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Ding Y, Hou D, Yin Y, Chen K, He J, Yan S, Li H, Xiong Y, Zhou W, Li M. Genetic dissection of Brassica napus seed vigor after aging. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:141. [PMID: 38789698 DOI: 10.1007/s00122-024-04648-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 05/10/2024] [Indexed: 05/26/2024]
Abstract
KEY MESSAGE Stable and novel QTLs that affect seed vigor under different storage durations were discovered, and BnaOLE4, located in the interval of cqSW-C2-3, increased seed vigor after aging. Seed vigor is an important trait in crop breeding; however, the underlying molecular regulatory mechanisms governing this trait in rapeseed remain largely unknown. In the present study, vigor-related traits were analyzed in seeds from a doubled haploid (DH) rapeseed (Brassica napus) population grown in 2 different environments using seeds stored for 7, 5, and 3 years under natural storage conditions. A total of 229 quantitative trait loci (QTLs) were identified and were found to explain 3.78%-17.22% of the phenotypic variance for seed vigor-related traits after aging. We further demonstrated that seed vigor-related traits were positively correlated with oil content (OC) but negatively correlated with unsaturated fatty acids (FAs). Some pleiotropic QTLs that collectively regulate OC, FAs, and seed vigor, such as uq.A8, uq.A3-2, uq.A9-2, and uq.C3-1, were identified. The transcriptomic results from extreme pools of DH lines with distinct seed vigor phenotypes during accelerated aging revealed that various biological pathways and metabolic processes (such as glutathione metabolism and reactive oxygen species) were involved in seed vigor. Through integration of QTL analysis and RNA-Seq, a regulatory network for the control of seed vigor was constructed. Importantly, a candidate (BnaOLE4) from cqSW-C2-3 was selected for functional analysis, and transgenic lines overexpressing BnaOLE4 showed increased seed vigor after artificial aging. Collectively, these results provide novel information on QTL and potential candidate genes for molecular breeding for improved seed storability.
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Affiliation(s)
- Yiran Ding
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan, 430074, China
| | - Dalin Hou
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan, 430074, China
| | - Yongtai Yin
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan, 430074, China
| | - Kang Chen
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan, 430074, China
| | - Jianjie He
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan, 430074, China
| | - Shuxiang Yan
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan, 430074, China
| | - Huaixin Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan, 430074, China
| | - Yiyi Xiong
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan, 430074, China
| | - Weixian Zhou
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan, 430074, China
| | - Maoteng Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China.
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan, 430074, China.
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Choudhary P, Pramitha L, Aggarwal PR, Rana S, Vetriventhan M, Muthamilarasan M. Biotechnological interventions for improving the seed longevity in cereal crops: progress and prospects. Crit Rev Biotechnol 2023; 43:309-325. [PMID: 35443842 DOI: 10.1080/07388551.2022.2027863] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Seed longevity is a measure of the viability of seeds during long-term storage and is crucial for germplasm conservation and crop improvement programs. Also, longevity is an important trait for ensuring food and nutritional security. Thus, a better understanding of various factors regulating seed longevity is requisite to improve this trait and to minimize the genetic drift during the regeneration of germplasm. In particular, seed deterioration of cereal crops during storage adversely affects agricultural productivity and food security. The irreversible process of seed deterioration involves a complex interplay between different genes and regulatory pathways leading to: loss of DNA integrity, membrane damage, inactivation of storage enzymes and mitochondrial dysfunction. Identifying the genetic determinants of seed longevity and manipulating them using biotechnological tools hold the key to ensuring prolonged seed storage. Genetics and genomics approaches had identified several genomic regions regulating the longevity trait in major cereals such as: rice, wheat, maize and barley. However, very few studies are available in other Poaceae members, including millets. Deploying omics tools, including genomics, proteomics, metabolomics, and phenomics, and integrating the datasets will pinpoint the precise molecular determinants affecting the survivability of seeds. Given this, the present review enumerates the genetic factors regulating longevity and demonstrates the importance of integrated omics strategies to dissect the molecular machinery underlying seed deterioration. Further, the review provides a roadmap for deploying biotechnological approaches to manipulate the genes and genomic regions to develop improved cultivars with prolonged storage potential.
