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Hou Z, Huang H, Wang Y, Chen L, Yue L, Liu B, Kong F, Yang H. Molecular Regulation of Shoot Architecture in Soybean. PLANT, CELL & ENVIRONMENT 2024. [PMID: 39254042 DOI: 10.1111/pce.15138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 08/02/2024] [Accepted: 08/21/2024] [Indexed: 09/11/2024]
Abstract
Soybean (Glycine max [L.] Merr.) serves as a major source of protein and oil for humans and animals. Shoot architecture, the spatial arrangement of a plant's above-ground organs, strongly affects crop yield and is therefore a critical agronomic trait. Unlike wheat and rice crops that have greatly benefitted from the Green Revolution, soybean yield has not changed significantly in the past six decades owing to its unique shoot architecture. Soybean is a pod-bearing crop with pods adhered to the nodes, and variation in shoot architecture traits, such as plant height, node number, branch number and number of seeds per pod, directly affects the number of pods and seeds per plant, thereby determining yield. In this review, we summarize the relationship between soybean yield and these major components of shoot architecture. We also describe the latest advances in identifying the genes and molecular mechanisms underlying soybean shoot architecture and discuss possible directions and approaches for breeding new soybean varieties with ideal shoot architecture and improved yield.
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Affiliation(s)
- Zhihong Hou
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Huan Huang
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Yanan Wang
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Liyu Chen
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Lin Yue
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Baohui Liu
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Fanjiang Kong
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Hui Yang
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
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Huang L, Gao G, Jiang C, Guo G, He Q, Zong Y, Liu C, Yang P. Generating homozygous mutant populations of barley microspores by ethyl methanesulfonate treatment. ABIOTECH 2023; 4:202-212. [PMID: 37970468 PMCID: PMC10638298 DOI: 10.1007/s42994-023-00108-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 05/31/2023] [Indexed: 11/17/2023]
Abstract
Induced mutations are important for genetic research and breeding. Mutations induced by physical or chemical mutagenesis are usually heterozygous during the early generations. However, mutations must be fixed prior to phenotyping or field trials, which requires additional rounds of self-pollination. Microspore culture is an effective method to produce double-haploid (DH) plants that are fixed homozygotes. In this study, we conducted ethyl methanesulfonate (EMS)-induced mutagenesis of microspore cultures of barley (Hordeum vulgare) cultivar 'Hua30' and landrace 'HTX'. The EMS concentrations were negatively correlated with the efficiency of callus induction and the frequency of mutant plant regeneration. The two genotypes showed different regeneration efficiencies. The phenotypic variation of the regenerated M1 plants and the presence of genome-wide nucleotide mutations, revealed by whole-genome sequencing, highlight the utility of EMS-induced mutagenesis of isolated microspore cultures for developing DH mutants. Genome-wide analysis of the mutation frequency in the regenerated plants revealed that a considerable proportion of mutations resulted from microspore culture (somaclonal variation) rather than EMS-induced mutagenesis. In addition to producing a population of 1972 homozygous mutant lines that are available for future field trials, this study lays the foundation for optimizing the regeneration efficiency of DH plants and the richness of mutations (mainly by fine-tuning the mutagen dosage).
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Affiliation(s)
- Linli Huang
- Biotech Research Institute, Shanghai Academy of Agricultural Sciences/Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai, 201106 China
| | - Guangqi Gao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Congcong Jiang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Guimei Guo
- Biotech Research Institute, Shanghai Academy of Agricultural Sciences/Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai, 201106 China
| | - Qiang He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Yingjie Zong
- Biotech Research Institute, Shanghai Academy of Agricultural Sciences/Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai, 201106 China
| | - Chenghong Liu
- Biotech Research Institute, Shanghai Academy of Agricultural Sciences/Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai, 201106 China
| | - Ping Yang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
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3
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Khan A, Khan NA, Bean SR, Chen J, Xin Z, Jiao Y. Variations in Total Protein and Amino Acids in the Sequenced Sorghum Mutant Library. PLANTS (BASEL, SWITZERLAND) 2023; 12:1662. [PMID: 37111885 PMCID: PMC10142022 DOI: 10.3390/plants12081662] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/05/2023] [Accepted: 04/12/2023] [Indexed: 06/19/2023]
Abstract
Sorghum (Sorghum bicolor) is the fifth most important cereal crop worldwide; however, its utilization in food products can be limited due to reduced nutritional quality related to amino acid composition and protein digestibility in cooked products. Low essential amino acid levels and digestibility are influenced by the composition of the sorghum seed storage proteins, kafirins. In this study, we report a core collection of 206 sorghum mutant lines with altered seed storage proteins. Wet lab chemistry analysis was conducted to evaluate the total protein content and 23 amino acids, including 19 protein-bound and 4 non-protein amino acids. We identified mutant lines with diverse compositions of essential and non-essential amino acids. The highest total protein content in these lines was almost double that of the wild-type (BTx623). The mutants identified in this study can be used as a genetic resource to improve the sorghum grain quality and determine the molecular mechanisms underlying the biosynthesis of storage protein and starch in sorghum seeds.
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Affiliation(s)
- Adil Khan
- Institute of Genomics for Crop Abiotic Stress Tolerance (IGCAST), Department of Plant and Soil Science, Texas Tech University, Lubbock, TX 79409, USA
| | - Nasir Ali Khan
- Institute of Genomics for Crop Abiotic Stress Tolerance (IGCAST), Department of Plant and Soil Science, Texas Tech University, Lubbock, TX 79409, USA
| | - Scott R. Bean
- Grain Quality and Structure Research Unit, Center for Grain and Animal Health Research, USDA-ARS, 1515 College Ave., Manhattan, KS 66502, USA
| | - Junping Chen
- Plant Stress and Germplasm Development Unit, Crop Systems Research Laboratory, USDA-ARS, 3810, 4th Street, Lubbock, TX 79424, USA
| | - Zhanguo Xin
- Plant Stress and Germplasm Development Unit, Crop Systems Research Laboratory, USDA-ARS, 3810, 4th Street, Lubbock, TX 79424, USA
| | - Yinping Jiao
- Institute of Genomics for Crop Abiotic Stress Tolerance (IGCAST), Department of Plant and Soil Science, Texas Tech University, Lubbock, TX 79409, USA
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Yu R, Niu Y, Wang X, Yang K, Han X, Liu Z, Qi Z, Yang Y. Construction of a density mutant collection in bitter gourd via new germplasms innovation and gene functional study. FRONTIERS IN PLANT SCIENCE 2022; 13:1069750. [PMID: 36483947 PMCID: PMC9724616 DOI: 10.3389/fpls.2022.1069750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 10/25/2022] [Indexed: 06/17/2023]
Abstract
Although a few studies have elucidated the creation of bitter gourd mutants, the suitable concentration and duration of ethyl methanesulfonate (EMS) mutagenesis have not been determined. In this study, mutant collection was conducted to create new germplasms and widen genetic diversity. By employing the seeds of the inbred line Y52 as the mutagenic material, EMS as the mutagen, and the suitable mutagenic conditions for bitter gourd seeds (EMS concentration 0.2%, mutagenic time 10 h), we mutated 10,000 seeds and acquired 3223 independent M1 lines. For the randomly selected 1000 M2 lines, 199 M2 lines with visible phenotypes were found, and 167 M2 lines were mutants of fruit shape, size, and tubercles. Furthermore, fourteen dwarf, eleven leaf color, five leaf shape, and eight meristem defect mutants were discovered in this mutant collection. In addition, three lines of 1253, 2284, and 3269 represented recessive mutants crossed with Y52. Furthermore, the yellow leaf lines of 2284 and 3269 were not mutated at the same gene locus. This study constructed a mutant collection through innovative new germplasms and provided valuable resources for bitter gourd breeding and functional gene research.
