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Yan X, Zhou W, Huang X, Ouyang J, Li S, Gao J, Wang X. RAL6 encodes a seed allergenic protein that positively regulates grain weight and seed germination. JOURNAL OF PLANT RESEARCH 2024:10.1007/s10265-024-01581-w. [PMID: 39242482 DOI: 10.1007/s10265-024-01581-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Accepted: 08/28/2024] [Indexed: 09/09/2024]
Abstract
The rice albumin (RAG) gene family belongs to the Tryp_alpha_amyl family. RAG2, specifically expressed in 14-21 DAP (days after pollination) seeds, regulates grain yield and quality. In this study, we identified another RAG family gene, RAL6, which exhibits specific expression in developing seeds, particularly in 7, 10, and 15 DAP seeds. Employing the CRISPR/Cas9 system, we analyzed functions of RAL6 and found that the ral6 lines (ral6-1, ral6-2, ral6-3, and ral6-4) displayed thinner seeds with significantly decreased 1000-grain weight and grain thickness compared to ZH11. Additionally, the cell width of spikelet cells, total protein and glutelin contents were significantly reduced in ral6. The germination assay and 1% TTC staining revealed a significant decrease in seed vigor among the ral6 lines. The alpha-amylase activity in ral6 mutant seeds was also markedly lower than in ZH11 seeds after 2 days of imbibition. Furthermore, co-expression analysis and GO annotation showed that co-expressed genes were involved in immune response, oligopeptide transport, and the glucan biosynthetic process. Collectively, our findings suggest that RAL6 plays a coordinating role in regulating grain weight and seed germination in rice.
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Affiliation(s)
- Xin Yan
- Key Laboratory of Molecular Biology and Gene Engineering of Jiangxi Province, College of life science, Nanchang University, Nanchang, 330031, China
| | - Wei Zhou
- College of Life Sciences, Xinyang Normal University, Xinyang, 464000, China
| | - Xirui Huang
- Key Laboratory of Molecular Biology and Gene Engineering of Jiangxi Province, College of life science, Nanchang University, Nanchang, 330031, China
| | - Jiexiu Ouyang
- Key Laboratory of Molecular Biology and Gene Engineering of Jiangxi Province, College of life science, Nanchang University, Nanchang, 330031, China
| | - Shaobo Li
- Key Laboratory of Molecular Biology and Gene Engineering of Jiangxi Province, College of life science, Nanchang University, Nanchang, 330031, China
| | - Jiadong Gao
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Guangzhou, 510640, China.
- Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510555, China.
| | - Xin Wang
- Key Laboratory of Molecular Biology and Gene Engineering of Jiangxi Province, College of life science, Nanchang University, Nanchang, 330031, China.
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Niu Y, Wang C, Suo W, Wang G, Zhao J, Wang Z, Zheng Y. Isopropylmalate synthase NtIPMS as a potential molecular marker for seed vigor in tobacco. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2023; 40:43-49. [PMID: 38213928 PMCID: PMC10777126 DOI: 10.5511/plantbiotechnology.23.0118a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 01/18/2023] [Indexed: 01/13/2024]
Abstract
Seed vigor is an important trait for tobacco production. However, the evaluation of seed vigor using molecular biomarkers is scarcely reported in tobacco. In this study, the development of molecular marker isopropylmalate synthase NtIPMS was conducted to detect seed ageing degree and seed priming effect in tobacco. Quantitative real-time PCR (qRT-PCR) analysis showed that the expression of NtIPMS was significantly induced at the initial imbibition stage during seed germination. The NtIPMS expression was positively correlated with the degree of seed ageing in non-pelleted and pelleted seeds. The mRNA level of NtIPMS was gradually increased with the increasing degree of seed ageing. The early best effect of gibberellin priming was observed in 30-h primed seeds, and the highest expression of NtIPMS was observed in 12-h primed seeds. The best stop time-point of seed priming is likely at the time 18 h after the relatively higher NtIPMS expression occurred during seed priming process. The NtIPMS mRNA detection has the potential usage as a potential molecular marker for the evaluation of seed vigor in tobacco.