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Affiliation(s)
- Pooja Choudhary
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Lydia Pramitha
- School of Agriculture and Biosciences, Karunya Institute of Technology and Sciences, Coimbatore, India
| | - Pooja Rani Aggarwal
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Sumi Rana
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Mani Vetriventhan
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India
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Jin Y, Wang B, Tian L, Zhao L, Guo S, Zhang H, Xu L, Han Z. Identification of miRNAs and their target genes associated with improved maize seed vigor induced by gibberellin. FRONTIERS IN PLANT SCIENCE 2022; 13:1008872. [PMID: 36176685 PMCID: PMC9514094 DOI: 10.3389/fpls.2022.1008872] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 08/18/2022] [Indexed: 06/16/2023]
Abstract
High seed vigor is crucial for agricultural production owing to its potential in high quality and yield of crops and a better understanding of the molecular mechanism associated with maize seed vigor is highly necessary. To better understand the involvement and regulatory mechanism of miRNAs correlated with maize seed vigor, small RNAs and degradome sequencing of two inbred lines Yu537A and Yu82 were performed. A total of 791 mature miRNAs were obtained with different expressions, among of which 505 miRNAs were newly identified and the rest miRNAs have been reported before by comparing the miRNAs with the sequences in miRbase database. Analysis of miRNA families showed maize seeds contain fewer miRNA families and larger miRNA families compared with animals, indicating that functions of miRNAs in maize seeds were more synergistic than animals. Degradome sequencing was used to identify the targets of miRNAs and the results showed a total of 6,196 targets were obtained. Function analysis of differentially expressed miRNAs and targets showed Glycan degradation and galactose metabolism were closely correlated with improved maize seed vigor. These findings provide valuable information to understand the involvement of miRNAs with maize seed vigor and these putative genes will be valuable resources for improving the seed vigor in future maize breeding.
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Affiliation(s)
- Yunqian Jin
- College of Agronomy, Henan University of Science and Technology, Luoyang, China
- State Key Laboratory of Cotton Biology / Institute of Cotton Research of Chinese Academy of Agricultural Sciences / School of Agricultural Sciences, Zhengzhou University, Henan, Zhengzhou, China / Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, Henan, China
| | - Bin Wang
- College of Agronomy, Henan University of Science and Technology, Luoyang, China
| | - Lei Tian
- College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Linxi Zhao
- College of Agronomy, Henan University of Science and Technology, Luoyang, China
| | - Shulei Guo
- Cereal Institute, Henan Academy of Agricultural Science/Henan Provincial Key Laboratory of Maize Biology, Zhengzhou, China
| | - Hengchao Zhang
- College of Agronomy, Henan University of Science and Technology, Luoyang, China
| | - Lengrui Xu
- College of Agronomy, Henan University of Science and Technology, Luoyang, China
| | - Zanping Han
- College of Agronomy, Henan University of Science and Technology, Luoyang, China
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Lin YX, Xu HJ, Yin GK, Zhou YC, Lu XX, Xin X. Dynamic Changes in Membrane Lipid Metabolism and Antioxidant Defense During Soybean ( Glycine max L. Merr.) Seed Aging. FRONTIERS IN PLANT SCIENCE 2022; 13:908949. [PMID: 35812982 PMCID: PMC9263854 DOI: 10.3389/fpls.2022.908949] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 06/07/2022] [Indexed: 06/15/2023]
Abstract
Seed viability depends upon the maintenance of functional lipids; however, how membrane lipid components dynamically change during the seed aging process remains obscure. Seed storage is accompanied by the oxidation of membrane lipids and loss of seed viability. Understanding membrane lipid changes and their effect on the cell membrane during seed aging can contribute to revealing the mechanism of seed longevity. In this study, the potential relationship between oxidative stress and membrane lipid metabolism was evaluated by using a non-targeted lipidomics approach during artificial aging of Glycine max L. Merr. Zhongdou No. 27 seeds. We determined changes in reactive oxygen species, malondialdehyde content, and membrane permeability and assessed antioxidant system activity. We found that decreased non-enzymatic antioxidant contents and catalase activity might lead to reactive oxygen species accumulation, resulting in higher electrolyte leakage and lipid peroxidation. The significantly decreased phospholipids and increased glycerolipids and lysophospholipids suggested that hydrolysis of phospholipids to form glycerolipids and lysophospholipids could be the primary pathway of membrane metabolism during seed aging. Moreover, the ratio of phosphatidylcholine to phosphatidylethanolamine, double bond index, and acyl chain length of phospholipids were found to jointly regulate membrane function. In addition, the observed changes in lipid metabolism suggest novel potential hallmarks of soybean seed aging, such as diacylglycerol 36:4; phosphatidylcholine 34:2, 36:2, and 36:4; and phosphatidylethanolamine 34:2. This knowledge can be of great significance for elucidating the molecular mechanism underlying seed aging and germplasm conservation.