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Affiliation(s)
- Renbo Yu
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
- Hainan Yazhou Bay Seed Lab, Hainan, China
- Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province, Hainan, China
| | - Yu Niu
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
- Hainan Yazhou Bay Seed Lab, Hainan, China
- Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province, Hainan, China
| | - Xiaoyi Wang
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Kaili Yang
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
- Hainan Yazhou Bay Seed Lab, Hainan, China
| | - Xu Han
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
- Hainan Yazhou Bay Seed Lab, Hainan, China
- Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province, Hainan, China
| | - Zhaohua Liu
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
- Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province, Hainan, China
| | - Zhiqiang Qi
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
- Hainan Yazhou Bay Seed Lab, Hainan, China
- Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province, Hainan, China
| | - Yan Yang
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
- Hainan Yazhou Bay Seed Lab, Hainan, China
- Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province, Hainan, China
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Song J, Wang X, Huang L, Li Z, Ren H, Wang J. Genetic dissection of the soybean dwarf mutant dm with integrated genomic, transcriptomic and methylomic analyses. FRONTIERS IN PLANT SCIENCE 2022; 13:1017672. [PMID: 36479521 PMCID: PMC9721362 DOI: 10.3389/fpls.2022.1017672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 10/07/2022] [Indexed: 06/17/2023]
Abstract
Plant height affects crop production and breeding practices, while genetic control of dwarfism draws a broad interest of researchers. Dwarfism in soybean (Glycine max) is mainly unexplored. Here, we characterized a dwarf mutant dm screened from ethyl methanesulfonate (EMS) mutated seeds of the soybean cultivar Zhongpin 661(ZP). Phenotypically, dm showed shorter and thinner stems, smaller leaves, and more nodes than ZP under greenhouse conditions. Genetically, whole-genome sequencing and comparison revealed that 210K variants of SNPs and InDel in ZP relative to the soybean reference genome Williams82, and EMS mutagenesis affected 636 genes with variants predicted to have a large impact on protein function in dm. Whole-genome methylation sequencing found 704 differentially methylated regions in dm. Further whole-genome RNA-Seq based transcriptomic comparison between ZP and dm leaves revealed 687 differentially expressed genes (DEGs), including 263 up-regulated and 424 down-regulated genes. Integrated omics analyses revealed 11 genes with both differential expressions and DNA variants, one gene with differential expression and differential methylation, and three genes with differential methylation and sequence variation, worthy of future investigation. Genes in cellulose, fatty acids, and energy-associated processes could be the key candidate genes for the dwarf phenotype. This study provides genetic clues for further understanding of the genetic control of dwarfism in soybean. The genetic resources could help to inbreed new cultivars with a desirable dwarf characteristic.
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Affiliation(s)
- Jian Song
- College of Life Science, Yangtze University, Jingzhou, China
- National Key Facility for Gene Resources and Genetic Improvement (NFCRI)/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xuewen Wang
- Department of Genetics, University of Georgia, Athens, AB, United States
| | - Lan Huang
- Department of Computer Science, Yangtze University, Jingzhou, China
| | - Zhongfeng Li
- National Key Facility for Gene Resources and Genetic Improvement (NFCRI)/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Honglei Ren
- National Key Facility for Gene Resources and Genetic Improvement (NFCRI)/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Soybean Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Jun Wang
- College of Agriculture, Yangtze University, Jingzhou, China
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Li X, Jia Y, Sun M, Ji Z, Zhang H, Qiu D, Cai Q, Xia Y, Yuan X, Chen X, Shen Z. MINI BODY1, encoding a MATE/DTX family transporter, affects plant architecture in mungbean ( Vigna radiata L.). FRONTIERS IN PLANT SCIENCE 2022; 13:1064685. [PMID: 36466236 PMCID: PMC9714821 DOI: 10.3389/fpls.2022.1064685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 11/01/2022] [Indexed: 06/17/2023]
Abstract
It has been shown that multidrug and toxic compound extrusion/detoxification (MATE/DTX) family transporters are involved in the regulation of plant development and stress response. Here, we characterized the mini body1 (mib1) mutants in mungbean, which gave rise to increased branches, pentafoliate compound leaves, and shortened pods. Map-based cloning revealed that MIB1 encoded a MATE/DTX family protein in mungbean. qRT-PCR analysis showed that MIB1 was expressed in all tissues of mungbean, with the highest expression level in the young inflorescence. Complementation assays in Escherichia coli revealed that MIB1 potentially acted as a MATE/DTX transporter in mungbean. It was found that overexpression of the MIB1 gene partially rescued the shortened pod phenotype of the Arabidopsis dtx54 mutant. Transcriptomic analysis of the shoot buds and young pods revealed that the expression levels of several genes involved in the phytohormone pathway and developmental regulators were altered in the mib1 mutants. Our results suggested that MIB1 plays a key role in the control of plant architecture establishment in mungbean.
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Affiliation(s)
- Xin Li
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Yahui Jia
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Mingzhu Sun
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Zikun Ji
- College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Hui Zhang
- National experimental Teaching Center for Plant Production, Nanjing Agricultural University, Nanjing, China
| | - Dan Qiu
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Qiao Cai
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Yan Xia
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Xingxing Yuan
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, China
| | - Xin Chen
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, China
| | - Zhenguo Shen
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
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Hudson K. Soybean Protein and Oil Variants Identified through a Forward Genetic Screen for Seed Composition. PLANTS (BASEL, SWITZERLAND) 2022; 11:2966. [PMID: 36365419 PMCID: PMC9656176 DOI: 10.3390/plants11212966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/25/2022] [Accepted: 10/31/2022] [Indexed: 06/16/2023]
Abstract
Mutagenesis remains an important tool in soybean biology. In classical plant mutation breeding, mutagenesis has been a trusted approach for decades, creating stable non-transgenic variation, and many mutations have been incorporated into germplasm for several crops, especially to introduce favorable seed composition traits. We performed a genetic screen for aberrant oil or protein composition of soybean seeds, and as a result isolated over 100 mutant lines for seed composition phenotypes, with particular interest in high protein or high oil phenotypes. These lines were followed for multiple seasons and generations to select the most stable traits for further characterization. Through backcrossing and outcrossing experiments, we determined that a subset of the lines showed recessive inheritance, while others showed a dominant inheritance pattern that suggests the involvement of multiple loci and genetic mechanisms. These lines can be used as a resource for future studies of the genetic control of seed protein and oil content in soybean.
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Affiliation(s)
- Karen Hudson
- USDA-ARS Crop Production and Pest Control Research Unit, 915 West State Street, West Lafayette, IN 47907, USA
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Zhu W, Yang C, Yong B, Wang Y, Li B, Gu Y, Wei S, An Z, Sun W, Qiu L, He C. An enhancing effect attributed to a nonsynonymous mutation in SOYBEAN SEED SIZE 1, a SPINDLY-like gene, is exploited in soybean domestication and improvement. THE NEW PHYTOLOGIST 2022; 236:1375-1392. [PMID: 36068955 DOI: 10.1111/nph.18461] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 08/12/2022] [Indexed: 05/26/2023]
Abstract
Soybean (Glycine max) was domesticated from its wild relative Glycine soja. One-hundred-seed weight is one of the most important domesticated traits determining soybean yield; however, its underlying genetic basis remains elusive. We characterized a soybean seed size 1 (sss1) mutant featuring large seeds compared to its wild-type background. Positional cloning revealed that the candidate gene GmSSS1 encoded a SPINDLY homolog and was co-located in a well-identified quantitative trait locus (QTL)-rich region on chromosome 19. Knocking out GmSSS1 resulted in small seeds, while overexpressing GmSSS1/Gmsss1 induced large seeds. Modulating GmSSS1/Gmsss1 in transgenic plants can positively influence cell expansion and cell division. Relative to GmSSS1, one mutation leading to an E to Q substitution at the 182nd residue in Gmsss1 conferred an enhancing effect on seed weight. GmSSS1 underwent diversification in wild-type and cultivated soybean, and the alleles encoding the Gmsss1-type substitution of 182nd -Q, which originated along the central and downstream parts of the Yellow River, were selected and expanded during soybean domestication and improvement. We cloned the causative gene for the sss1 mutant, which is linked with a seed weight QTL, identified an elite allele of this gene for increasing seed weight, and provided new insights into soybean domestication and breeding.
