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Wang AB, Baskin CC, Baskin JM, Ding J. Environmental and seed-position effects on viability and germination of buried seeds of an invasive diaspore-heteromorphic annual grass. PHYSIOLOGIA PLANTARUM 2024; 176:e14353. [PMID: 38801018 DOI: 10.1111/ppl.14353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 05/02/2024] [Accepted: 05/06/2024] [Indexed: 05/29/2024]
Abstract
Environmental factors, such as temperature and moisture, and plant factors, such as seed position on the mother plant, can affect seed viability and germination. However, little is known about the viability and germination of seeds in different positions on the mother plant after burial in soil under natural environmental conditions. Here, diaspores from three positions on a compound spike and seeds from two/three positions in a diaspore of the invasive diaspore-heteromorphic annual grass Aegilops tauschii were buried at four depths for more than 2 years (1-26 months) under natural conditions and viability and germination monitored monthly. Viability of seeds in each diaspore/seed position decreased as burial depth and duration increased and was associated with changes in soil temperature and moisture. Germination was highest at 2 cm and lowest at 10 cm soil depths, with peaks and valleys in autumn/spring and winter/summer, respectively. Overall, seeds in distal diaspore and distal seed positions had higher germination percentages than those in basal diaspore and basal seed positions, but basal ones lived longer than distal ones. Chemical content of fresh diaspores/seeds was related to diaspore/seed position effects on seed germination and viability during burial. We conclude that seeds in distal diaspores/seed positions have a 'high risk' strategy and those in basal positions a 'low risk' strategy. The two risk strategies may act as a bet-hedging strategy that spreads risks of germination failure in the soil seed bank over time, thereby facilitating the survival and invasiveness of A. tauschii.
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Affiliation(s)
- Ai Bo Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Carol C Baskin
- Department of Biology, University of Kentucky, Lexington, KY, USA
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, USA
| | - Jerry M Baskin
- Department of Biology, University of Kentucky, Lexington, KY, USA
| | - Jianqing Ding
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
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2
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Liu C, He S, Chen J, Wang M, Li Z, Wei L, Chen Y, Du M, Liu D, Li C, An C, Bhadauria V, Lai J, Zhu W. A dual-subcellular localized β-glucosidase confers pathogen and insect resistance without a yield penalty in maize. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1017-1032. [PMID: 38012865 PMCID: PMC10955503 DOI: 10.1111/pbi.14242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/23/2023] [Accepted: 11/11/2023] [Indexed: 11/29/2023]
Abstract
Maize is one of the most important crops for food, cattle feed and energy production. However, maize is frequently attacked by various pathogens and pests, which pose a significant threat to maize yield and quality. Identification of quantitative trait loci and genes for resistance to pests will provide the basis for resistance breeding in maize. Here, a β-glucosidase ZmBGLU17 was identified as a resistance gene against Pythium aphanidermatum, one of the causal agents of corn stalk rot, by genome-wide association analysis. Genetic analysis showed that both structural variations at the promoter and a single nucleotide polymorphism at the fifth intron distinguish the two ZmBGLU17 alleles. The causative polymorphism near the GT-AG splice site activates cryptic alternative splicing and intron retention of ZmBGLU17 mRNA, leading to the downregulation of functional ZmBGLU17 transcripts. ZmBGLU17 localizes in both the extracellular matrix and vacuole and contribute to the accumulation of two defence metabolites lignin and DIMBOA. Silencing of ZmBGLU17 reduces maize resistance against P. aphanidermatum, while overexpression significantly enhances resistance of maize against both the oomycete pathogen P. aphanidermatum and the Asian corn borer Ostrinia furnacalis. Notably, ZmBGLU17 overexpression lines exhibited normal growth and yield phenotype in the field. Taken together, our findings reveal that the apoplastic and vacuolar localized ZmBGLU17 confers resistance to both pathogens and insect pests in maize without a yield penalty, by fine-tuning the accumulation of lignin and DIMBOA.