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Affiliation(s)
- Yi-xin Lin
- National Crop Genebank, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Agriculture, Fujian Agricultural and Forestry University, Fuzhou, China
| | - Hai-jin Xu
- National Crop Genebank, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Agriculture, Fujian Agricultural and Forestry University, Fuzhou, China
| | - Guang-kun Yin
- National Crop Genebank, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuan-chang Zhou
- College of Agriculture, Fujian Agricultural and Forestry University, Fuzhou, China
| | - Xin-xiong Lu
- National Crop Genebank, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xia Xin
- National Crop Genebank, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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Wei J, Fang Y, Jiang H, Wu XT, Zuo JH, Xia XC, Li JQ, Stich B, Cao H, Liu YX. Combining QTL mapping and gene co-expression network analysis for prediction of candidate genes and molecular network related to yield in wheat. BMC PLANT BIOLOGY 2022; 22:288. [PMID: 35698038 PMCID: PMC9190149 DOI: 10.1186/s12870-022-03677-8] [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: 02/27/2022] [Accepted: 05/27/2022] [Indexed: 05/21/2023]
Abstract
BACKGROUND Wheat (Triticum aestivum L.) is an important cereal crop. Increasing grain yield for wheat is always a priority. Due to the complex genome of hexaploid wheat with 21 chromosomes, it is difficult to identify underlying genes by traditional genetic approach. The combination of genetics and omics analysis has displayed the powerful capability to identify candidate genes for major quantitative trait loci (QTLs), but such studies have rarely been carried out in wheat. In this study, candidate genes related to yield were predicted by a combined use of linkage mapping and weighted gene co-expression network analysis (WGCNA) in a recombinant inbred line population. RESULTS QTL mapping was performed for plant height (PH), spike length (SL) and seed traits. A total of 68 QTLs were identified for them, among which, 12 QTLs were stably identified across different environments. Using RNA sequencing, we scanned the 99,168 genes expression patterns of the whole spike for the recombinant inbred line population. By the combined use of QTL mapping and WGCNA, 29, 47, 20, 26, 54, 46 and 22 candidate genes were predicted for PH, SL, kernel length (KL), kernel width, thousand kernel weight, seed dormancy, and seed vigor, respectively. Candidate genes for different traits had distinct preferences. The known PH regulation genes Rht-B and Rht-D, and the known seed dormancy regulation genes TaMFT can be selected as candidate gene. Moreover, further experiment revealed that there was a SL regulatory QTL located in an interval of about 7 Mbp on chromosome 7A, named TaSL1, which also involved in the regulation of KL. CONCLUSIONS A combination of QTL mapping and WGCNA was applied to predicted wheat candidate genes for PH, SL and seed traits. This strategy will facilitate the identification of candidate genes for related QTLs in wheat. In addition, the QTL TaSL1 that had multi-effect regulation of KL and SL was identified, which can be used for wheat improvement. These results provided valuable molecular marker and gene information for fine mapping and cloning of the yield-related trait loci in the future.
