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Cho Y, Kim JY, Kim SK, Kim SY, Kim N, Lee J, Park JL. Whole-genome sequencing analysis of soybean diversity across different countries and selection signature of Korean soybean accession. G3 (BETHESDA, MD.) 2024; 14:jkae118. [PMID: 38833595 PMCID: PMC11304964 DOI: 10.1093/g3journal/jkae118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 04/24/2024] [Accepted: 05/20/2024] [Indexed: 06/06/2024]
Abstract
Soybean is an important agricultural crop known for its high protein and oil content, contributing to essential nutritional and health benefits for humans. Domesticated in China over 5,000 years ago, soybean has since adapted to diverse environments and spread worldwide. This study aimed to investigate the genomic characteristics and population structures of 2,317 publicly available soybean whole-genome sequences from diverse geographical regions, including China, Korea, Japan, Europe, North America, and South America. We used large-scale whole-genome sequencing data to perform high-resolution analyses to reveal the genetic characteristics of soybean accessions. Soybean accessions from China and Korea exhibited landrace characteristics, indicating higher genetic diversity and adaptation to local environments. On the other hand, soybean accessions from Japan, the European Union, and South America were found to have low genetic diversity due to artificial selection and breeding for agronomic traits. We also identified key variants and genes associated with the ability to adapt to different environments. In Korean soybean accessions, we observed strong selection signals for isoflavone synthesis, an adaptive trait critical for improving soybean adaptability, survival, and reproductive success by mitigating environmental stress. Identifying specific genomic regions showing unique patterns of selective sweeps for genes such as HIDH, CYP73A11, IFS1, and CYP81E11 associated with isoflavone synthesis provided valuable insights into potential adaptation mechanisms. Our research has significantly improved our understanding of soybean diversity at the genetic level. We have identified key genetic variants and genes influencing adaptability, laying the foundation for future advances in genomics-based breeding programs and crop improvement efforts.
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Affiliation(s)
- Youngbeom Cho
- Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon 34141, Republic of Korea
- Aging Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Jae-Yoon Kim
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Seon-Kyu Kim
- Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon 34141, Republic of Korea
- Aging Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Seon-Young Kim
- Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon 34141, Republic of Korea
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Namshin Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Jinhyuk Lee
- Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon 34141, Republic of Korea
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Jong-Lyul Park
- Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon 34141, Republic of Korea
- Aging Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
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Zhu X, Wang H, Li Y, Rao D, Wang F, Gao Y, Zhong W, Zhao Y, Wu S, Chen X, Qiu H, Zhang W, Xia Z. A Novel 10-Base Pair Deletion in the First Exon of GmHY2a Promotes Hypocotyl Elongation, Induces Early Maturation, and Impairs Photosynthetic Performance in Soybean. Int J Mol Sci 2024; 25:6483. [PMID: 38928189 PMCID: PMC11203641 DOI: 10.3390/ijms25126483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 06/03/2024] [Accepted: 06/07/2024] [Indexed: 06/28/2024] Open
Abstract
Plants photoreceptors perceive changes in light quality and intensity and thereby regulate plant vegetative growth and reproductive development. By screening a γ irradiation-induced mutant library of the soybean (Glycine max) cultivar "Dongsheng 7", we identified Gmeny, a mutant with elongated nodes, yellowed leaves, decreased chlorophyll contents, altered photosynthetic performance, and early maturation. An analysis of bulked DNA and RNA data sampled from a population segregating for Gmeny, using the BVF-IGV pipeline established in our laboratory, identified a 10 bp deletion in the first exon of the candidate gene Glyma.02G304700. The causative mutation was verified by a variation analysis of over 500 genes in the candidate gene region and an association analysis, performed using two populations segregating for Gmeny. Glyma.02G304700 (GmHY2a) is a homolog of AtHY2a in Arabidopsis thaliana, which encodes a PΦB synthase involved in the biosynthesis of phytochrome. A transcriptome analysis of Gmeny using the Kyoto Encyclopedia of Genes and Genomes (KEGG) revealed changes in multiple functional pathways, including photosynthesis, gibberellic acid (GA) signaling, and flowering time, which may explain the observed mutant phenotypes. Further studies on the function of GmHY2a and its homologs will help us to understand its profound regulatory effects on photosynthesis, photomorphogenesis, and flowering time.