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Affiliation(s)
- Weiwei Zhu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Road 19, Beijing, 100049, China
| | - Ce Yang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Road 19, Beijing, 100049, China
| | - Bin Yong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Road 19, Beijing, 100049, China
| | - Yan Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
| | - Bingbing Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Road 19, Beijing, 100049, China
| | - Yongzhe Gu
- National Key Facility for Gene Resources and Genetic Improvement/Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Siming Wei
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Road 19, Beijing, 100049, China
| | - Zhenghong An
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Road 19, Beijing, 100049, China
| | - Wenkai Sun
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Road 19, Beijing, 100049, China
| | - Lijuan Qiu
- National Key Facility for Gene Resources and Genetic Improvement/Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Chaoying He
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Road 19, Beijing, 100049, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
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Su B, Wu H, Guo Y, Gao H, Wei Z, Zhao Y, Qiu L. GmIAA27 Encodes an AUX/IAA Protein Involved in Dwarfing and Multi-Branching in Soybean. Int J Mol Sci 2022; 23:ijms23158643. [PMID: 35955771 PMCID: PMC9368862 DOI: 10.3390/ijms23158643] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/25/2022] [Accepted: 08/01/2022] [Indexed: 11/16/2022] Open
Abstract
Soybean plant height and branching affect plant architecture and yield potential in soybean. In this study, the mutant dmbn was obtained by treating the cultivar Zhongpin 661 with ethylmethane sulfonate. The dmbn mutant plants were shorter and more branched than the wild type. The genetic analysis showed that the mutant trait was controlled by a semi-dominant gene. The candidate gene was fine-mapped to a 91 kb interval on Chromosome 9 by combining BSA-seq and linkage analysis. Sequence analysis revealed that Glyma.09g193000 encoding an Aux/IAA protein (GmIAA27) was mutated from C to T in the second exon of the coding region, resulting to amino acid substitution of proline to leucine. Overexpression of the mutant type of this gene in Arabidopsis thaliana inhibited apical dominance and promoted lateral branch development. Expression analysis of GmIAA27 and auxin response genes revealed that some GH3 genes were induced. GmIAA27 relies on auxin to interact with TIR1, whereas Gmiaa27 cannot interact with TIR1 owing to the mutation in the degron motif. Identification of this unique gene that controls soybean plant height and branch development provides a basis for investigating the mechanisms regulating soybean plant architecture development.
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Affiliation(s)
- Bohong Su
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (B.S.); (H.W.)
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.G.); (H.G.); (Y.Z.)
| | - Haitao Wu
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (B.S.); (H.W.)
| | - Yong Guo
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.G.); (H.G.); (Y.Z.)
| | - Huawei Gao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.G.); (H.G.); (Y.Z.)
| | - Zhongyan Wei
- Institute of Plant Virology, Ningbo University, Ningbo 315211, China;
| | - Yuyang Zhao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.G.); (H.G.); (Y.Z.)
| | - Lijuan Qiu
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (B.S.); (H.W.)
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.G.); (H.G.); (Y.Z.)
- Correspondence: ; Tel.: +86-8210-5843
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10
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Zhang M, Zhang X, Jiang X, Qiu L, Jia G, Wang L, Ye W, Song Q. iSoybean: A database for the mutational fingerprints of soybean. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1435-1437. [PMID: 35579453 PMCID: PMC9342614 DOI: 10.1111/pbi.13844] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 05/07/2022] [Accepted: 05/12/2022] [Indexed: 05/25/2023]
Affiliation(s)
- Mengzhu Zhang
- Stake Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingJiangsuChina
| | - Xiyu Zhang
- Stake Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingJiangsuChina
| | - Xinyu Jiang
- Stake Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingJiangsuChina
| | - Lei Qiu
- Jiamusi Branch of Heilongjiang Academy of Agricultural SciencesJiamusiHeilongjiangChina
| | - Guanghong Jia
- Stake Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingJiangsuChina
| | - Longfei Wang
- Stake Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingJiangsuChina
| | - Wenxue Ye
- Stake Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingJiangsuChina
| | - Qingxin Song
- Stake Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingJiangsuChina
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11
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Islam N, Krishnan HB, Natarajan SS. Protein profiling of fast neutron soybean mutant seeds reveals differential accumulation of seed and iron storage proteins. PHYTOCHEMISTRY 2022; 200:113214. [PMID: 35469783 DOI: 10.1016/j.phytochem.2022.113214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 04/18/2022] [Accepted: 04/19/2022] [Indexed: 06/14/2023]
Abstract
A fast neutron (FN) radiated mutant soybean (Glycine max (L.) Merr., Fabaceae) displaying large duplications exhibited an increase in total seed protein content. A tandem mass tag (TMT) based protein profiling of matured seeds resulted in the identification of 4338 proteins. Gene duplication resulted in a significant increase in several seed storage proteins and protease inhibitors. Among the storage proteins, basic 7 S globulin, glycinin G4, and beta-conglycinin showed higher abundance in matured FN mutant seeds in addition to protease inhibitors. A significantly higher abundance of L-ascorbate peroxidases, acid phosphatases, and iron storage proteins was also observed. A higher amount of albumin, sucrose synthase, iron storage, and ascorbate family proteins in the mutant seeds was observed at the mid-stage of seed filling. We anticipate that the duplicated genes might have a cascading effect on the genome constituents, thus, resulting in increased storage and iron-containing protein content in the mutant seeds.
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Affiliation(s)
- Nazrul Islam
- Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD, 20705, USA
| | - Hari B Krishnan
- Plant Genetics Research Unit, USDA-ARS, University of Missouri, Columbia, MO, 65211, USA
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12
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Comparison between Germinated Seed and Isolated Microspore EMS Mutagenesis in Chinese Cabbage (Brassica rapa L. ssp. pekinensis). HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8030232] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Mutagenesis is an important tool for breeding and genomic research. In this study, the germinated seeds and isolated microspores of a double haploid line ‘FT’ were treated with EMS, respectively, with the aim of comparing the effects of the two approaches on generating mutants in Chinese cabbage. For microspore EMS mutagenesis, the isolated microspores were treated with 0.12% EMS for 20 min, a total of 1268 plantlets were obtained, and 15 M1 mutants were screened with a mutation frequency of 1.2%. For seed EMS mutagenesis, 7800 germinated seeds were treated with 0.8% EMS for 12 h, and a total of 701 M2 mutants were screened, with a mutation frequency of 18.78%. In total, 716 mutants with heritable morphological variation including leaf color, leaf shape, leafy head, bolting, and fertility, were obtained from the EMS mutagenesis experiments. Homozygous mutant plants could be screened from M1 lines by microspore mutagenesis, and M2 lines by seed mutagenesis. The mutation frequency was higher in seed mutagenesis than in microspore mutagenesis. Based on these results, we propose that seed EMS mutagenesis is more suitable to generate a large-scale mutant library, and the microspore EMS mutagenesis is conducive to rapidly obtaining homozygous mutants.
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13
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Zhang M, Liu S, Wang Z, Yuan Y, Zhang Z, Liang Q, Yang X, Duan Z, Liu Y, Kong F, Liu B, Ren B, Tian Z. Progress in soybean functional genomics over the past decade. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:256-282. [PMID: 34388296 PMCID: PMC8753368 DOI: 10.1111/pbi.13682] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 08/04/2021] [Accepted: 08/09/2021] [Indexed: 05/24/2023]
Abstract
Soybean is one of the most important oilseed and fodder crops. Benefiting from the efforts of soybean breeders and the development of breeding technology, large number of germplasm has been generated over the last 100 years. Nevertheless, soybean breeding needs to be accelerated to meet the needs of a growing world population, to promote sustainable agriculture and to address future environmental changes. The acceleration is highly reliant on the discoveries in gene functional studies. The release of the reference soybean genome in 2010 has significantly facilitated the advance in soybean functional genomics. Here, we review the research progress in soybean omics (genomics, transcriptomics, epigenomics and proteomics), germplasm development (germplasm resources and databases), gene discovery (genes that are responsible for important soybean traits including yield, flowering and maturity, seed quality, stress resistance, nodulation and domestication) and transformation technology during the past decade. At the end, we also briefly discuss current challenges and future directions.
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Affiliation(s)
- Min Zhang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
| | - Shulin Liu
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
| | - Zhao Wang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yaqin Yuan
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Zhifang Zhang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Qianjin Liang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xia Yang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Zongbiao Duan
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yucheng Liu
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
| | - Fanjiang Kong
- Innovative Center of Molecular Genetics and EvolutionSchool of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Baohui Liu
- Innovative Center of Molecular Genetics and EvolutionSchool of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Bo Ren
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
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14
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Islam N, Krishnan HB, Natarajan S. Proteomic Profiling of Fast Neutron-Induced Soybean Mutant Unveiled Pathways Associated with Increased Seed Protein Content. J Proteome Res 2020; 19:3936-3944. [PMID: 32819100 DOI: 10.1021/acs.jproteome.0c00160] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Mutagenesis through fast neutron (FN) radiation of soybean resulted in a mutant with a 15% increase in seed protein content. A comparative genomic hybridization analysis confirmed that the mutant is lacking 24 genes located at chromosomes 5 and 10. A tandem mass tag-based proteomic profiling of the wild type and the FN mutant revealed 3,502 proteins, of which 206 proteins exhibited increased abundance and 214 proteins showed decreased abundance. Among the abundant proteins, basic 7S globulin increased fourfold, followed by vacuolar-sorting receptor and protein transporters. The differentially expressed proteins were mapped on the global metabolic pathways. It was observed that there was an enrichment of 29 ribosomal proteins, 16 endoplasmic reticular proteins, and several proteins in export metabolic pathways. The deletion of the sequence-specific DNA binding transcription factor along with 23 other genes may have altered the negative regulation of protein syntheses processes, resulting in an increase in the overall protein content of the mutant seed. This mutant is a valuable resource for researchers to understand the metabolic pathways that may affect an increase in seed protein content (the mass spectrometry data files were submitted to massive.ucsd.edu # MassIVE MSV000084228).
