAs regulate seed aging remains unknown. In this study, we performed whole transcriptome strand-specific RNA sequencing of samples from rice embryos, analyzed the differences in expression of rice seed lncRNAs before and after artificial aging treatment (AAT), and systematically screened 6002 rice lncRNAs. During the AAT period, the expression levels of most lncRNAs (454) were downregulated and only four were upregulated among the 458 differentially expressed lncRNAs (DELs). Cis- or trans-regulated target genes of the four upregulated lncRNAs were mainly related to base repair, while 454 downregulated lncRNAs were related to plant-pathogen interaction, plant hormones, energy metabolism, and secondary metabolism. The pathways of DEL target genes were similar with those of differentially expressed mRNAs (DEGs). A competing endogenous RNA (ceRNA) network composed of 34 lncRNAs, 24 microRNAs (miRNA), and 161 mRNAs was obtained. The cDNA sequence of lncRNA LNC_037529 was obtained by rapid amplification of cDNA ends (RACE) cloning with a total length of 1325 bp, a conserved 5' end, and a non-conserved 3' end. Together, our findings indicate that genome-wide selection for lncRNA downregulation was an important mechanism for rice seed aging. LncRNAs can be used as markers of seed aging in rice. These findings provide a future path to decipher the underlying mechanism associated with lncRNAs in seed aging.
Collapse
Affiliation(s)
- Yixin Zhang
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Fan Fan
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Qunjie Zhang
- Guangdong Key Lab for Crop Germplasm Resources Preservation and Utilization/Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Yongjian Luo
- Guangdong Key Lab for Crop Germplasm Resources Preservation and Utilization/Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Qinjian Liu
- Guangdong Key Lab for Crop Germplasm Resources Preservation and Utilization/Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Jiadong Gao
- Guangdong Key Lab for Crop Germplasm Resources Preservation and Utilization/Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Jun Liu
- Guangdong Key Lab for Crop Germplasm Resources Preservation and Utilization/Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Guanghui Chen
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Haiqing Zhang
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| |
Collapse
|
|
10
|
Deterioration in the Quality of Recalcitrant Quercus robur Seeds during Six Months of Storage at Subzero Temperatures: Ineffective Activation of Prosurvival Mechanisms and Evidence of Freezing Stress from an Untargeted Metabolomic Study. Metabolites 2022; 12:metabo12080756. [PMID: 36005628 PMCID: PMC9413681 DOI: 10.3390/metabo12080756] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/09/2022] [Accepted: 08/15/2022] [Indexed: 11/25/2022] Open
Abstract
Pedunculate oak (Quercus robur L.) is an economically important forest-forming species in Poland that produces seeds that are sensitive to desiccation; therefore, short-lived seeds are classified as recalcitrant. Such seeds display active metabolism throughout storage. Acorns stored under controlled conditions (moisture content of 40%, temperature −3 °C) maintain viability for up to 1.5–2 years. Meanwhile, oaks only produce large numbers of seeds every few years during so-called mast years. This results in a scarcity of good-quality seeds for continuous nursery production and restoration. The recalcitrant storage behavior and the requirements of foresters make it necessary to develop a new protocol for longer acorn storage at lower temperatures. Two storage temperatures were tested: −3 °C (currently used in forest practice) and −7 °C. Our results showed that acorns stored for six months exhibited deterioration and reduced germination capacity, as well as reduced seedling performance, particularly when acorns were stored at −7 °C. To elucidate the decrease in quality during storage, an untargeted metabolomics study was performed for the first time and supported with the analysis of carbohydrates and percentages of carbon (C) and nitrogen (N). Embryonic axes were characterized by a lower C:N ratio and higher hydration. A total of 1985 metabolites were detected, and 303 were successfully identified and quantified, revealing 44 known metabolites that displayed significantly up- or downregulated abundance. We demonstrated for the first time that the significant deterioration of seed germination potential, particularly in seeds stored at −7 °C, was accompanied by an increased abundance of phenolic compounds and carbohydrates but also amino acids and phosphorylated monosaccharides, particularly in the embryonic axes. The increased abundance of defense-related metabolites (1,2,4-Benzenetriol; BTO), products of ascorbic acid degradation (threonic and isothreonic acid), as well as antifreezing compounds (sugar alcohols, predominantly threitol), was reported in seed stored at −7 °C. We hypothesize that seed deterioration was caused by freezing stress experienced during six months of storage at −7 °C, a decline in antioxidative potential and the unsuccessful rerouting of the energy-production pathways. Additionally, our data are a good example of the application of high-throughput metabolomic tools in forest management.