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Affiliation(s)
- Xiaobin Zhu
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China; (X.Z.); (H.W.); (Y.L.); (F.W.); (Y.G.); (W.Z.); (Y.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haiyan Wang
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China; (X.Z.); (H.W.); (Y.L.); (F.W.); (Y.G.); (W.Z.); (Y.Z.)
| | - Yuzhuo Li
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China; (X.Z.); (H.W.); (Y.L.); (F.W.); (Y.G.); (W.Z.); (Y.Z.)
| | - Demin Rao
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, Changchun 132102, China; (D.R.); (H.Q.); (W.Z.)
| | - Feifei Wang
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China; (X.Z.); (H.W.); (Y.L.); (F.W.); (Y.G.); (W.Z.); (Y.Z.)
| | - Yi Gao
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China; (X.Z.); (H.W.); (Y.L.); (F.W.); (Y.G.); (W.Z.); (Y.Z.)
| | - Weiyu Zhong
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China; (X.Z.); (H.W.); (Y.L.); (F.W.); (Y.G.); (W.Z.); (Y.Z.)
| | - Yujing Zhao
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China; (X.Z.); (H.W.); (Y.L.); (F.W.); (Y.G.); (W.Z.); (Y.Z.)
| | - Shihao Wu
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (S.W.); (X.C.)
| | - Xin Chen
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (S.W.); (X.C.)
| | - Hongmei Qiu
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, Changchun 132102, China; (D.R.); (H.Q.); (W.Z.)
| | - Wei Zhang
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, Changchun 132102, China; (D.R.); (H.Q.); (W.Z.)
| | - Zhengjun Xia
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China; (X.Z.); (H.W.); (Y.L.); (F.W.); (Y.G.); (W.Z.); (Y.Z.)
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Yang Y, Wang L, Zhang D, Che Z, Wang Q, Cui R, Zhao W, Huang F, Zhang H, Cheng H, Yu D. Soybean type-B response regulator GmRR1 mediates phosphorus uptake and yield by modifying root architecture. PLANT PHYSIOLOGY 2024; 194:1527-1544. [PMID: 37882637 DOI: 10.1093/plphys/kiad570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 09/21/2023] [Accepted: 09/22/2023] [Indexed: 10/27/2023]
Abstract
Phosphorus (P) plays a pivotal role in plant growth and development. Low P stress can greatly hamper plant growth. Here, we identified a QTL (named QPH-9-1), which is associated with P efficiency across multiple environments through linkage analysis and genome-wide association study. Furthermore, we successfully cloned the underlying soybean (Glycine max) gene GmRR1 (a soybean type-B Response Regulator 1) that encodes a type-B response regulator protein. Knockout of GmRR1 resulted in a substantial increase in plant height, biomass, P uptake efficiency, and yield-related traits due to the modification of root structure. In contrast, overexpression of GmRR1 in plants resulted in a decrease in these phenotypes. Further analysis revealed that knockout of GmRR1 substantially increased the levels of auxin and ethylene in roots, thereby promoting root hair formation and growth by promoting the formation of root hair primordium and lengthening the root apical meristem. Yeast two-hybrid, bimolecular fluorescence complementation, and dual-luciferase assays demonstrated an interaction between GmRR1 and Histidine-containing Phosphotransmitter protein 1. Expression analysis suggested that these proteins coparticipated in response to low P stress. Analysis of genomic sequences showed that GmRR1 underwent a selection during soybean domestication. Taken together, this study provides further insights into how plants respond to low P stress by modifying root architecture through phytohormone pathways.