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Affiliation(s)
- Nazrul Islam
- Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville, Maryland 20705, United States
| | - Hari B Krishnan
- Plant Genetics Research Unit, USDA-ARS, University of Missouri, Columbia, Missouri 65211, United States
| | - Savithiry Natarajan
- Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville, Maryland 20705, United States
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15
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Kato S, Yokota Y, Suzuki R, Fujisawa Y, Sayama T, Kaga A, Anai T, Komatsu K, Oki N, Kikuchi A, Ishimoto M. Identification of a cytochrome P450 hydroxylase, CYP81E22, as a causative gene for the high sensitivity of soybean to herbicide bentazon. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:2105-2115. [PMID: 32200415 DOI: 10.1007/s00122-020-03580-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 03/12/2020] [Indexed: 06/10/2023]
Abstract
KEY MESSAGE A frame shift invoked by a single-base deletion in the gene encoding a cytochrome P450 hydroxylase, CYP81E22, causes the loss of bentazon detoxification function in soybean. Bentazon is an effective herbicide in soybean cultivation applied at post-emergence stages for control of several broadleaf weeds. However, some soybean cultivars are highly sensitive to bentazon and are killed upon application. In this study, the gene related to the high sensitivity of soybean cultivars to bentazon was mapped to chromosome 16, and its location was narrowed down to a 257-kb region where three cytochrome P450 genes were located. In these genes, a single-base deletion of cytosine was detected in the coding region of Glyma.16G149300, CYP81E22, at + 1465 bp downstream from the translation start codon, leading to a frame shift in the open reading frame and creating a premature stop codon. This stop codon resulted in the loss of more than half of the P450, and consequently, the remaining molecule failed to form a functioning protein. This single-base deletion was common among the highly sensitive cultivars screened from the soybean mini-core collection and other previously reported highly sensitive cultivars. Furthermore, we screened plant lines from the targeting-induced local lesions in genomes library of the soybean cultivar Enrei based on a modelled 3D structure of CYP81E22. The lines with mutations in Glyma.16G149300 were highly sensitive to bentazon, which provides strong evidence that Glyma.16G149300 is the gene responsible for high sensitivity to bentazon.
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Affiliation(s)
- Shin Kato
- Tohoku Agricultural Research Center, National Agriculture and Food Research Organization (NARO), 297 Uenodai, Kariwano, Daisen, Akita, 019-2112, Japan
| | - Yuko Yokota
- Institute of Crop Science, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Rintaro Suzuki
- Advanced Analysis Center, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
| | - Yukiko Fujisawa
- Institute of Crop Science, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Takashi Sayama
- Institute of Crop Science, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
- Western Region Agricultural Research Center, NARO, 1-3-1 Senyu-cho, Zentsuji, Kagawa, 765-8508, Japan
| | - Akito Kaga
- Institute of Crop Science, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Toyoaki Anai
- Faculty of Agriculture, Saga University, Saga, 840-8502, Japan
| | - Kunihiko Komatsu
- Western Region Agricultural Research Center, NARO, 1-3-1 Senyu-cho, Zentsuji, Kagawa, 765-8508, Japan
| | - Nobuhiko Oki
- Kyushu Okinawa Agricultural Research Center, NARO, 2421 Suya, Koshi, Kumamoto, 861-1192, Japan
| | - Akio Kikuchi
- Tohoku Agricultural Research Center, National Agriculture and Food Research Organization (NARO), 297 Uenodai, Kariwano, Daisen, Akita, 019-2112, Japan
| | - Masao Ishimoto
- Institute of Crop Science, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan.
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16
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García-Calderón M, Pérez-Delgado CM, Palove-Balang P, Betti M, Márquez AJ. Flavonoids and Isoflavonoids Biosynthesis in the Model Legume Lotus japonicus; Connections to Nitrogen Metabolism and Photorespiration. PLANTS 2020; 9:plants9060774. [PMID: 32575698 PMCID: PMC7357106 DOI: 10.3390/plants9060774] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/17/2020] [Accepted: 06/18/2020] [Indexed: 12/11/2022]
Abstract
Phenylpropanoid metabolism represents an important metabolic pathway from which originates a wide number of secondary metabolites derived from phenylalanine or tyrosine, such as flavonoids and isoflavonoids, crucial molecules in plants implicated in a large number of biological processes. Therefore, various types of interconnection exist between different aspects of nitrogen metabolism and the biosynthesis of these compounds. For legumes, flavonoids and isoflavonoids are postulated to play pivotal roles in adaptation to their biological environments, both as defensive compounds (phytoalexins) and as chemical signals in symbiotic nitrogen fixation with rhizobia. In this paper, we summarize the recent progress made in the characterization of flavonoid and isoflavonoid biosynthetic pathways in the model legume Lotus japonicus (Regel) Larsen under different abiotic stress situations, such as drought, the impairment of photorespiration and UV-B irradiation. Emphasis is placed on results obtained using photorespiratory mutants deficient in glutamine synthetase. The results provide different types of evidence showing that an enhancement of isoflavonoid compared to standard flavonol metabolism frequently occurs in Lotus under abiotic stress conditions. The advance produced in the analysis of isoflavonoid regulatory proteins by the use of co-expression networks, particularly MYB transcription factors, is also described. The results obtained in Lotus japonicus plants can be also extrapolated to other cultivated legume species, such as soybean, of extraordinary agronomic importance with a high impact in feeding, oil production and human health.
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Affiliation(s)
- Margarita García-Calderón
- Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Química, Universidad de Sevilla, Calle Profesor García González, 1, 41012-Sevilla, Spain; (M.G.-C.); (C.M.P.-D.); (M.B.)
| | - Carmen M. Pérez-Delgado
- Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Química, Universidad de Sevilla, Calle Profesor García González, 1, 41012-Sevilla, Spain; (M.G.-C.); (C.M.P.-D.); (M.B.)
| | - Peter Palove-Balang
- Institute of Biology and Ecology, Faculty of Science, P.J. Šafárik University in Košice, Mánesova 23, SK-04001 Košice, Slovakia;
| | - Marco Betti
- Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Química, Universidad de Sevilla, Calle Profesor García González, 1, 41012-Sevilla, Spain; (M.G.-C.); (C.M.P.-D.); (M.B.)
| | - Antonio J. Márquez
- Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Química, Universidad de Sevilla, Calle Profesor García González, 1, 41012-Sevilla, Spain; (M.G.-C.); (C.M.P.-D.); (M.B.)
- Correspondence: ; Tel.: +34-954557145
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17
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Sarkar MAR, Otsu W, Suzuki A, Hashimoto F, Anai T, Watanabe S. Single-base deletion in GmCHR5 increases the genistein-to-daidzein ratio in soybean seed. BREEDING SCIENCE 2020; 70:265-276. [PMID: 32714048 PMCID: PMC7372027 DOI: 10.1270/jsbbs.19134] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 12/03/2019] [Indexed: 06/11/2023]
Abstract
Novel mutant alleles related to isoflavone content are useful for breeding programs to improve the disease resistance and nutritional content of soybean. However, identification of mutant alleles from high-density mutant libraries is expensive and time-consuming because soybean has a large, complicated genome. Here, we identified the gene responsible for increased genistein-to-daidzein ratio in seed of the mutant line F333ES017D9. For this purpose, we used a time- and cost-effective approach based on selective genotyping of a small number of F2 plants showing the mutant phenotype with nearest-neighboring-nucleotide substitution-high-resolution melting analysis markers, followed by alignment of short reads obtained by next-generation sequencing analysis with the identified locus. In the mutant line, GmCHR5 harbored a single-base deletion that caused a change in the substrate flow in the isoflavone biosynthetic pathway towards genistein. Mutated GmCHR5 was expressed at a lower level during seed development than wild-type GmCHR5. Ectopic overexpression of GmCHR5 increased the production of daidzein derivatives in both the wild-type and mutant plants. The present strategy will be useful for accelerating identification of mutant alleles responsible for traits of interest in agronomically important crops.