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Affiliation(s)
- Jun Wei
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yu Fang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hao Jiang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Xing-Ting Wu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jing-Hong Zuo
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xian-Chun Xia
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jin-Quan Li
- Strube Research GmbH & Co., KG, 38387, S ̈ollingen, Germany
| | - Benjamin Stich
- Institute of Quantitative Genetics and Genomics of Plants, Heinrich Heine University, D ̈usseldorf, Germany
| | - Hong Cao
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Yong-Xiu Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Genetic Aspects and Molecular Causes of Seed Longevity in Plants—A Review. PLANTS 2022; 11:plants11050598. [PMID: 35270067 PMCID: PMC8912819 DOI: 10.3390/plants11050598] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 02/17/2022] [Accepted: 02/22/2022] [Indexed: 12/19/2022]
Abstract
Seed longevity is the most important trait related to the management of gene banks because it governs the regeneration cycle of seeds. Thus, seed longevity is a quantitative trait. Prior to the discovery of molecular markers, classical genetic studies have been performed to identify the genetic determinants of this trait. Post-2000 saw the use of DNA-based molecular markers and modern biotechnological tools, including RNA sequence (RNA-seq) analysis, to understand the genetic factors determining seed longevity. This review summarizes the most important and relevant genetic studies performed in Arabidopsis (24 reports), rice (25 reports), barley (4 reports), wheat (9 reports), maize (8 reports), soybean (10 reports), tobacco (2 reports), lettuce (1 report) and tomato (3 reports), in chronological order, after discussing some classical studies. The major genes identified and their probable roles, where available, are debated in each case. We conclude by providing information about many different collections of various crops available worldwide for advanced research on seed longevity. Finally, the use of new emerging technologies, including RNA-seq, in seed longevity research is emphasized by providing relevant examples.
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Chen X, Börner A, Xin X, Nagel M, He J, Li J, Li N, Lu X, Yin G. Comparative Proteomics at the Critical Node of Vigor Loss in Wheat Seeds Differing in Storability. FRONTIERS IN PLANT SCIENCE 2021; 12:707184. [PMID: 34527008 PMCID: PMC8435634 DOI: 10.3389/fpls.2021.707184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 08/10/2021] [Indexed: 06/13/2023]
Abstract
The critical node (CN, 85% germination) of seed viability is an important threshold for seed regeneration decisions after long-term conservation. Dependent on the germplasm, the storage period until CN is reached varies and information on the divergence of the proteomic profiles is limited. Therefore, the study aims to identify key proteins and mechanisms relevant for a long plateau phase and a late CN during artificial seed aging of wheat. Seeds of the storage-tolerant genotype (ST) TRI 23248, and the storage-sensitive genotype (SS) TRI 10230 were exposed to artificial ageing (AA) and extracted embryos of imbibed seeds were analyzed using an iTRAQ-based proteomic technique. ST and SS required AA for 24 and 18 days to reach the CN, respectively. Fifty-seven and 165 differentially abundant proteins (DAPs) were observed in the control and aged groups, respectively. Interestingly, a higher activity in metabolic processes, protein synthesis, transcription, cell growth/division, and signal transduction were already found in imbibed embryos of control ST seeds. After AA, 132 and 64 DAPs were accumulated in imbibed embryos of both aged ST and SS seeds, respectively, which were mainly associated with cell defense, rescue, and metabolism. Moreover, 78 DAPs of ST appeared before CN and were mainly enriched in biological pathways related to the maintenance of redox and carbon homeostasis and they presented a stronger protein translation ability. In contrast, in SS, only 3 DAPs appeared before CN and were enriched only in the structural constituents of the cytoskeleton. In conclusion, a longer span of plateau phase might be obtained in seeds when proteins indicate an intense stress response before CN and include the effective maintenance of cellular homeostasis, and avoidance of excess accumulation of cytotoxic compounds. Although key proteins, inherent factors and the precise regulatory mechanisms need to be further investigated, the found proteins may also have functional potential roles during long-term seed conservation.