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Affiliation(s)
- Yuming Yang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
- School of Agriculture, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Li Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
- School of Agriculture, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Dan Zhang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
| | - Zhijun Che
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
- School of Agriculture, Ningxia University, Yinchuan 750021, China
| | - Qing Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Ruifan Cui
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
| | - Wei Zhao
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Fang Huang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Hengyou Zhang
- Northeast Institute of Geography and Agroecology, Key Laboratory of Soybean Molecular Design Breeding, Chinese Academy of Sciences, Harbin 150081, China
| | - Hao Cheng
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Deyue Yu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
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Talib N, Mohamad NE, Yeap SK, Ho CL, Masarudin MJ, Abd-Aziz S, Izham MNM, Kumar MR, Hussin Y, Alitheen NB. Anti-Diabetic Effect of Lactobacillus Paracasei Isolated from Malaysian Water Kefir Grains. Probiotics Antimicrob Proteins 2023:10.1007/s12602-023-10159-2. [PMID: 37755545 DOI: 10.1007/s12602-023-10159-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/12/2023] [Indexed: 09/28/2023]
Abstract
The prevalence of type 2 diabetes mellitus (T2DM) is alarming because it is always linked to the increase in chronic diseases, mortality, and socioeconomic burden. Water kefir has a wide range of functional and probiotic characteristics attributed to the microorganisms present in the kefir grains. The present study aims to evaluate the in vivo anti-diabetic potential of the isolated Lactobacillus paracasei from Malaysian water kefir grains (MWKG) which was reported to have excellent probiotic properties and high antioxidant activities as reported previously. High-fat diet/streptozotocin (HFD/STZ) induction was used to obtain a T2DM model followed by treatment with the isolated L. paracasei from MWKG. The levels of glucose, insulin, and in vivo liver antioxidants were quantified after 14 weeks. Gene expression analysis of the liver was also carried out using microarray analysis, and several genes were selected for validation using quantitative real-time PCR. Insulin tolerance test demonstrated that the L. paracasei isolated from the MWKG alleviated T2DM by improving the area under the curve of the insulin tolerance test whereby low-dose and high-dose concentrations treated groups showed 2424.50 ± 437.02 mmol/L·min and 2017.50 ± 347.09 mmol/L·min, respectively, compared to untreated diabetic mice which was 3884.50 ± 39.36 mmol/L·min. Additionally, treatment with the isolated L. paracasei from MWKG regulated the expression of several genes related to glucose homeostasis and lipid metabolism in diabetic mice. These results suggested that the isolated L. paracasei from MWKG could be a potential dietary supplement for T2DM.
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Affiliation(s)
- Noorshafadzilah Talib
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor Darul Ehsan, Malaysia
| | - Nurul Elyani Mohamad
- Biotechnology Research Institute, Universiti Malaysia Sabah, 88400, Kota Kinabalu, Sabah, Malaysia
| | - Swee Keong Yeap
- China-ASEAN College of Marine Sciences, Xiamen University Malaysia, 43900, Sepang, Malaysia
| | - Chai Ling Ho
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor Darul Ehsan, Malaysia
| | - Mas Jaffri Masarudin
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor Darul Ehsan, Malaysia
- UPM-MAKNA Cancer Research Laboratory, Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor Darul Ehsan, Malaysia
| | - Suraini Abd-Aziz
- Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor Darul Ehsan, Malaysia
| | - Mira Nadiah Mohd Izham
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor Darul Ehsan, Malaysia
| | - Muganti Rajah Kumar
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor Darul Ehsan, Malaysia
| | - Yazmin Hussin
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor Darul Ehsan, Malaysia
| | - Noorjahan Banu Alitheen
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor Darul Ehsan, Malaysia.
- UPM-MAKNA Cancer Research Laboratory, Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor Darul Ehsan, Malaysia.
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Lee Y, Woo DU, Kang YJ. SoyDBean: a database for SNPs reconciliation by multiple versions of soybean reference genomes. Sci Rep 2023; 13:15712. [PMID: 37735613 PMCID: PMC10514325 DOI: 10.1038/s41598-023-42898-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 09/15/2023] [Indexed: 09/23/2023] Open
Abstract
Due to the development of sequence technology and decreased cost, many whole genome sequences have been obtained. As a result, extensive genetic variations have been discovered from many populations and germplasms to understand the genetic diversity of soybean (Glycine max [L.] Merr.). However, assessing the quality of variation is essential because the published variants were collected using different bioinformatic methods and parameters. Furthermore, despite the enhanced genome contiguity and more efficient filling of "N" stretches in the new reference genome, there remains a dearth of endeavors to verify the caliber of variations present in it. The primary goal of this research was to discern a dependable set of SNPs that can withstand reconciliation across multiple reference genomes. Additionally, the investigation aimed to reconfirm the variations through the utilization of numerous whole genome sequencing data obtained from publicly available databases. Based on the result, we created datasets that comprised the thoroughly verified SNP coordinates between the reference assemblies. The resulting "SoyDBean" database is now publicly accessible through the following URL: http://soydbean.plantprofile.net/ .