Collapse
|
|
11
|
Zhou S, Huang K, Zhou Y, Hu Y, Xiao Y, Chen T, Yin M, Liu Y, Xu M, Jiang X. Degradome sequencing reveals an integrative miRNA-mediated gene interaction network regulating rice seed vigor. BMC PLANT BIOLOGY 2022; 22:269. [PMID: 35650544 PMCID: PMC9158300 DOI: 10.1186/s12870-022-03645-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 05/11/2022] [Indexed: 05/14/2023]
Abstract
BACKGROUND It is well known that seed vigor is essential for agricultural production and rice (Oryza sativa L.) is one of the most important crops in the world. Though we previously reported that miR164c regulates rice seed vigor, but whether and how other miRNAs cooperate with miR164c to regulate seed vigor is still unknown. RESULTS Based on degradome data of six RNA samples isolated from seeds of the wild-type (WT) indica rice cultivar 'Kasalath' as well as two modified lines in 'Kasalath' background (miR164c-silenced line [MIM164c] and miR164c overexpression line [OE164c]), which were subjected to either no aging treatment or an 8-day artificial aging treatment, 1247 different target transcripts potentially cleaved by 421 miRNAs were identified. The miRNA target genes were functionally annotated via GO and KEGG enrichment analyses. By STRING database assay, a miRNA-mediated gene interaction network regulating seed vigor in rice was revealed, which comprised at least four interconnected pathways: the miR5075-mediated oxidoreductase related pathway, the plant hormone related pathway, the miR164e related pathway, and the previously reported RPS27AA related pathway. Knockout and overexpression of the target gene Os02g0817500 of miR5075 decreased and enhanced seed vigor, respectively. By Y2H assay, the proteins encoded by five seed vigor-related genes, Os08g0295100, Os07g0633100, REFA1, OsPER1 and OsGAPC3, were identified to interact with Os02g0817500. CONCLUSIONS miRNAs cooperate to regulate seed vigor in rice via an integrative gene interaction network comprising miRNA target genes and other functional genes. The result provided a basis for fully understanding the molecular mechanisms of seed vigor regulation.
Collapse
Affiliation(s)
- Shiqi Zhou
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Kerui Huang
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, Changsha, 410081, China
- College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde, 415000, China
| | - Yan Zhou
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Yingqian Hu
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Yuchao Xiao
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Ting Chen
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Mengqi Yin
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Yan Liu
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Mengliang Xu
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, Changsha, 410081, China
| | - Xiaocheng Jiang
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China.
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, Changsha, 410081, China.
| |
Collapse
|
|
12
|
Kim DS, Kim QW, Kim H, Kim HJ. Changes in the chemical, physical, and sensory properties of rice according to its germination rate. Food Chem 2022; 388:133060. [PMID: 35483295 DOI: 10.1016/j.foodchem.2022.133060] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 03/08/2022] [Accepted: 04/21/2022] [Indexed: 01/04/2023]
Abstract
This study aimed to decipher the association among the physicochemical properties, sensory quality, and germination rate of rice samples stored at different storage conditions and for different durations (stored at 10, 20, and 30 °C for 8 months). The germination rate of the samples varied from 0.3 to 98.7%. A reduced germination rate increased the lipid oxidation, hardness, and most pasting properties of rice, whereas seed viability, moisture content, and adhesiveness were reduced. Amylose and protein contents were not influenced by the changes in germination rate. However, with a decrease in germination rate, the surface endosperm cells were aggregated, whereas the sizes of inner endosperm cells in cooked rice were reduced. Several metabolites involved in rice sensory quality were also altered, and a related pathway was proposed. Collectively, these results suggest that germination rate could serve as a potential indicator to track the changes in rice quality.
Collapse
Affiliation(s)
- Dong-Shin Kim
- Institute of Animal Medicine, Gyeongsang National University, 501 Jinjudaero, Jinju, Gyeongsang, Republic of Korea
| | - Qui Woung Kim
- Korea Food Research Institute, Research Group of Consumer Safety, 245 Nongsaengmyeong-ro, Iseo-myeon, Wanju-Gun, Jeollabuk-do 55365, Republic of Korea
| | - Hoon Kim
- Korea Food Research Institute, Research Group of Consumer Safety, 245 Nongsaengmyeong-ro, Iseo-myeon, Wanju-Gun, Jeollabuk-do 55365, Republic of Korea.
| | - Hyun-Jin Kim
- Institute of Animal Medicine, Gyeongsang National University, 501 Jinjudaero, Jinju, Gyeongsang, Republic of Korea; Division of Applied Life Sciences (BK21 Four), Department of Food Science & Technology, and Institute of Agriculture and Life Science, Gyeongsang National University, 501 Jinjudaero, Jinju, Gyeongsang, Republic of Korea.
| |
Collapse
|