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Affiliation(s)
- Xiuling Chen
- National Crop Genebank, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Applied Technology Research and Development Center for Sericulture and Special Local Products of Hebei Universities, Institute of Sericulture, Chengde Medical University, Chengde, China
| | - Andreas Börner
- Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Xia Xin
- National Crop Genebank, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Manuela Nagel
- Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Juanjuan He
- National Crop Genebank, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jisheng Li
- Applied Technology Research and Development Center for Sericulture and Special Local Products of Hebei Universities, Institute of Sericulture, Chengde Medical University, Chengde, China
| | - Na Li
- Applied Technology Research and Development Center for Sericulture and Special Local Products of Hebei Universities, Institute of Sericulture, Chengde Medical University, Chengde, China
| | - Xinxiong Lu
- National Crop Genebank, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guangkun Yin
- National Crop Genebank, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
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Yuan Z, Fan K, Wang Y, Tian L, Zhang C, Sun W, He H, Yu S. OsGRETCHENHAGEN3-2 modulates rice seed storability via accumulation of abscisic acid and protective substances. PLANT PHYSIOLOGY 2021; 186:469-482. [PMID: 33570603 PMCID: PMC8154041 DOI: 10.1093/plphys/kiab059] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 01/26/2021] [Indexed: 05/23/2023]
Abstract
Seed storability largely determines the vigor of seeds during storage and is significant in agriculture and ecology. However, the underlying genetic basis remains unclear. In the present study, we report the cloning and characterization of the rice (Oryza sativa) indole-3-acetic acid (IAA)-amido synthetase gene GRETCHEN HAGEN3-2 (OsGH3-2) associated with seed storability. OsGH3-2 was identified by performing a genome-wide association study in rice germplasms with linkage mapping in chromosome substitution segment lines, contributing to the wide variation of seed viability in the populations after long periods of storage and artificial ageing. OsGH3-2 was dominantly expressed in the developing seeds and catalyzed IAA conjugation to amino acids, forming inactive auxin. Transgenic overexpression, knockout, and knockdown experiments demonstrated that OsGH3-2 affected seed storability by regulating the accumulation level of abscisic acid (ABA). Overexpression of OsGH3-2 significantly decreased seed storability, while knockout or knockdown of the gene enhanced seed storability compared with the wild-type. OsGH3-2 acted as a negative regulator of seed storability by modulating many genes related to the ABA pathway and probably subsequently late embryogenesis-abundant proteins at the transcription level. These findings shed light on the molecular mechanisms underlying seed storability and will facilitate the improvement of seed vigor by genomic breeding and gene-editing approaches in rice.
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Affiliation(s)
- Zhiyang Yuan
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Kai Fan
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuntong Wang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Li Tian
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Chaopu Zhang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Wenqiang Sun
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Hanzi He
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Sibin Yu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
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Shi H, Guan W, Shi Y, Wang S, Fan H, Yang J, Chen W, Zhang W, Sun D, Jing R. QTL mapping and candidate gene analysis of seed vigor-related traits during artificial aging in wheat (Triticum aestivum). Sci Rep 2020; 10:22060. [PMID: 33328518 PMCID: PMC7745025 DOI: 10.1038/s41598-020-75778-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 10/15/2020] [Indexed: 11/23/2022] Open
Abstract
High vigor seeds have greater yield potential than those with low vigor; however, long-term storage leads to a decline in this trait. The objective of this study was to identify quantitative trait loci (QTLs) for seed vigor-related traits under artificial aging conditions using a high-density genetic linkage map of wheat (Triticum aestivum) and mine the related candidate genes. A doubled haploid population, derived from a cross between Hanxuan 10 × Lumai 14, was used as the experimental material. Six controlled-environment treatments were set up, i.e. the seeds were aged for 0, 24, 36, 48, 60, and 72 h at a high temperature (48 °C) and under high humidity (relative humidity 100%). Eight traits including seed germination percentage, germination energy, germination index, seedling length, root length, seedling weight, vigor index, and simple vigor index were measured. With the prolongation of artificial aging treatment, these traits showed a continuous downward trend and significant correlations were observed between most of them. A total of 49 additive QTLs for seed vigor-related traits were mapped onto 12 chromosomes (1B, 2D, 3A, 3B, 3D, 4A, 4D, 5A, 5B, 5D, 6D, and 7A); and each one accounted for 6.01–17.18% of the phenotypic variations. Twenty-five pairs of epistatic QTLs were detected on all chromosomes, except for 5D, 6A, and 7D, and each epistasis accounted for 7.35–26.06% of the phenotypic variations. Three additive QTL hot spots were found on chromosomes 5A, 5B, and 5D, respectively. 13 QTLs, QGEe5B, QGIe5B, QSLc5B, QSLd5B, QSLf5B, QRLd5B, QRLe5B, QRLf5B, QVId5B, QVIe5B, QVIf5B, QSVId5B, and QSVIe5B, were located in the marker interval AX-94643729 ~ AX-110529646 on 5B and the physical interval 707,412,449–710,959,479 bp. Genes including TRAESCS5B01G564900, TRAESCS5B01G564200, TRAESCS5B01G562600, TraesCS5B02G562700, TRAESCS5B01G561300, TRAESCS5B01G561400, and TRAESCS5B01G562100, located in this marker interval, were found to be involved in regulating the processes of carbohydrate and lipid metabolism, transcription, and cell division during the germination of aging seeds, thus they were viewed as candidate genes for seed viability-related traits. These findings provide the basis for the seed-based cloning and functional identification of related candidate genes for seed vigor.