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Affiliation(s)
- Yejin Lee
- Division of Bio and Medical Bigdata Department (BK4 Program), Gyeongsang National University, 501, Jinju-daero, Jinju-si, Gyeongsangnam-do, 52828, Republic of Korea
- Division of Life Science Department, Gyeongsang National University, Jinju, Republic of Korea
| | - Dong U Woo
- Division of Bio and Medical Bigdata Department (BK4 Program), Gyeongsang National University, 501, Jinju-daero, Jinju-si, Gyeongsangnam-do, 52828, Republic of Korea
- Division of Life Science Department, Gyeongsang National University, Jinju, Republic of Korea
| | - Yang Jae Kang
- Division of Bio and Medical Bigdata Department (BK4 Program), Gyeongsang National University, 501, Jinju-daero, Jinju-si, Gyeongsangnam-do, 52828, Republic of Korea.
- Division of Life Science Department, Gyeongsang National University, Jinju, Republic of Korea.
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Wang L, Yang Y, Yang Z, Li W, Hu D, Yu H, Li X, Cheng H, Kan G, Che Z, Zhang D, Zhang H, Wang H, Huang F, Yu D. GmFtsH25 overexpression increases soybean seed yield by enhancing photosynthesis and photosynthates. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:1026-1040. [PMID: 36349957 DOI: 10.1111/jipb.13405] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 11/08/2022] [Indexed: 06/16/2023]
Abstract
Increasing plant photosynthetic capacity is a promising approach to boost yields, but it is particularly challenging in C3 crops, such as soybean (Glycine max (L.) Merr.). Here, we identified GmFtsH25, encoding a member of the filamentation temperature-sensitive protein H protease family, as a major gene involved in soybean photosynthesis, using linkage mapping and a genome-wide association study. Overexpressing GmFtsH25 resulted in more grana thylakoid stacks in chloroplasts and increased photosynthetic efficiency and starch content, while knocking out GmFtsH25 produced the opposite phenotypes. GmFtsH25 interacted with photosystem I light harvesting complex 2 (GmLHCa2), and this interaction may contribute to the observed enhanced photosynthesis. GmFtsH25 overexpression lines had superior yield traits, such as yield per plant, compared to the wild type and knockout lines. Additionally, we identified an elite haplotype of GmFtsH25, generated by natural mutations, which appears to have been selected during soybean domestication. Our study sheds light on the molecular mechanism by which GmFtsH25 modulates photosynthesis and provides a promising strategy for improving the yields of soybean and other crops.
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Affiliation(s)
- Li Wang
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yuming Yang
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Zhongyi Yang
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wenlong Li
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Dezhou Hu
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Huilian Yu
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiao Li
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hao Cheng
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Guizhen Kan
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhijun Che
- School of Agriculture, Ningxia University, Yinchuan, 750021, China
| | - Dan Zhang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Hengyou Zhang
- Northeast Institute of Geography and Agroecology, Key Laboratory of Soybean Molecular Design Breeding, the Chinese Academy of Sciences, Harbin, 150081, China
| | - Hui Wang
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Fang Huang
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Deyue Yu
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
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Yang Y, Wang R, Wang L, Cui R, Zhang H, Che Z, Hu D, Chu S, Jiao Y, Yu D, Zhang D. GmEIL4 enhances soybean (Glycine max) phosphorus efficiency by improving root system development. PLANT, CELL & ENVIRONMENT 2023; 46:592-606. [PMID: 36419232 DOI: 10.1111/pce.14497] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 11/01/2022] [Accepted: 11/22/2022] [Indexed: 06/16/2023]
Abstract
Phosphorus (P) deficiency seriously affects plant growth and development and ultimately limits the quality and yield of crops. Here, a new P efficiency-related major quantitative trait locus gene, GmEIL4 (encoding an ethylene-insensitive 3-like 1 protein), was cloned at qP2, which was identified by linkage analysis and genome-wide association study across four environments. Overexpressing GmEIL4 significantly improved the P uptake efficiency by increasing the number, length and surface area of lateral roots of hairy roots in transgenic soybeans, while interfering with GmEIL4 resulted in poor root phenotypic characteristics compared with the control plants under low P conditions. Interestingly, we found that GmEIL4 interacted with EIN3-binding F box protein 1 (GmEBF1), which may regulate the root response to low P stress. We conclude that the expression of GmEIL4 was induced by low-P stress and that overexpressing GmEIL4 improved P accumulation by regulating root elongation and architecture. Analysis of allele variation of GmEIL4 in 894 soybean accessions suggested that GmEIL4 is undergoing artificial selection during soybean evolution, which will benefit soybean production. Together, this study further elucidates how plants respond to low P stress by modifying root structure and provides insight into the great potential of GmEIL4 in crop P-efficient breeding.