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Affiliation(s)
- Chuang Liu
- China Key Laboratory of Pest Monitoring and Green Management, MOA, and College of Plant ProtectionChina Agricultural UniversityBeijingChina
| | - Shengfeng He
- China Key Laboratory of Pest Monitoring and Green Management, MOA, and College of Plant ProtectionChina Agricultural UniversityBeijingChina
| | - Junbin Chen
- China Key Laboratory of Pest Monitoring and Green Management, MOA, and College of Plant ProtectionChina Agricultural UniversityBeijingChina
| | - Mingyu Wang
- China Key Laboratory of Pest Monitoring and Green Management, MOA, and College of Plant ProtectionChina Agricultural UniversityBeijingChina
| | - Zhenju Li
- China Key Laboratory of Pest Monitoring and Green Management, MOA, and College of Plant ProtectionChina Agricultural UniversityBeijingChina
| | - Luyang Wei
- China Key Laboratory of Pest Monitoring and Green Management, MOA, and College of Plant ProtectionChina Agricultural UniversityBeijingChina
| | - Yan Chen
- China Key Laboratory of Pest Monitoring and Green Management, MOA, and College of Plant ProtectionChina Agricultural UniversityBeijingChina
| | - Meida Du
- China Key Laboratory of Pest Monitoring and Green Management, MOA, and College of Plant ProtectionChina Agricultural UniversityBeijingChina
| | - Dandan Liu
- China Key Laboratory of Pest Monitoring and Green Management, MOA, and College of Plant ProtectionChina Agricultural UniversityBeijingChina
| | - Cai Li
- China Key Laboratory of Pest Monitoring and Green Management, MOA, and College of Plant ProtectionChina Agricultural UniversityBeijingChina
| | - Chunju An
- China Key Laboratory of Pest Monitoring and Green Management, MOA, and College of Plant ProtectionChina Agricultural UniversityBeijingChina
- State Key Laboratory of Maize Bio‐breedingChina Agricultural UniversityBeijingChina
| | - Vijai Bhadauria
- China Key Laboratory of Pest Monitoring and Green Management, MOA, and College of Plant ProtectionChina Agricultural UniversityBeijingChina
| | - Jinsheng Lai
- State Key Laboratory of Maize Bio‐breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
| | - Wangsheng Zhu
- China Key Laboratory of Pest Monitoring and Green Management, MOA, and College of Plant ProtectionChina Agricultural UniversityBeijingChina
- State Key Laboratory of Maize Bio‐breedingChina Agricultural UniversityBeijingChina
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Liu T, Liu X, He J, Dong K, Zhang L, Li Y, Ren R, Yang T. Comparative transcriptome analysis and genetic dissection of vegetative branching traits in foxtail millet (Setaria italica). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:39. [PMID: 38294546 DOI: 10.1007/s00122-023-04524-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 12/11/2023] [Indexed: 02/01/2024]
Abstract
KEY MESSAGE Two major genetic loci, qTN5.1 and qAB9.1, were identified and finely mapped to the 255 Kb region with one potential candidate gene for tiller number and the 521 Kb region with eight candidate genes for axillary branch number, respectively. Vegetative branching including tillering and axillary branching are vital traits affecting both the plant architecture and the biomass in cereal crops. However, the mechanism underlying the formation of vegetative branching in foxtail millet is largely unknown. Here, a foxtail millet cultivar and its bushy wild relative Setaria viridis accession were used to construct segregating populations to identify candidate genes regulating tiller number and axillary branch number. Transcriptome analysis using vegetative branching bud samples of parental accessions was performed, and key differentially expressed genes and pathways regulating vegetative branching were pointed out. Bulk segregant analysis on their F2:3 segregating population was carried out, and a major QTL for tiller number (qTN5.1) and two major QTLs for axillary branch number (qAB2.1 and qAB9.1) were detected. Fine-mapping strategy was further performed on F2:4 segregate population, and Seita.5G356600 encoding β-glucosidase 11 was identified as the promising candidate gene for qTN5.1, and eight genes, especially Seita.9G125300 and Seita.9G125400 annotated as B-S glucosidase 44, were finally identified as candidate genes for regulating axillary branching. Findings in this study will help to elucidate the genetic basis of the vegetative branching formation of foxtail millet and lay a foundation for breeding foxtail millet varieties with ideal vegetative branching numbers.
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Affiliation(s)
- Tianpeng Liu
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, China
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Xueying Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Jihong He
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, China
| | - Kongjun Dong
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, China
| | - Lei Zhang
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, China
| | - Yawei Li
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, China
| | - Ruiyu Ren
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, China
| | - Tianyu Yang
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, China.