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Affiliation(s)
- Yongzhi Niu
- Yuxi Zhongyan Seed Company Ltd., Seed Engineering Technology Center of Yunnan Province, Yuxi 653100, China
| | - Chengjing Wang
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Wenlong Suo
- Yuxi Zhongyan Seed Company Ltd., Seed Engineering Technology Center of Yunnan Province, Yuxi 653100, China
| | - Guoping Wang
- Yuxi Zhongyan Seed Company Ltd., Seed Engineering Technology Center of Yunnan Province, Yuxi 653100, China
| | - Jia Zhao
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Zhoufei Wang
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Yunye Zheng
- Yuxi Zhongyan Seed Company Ltd., Seed Engineering Technology Center of Yunnan Province, Yuxi 653100, China
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Transcriptomics View over the Germination Landscape in Biofortified Rice. Genes (Basel) 2021; 12:genes12122013. [PMID: 34946962 PMCID: PMC8700799 DOI: 10.3390/genes12122013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/14/2021] [Accepted: 12/15/2021] [Indexed: 12/29/2022] Open
Abstract
Hidden hunger, or micronutrient deficiency, is a worldwide problem. Several approaches are employed to alleviate its effects (e.g., promoting diet diversity, use of dietary supplements, chemical fortification of processed food), and among these, biofortification is considered as one of the most cost-effective and highly sustainable. Rice is one of the best targets for biofortification since it is a staple food for almost half of the world’s population as a high-energy source but with low nutritional value. Multiple biofortified rice lines have been produced during the past decades, while few studies also reported modifications in germination behavior (in terms of enhanced or decreased germination percentage or speed). It is important to underline that rapid, uniform germination, and seedling establishment are essential prerequisites for crop productivity. Combining the two traits, biofortified, highly-nutritious seeds with improved germination behavior can be envisaged as a highly-desired target for rice breeding. To this purpose, information gathered from transcriptomics studies can reveal useful insights to unveil the molecular players governing both traits. The present review aims to provide an overview of transcriptomics studies applied at the crossroad between biofortification and seed germination, pointing out potential candidates for trait pyramiding.
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Sarkar D, Maranas CD. SNPeffect: identifying functional roles of SNPs using metabolic networks. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:512-531. [PMID: 32167625 PMCID: PMC9328443 DOI: 10.1111/tpj.14746] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 02/20/2020] [Indexed: 05/04/2023]
Abstract
Genetic sources of phenotypic variation have been a focus of plant studies aimed at improving agricultural yield and understanding adaptive processes. Genome-wide association studies identify the genetic background behind a trait by examining associations between phenotypes and single-nucleotide polymorphisms (SNPs). Although such studies are common, biological interpretation of the results remains a challenge; especially due to the confounding nature of population structure and the systematic biases thus introduced. Here, we propose a complementary analysis (SNPeffect) that offers putative genotype-to-phenotype mechanistic interpretations by integrating biochemical knowledge encoded in metabolic models. SNPeffect is used to explain differential growth rate and metabolite accumulation in A. thaliana and P. trichocarpa accessions as the outcome of SNPs in enzyme-coding genes. To this end, we also constructed a genome-scale metabolic model for Populus trichocarpa, the first for a perennial woody tree. As expected, our results indicate that growth is a complex polygenic trait governed by carbon and energy partitioning. The predicted set of functional SNPs in both species are associated with experimentally characterized growth-determining genes and also suggest putative ones. Functional SNPs were found in pathways such as amino acid metabolism, nucleotide biosynthesis, and cellulose and lignin biosynthesis, in line with breeding strategies that target pathways governing carbon and energy partition.