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Affiliation(s)
- Yuming Yang
- Department of Agriculture, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Ruiyang Wang
- Department of Agriculture, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Li Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, China
| | - Ruifan Cui
- Department of Agriculture, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Hengyou Zhang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | | | - Dandan Hu
- Department of Agriculture, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Shanshan Chu
- Department of Agriculture, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Yongqing Jiao
- Department of Agriculture, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Deyue Yu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, China
| | - Dan Zhang
- Department of Agriculture, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, China
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Liang R, Ji X, Sheng Z, Liu J, Qiang S, Song X. Fitness and Rhizobacteria of F2, F3 Hybrids of Herbicide-Tolerant Transgenic Soybean and Wild Soybean. PLANTS (BASEL, SWITZERLAND) 2022; 11:3184. [PMID: 36432913 PMCID: PMC9693618 DOI: 10.3390/plants11223184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/10/2022] [Accepted: 11/15/2022] [Indexed: 06/16/2023]
Abstract
The introduction of herbicide-tolerant (HT) transgenic soybeans (Glycine max (L.) Merr.) into farming systems raises great concern that transgenes may flow to endemic wild soybeans (Glycine soja Sieb. et Zucc.) via pollen, which may increase the ecological risks by increasing the fitness of hybrids under certain conditions and threaten the genetic diversity of wild soybean populations. In order to demonstrate the potential risk of gene flow from the HT soybean to the wild soybean, the fitness of F2 and F3 hybrids obtained from two wild soybean populations (HLJHRB-1, JSCZ) collected from China and the HT soybean was measured under farmland and wasteland soil conditions, as well as with or without weed competition. Compared with their wild progenitors, the F2 and F3 hybrids of HLJHRB-1 displayed a higher emergence rate, higher aboveground dry biomass, more pods and filled-seed plants, as well as better composite fitness under four planting conditions. The F2 and F3 hybrids of JSCZ also displayed a higher emergence rate, higher aboveground dry biomass, more pods, and more filled seeds per plant under mixed planting, whereas these characteristics were lower under pure planting conditions in wasteland and farmland soil. Therefore, the composite fitness of JSCZ hybrids was higher or lower depending on the planting conditions. Furthermore, the soil microbial communities of the F3 of HLJHRB-1, JSCZ, and the wild soybean were investigated with 16S rDNA sequencing, which showed that low alpha diversity of rhizobacteria was relative to high fitness, and Rhizobium played an important role in promoting F3 plant growth.
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Goettel W, Zhang H, Li Y, Qiao Z, Jiang H, Hou D, Song Q, Pantalone VR, Song BH, Yu D, An YQC. POWR1 is a domestication gene pleiotropically regulating seed quality and yield in soybean. Nat Commun 2022; 13:3051. [PMID: 35650185 PMCID: PMC9160092 DOI: 10.1038/s41467-022-30314-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Accepted: 04/25/2022] [Indexed: 11/09/2022] Open
Abstract
Seed protein, oil content and yield are highly correlated agronomically important traits that essentially account for the economic value of soybean. The underlying molecular mechanisms and selection of these correlated seed traits during soybean domestication are, however, less known. Here, we demonstrate that a CCT gene, POWR1, underlies a large-effect protein/oil QTL. A causative TE insertion truncates its CCT domain and substantially increases seed oil content, weight, and yield while decreasing protein content. POWR1 pleiotropically controls these traits likely through regulating seed nutrient transport and lipid metabolism genes. POWR1 is also a domestication gene. We hypothesize that the TE insertion allele is exclusively fixed in cultivated soybean due to selection for larger seeds during domestication, which significantly contributes to shaping soybean with increased yield/seed weight/oil but reduced protein content. This study provides insights into soybean domestication and is significant in improving seed quality and yield in soybean and other crop species.