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Rates ADB, Cesarino I. Pour some sugar on me: The diverse functions of phenylpropanoid glycosylation. JOURNAL OF PLANT PHYSIOLOGY 2023; 291:154138. [PMID: 38006622 DOI: 10.1016/j.jplph.2023.154138] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 11/06/2023] [Indexed: 11/27/2023]
Abstract
The phenylpropanoid metabolism is the source of a vast array of specialized metabolites that play diverse functions in plant growth and development and contribute to all aspects of plant interactions with their surrounding environment. These compounds protect plants from damaging ultraviolet radiation and reactive oxygen species, provide mechanical support for the plants to stand upright, and mediate plant-plant and plant-microorganism communications. The enormous metabolic diversity of phenylpropanoids is further expanded by chemical modifications known as "decorative reactions", including hydroxylation, methylation, glycosylation, and acylation. Among these modifications, glycosylation is the major driving force of phenylpropanoid structural diversification, also contributing to the expansion of their properties. Phenylpropanoid glycosylation is catalyzed by regioselective uridine diphosphate (UDP)-dependent glycosyltransferases (UGTs), whereas glycosyl hydrolases known as β-glucosidases are the major players in deglycosylation. In this article, we review how the glycosylation process affects key physicochemical properties of phenylpropanoids, such as molecular stability and solubility, as well as metabolite compartmentalization/storage and biological activity/toxicity. We also summarize the recent knowledge on the functional implications of glycosylation of different classes of phenylpropanoid compounds. A balance of glycosylation/deglycosylation might represent an essential molecular mechanism to regulate phenylpropanoid homeostasis, allowing plants to dynamically respond to diverse environmental signals.
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Affiliation(s)
- Arthur de Barros Rates
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, 05508-090, São Paulo, Brazil
| | - Igor Cesarino
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, 05508-090, São Paulo, Brazil; Synthetic and Systems Biology Center, InovaUSP, Avenida Professor Lucio Martins Rodrigues 370, 05508-020, São Paulo, Brazil.
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Li S, Li Q, Cao J, Qu G, Jiang W. Comparative transcriptomic analysis provides novel insights into the difference in textural alteration between mealy and crisp apple patterns. Food Res Int 2023; 169:112941. [PMID: 37254365 DOI: 10.1016/j.foodres.2023.112941] [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: 03/09/2023] [Revised: 04/28/2023] [Accepted: 05/02/2023] [Indexed: 06/01/2023]
Abstract
Mealiness is a common textural deterioration of several fruit after harvest. To unravel the underlying mechanism involved in mealiness, biochemical characterization and global transcriptomic profiling were comparatively performed between mealy 'Hongjiangjun' (HJJ) and crisp 'Fuji' apples. Sensory evaluation and SEM-based microstructure observation showed that HJJ apples appeared to be mealy in only 3 d at 23 ± 1 °C, while Fuji apples did not appear to be mealy even after 28 d of storage. Textural deterioration and ethylene burst occurred more sharply in HJJ apples than in Fuji apples during storage. The results obtained from the dimensional RNA-sequencing analysis showed that a much stronger upregulation of the transcription of genes encoding polygalacturonase (PG), pectin acetylesterase (PAE), pectinesterase (PE), β-galactosidase (GAL), α-l-arabinofuranase (AF), and expansin (EXP) was observed in the pair of mealy HJJ apples vs. harvest than in the pair of Fuji apples after 28 d vs. harvest. The gene expression of ethylene responsive factor (ERF) was found to be strongly upregulated in HJJ apples compared with Fuji apples, which may mediate the regulation of downstream genes encoding cell wall-modifying enzymes. Weighted gene co-expression network analysis showed that the transcription factors MdbHLH63 and MdERF-like, and a constructure gene of MdGAL had strong connectivity with mealiness. Validation by qRT-PCR further confirmed the main findings obtained by RNA-sequencing. The occurrence of apple mealiness involves altered expression patterns of cell wall-modifying enzymes as well as MdbHLH63 and MdERF-like, which are core genes regulating the mealiness process. The above findings provide global insight into the difference in textural alteration between mealy and crisp apple patterns.
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Affiliation(s)
- Shihao Li
- College of Food Science and Nutritional Engineering, China Agricultural University, 17, Qinghuadonglu Road, Beijing 100083, PR China
| | - Qianqian Li
- College of Food Science and Nutritional Engineering, China Agricultural University, 17, Qinghuadonglu Road, Beijing 100083, PR China; Institute of Quality Standard and Testing Technology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, PR China
| | - Jiankang Cao
- College of Food Science and Nutritional Engineering, China Agricultural University, 17, Qinghuadonglu Road, Beijing 100083, PR China.