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Affiliation(s)
- Huawei Shi
- College of Agronomy, Shanxi Agricultural University, Taigu, 030801, People's Republic of China
| | - Wanghui Guan
- College of Agronomy, Shanxi Agricultural University, Taigu, 030801, People's Republic of China
| | - Yugang Shi
- College of Agronomy, Shanxi Agricultural University, Taigu, 030801, People's Republic of China
| | - Shuguang Wang
- College of Agronomy, Shanxi Agricultural University, Taigu, 030801, People's Republic of China
| | - Hua Fan
- College of Agronomy, Shanxi Agricultural University, Taigu, 030801, People's Republic of China
| | - Jinwen Yang
- College of Agronomy, Shanxi Agricultural University, Taigu, 030801, People's Republic of China
| | - Weiguo Chen
- College of Agronomy, Shanxi Agricultural University, Taigu, 030801, People's Republic of China
| | - Wenjun Zhang
- College of Agronomy, Shanxi Agricultural University, Taigu, 030801, People's Republic of China
| | - Daizhen Sun
- College of Agronomy, Shanxi Agricultural University, Taigu, 030801, People's Republic of China.
| | - Ruilian Jing
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China.
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Li W, He X, Chen Y, Jing Y, Shen C, Yang J, Teng W, Zhao X, Hu W, Hu M, Li H, Miller AJ, Tong Y. A wheat transcription factor positively sets seed vigour by regulating the grain nitrate signal. THE NEW PHYTOLOGIST 2020; 225:1667-1680. [PMID: 31581317 PMCID: PMC7004088 DOI: 10.1111/nph.16234] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 09/22/2019] [Indexed: 05/12/2023]
Abstract
Seed vigour and early establishment are important factors determining the yield of crops. A wheat nitrate-inducible NAC transcription factor, TaNAC2, plays a critical role in promoting crop growth and nitrogen use efficiency (NUE), and now its role in seed vigour is revealed. A TaNAC2 regulated gene was identified that is a NRT2-type nitrate transporter TaNRT2.5 with a key role in seed vigour. Overexpressing TaNAC2-5A increases grain nitrate concentration and seed vigour by directly binding to the promoter of TaNRT2.5-3B and positively regulating its expression. TaNRT2.5 is expressed in developing grain, particularly the embryo and husk. In Xenopus oocyte assays TaNRT2.5 requires a partner protein TaNAR2.1 to give nitrate transport activity, and the transporter locates to the tonoplast in a tobacco leaf transient expression system. Furthermore, in the root TaNRT2.5 and TaNRT2.1 function in post-anthesis acquisition of soil nitrate. Overexpression of TaNRT2.5-3B increases seed vigour, grain nitrate concentration and yield, whereas RNA interference of TaNRT2.5 has the opposite effects. The TaNAC2-NRT2.5 module has a key role in regulating grain nitrate accumulation and seed vigour. Both genes can potentially be used to improve grain yield and NUE in wheat.