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Affiliation(s)
- Wolfgang Goettel
- US Department of Agriculture, Agricultural Research Service, Midwest Area, Plant Genetics Research Unit, 975N Warson Rd, St. Louis, MO, 63132, USA
| | - Hengyou Zhang
- Donald Danforth Plant Science Center, 975N Warson Rd, St. Louis, MO, 63132, USA
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China
| | - Ying Li
- Donald Danforth Plant Science Center, 975N Warson Rd, St. Louis, MO, 63132, USA
| | - Zhenzhen Qiao
- Donald Danforth Plant Science Center, 975N Warson Rd, St. Louis, MO, 63132, USA
| | - He Jiang
- Donald Danforth Plant Science Center, 975N Warson Rd, St. Louis, MO, 63132, USA
| | - Dianyun Hou
- US Department of Agriculture, Agricultural Research Service, Midwest Area, Plant Genetics Research Unit, 975N Warson Rd, St. Louis, MO, 63132, USA
- College of Agriculture, Henan University of Science and Technology, Luoyang, Henan, 471023, China
| | - Qijian Song
- US Department of Agriculture, Agricultural Research Service, Soybean Genomics and Improvement Laboratory, Beltsville, MD, 20705, USA
| | - Vincent R Pantalone
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| | - Bao-Hua Song
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Deyue Yu
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Yong-Qiang Charles An
- US Department of Agriculture, Agricultural Research Service, Midwest Area, Plant Genetics Research Unit, 975N Warson Rd, St. Louis, MO, 63132, USA.
- Donald Danforth Plant Science Center, 975N Warson Rd, St. Louis, MO, 63132, USA.
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Cao P, Zhao Y, Wu F, Xin D, Liu C, Wu X, Lv J, Chen Q, Qi Z. Multi-Omics Techniques for Soybean Molecular Breeding. Int J Mol Sci 2022; 23:4994. [PMID: 35563386 PMCID: PMC9099442 DOI: 10.3390/ijms23094994] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 04/22/2022] [Accepted: 04/28/2022] [Indexed: 02/04/2023] Open
Abstract
Soybean is a major crop that provides essential protein and oil for food and feed. Since its origin in China over 5000 years ago, soybean has spread throughout the world, becoming the second most important vegetable oil crop and the primary source of plant protein for global consumption. From early domestication and artificial selection through hybridization and ultimately molecular breeding, the history of soybean breeding parallels major advances in plant science throughout the centuries. Now, rapid progress in plant omics is ushering in a new era of precision design breeding, exemplified by the engineering of elite soybean varieties with specific oil compositions to meet various end-use targets. The assembly of soybean reference genomes, made possible by the development of genome sequencing technology and bioinformatics over the past 20 years, was a great step forward in soybean research. It facilitated advances in soybean transcriptomics, proteomics, metabolomics, and phenomics, all of which paved the way for an integrated approach to molecular breeding in soybean. In this review, we summarize the latest progress in omics research, highlight novel findings made possible by omics techniques, note current drawbacks and areas for further research, and suggest that an efficient multi-omics approach may accelerate soybean breeding in the future. This review will be of interest not only to soybean breeders but also to researchers interested in the use of cutting-edge omics technologies for crop research and improvement.
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Affiliation(s)
- Pan Cao
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (P.C.); (Y.Z.); (F.W.); (D.X.); (C.L.)
| | - Ying Zhao
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (P.C.); (Y.Z.); (F.W.); (D.X.); (C.L.)
| | - Fengjiao Wu
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (P.C.); (Y.Z.); (F.W.); (D.X.); (C.L.)
| | - Dawei Xin
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (P.C.); (Y.Z.); (F.W.); (D.X.); (C.L.)
| | - Chunyan Liu
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (P.C.); (Y.Z.); (F.W.); (D.X.); (C.L.)
| | - Xiaoxia Wu
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (P.C.); (Y.Z.); (F.W.); (D.X.); (C.L.)
| | - Jian Lv
- Department of Innovation, Syngenta Biotechnology China, Beijing 102206, China
| | - Qingshan Chen
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (P.C.); (Y.Z.); (F.W.); (D.X.); (C.L.)
| | - Zhaoming Qi
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (P.C.); (Y.Z.); (F.W.); (D.X.); (C.L.)
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