| | - Guiqin Qu
- College of Food Science and Nutritional Engineering, China Agricultural University, 17, Qinghuadonglu Road, Beijing 100083, PR China
| | - Weibo Jiang
- College of Food Science and Nutritional Engineering, China Agricultural University, 17, Qinghuadonglu Road, Beijing 100083, PR China
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Miao W, Yang Y, Wu M, Huang G, Ge L, Liu Y, Guan Z, Chen S, Fang W, Chen F, Zhao S. Potential pathways and genes expressed in Chrysanthemum in response to early fusarium oxysporum infection. BMC PLANT BIOLOGY 2023; 23:312. [PMID: 37308810 DOI: 10.1186/s12870-023-04331-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 06/05/2023] [Indexed: 06/14/2023]
Abstract
BACKGROUND Chrysanthemum Fusarium wilt is a common fungal disease caused by Fusarium oxysporum, which causes continuous cropping obstacles and huge losses to the chrysanthemum industry. The defense mechanism of chrysanthemum against F. oxysporum remains unclear, especially during the early stages of the disease. Therefore, in the present study, we analyzed chrysanthemum 'Jinba' samples inoculated with F. oxysporum at 0, 3, and 72 h using RNA-seq. RESULTS The results revealed that 7985 differentially expressed genes (DEGs) were co-expressed at 3 and 72 h after F. oxysporum infection. We analyzed the identified DEGs using Kyoto Encyclopedia of Genes and Genomes and Gene Ontology. The DEGs were primarily enriched in "Plant pathogen interaction", "MAPK signaling pathway", "Starch and sucrose metabolism", and "Biosynthesis of secondary metabolites". Genes related to the synthesis of secondary metabolites were upregulated in chrysanthemum early during the inoculation period. Furthermore, peroxidase, polyphenol oxidase, and phenylalanine ammonia-lyase enzymes were consistently produced to accumulate large amounts of phenolic compounds to resist F. oxysporum infection. Additionally, genes related to the proline metabolic pathway were upregulated, and proline levels accumulated within 72 h, regulating osmotic balance in chrysanthemum. Notably, the soluble sugar content in chrysanthemum decreased early during the inoculation period; we speculate that this is a self-protective mechanism of chrysanthemums for inhibiting fungal reproduction by reducing the sugar content in vivo. In the meantime, we screened for transcription factors that respond to F. oxysporum at an early stage and analyzed the relationship between WRKY and DEGs in the "Plant-pathogen interaction" pathway. We screened a key WRKY as a research target for subsequent experiments. CONCLUSION This study revealed the relevant physiological responses and gene expression changes in chrysanthemum in response to F. oxysporum infection, and provided a relevant candidate gene pool for subsequent studies on chrysanthemum Fusarium wilt.
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Affiliation(s)
- Weihao Miao
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Key laboratory of landscaping, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, 210014, Jiangsu, PR China
| | - Yanrong Yang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Key laboratory of landscaping, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, 210014, Jiangsu, PR China
| | - Mengtong Wu
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Key laboratory of landscaping, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, 210014, Jiangsu, PR China
| | - Gan Huang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Key laboratory of landscaping, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, 210014, Jiangsu, PR China
| | - Lijiao Ge
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Key laboratory of landscaping, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, 210014, Jiangsu, PR China
| | - Ye Liu
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Key laboratory of landscaping, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, 210014, Jiangsu, PR China
| | - Zhiyong Guan
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Key laboratory of landscaping, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, 210014, Jiangsu, PR China
| | - Sumei Chen
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Key laboratory of landscaping, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, 210014, Jiangsu, PR China
| | - Weimin Fang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Key laboratory of landscaping, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, 210014, Jiangsu, PR China
| | - Fadi Chen
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Key laboratory of landscaping, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, 210014, Jiangsu, PR China
| | - Shuang Zhao
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
- Key laboratory of landscaping, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China.
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, 210014, Jiangsu, PR China.
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Toyooka K, Goto Y, Hashimoto K, Wakazaki M, Sato M, Hirai MY. Endoplasmic Reticulum Bodies in the Lateral Root Cap Are Involved in the Direct Transport of Beta-Glucosidase to Vacuoles. PLANT & CELL PHYSIOLOGY 2023; 64:461-473. [PMID: 36617247 DOI: 10.1093/pcp/pcac177] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 12/22/2022] [Accepted: 01/05/2023] [Indexed: 05/17/2023]
Abstract
Programmed cell death (PCD) in lateral root caps (LRCs) is crucial for maintaining root cap functionality. Endoplasmic reticulum (ER) bodies play important roles in plant immunity and PCD. However, the distribution of ER bodies and their communication with vacuoles in the LRC remain elusive. In this study, we investigated the ultrastructure of LRC cells of wild-type and transgenic Arabidopsis lines using an auto-acquisition transmission electron microscope (TEM) system and high-pressure freezing. Gigapixel-scale high-resolution TEM imaging of the transverse and longitudinal sections of roots followed by three-dimensional imaging identified sausage-shaped structures budding from the ER. These were subsequently identified as ER bodies using GFPh transgenic lines expressing green fluorescent protein (GFP) fused with an ER retention signal (HDEL). Immunogold labeling using an anti-GFP antibody detected GFP signals in the ER bodies and vacuoles. The fusion of ER bodies with vacuoles in LRC cells was identified using correlative light and electron microscopy. Imaging of the root tips of a GFPh transgenic line with a PYK10 promoter revealed the localization of PYK10, a member of the β-glucosidase family with an ER retention signal, in the ER bodies in the inner layer along with a fusion of ER bodies with vacuoles in the middle layer and collapse of vacuoles in the outer layer of the LRC. These findings suggest that ER bodies in LRC directly transport β-glucosidases to the vacuoles, and that a subsequent vacuolar collapse triggered by an unknown mechanism releases protective substances to the growing root tip to protect it from the invaders.