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Affiliation(s)
- Md. Abdur Rauf Sarkar
- The United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
- Faculty of Agriculture, Saga University, 1 Honjo-machi, Saga, Saga 840-8502, Japan
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Wakana Otsu
- Faculty of Agriculture, Saga University, 1 Honjo-machi, Saga, Saga 840-8502, Japan
| | - Akihiro Suzuki
- The United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
- Faculty of Agriculture, Saga University, 1 Honjo-machi, Saga, Saga 840-8502, Japan
| | - Fumio Hashimoto
- The United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Toyoaki Anai
- The United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
- Faculty of Agriculture, Saga University, 1 Honjo-machi, Saga, Saga 840-8502, Japan
| | - Satoshi Watanabe
- The United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
- Faculty of Agriculture, Saga University, 1 Honjo-machi, Saga, Saga 840-8502, Japan
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18
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Liu S, Zhang M, Feng F, Tian Z. Toward a "Green Revolution" for Soybean. MOLECULAR PLANT 2020; 13:688-697. [PMID: 32171732 DOI: 10.1016/j.molp.2020.03.002] [Citation(s) in RCA: 112] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 02/03/2020] [Accepted: 03/06/2020] [Indexed: 05/25/2023]
Abstract
Soybean (Glycine max), as an economically important food and oilseedcrop, is a major source of plant proteins and oils. Although considerable progress has been made in increasing the yields of rice, wheat, and maize through the "Green Revolution", little improvements have been made for soybean. With the increasing demand of soybean production and the rapid development of crop breeding technologies, time has come for this important crop to undergo a Green Revolution. Here, we briefly summarize the history of crop breeding and Green Revolution in other crops. We then discuss the possible directions and potential approaches toward achieving a Green Revolution for soybean. We provide our views and perspectives on how to breed new soybean varieties with improved yield.
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Affiliation(s)
- Shulin Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Min Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Feng Feng
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
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19
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Bai M, Yuan J, Kuang H, Gong P, Li S, Zhang Z, Liu B, Sun J, Yang M, Yang L, Wang D, Song S, Guan Y. Generation of a multiplex mutagenesis population via pooled CRISPR-Cas9 in soya bean. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:721-731. [PMID: 31452351 PMCID: PMC7004907 DOI: 10.1111/pbi.13239] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 07/17/2019] [Accepted: 08/15/2019] [Indexed: 05/08/2023]
Abstract
The output of genetic mutant screenings in soya bean [Glycine max (L.) Merr.] has been limited by its paleopolypoid genome. CRISPR-Cas9 can generate multiplex mutants in crops with complex genomes. Nevertheless, the transformation efficiency of soya bean remains low and, hence, remains the major obstacle in the application of CRISPR-Cas9 as a mutant screening tool. Here, we report a pooled CRISPR-Cas9 platform to generate soya bean multiplex mutagenesis populations. We optimized the key steps in the screening protocol, including vector construction, sgRNA assessment, pooled transformation, sgRNA identification and gene editing verification. We constructed 70 CRISPR-Cas9 vectors to target 102 candidate genes and their paralogs which were subjected to pooled transformation in 16 batches. A population consisting of 407 T0 lines was obtained containing all sgRNAs at an average mutagenesis frequency of 59.2%, including 35.6% lines carrying multiplex mutations. The mutation frequency in the T1 progeny could be increased further despite obtaining a transgenic chimera. In this population, we characterized gmric1/gmric2 double mutants with increased nodule numbers and gmrdn1-1/1-2/1-3 triple mutant lines with decreased nodulation. Our study provides an advanced strategy for the generation of a targeted multiplex mutant population to overcome the gene redundancy problem in soya bean as well as in other major crops.
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Affiliation(s)
- Mengyan Bai
- College of Resources and EnvironmentFujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Juehui Yuan
- College of Resources and EnvironmentFujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Huaqin Kuang
- FAFU‐UCR Joint Center for Horticultural Biology and MetabolomicsHaixia Institute of Science and TechnologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Pingping Gong
- FAFU‐UCR Joint Center for Horticultural Biology and MetabolomicsHaixia Institute of Science and TechnologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Suning Li
- FAFU‐UCR Joint Center for Horticultural Biology and MetabolomicsHaixia Institute of Science and TechnologyFujian Agriculture and Forestry UniversityFuzhouChina
- College of Life SciencesFujian Agriculture and Forestry UniversityFuzhouChina
| | - Zhihui Zhang
- College of Resources and EnvironmentFujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyFujian Agriculture and Forestry UniversityFuzhouChina
- FAFU‐UCR Joint Center for Horticultural Biology and MetabolomicsHaixia Institute of Science and TechnologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Bo Liu
- College of Resources and EnvironmentFujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyFujian Agriculture and Forestry UniversityFuzhouChina
- FAFU‐UCR Joint Center for Horticultural Biology and MetabolomicsHaixia Institute of Science and TechnologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Jiafeng Sun
- College of Resources and EnvironmentFujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyFujian Agriculture and Forestry UniversityFuzhouChina
- FAFU‐UCR Joint Center for Horticultural Biology and MetabolomicsHaixia Institute of Science and TechnologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Maoxiang Yang
- College of Resources and EnvironmentFujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyFujian Agriculture and Forestry UniversityFuzhouChina
- FAFU‐UCR Joint Center for Horticultural Biology and MetabolomicsHaixia Institute of Science and TechnologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Lan Yang
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi ProvinceCollege of Life ScienceNanchang UniversityJiangxiChina
| | - Dong Wang
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi ProvinceCollege of Life ScienceNanchang UniversityJiangxiChina
| | - Shikui Song
- FAFU‐UCR Joint Center for Horticultural Biology and MetabolomicsHaixia Institute of Science and TechnologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Yuefeng Guan
- FAFU‐UCR Joint Center for Horticultural Biology and MetabolomicsHaixia Institute of Science and TechnologyFujian Agriculture and Forestry UniversityFuzhouChina
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20
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Gao YL, Yao XF, Li WZ, Song ZB, Wang BW, Wu YP, Shi JL, Liu GS, Li YP, Liu CM. An efficient TILLING platform for cultivated tobacco. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020; 62:165-180. [PMID: 30697931 DOI: 10.1111/jipb.12784] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 01/23/2019] [Indexed: 06/09/2023]
Abstract
Targeting-induced local lesions in genomes (TILLING) is a powerful reverse-genetics tool that enables high-throughput screening of genomic variations in plants. Although TILLING has been developed for many diploid plants, the technology has been used in very few polyploid species due to their genomic complexity. Here, we established an efficient capillary electrophoresis-based TILLING platform for allotetraploid cultivated tobacco (Nicotiana tabacum L.) using an ethyl methanesulfonate (EMS)-mutagenized population of 1,536 individuals. We optimized the procedures for endonuclease preparation, leaf tissue sampling, DNA extraction, normalization, pooling, PCR amplification, heteroduplex formation, and capillary electrophoresis. In a test screen using seven target genes with eight PCR fragments, we obtained 118 mutants. The mutation density was estimated to be approximately one mutation per 106 kb on average. Phenotypic analyses showed that mutations in two heavy metal transporter genes, HMA2S and HMA4T, led to reduced accumulation of cadmium and zinc, which was confirmed independently using CRISPR/Cas9 to generate knockout mutants. Our results demonstrate that this powerful TILLING platform (available at http://www.croptilling.org) can be used in tobacco to facilitate functional genomics applications.