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Affiliation(s)
- Wenjing Li
- The State Key Laboratory for Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesBeijing100101China
- University of Chinese Academy of SciencesBeijing100049China
- CAS‐JIC Centre of Excellence for Plant and Microbial Science (CEPAMS)Shanghai Institutes for Biological SciencesChinese Academy of Sciences (CAS)Shanghai200032China
| | - Xue He
- The State Key Laboratory for Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesBeijing100101China
- CAS‐JIC Centre of Excellence for Plant and Microbial Science (CEPAMS)Shanghai Institutes for Biological SciencesChinese Academy of Sciences (CAS)Shanghai200032China
| | - Yi Chen
- CAS‐JIC Centre of Excellence for Plant and Microbial Science (CEPAMS)Shanghai Institutes for Biological SciencesChinese Academy of Sciences (CAS)Shanghai200032China
- Department of Metabolic BiologyJohn Innes CentreNorwich Research ParkNorwichNR4 7UHUK
| | - Yanfu Jing
- The State Key Laboratory for Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesBeijing100101China
- University of Chinese Academy of SciencesBeijing100049China
| | - Chuncai Shen
- The State Key Laboratory for Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesBeijing100101China
- University of Chinese Academy of SciencesBeijing100049China
| | - Junbo Yang
- The State Key Laboratory for Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesBeijing100101China
- University of Chinese Academy of SciencesBeijing100049China
| | - Wan Teng
- The State Key Laboratory for Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesBeijing100101China
| | - Xueqiang Zhao
- The State Key Laboratory for Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesBeijing100101China
| | - Weijuan Hu
- The State Key Laboratory for Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesBeijing100101China
| | - Mengyun Hu
- The Institute for Cereal and Oil CropsHebei Academy of Agriculture and Forestry SciencesShijiazhuang050035China
| | - Hui Li
- The Institute for Cereal and Oil CropsHebei Academy of Agriculture and Forestry SciencesShijiazhuang050035China
| | - Anthony J. Miller
- CAS‐JIC Centre of Excellence for Plant and Microbial Science (CEPAMS)Shanghai Institutes for Biological SciencesChinese Academy of Sciences (CAS)Shanghai200032China
- Department of Metabolic BiologyJohn Innes CentreNorwich Research ParkNorwichNR4 7UHUK
| | - Yiping Tong
- The State Key Laboratory for Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesBeijing100101China
- CAS‐JIC Centre of Excellence for Plant and Microbial Science (CEPAMS)Shanghai Institutes for Biological SciencesChinese Academy of Sciences (CAS)Shanghai200032China
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Zhang X, Hina A, Song S, Kong J, Bhat JA, Zhao T. Whole-genome mapping identified novel "QTL hotspots regions" for seed storability in soybean (Glycine max L.). BMC Genomics 2019; 20:499. [PMID: 31208334 PMCID: PMC6580613 DOI: 10.1186/s12864-019-5897-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 06/11/2019] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Seed aging in soybean is a serious challenge for agronomic production and germplasm preservation. However, its genetic basis remains largely unclear in soybean. Unraveling the genetic mechanism involved in seed aging, and enhancing seed storability is an imperative goal for soybean breeding. The aim of this study is to identify quantitative trait loci (QTLs) using high-density genetic linkage maps of soybean for seed storability. In this regard, two recombinant inbred line (RIL) populations derived from Zhengyanghuangdou × Meng 8206 (ZM6) and Linhefenqingdou × Meng 8206 (LM6) crosses were evaluated for three seed-germination related traits viz., germination rate (GR), normal seedling length (SL) and normal seedling fresh weight (FW) under natural and artificial aging conditions to map QTLs for seed storability. RESULTS A total of 34 QTLs, including 13 QTLs for GR, 11 QTLs for SL and 10 QTLs for FW, were identified on 11 chromosomes with the phenotypic variation ranged from 7.30 to 23.16% under both aging conditions. All these QTLs were novel, and 21 of these QTLs were clustered in five QTL-rich regions on four different chromosomes viz., Chr3, Chr5, Chr17 &Chr18, among them the highest concentration of seven and six QTLs were found in "QTL hotspot A" (Chr17) and "QTL hotspot B" (Chr5), respectively. Furthermore, QTLs within all the five QTL clusters are linked to at least two studied traits, which is also supported by highly significant correlation between the three germination-related traits. QTLs for seed-germination related traits in "QTL hotspot B" were found in both RIL populations and aging conditions, and also QTLs underlying "QTL hotspot A" are identified in both RIL populations under artificial aging condition. These are the stable genomic regions governing the inheritance of seed storability in soybean, and will be the main focus for soybean breeders. CONCLUSION This study uncovers the genetic basis of seed storability in soybean. The newly identified QTLs provides valuable information, and will be main targets for fine mapping, candidate gene identification and marker-assisted breeding. Hence, the present study is the first report for the comprehensive and detailed investigation of genetic architecture of seed storability in soybean.
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Affiliation(s)
- Xi Zhang
- Soybean Research Institution, National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Aiman Hina
- Soybean Research Institution, National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Shiyu Song
- Soybean Research Institution, National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Jiejie Kong
- Soybean Research Institution, National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Javaid Akhter Bhat
- Soybean Research Institution, National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Tuanjie Zhao
- Soybean Research Institution, National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
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