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Affiliation(s)
- Kiminori Toyooka
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045 Japan
| | - Yumi Goto
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045 Japan
| | - Kei Hashimoto
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045 Japan
| | - Mayumi Wakazaki
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045 Japan
| | - Mayuko Sato
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045 Japan
| | - Masami Yokota Hirai
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045 Japan
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601 Japan
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8
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Malviya R, Dey S, Pandey A, Gayen D. Genome-wide identification and expression pattern analysis of lipoxygenase genes of chickpea (Cicer arietinum L.) in response to accelerated aging. Gene 2023; 874:147482. [PMID: 37187244 DOI: 10.1016/j.gene.2023.147482] [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: 01/05/2023] [Revised: 03/30/2023] [Accepted: 05/09/2023] [Indexed: 05/17/2023]
Abstract
Seed aging is a major problem which is caused by various factors such as unfavorable physiological, biochemical, and metabolic alterations in seed cells. Lipoxygenase (LOXs), an oxidoreductase enzyme that catalyzes the oxidation of polyunsaturated fatty acids, acts as a negative regulator in seed viability and vigour during storage. In this study, we identified ten putative LOX gene family members in the chickpea genome, designated as "CaLOX" which are mainly located in the cytoplasm and chloroplast. These genes share different physiochemical properties and similarities in their gene structures and conserved functional regions. The promoter region contained the cis-regulatory elements and transcription binding factors, which were mainly linked to biotic and abiotic stress, hormones, and light responsiveness. In this study, chickpea seeds were treated with accelerated aging treatment for 0, 2, and 4 days at 45°C and 85 % relative humidity. Increased level of reactive oxygen species, malondialdehyde, electrolyte leakage, proline, lipoxygenase (LOX) activity, and decreased catalase activity indicates cellular dysfunction and demonstrated seed deterioration. Quantitative real-time analysis reveals that 6 CaLOX genes were upregulated, and 4 CaLOX genes were downregulated during the seed aging process in chickpea. This comprehensive study will reveal the role of the CaLOX gene in response to aging treatment. The identified gene may be used to develop better-quality seeds in chickpea.
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Affiliation(s)
- Rinku Malviya
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, NH-8 Bandarsindri, Tehsil- Kishangarh, Dist- Ajmer, 305817
| | - Sharmistha Dey
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, NH-8 Bandarsindri, Tehsil- Kishangarh, Dist- Ajmer, 305817
| | - Anuradha Pandey
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, NH-8 Bandarsindri, Tehsil- Kishangarh, Dist- Ajmer, 305817
| | - Dipak Gayen
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, NH-8 Bandarsindri, Tehsil- Kishangarh, Dist- Ajmer, 305817.
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Xing M, Peng Z, Guan C, Guan M. Comparative study on abortion characteristics of Nsa CMS and Pol CMS and analysis of long non-coding RNAs related to pollen abortion in Brassica napus. PLoS One 2023; 18:e0284287. [PMID: 37053132 PMCID: PMC10101420 DOI: 10.1371/journal.pone.0284287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 03/28/2023] [Indexed: 04/14/2023] Open
Abstract
Cytoplasmic male sterile system (CMS) is one of the important methods for the utilization of heterosisin Brassica napus. The involvement of long non-coding RNAs (lncRNAs) in anther and pollen development in B.napus has been recognized, but there is little data on the involvement of lncRNAs in pollen abortion in different types of rapeseed CMS. The present study compared the cytological, physiological and biochemical characteristics of Nsa CMS (1258A) and Pol CMS (P5A) during pollen abortion, and high-throughput sequencing of flower buds of different sizes before and after pollen abortion. The results showed that insufficient energy supply was an important physiological basis for 1258A and P5A pollen abortion, and 1258A had excessive ROS (reactive oxygen species) accumulation in the stage of pollen abortion. Functional analysis showed that Starch and sucrose metabolism and Sulfur metabolism were significantly enriched before and after pollen abortion in 1258A and P5A, and a large number of genes were down-regulated. In 1258A, 227 lncRNAs had cis-targeting regulation, and 240 cis-target genes of the lncRNAs were identified. In P5A, 116 lncRNAs had cis-targeting regulation, and 101 cis-target genes of the lncRNAs were identified. There were five lncRNAs cis-target genes in 1258A and P5A during pollen abortion, and LOC106445716 encodes β-D-glucopyranosyl abscisate β-glucosidase and could regulate pollen abortion. Taken together, this study, provides a new perspective for lncRNAs to participate in the regulation of Nsa CMS and Pol CMS pollen abortion.