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Affiliation(s)
- Yu-Long Gao
- Key Laboratory of Tobacco Biotechnological Breeding, National Tobacco Genetic Engineering Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, China
| | - Xue-Feng Yao
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- The University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wen-Zheng Li
- Key Laboratory of Tobacco Biotechnological Breeding, National Tobacco Genetic Engineering Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, China
| | - Zhong-Bang Song
- Key Laboratory of Tobacco Biotechnological Breeding, National Tobacco Genetic Engineering Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, China
| | - Bing-Wu Wang
- Key Laboratory of Tobacco Biotechnological Breeding, National Tobacco Genetic Engineering Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, China
| | - Yu-Ping Wu
- Key Laboratory of Tobacco Biotechnological Breeding, National Tobacco Genetic Engineering Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, China
| | - Jun-Li Shi
- Key Laboratory of Tobacco Biotechnological Breeding, National Tobacco Genetic Engineering Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, China
| | - Guan-Shan Liu
- Tobacco Research Institute, the Chinese Agriculture Academy of Sciences, Qingdao, 266101, China
| | - Yong-Ping Li
- Key Laboratory of Tobacco Biotechnological Breeding, National Tobacco Genetic Engineering Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, China
| | - Chun-Ming Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- Institute of Crop Sciences, the Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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21
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Zhou Z, Lakhssassi N, Cullen MA, El Baz A, Vuong TD, Nguyen HT, Meksem K. Assessment of Phenotypic Variations and Correlation among Seed Composition Traits in Mutagenized Soybean Populations. Genes (Basel) 2019; 10:E975. [PMID: 31783508 PMCID: PMC6947669 DOI: 10.3390/genes10120975] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 11/22/2019] [Accepted: 11/22/2019] [Indexed: 01/31/2023] Open
Abstract
Soybean [Glycine max (L.) Merr.] seed is a valuable source of protein and oil worldwide. Traditionally, the natural variations were heavily used in conventional soybean breeding programs to select desired traits. However, traditional plant breeding is encumbered with low frequencies of spontaneous mutations. In mutation breeding, genetic variations from induced mutations provide abundant sources of alterations in important soybean traits; this facilitated the development of soybean germplasm with modified seed composition traits to meet the different needs of end users. In this study, a total of 2366 'Forrest'-derived M2 families were developed for both forward and reverse genetic studies. A subset of 881 M3 families was forward genetically screened to measure the contents of protein, oil, carbohydrates, and fatty acids. A total of 14 mutants were identified to have stable seed composition phenotypes observed in both M3 and M4 generations. Correlation analyses have been conducted among ten seed composition traits and compared to a collection of 103 soybean germplasms. Mainly, ethyl methanesulfonate (EMS) mutagenesis had a strong impact on the seed-composition correlation that was observed among the 103 soybean germplasms, which offers multiple benefits for the soybean farmers and industry to breed for desired multiple seed phenotypes.
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Affiliation(s)
- Zhou Zhou
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (Z.Z.); (N.L.); (M.A.C.); (A.E.B.)
| | - Naoufal Lakhssassi
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (Z.Z.); (N.L.); (M.A.C.); (A.E.B.)
| | - Mallory A. Cullen
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (Z.Z.); (N.L.); (M.A.C.); (A.E.B.)
| | - Abdelhalim El Baz
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (Z.Z.); (N.L.); (M.A.C.); (A.E.B.)
| | - Tri D. Vuong
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA; (T.D.V.); (H.T.N.)
| | - Henry T. Nguyen
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA; (T.D.V.); (H.T.N.)
| | - Khalid Meksem
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (Z.Z.); (N.L.); (M.A.C.); (A.E.B.)
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22
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Afzal M, Alghamdi SS, Migdadi HH, Khan MA, Nurmansyah, Mirza SB, El-Harty E. Legume genomics and transcriptomics: From classic breeding to modern technologies. Saudi J Biol Sci 2019; 27:543-555. [PMID: 31889880 PMCID: PMC6933173 DOI: 10.1016/j.sjbs.2019.11.018] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 11/16/2019] [Accepted: 11/17/2019] [Indexed: 02/06/2023] Open
Abstract
Legumes are essential and play a significant role in maintaining food standards and augmenting physiochemical soil properties through the biological nitrogen fixation process. Biotic and abiotic factors are the main factors limiting legume production. Classical breeding methodologies have been explored extensively about the problem of truncated yield in legumes but have not succeeded at the desired rate. Conventional breeding improved legume genotypes but with more resources and time. Recently, the invention of next-generation sequencing (NGS) and high-throughput methods for genotyping have opened new avenues for research and developments in legume studies. During the last decade, genome sequencing for many legume crops documented. Sequencing and re-sequencing of important legume species have made structural variation and functional genomics conceivable. NGS and other molecular techniques such as the development of markers; genotyping; high density genetic linkage maps; quantitative trait loci (QTLs) identification, expressed sequence tags (ESTs), single nucleotide polymorphisms (SNPs); and transcription factors incorporated into existing breeding technologies have made possible the accurate and accelerated delivery of information for researchers. The application of genome sequencing, RNA sequencing (transcriptome sequencing), and DNA sequencing (re-sequencing) provide considerable insights for legume development and improvement programs. Moreover, RNA-Seq helps to characterize genes, including differentially expressed genes, and can be applied for functional genomics studies, especially when there is limited information available for the studied genomes. Genome-based crop development studies and the availability of genomics data as well as decision-making gears look be specific for breeding programs. This review mainly presents an overview of the path from classical breeding to new emerging genomics tools, which will trigger and accelerate genomics-assisted breeding for recognition of novel genes for yield and quality characters for sustainable legume crop production.
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Affiliation(s)
- Muhammad Afzal
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Salem S Alghamdi
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Hussein H Migdadi
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Muhammad Altaf Khan
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Nurmansyah
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Shaher Bano Mirza
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University (BAU), Istanbul, Turkey.,Department of Biosciences, COMSATS Institute of Information Technology (CIIT), Chak Shahzad, Islamabad, Pakistan
| | - Ehab El-Harty
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
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23
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Islam N, Stupar RM, Qijian S, Luthria DL, Garrett W, Stec AO, Roessler J, Natarajan SS. Genomic changes and biochemical alterations of seed protein and oil content in a subset of fast neutron induced soybean mutants. BMC PLANT BIOLOGY 2019; 19:420. [PMID: 31604426 PMCID: PMC6790046 DOI: 10.1186/s12870-019-1981-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 08/19/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Soybean is subjected to genetic manipulation by breeding, mutation, and transgenic approaches to produce value-added quality traits. Among those genetic approaches, mutagenesis through fast neutrons radiation is intriguing because it yields a variety of mutations, including single/multiple gene deletions and/or duplications. Characterizing the seed composition of the fast neutron mutants and its relationship with gene mutation is useful towards understanding oil and protein traits in soybean. RESULTS From a large population of fast neutron mutagenized plants, we selected ten mutants based on a screening of total oil and protein content using near infra-red spectroscopy. These ten mutants were regrown, and the seeds were analyzed for oil by GC-MS, protein profiling by SDS-PAGE and gene mapping by comparative genomic hybridization. The mutant 2R29C14Cladecr233cMN15 (nicknamed in this study as L10) showed higher protein and lower oil content compared to the wild type, followed by three other lines (nicknamed in this study as L03, L05, and L06). We characterized the fatty acid methyl esters profile of the trans-esterified oil and found the presence of five major fatty acids (palmitic, stearic, oleic, linoleic, and linolenic acids) at varying proportions among the mutants. Protein profile using SDS-PAGE of the ten mutants did exhibit discernable variation between storage (glycinin and β-conglycinin) and anti-nutritional factor (trypsin inhibitor) proteins. In addition, we physically mapped the position of the gene deletions or duplications in each mutant using comparative genomic hybridization. CONCLUSION Characterization of oil and protein profile in soybean fast neutron mutants will assist scientist and breeders to develop new value-added soybeans with improved protein and oil quality traits.
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Affiliation(s)
- Nazrul Islam
- Soybean Genomics and Improvement Laboratory, USDA-ARS, NEA, 10300, Baltimore Avenue, Beltsville, MD, USA
| | - Robert M Stupar
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, USA
| | - Song Qijian
- Soybean Genomics and Improvement Laboratory, USDA-ARS, NEA, 10300, Baltimore Avenue, Beltsville, MD, USA
| | - Devanand L Luthria
- Food Composition and Methods Development Laboratory, USDA-ARS, NEA, Beltsville, MD, USA
| | - Wesley Garrett
- Animal Biosciences & Biotechnology Laboratory, USDA-ARS, NEA, Beltsville, MD, USA
| | - Adrian O Stec
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, USA
| | - Jeff Roessler
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, USA
| | - Savithiry S Natarajan
- Soybean Genomics and Improvement Laboratory, USDA-ARS, NEA, 10300, Baltimore Avenue, Beltsville, MD, USA.