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Affiliation(s)
- Debolina Sarkar
- Department of Chemical EngineeringPennsylvania State UniversityUniversity ParkPAUSA
| | - Costas D. Maranas
- Department of Chemical EngineeringPennsylvania State UniversityUniversity ParkPAUSA
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He Y, Cheng J, He Y, Yang B, Cheng Y, Yang C, Zhang H, Wang Z. Influence of isopropylmalate synthase OsIPMS1 on seed vigour associated with amino acid and energy metabolism in rice. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:322-337. [PMID: 29947463 PMCID: PMC6335077 DOI: 10.1111/pbi.12979] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 06/24/2018] [Indexed: 05/21/2023]
Abstract
Seed vigour is an imperative trait for the direct seeding of rice. Isopropylmalate synthase (IPMS) catalyses the committed step of leucine (Leu) biosynthesis, but its effect on seed vigour remains unclear. In this study, rice OsIPMS1 and OsIPMS2 was cloned, and the roles of OsIPMS1 in seed vigour were mainly investigated. OsIPMS1 and OsIPMS2 catalyse Leu biosynthesis, and Leu feedback inhibits their IPMS activities. Disruption of OsIPMS1 resulted in low seed vigour under various conditions, which might be tightly associated with the reduction of amino acids in germinating seeds. Eleven amino acids that associated with stress tolerance, GA biosynthesis and tricarboxylic acid (TCA) cycle were significantly reduced in osipms1 mutants compared with those in wide type (WT) during seed germination. Transcriptome analysis indicated that a total of 1209 differentially expressed genes (DEGs) were altered in osipms1a mutant compared with WT at the early germination stage, wherein most of the genes were involved in glycolysis/gluconeogenesis, protein processing, pyruvate, carbon, fructose and mannose metabolism. Further analysis confirmed that the regulation of OsIPMS1 in seed vigour involved in starch hydrolysis, glycolytic activity and energy levels in germinating seeds. The effects of seed priming were tightly associated with the mRNA levels of OsIPMS1 in priming seeds. The OsIPMS1 might be used as a biomarker to determine the best stop time-point of seed priming in rice. This study provides novel insights into the function of OsIPMS1 on seed vigour and should have practical applications in seed priming of rice.
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Affiliation(s)
- Yongqi He
- The Laboratory of Seed Science and TechnologyState Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingChina
| | - Jinping Cheng
- The Laboratory of Seed Science and TechnologyState Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingChina
| | - Ying He
- The Laboratory of Seed Science and TechnologyState Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingChina
| | - Bin Yang
- The Laboratory of Seed Science and TechnologyState Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingChina
| | - Yanhao Cheng
- The Laboratory of Seed Science and TechnologyState Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingChina
| | - Can Yang
- The Laboratory of Seed Science and TechnologyState Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingChina
| | - Hongsheng Zhang
- The Laboratory of Seed Science and TechnologyState Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingChina
| | - Zhoufei Wang
- The Laboratory of Seed Science and TechnologyState Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingChina
- The Laboratory of Seed Science and TechnologyGuangdong Key Laboratory of Plant Molecular BreedingState Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
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Ren XX, Xue JQ, Wang SL, Xue YQ, Zhang P, Jiang HD, Zhang XX. Proteomic analysis of tree peony (Paeonia ostii 'Feng Dan') seed germination affected by low temperature. JOURNAL OF PLANT PHYSIOLOGY 2018; 224-225:56-67. [PMID: 29597068 DOI: 10.1016/j.jplph.2017.12.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 12/22/2017] [Accepted: 12/22/2017] [Indexed: 06/08/2023]
Abstract
Seed germination is a critical process that is influenced by various factors. In the present study, the effect of low temperature (4 °C) on tree peony seed germination was investigated. Compared to seeds maintained at 25 °C, germination was inhibited when seeds were kept at 4 °C. Furthermore, low-temperature exposure of seeds resulted in a delay in water uptake, starch degradation, and soluble sugar consumption and a subsequent increase in soluble protein levels. Two-dimensional gel electrophoresis (2-DE) proteomic analysis identified 100 protein spots. Comparative analysis indicated that low-temperature exposure apparently mainly affected glycolysis and the tricarboxylic acid (TCA) cycle, while also significantly affecting proteometabolism-related factors. Moreover, low-temperature exposure led to the induction of abscisic acid, whereas the gibberellin pathway was not affected. Further comparison of the two temperature conditions showed that low-temperature exposure delays carbohydrate metabolism, adenosine triphosphate (ATP) production, respiration, and proteolysis and increases defense response factors. To further examine the obtained proteomic findings, four genes were evaluated by quantitative polymerase chain reaction (qPCR). The obtained transcriptional results for the GAPC gene coincided with the translational results, thus further suggesting that the delay in glycolysis may play a key role in low-temperature-induced inhibition of seed germination. However, the other three genes examined, which included FPP synthase, PCNT115, and endochitinase, showed non-correlative transcriptional and translational profiles. Our results suggest that the exposure of tree peony seeds to low temperature results in a delay in the degradation of starch and other metabolites, which in turn affects glycolysis and some other processes, thereby ultimately inhibiting seed germination.
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Affiliation(s)
- Xiu-Xia Ren
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jing-Qi Xue
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shun-Li Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yu-Qian Xue
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ping Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hai-Dong Jiang
- College of Agriculture, Nanjing Agricultural University, Nanjing, China.
| | - Xiu-Xin Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China.
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