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Affiliation(s)
- Man Xing
- Hunan Branch of National Oilseed Crops Improvement Center, Changsha, China
- College of Agriculture, Hunan Agricultural University, Changsha, China
| | - Zechuan Peng
- Hunan Branch of National Oilseed Crops Improvement Center, Changsha, China
- College of Agriculture, Hunan Agricultural University, Changsha, China
| | - Chunyun Guan
- Hunan Branch of National Oilseed Crops Improvement Center, Changsha, China
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Changsha, China
| | - Mei Guan
- Hunan Branch of National Oilseed Crops Improvement Center, Changsha, China
- College of Agriculture, Hunan Agricultural University, Changsha, China
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Changsha, China
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10
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Shao Z, Liu N, Wang W, Zhu L. β-Glucosidases as dominant dose-dependent regulators of Oryza sativa L. in response to typical organic pollutant exposures. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 309:119709. [PMID: 35841992 DOI: 10.1016/j.envpol.2022.119709] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 06/15/2022] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
Understanding the metabolic defense and compensation to maintain homeostasis is crucial for assessing the potential health risk of organic pollutants in crops. Currently, limited understanding is available regarding the targeted metabolic pathways and response mechanism under contaminant stress. This study showed that ciprofloxacin (CIP) at the environmental concentrations (1, 5, 25, 50 mg/L) did not significantly inhibit growth or cause severe oxidative damage to rice (Oryza sativa L.). Instead, the increment in CIP concentration induced a series of sequential metabolic disorders, which were characterized predominantly by primary and secondary metabolic disturbances, including phenylpropanoid biosynthesis, the carbohydrate, lipid and amino acid metabolism. After CIP in vivo exceeded a certain threshold level (>0.29 mg/g dry weight), β-glucosidases (BGLUs) mediated the transition from the activation of the genes related to phenylpropanoid biosynthesis to the inhibition of the genes related to carbohydrate metabolism in rice. In particular, starch and sucrose metabolism showed the most profound perturbation stressed by environmental concentrations of CIP (5 mg/L) and other tested organic pollutants (10 μg/L of tricyclazole, thiamethoxam, polybrominated diphenyl ethers, and polychlorinated biphenyls). Besides, the key genes encoding endoglucanase and BGLU were significantly downregulated (|log2FC| > 3.0) under 100 μg/L of other tested organic pollutants, supporting the transition from the activation of secondary defense metabolism to the disruption of primary energy metabolism. Thus, in addition to bioaccumulation, changes in BGLU activity and starch and sucrose metabolism can reflect the potential adverse effects of pollutants on rice. This study explained the stepwise metabolic and transcriptional responses of rice to organic pollutants, which provided a new reference for the comprehensive evaluation of their environmental risks.
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Affiliation(s)
- Zexi Shao
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou, Zhejiang, 310058, China
| | - Na Liu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou, Zhejiang, 310058, China
| | - Wei Wang
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou, Zhejiang, 310058, China
| | - Lizhong Zhu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou, Zhejiang, 310058, China.
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11
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Liu F, Li N, Yu Y, Chen W, Yu S, He H. Insights into the Regulation of Rice Seed Storability by Seed Tissue-Specific Transcriptomic and Metabolic Profiling. PLANTS 2022; 11:plants11121570. [PMID: 35736721 PMCID: PMC9231264 DOI: 10.3390/plants11121570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/11/2022] [Accepted: 06/12/2022] [Indexed: 11/26/2022]
Abstract
Non-dormant seeds are continuously aging and deteriorating during storage, leading to declining seed vigor, which is a challenge for the rice seed industry. Improving the storability of seeds is of great significance to ensure the quality of rice and national food security. Through a set of chromosome segment substitution lines population constructed using japonica rice NIP as donor parent and indica rice ZS97 as recurrent parent, we performed seed storability QTL analysis and selected four non-storable NILs to further investigate the storability regulatory mechanisms underlying it. The seeds were divided into four tissues, which were the embryo, endosperm, aleurone layer, and hull, and tissue-specific transcriptome and metabolome analyses were performed on them. By exploring the common differentially expressed genes and differentially accumulated metabolites, as well as the KEGG pathway of the four non-storable NILs, we revealed that the phenylpropanoid biosynthesis pathway and diterpenoid biosynthesis pathway played a central role in regulating seed storability. Integrated analysis pinpointed 12 candidate genes that may take part in seed storability. The comprehensive analysis disclosed the divergent and synergistic effect of different seed tissues in the regulation of rice storability.