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24
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Liu S, Ge F, Huang W, Lightfoot DA, Peng D. Effective identification of soybean candidate genes involved in resistance to soybean cyst nematode via direct whole genome re-sequencing of two segregating mutants. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:2677-2687. [PMID: 31250041 DOI: 10.1007/s00122-019-03381-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 06/14/2019] [Indexed: 06/09/2023]
Abstract
KEY MESSAGE Three soybean candidate genes involved in resistance to soybean cyst nematode race 4 were identified via direct whole genome re-sequencing of two segregating mutants. The genes conferring resistance to soybean cyst nematode (SCN) race 4 (Hg type 1.2.3.5.7) in soybean (Glycine max L. Merr.) remains unknown. Next generation sequencing-based methods identify a wide range of targets, it is difficult to identify genes underlying traits. Use of the MutMap and QTL-seq methods to identify trait candidate genes needs backcrossing and is very time-consuming. Here we report a simple method to effectively identify candidate genes involved in resistance to SCN race 4. Two ethane methylsulfonate mutagenized mutants of soybean 'PI 437654', whose SCN race 4-infection phenotype altered, were selected. Six relevant whole genomes were re-sequenced, and then calling of genomic variants (SNPs and InDels) was conducted and compared to 'Williams 82'. The comparison eliminated many genomic variants from the mutant lines that overlapped two non-phenotypic but mutant progeny plants, wild-type PI 437654 and 'Zhonghuang 13'. Finally, only 27 mutations were found among 10 genes. Of these 10 genes, 3 genes, Glyma.09g054000, Glyma.16g065700 and Glyma.18g192200 were overlapped between two phenotypic mutant progeny plants. Therefore, the three genes may be the candidate genes involved in resistance of PI 437654 to soybean cyst nematode race 4. This method simplifies the effective identification of candidate genes.
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Affiliation(s)
- Shiming Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China.
- College of Plant Protection, Hunan Agricultural University, Changsha, 410128, People's Republic of China.
| | - Fengyong Ge
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China
| | - Wenkun Huang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China
| | - David A Lightfoot
- College of Agricultural Sciences, Southern Illinois University, Carbondale, IL, 62901, USA
| | - Deliang Peng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China
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25
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Krishnamurthy P, Fujisawa Y, Takahashi Y, Abe H, Yamane K, Mukaiyama K, Son HR, Hiraga S, Kaga A, Anai T, Tsukamoto C, Ishimoto M. High-Throughput Screening and Characterization of a High-Density Soybean Mutant Library Elucidate the Biosynthesis Pathway of Triterpenoid Saponins. PLANT & CELL PHYSIOLOGY 2019; 60:1082-1097. [PMID: 30753604 DOI: 10.1093/pcp/pcz025] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 01/31/2019] [Indexed: 05/21/2023]
Abstract
Triterpenes (C30) constitute one of the diverse class of natural products with potential applications in food, cosmetic and pharmaceutical industries. Soyasaponins are oleanane-type triterpenoids widespread among legumes and particularly abundant in soybean seeds. They have associated with various pharmacological implications and undesirable taste properties of soybean-based food products. Uncovering the biosynthetic genes of soyasaponins will provide new opportunities to control the pathway for human benefits. However, the pathway of soyasaponin biosynthesis has not been fully elucidated in part because of a paucity of natural mutants. Here, we applied a structured high-density soybean mutant library for the forward genetic screening of triterpenoid biosynthesis. The seed soyasaponin polymorphism in the mutant library was evaluated using a high-throughput thin-layer chromatography and liquid chromatography tandem mass spectrometry analysis. This screening identified 35 mutants (3.85% of 909 mutant lines) with seven unusual soyasaponin phenotypes (Categories 1-7), which was greater than the number of natural mutants reported previously (22 mutants, 0.18% of ∼12,428 accessions). Nine unique intermediates of soyasaponin biosynthesis were identified and their chemical structures were estimated based on their MS/MS fragment patterns. Based on published information, 19 mutants could be associated with loss of function of four individual soyasaponin biosynthesis genes identified through expressed sequence tag mining or positional cloning, whereas the remaining 16 mutants were novel and may facilitate discovery of the unknown biosynthetic genes of soyasaponins. Our approach and library may help to identify new phenotype materials and causative genes associated with specialized metabolite production and other traits.
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Affiliation(s)
| | | | - Yuya Takahashi
- Faculty of Agriculture, Iwate University, Morioka, Iwate, Japan
| | - Hanako Abe
- Faculty of Agriculture, Iwate University, Morioka, Iwate, Japan
| | - Kentaro Yamane
- Faculty of Agriculture, Iwate University, Morioka, Iwate, Japan
| | | | - Hae-Reon Son
- Faculty of Agriculture, Iwate University, Morioka, Iwate, Japan
| | - Susumu Hiraga
- Institute of Crop Science, NARO, Tsukuba, Ibaraki, Japan
| | - Akito Kaga
- Institute of Crop Science, NARO, Tsukuba, Ibaraki, Japan
| | - Toyoaki Anai
- Faculty of Agriculture, Saga University, Saga, Japan
| | | | - Masao Ishimoto
- Institute of Crop Science, NARO, Tsukuba, Ibaraki, Japan
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26
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Jiao K, Li X, Guo Y, Guan Y, Guo W, Luo D, Hu Z, Shen Z. Regulation of compound leaf development in mungbean (Vigna radiata L.) by CUP-SHAPED COTYLEDON/NO APICAL MERISTEM (CUC/NAM) gene. PLANTA 2019; 249:765-774. [PMID: 30390139 DOI: 10.1007/s00425-018-3038-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Accepted: 10/31/2018] [Indexed: 05/09/2023]
Abstract
The results provide a significant verification of functional redundancy and diversity of CUC/NAM genes in legumes. The CUP-SHAPED COTYLEDON/NO APICAL MERISTEM (CUC/NAM) orthologs play key roles for plant organ boundary formation and organ development. Here, we performed a forward screen of the gamma irradiation mutagenesis population in mungbean and characterised a mutant, reduced rachis and fused leaflets (rrf1), which gave rise to the formation of compound leaves with reduced rachis and fused leaflets. Map-based cloning revealed that RRF1 encoded a CUC/NAM protein in mungbean. Phylogenetic analysis indicated that legume CUC1/CUC2 genes were classified as belonging to two subclades, and there are different copies of CUC1/CUC2 genes in legumes. Transcriptomic analysis showed that expression levels of a set of developmental regulators, including class I KNOTTED-LIKE HOMEOBOXI (KNOXI) gene and LATERAL ORGAN BOUNDARIES DOMAIN (LBD) gene, were altered in rrf1 mutants compared to the wild-type plants. Furthermore, rrf1 genetically interacted with heptafoliate leaflets1 (hel1), a mutant displaying a seven-leaflet compound leaf, to regulate leaf development in mungbean. Our results suggest functional redundancy and diversity of two subclades of CUC1/CUC2 genes in legumes, following the duplication of an ancestral gene.
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Affiliation(s)
- Keyuan Jiao
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy, Jinan University, Guangzhou, China
| | - Xin Li
- Laboratory Center of Life Sciences, College of Life Sciences, Nanjing Agricultural University, Nanjing, China.
| | - Yafang Guo
- Laboratory Center of Life Sciences, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Yining Guan
- Laboratory Center of Life Sciences, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Wuxiu Guo
- Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Da Luo
- Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Zhubing Hu
- State Key Laboratory of Cotton Biology, Department of Biology, Institute of Plant Stress Biology, Henan University, Kaifeng, China
| | - Zhenguo Shen
- Laboratory Center of Life Sciences, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
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27
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Sun J, Luu NS, Chen Z, Chen B, Cui X, Wu J, Zhang Z, Lu T. Generation and Characterization of a Foxtail Millet ( Setaria italica) Mutant Library. FRONTIERS IN PLANT SCIENCE 2019; 10:369. [PMID: 31001298 PMCID: PMC6455083 DOI: 10.3389/fpls.2019.00369] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 03/11/2019] [Indexed: 05/20/2023]
Abstract
Foxtail millet (Setaria italica) is attractive to plant scientists as a model plant because of several distinct characteristics, such as its short stature, rapid life cycle, sufficient seed production per plant, self-compatibility, true diploid nature, high photosynthetic efficiency, small genome size, and tolerance to abiotic and biotic stress. However, the study on the genetic resources of foxtail millet largely lag behind those of the other model plants such as Arabidopsis, rice and maize. Mutagenized populations cannot only create new germplasm resources, but also provide materials for gene function research. In this manuscript, an ethyl methanesulfonate (EMS)-induced foxtail millet population comprising ∼15,000 individual M1 lines was established. Total 1353 independent lines with diverse abnormal phenotypes of leaf color, plant morphologies and panicle shapes were identified in M2. Resequencing of sixteen randomly selected M2 plants showed an average estimated mutation density of 1 loci/213 kb. Moreover, we provided an example for rapid cloning of the WP1 gene by a map-based cloning method. A white panicle mutant, named as wp1.a, exhibited significantly reduced chlorophyll (Chl) and carotenoid contents in leaf and panicle. Map-based cloning results showed an eight-base pair deletion located at the sixth exon of wp1.a in LOC101786849, which caused the premature termination. WP1 encoded phytoene synthase. Moreover, the sequencing analysis and cross test verified that a white panicle mutant wp1.b was an allelic mutant of wp1.a. The filed phenotypic observation and gene cloning example showed that our foxtail millet EMS-induced mutant population would be used as an important resource for functional genomics studies of foxtail millet.