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Affiliation(s)
- Fangzhou Liu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (F.L.); (N.L.); (Y.Y.); (W.C.); (S.Y.)
| | - Nannan Li
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (F.L.); (N.L.); (Y.Y.); (W.C.); (S.Y.)
- Weizhai Town Agricultural Comprehensive Service Station, Fuyang 236418, China
| | - Yuye Yu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (F.L.); (N.L.); (Y.Y.); (W.C.); (S.Y.)
- Glbizzia Bioinformatics Institute, Beijing 102629, China
| | - Wei Chen
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (F.L.); (N.L.); (Y.Y.); (W.C.); (S.Y.)
| | - Sibin Yu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (F.L.); (N.L.); (Y.Y.); (W.C.); (S.Y.)
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Hanzi He
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (F.L.); (N.L.); (Y.Y.); (W.C.); (S.Y.)
- Correspondence:
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12
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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.
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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.
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13
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Chen DG, Zhou XQ, Chen K, Chen PL, Guo J, Liu CG, Chen YD. Fine-mapping and candidate gene analysis of a major locus controlling leaf thickness in rice ( Oryza sativa L.). MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:6. [PMID: 35103045 PMCID: PMC8792131 DOI: 10.1007/s11032-022-01275-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 01/13/2022] [Indexed: 05/16/2023]
Abstract
UNLABELLED Leaf thickness is an important trait in rice (Oryza sativa L.). It affects both photosynthesis and sink-resource efficiency. However, compared to leaf length and length width, reports seldom focused on leaf thickness due to the complicated measurement and minor difference. To identify the quantitative trait loci (QTL) and explore the genetic mechanism regulating the natural variation of leaf thickness, we crossed a high leaf thickness variety Aixiuzhan (AXZ) to a thin leaf thickness variety Yangdao No.6 (YD 6) and evaluated 585 F2 individuals. We further use bulked sergeant analysis with whole-genome resequencing (BSA-seq) to identify five genomic regions, including chromosomes 1, 6, 9, 10, and 12. These regions represented significant allele frequency differentiation between thick and thin leaf thickness among the mixed pool offspring. Moreover, we conducted a linkage mapping using 276 individuals derived from the F2 population. We fine-mapped and confirmed that chromosome 9 contributed the primary explanation of phenotypic variance. We fine-mapped the candidate regions and confirmed that the chromosome 9 region contributed to flag leaf thickness in rice. We observed the virtual cellular slices and found that the bundle sheath cells in YD 6 flag leaf veins are fewer than AXZ. We analyzed the potential regions on chromosome 9 and narrowed the QTL candidate intervals in the 928-kb region. Candidate genes of this major QTL were listed as potentially controlled leaf thickness. These results provide promising evidence that cloning leaf thickness is associated with yield production in rice. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s11032-022-01275-y.
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Affiliation(s)
- Da-gang Chen
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 People’s Republic of China
| | - Xin-qiao Zhou
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 People’s Republic of China
| | - Ke Chen
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 People’s Republic of China
| | - Ping-li Chen
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 People’s Republic of China
| | - Jie Guo
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 People’s Republic of China
| | - Chuan-guang Liu
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 People’s Republic of China
| | - You-ding Chen
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 People’s Republic of China
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14
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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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15
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Zhao M, Hu B, Fan Y, Ding G, Yang W, Chen Y, Chen Y, Xie J, Zhang F. Identification, Analysis, and Confirmation of Seed Storability-Related Loci in Dongxiang Wild Rice ( Oryza rufipogon Griff.). Genes (Basel) 2021; 12:genes12111831. [PMID: 34828437 PMCID: PMC8622159 DOI: 10.3390/genes12111831] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 11/15/2021] [Accepted: 11/18/2021] [Indexed: 12/02/2022] Open
Abstract
Dongxiang wild rice (Oryza rufipogon Griff.) (DXWR) has strong seed storability and identifying its elite gene resources may facilitate genetic improvements in rice seed storability. In this study, we developed two backcross inbred lines (BILs) populations, with DXWR as a common donor parent and two rice varieties (F6 and R974) as recipient parents. Bulked segregant analysis via whole genome sequencing (BSA-seq) was used to identify seed storability-related loci in the DXWR and F6 population. Two main genomic regions containing 18,550,000–20,870,000 bp on chromosome 4 and 7,860,000–9,780,000 bp on chromosome 9 were identified as candidate loci of DXWR seed storability; these overlapped partially with seed storability-related quantitative trait loci (QTLs) discovered in previous studies, suggesting that these loci may provide important regions for isolating the responsible genes. In total, 448 annotated genes were predicted within the identified regions, of which 274 and 82 had nonsynonymous and frameshift mutations, respectively. We detected extensive metabolic activities and cellular processes during seed storability and confirmed the effects of the seed storability-related candidate loci using four BILs from DXWR and R974. These results may facilitate the cloning of DXWR seed storability-related genes, thereby elucidating rice seed storability and its improvement potential.
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Affiliation(s)
- Minmin Zhao
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China; (M.Z.); (G.D.); (Y.C.)
| | - Biaolin Hu
- Rice National Engineering Laboratory, Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330022, China;
| | - Yuanwei Fan
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China;
| | - Gumu Ding
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China; (M.Z.); (G.D.); (Y.C.)
| | - Wanling Yang
- Jiangxi Provincial Key Lab of Protection and Utilization of Subtropical Plant Resources, Nanchang 330022, China; (W.Y.); (Y.C.)
| | - Yong Chen
- Jiangxi Provincial Key Lab of Protection and Utilization of Subtropical Plant Resources, Nanchang 330022, China; (W.Y.); (Y.C.)
| | - Yanhong Chen
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China; (M.Z.); (G.D.); (Y.C.)
| | - Jiankun Xie
- Jiangxi Provincial Key Lab of Protection and Utilization of Subtropical Plant Resources, Nanchang 330022, China; (W.Y.); (Y.C.)
- Correspondence: (J.X.); (F.Z.)
| | - Fantao Zhang
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China; (M.Z.); (G.D.); (Y.C.)
- Correspondence: (J.X.); (F.Z.)
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16
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Bian Z, Wang D, Liu Y, Xi Y, Wang X, Meng S. Analysis of Populus glycosyl hydrolase family I members and their potential role in the ABA treatment and drought stress response. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 163:178-188. [PMID: 33848930 DOI: 10.1016/j.plaphy.2021.03.057] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Accepted: 03/28/2021] [Indexed: 06/12/2023]
Abstract
Glycoside hydrolase family 1 (GH1) β-glucosidases (BGLUs) are encoded by a large number of genes and are involved in many developmental processes and stress responses in plants. Due to their importance in plant growth and development, genome-wide analyses have been conducted in the model plant species Arabidopsis thaliana, rice and maize but not in woody plant species, which have important economic and ecological value. In this study, we systematically analyzed Populus BGLUs (PtBGLUs) and demonstrated the involvement of several genes under stress conditions. Forty-four PtBGLUs were identified in Populus databases; these genes were located on 11 chromosomes, and the proteins of several PtBGLU genes were highly similar. More than 90% of PtBGLUs contain three conserved motifs. Collinearity results showed that 44 PtBGLU genes resulted from 12 tandem and 5 segmental duplication events. Phylogenetic analysis revealed that 128 BGLU genes from Populus trichocarpa, A. thaliana and Oryza sativa could be classified into 4 subgroups and subgroup Ⅱ and Ⅳ were differently having PtBGLUs and AtBGLUs. We further investigated whether several PtBGLUs responded to drought stress and ABA treatment, and the results showed that most of the selected BGLU genes were expressed in response to stress, which is consistent with previous studies involving rice and Arabidopsis homologous genes. Large numbers of stress-, hormone-, and development-related elements in the PtBGLU promoters suggest that BGLU genes may be involved in complex networks. Taken together, our results provide valuable information for an improved understanding of β-glucosidase function in woody plants.
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Affiliation(s)
- Zhan Bian
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, Guangdong, 510520, China.
| | - Dongli Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, Guangdong, 510520, China.
| | - Yunshan Liu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, Guangdong, 510520, China; College of Biology and Food Engineering, Chongqing Three Gorges University, Wanzhou, Chongqing, 404100, China
| | - Yimin Xi
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, Guangdong, 510520, China
| | - Xiaoling Wang
- Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, Jiangxi, 330096, China.
| | - Sen Meng
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, Guangdong, 510520, China.
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17
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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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