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Affiliation(s)
| | | | | | | | | | | | | | - Tiegang Lu
- *Correspondence: Zhiguo Zhang, Tiegang Lu,
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28
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Jiao K, Li X, Su S, Guo W, Guo Y, Guan Y, Hu Z, Shen Z, Luo D. Genetic control of compound leaf development in the mungbean ( Vigna radiata L.). HORTICULTURE RESEARCH 2019; 6:23. [PMID: 30729013 PMCID: PMC6355865 DOI: 10.1038/s41438-018-0088-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Revised: 07/25/2018] [Accepted: 08/07/2018] [Indexed: 05/09/2023]
Abstract
Many studies suggest that there are distinct regulatory processes controlling compound leaf development in different clades of legumes. Loss of function of the LEAFY (LFY) orthologs results in a reduction of leaf complexity to different degrees in inverted repeat-lacking clade (IRLC) and non-IRLC species. To further understand the role of LFY orthologs and the molecular mechanism in compound leaf development in non-IRLC plants, we studied leaf development in unifoliate leaf (un) mutant, a classical mutant of mungbean (Vigna radiata L.), which showed a complete conversion of compound leaves into simple leaves. Our analysis revealed that UN encoded the mungbean LFY ortholog (VrLFY) and played a significant role in leaf development. In situ RNA hybridization results showed that STM-like KNOXI genes were expressed in compound leaf primordia in mungbean. Furthermore, increased leaflet number in heptafoliate leaflets1 (hel1) mutants was demonstrated to depend on the function of VrLFY and KNOXI genes in mungbean. Our results suggested that HEL1 is a key factor coordinating distinct processes in the control of compound leaf development in mungbean and its related non-IRLC legumes.
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Affiliation(s)
- Keyuan Jiao
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy, Jinan University, Guangzhou, China
| | - Xin Li
- College of Life Sciences, Laboratory Center of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Shihao Su
- Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Wuxiu Guo
- Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Yafang Guo
- College of Life Sciences, Laboratory Center of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Yining Guan
- College of Life Sciences, Laboratory Center of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Zhubing Hu
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, Kaifeng, China
| | - Zhenguo Shen
- College of Life Sciences, Laboratory Center of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Da Luo
- Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
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29
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Li ZF, Guo Y, Ou L, Hong H, Wang J, Liu ZX, Guo B, Zhang L, Qiu L. Identification of the dwarf gene GmDW1 in soybean (Glycine max L.) by combining mapping-by-sequencing and linkage analysis. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:1001-1016. [PMID: 29550969 PMCID: PMC5895683 DOI: 10.1007/s00122-017-3044-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 12/17/2017] [Indexed: 05/10/2023]
Abstract
KEY MESSAGE GmDW1 encodes an ent-kaurene synthase (KS) acting at the early step of the biosynthesis pathway for gibberellins (GAs) and regulates the development of plant height in soybean. Plant height is an important component of plant architecture, and significantly affects crop breeding practices and yield. Here, we report the characterization of an EMS-induced dwarf mutant (dw) of the soybean cultivar Zhongpin 661 (ZDD23893). The dw mutant displayed reduced plant height and shortened internodes, both of which were mainly attributed to the longitudinally decreased cell length. The bioactive GA1 (gibberellin A1) and GA4 (gibberellin A4) were not detectable in the stem of dw, and the dwarf phenotype could be rescued by treatment with exogenous GA3. Genetic analysis showed that the dwarf trait of dw was controlled by a recessive nuclear gene. By combining linkage analysis and mapping-by-sequencing, we mapped the GmDW1 gene to an approximately 460-kb region on chromosome (Chr.) 8, containing 36 annotated genes in the reference Willliams 82 genome. Of these genes, we identified two nonsynonymous single nucleotide polymorphisms (SNPs) that are present in the encoding regions of Gmdw1 and Glyma.08G165100 in dw, respectively. However, only the SNP mutation (T>A) at nucleotide 1224 in Gmdw1 cosegregated with the dwarf phenotype. GmDW1 encodes an ent-kaurene synthase, and was expressed in various tissues including root, stem, and leaf. Further phenotypic analysis of the allelic variations in soybean accessions strongly indicated that GmDW1 is responsible for the dwarf phenotype in dw. Our results provide important information for improving our understanding of the genetics of soybean plant height and crop breeding.
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Affiliation(s)
- Zhong-Feng Li
- National Key Facility for Gene Resources and Genetic Improvement/Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture, Institute of Crop Sciences, Chinese Academy of Agricultural Science, No. 12 Zhongguancun South Street, Haidian District, Beijing, 100081, People's Republic of China
| | - Yong Guo
- National Key Facility for Gene Resources and Genetic Improvement/Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture, Institute of Crop Sciences, Chinese Academy of Agricultural Science, No. 12 Zhongguancun South Street, Haidian District, Beijing, 100081, People's Republic of China
| | - Lin Ou
- College of Agriculture, Yangzi University, Jingzhou, 434025, People's Republic of China
| | - Huilong Hong
- National Key Facility for Gene Resources and Genetic Improvement/Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture, Institute of Crop Sciences, Chinese Academy of Agricultural Science, No. 12 Zhongguancun South Street, Haidian District, Beijing, 100081, People's Republic of China
| | - Jun Wang
- College of Agriculture, Yangzi University, Jingzhou, 434025, People's Republic of China
| | - Zhang-Xiong Liu
- National Key Facility for Gene Resources and Genetic Improvement/Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture, Institute of Crop Sciences, Chinese Academy of Agricultural Science, No. 12 Zhongguancun South Street, Haidian District, Beijing, 100081, People's Republic of China
| | - Bingfu Guo
- National Key Facility for Gene Resources and Genetic Improvement/Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture, Institute of Crop Sciences, Chinese Academy of Agricultural Science, No. 12 Zhongguancun South Street, Haidian District, Beijing, 100081, People's Republic of China
| | - Lijuan Zhang
- National Key Facility for Gene Resources and Genetic Improvement/Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture, Institute of Crop Sciences, Chinese Academy of Agricultural Science, No. 12 Zhongguancun South Street, Haidian District, Beijing, 100081, People's Republic of China
| | - Lijuan Qiu
- National Key Facility for Gene Resources and Genetic Improvement/Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture, Institute of Crop Sciences, Chinese Academy of Agricultural Science, No. 12 Zhongguancun South Street, Haidian District, Beijing, 100081, People's Republic of China.
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Song J, Li Z, Liu Z, Guo Y, Qiu LJ. Next-Generation Sequencing from Bulked-Segregant Analysis Accelerates the Simultaneous Identification of Two Qualitative Genes in Soybean. FRONTIERS IN PLANT SCIENCE 2017; 8:919. [PMID: 28620406 PMCID: PMC5449466 DOI: 10.3389/fpls.2017.00919] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 05/16/2017] [Indexed: 05/03/2023]
Abstract
Next-generation sequencing (NGS)-based bulked-segregant analysis (BSA) approaches have been proven successful for rapidly mapping genes in plant species. However, most such methods are based on mutants and usually only one gene controlling the mutant phenotype is identified. In this study, NGS-based BSA was employed to map simultaneously two qualitative genes controlling cotyledon color of seed in soybean. Yellow-cotyledon (YC) and green-cotyledon (GC) bulks from progenies of a biparental population (Zhonghuang 30 × Jiyu 102) were sequenced. The SNP-index of each SNP locus in YC and GC bulks was calculated and two genomic regions on chromosomes 1 and 11 harboring, respectively, loci qCC1 and qCC2 were identified by Δ(SNP-index) analysis. These two BSA-seq-derived loci were further validated with SSR markers and fine-mapped. qCC1 was mapped to a 30.7-kb region containing four annotated genes and qCC2 was mapped to a 67.7-kb region with nine genes. These two regions contained, respectively, genes D1 and D2, which had previously been identified by homology-based cloning as being associated with cotyledon color. Sequence analysis of the NGS data also identified a frameshift deletion in the coding region of D1. These results suggested that BSA-seq could accelerate the mapping of loci controlling qualitative traits, even if a trait is controlled by more than one locus.
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Affiliation(s)
| | | | | | - Yong Guo
- *Correspondence: Li-Juan Qiu, Yong Guo,
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