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Zhao Q, Zhao D, Wang Y, Li Y, Ni C, Su Z, Lian P, Liu S, Liu H, Zhang J, Yao D. Exploration of GmDof11- lncRNA13082 Module Regulating Oil Synthesis in Plants. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:16889-16899. [PMID: 39021146 DOI: 10.1021/acs.jafc.4c03084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Soybean (Glycine max [Linn.] Merr.) is an important oilseed crop. Although transcription factors (TFs) can coordinate the expression of mRNA and lncRNA, their coordination in the soybean oil synthesis pathway remains unclear. This study examined the interaction between the TF GmDof11 and lncRNA13082 and found that overexpression of GmDof11 led to an increase in the number of Arabidopsis seeds, thousand seed weight, crude protein, hydrolysis amino acid, and soluble sugar. Additionally, it reduced the triglyceride and starch contents and affected the proportion of fatty acids, increasing the contents of palmitic acid, stearic acid, and linolenic acid. The yeast two-hybrid experiments revealed that GmDof11 interacts with GmBCCP1, GmLEC1b, and GmFAB2 proteins. In the RT-qPCR analysis of transgenic soybean roots, it was found that GmDof11 can activate the production of lncRNA13082 and work in conjunction with lncRNA13082 to oversee oil synthesis and nutrient storage. Our research provides robust theoretical evidence for a comprehensive resolution of TF-lncRNA regulation in the soybean oil synthesis network.
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Affiliation(s)
- Qiuzhu Zhao
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, Jilin, China
- College of Agronomy, Jilin Agricultural University, Changchun 130118, Jilin, China
| | - Dingyi Zhao
- College of Agronomy, Jilin Agricultural University, Changchun 130118, Jilin, China
| | - Yashuo Wang
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, Jilin, China
| | - Yuxin Li
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, Jilin, China
| | - Chang Ni
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, Jilin, China
| | - Zitong Su
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, Jilin, China
| | - Panhang Lian
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, Jilin, China
| | - Shuying Liu
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, Jilin, China
| | - Huijing Liu
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, Jilin, China
| | - Jun Zhang
- College of Agronomy, Jilin Agricultural University, Changchun 130118, Jilin, China
| | - Dan Yao
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, Jilin, China
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Zhong K, Zhang P, Wei X, Platre MP, He W, Zhang L, Małolepszy A, Cao M, Hu S, Tang S, Li B, Hu P, Busch W. Natural variation of TBR confers plant zinc toxicity tolerance through root cell wall pectin methylesterification. Nat Commun 2024; 15:5823. [PMID: 38992052 PMCID: PMC11239920 DOI: 10.1038/s41467-024-50106-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 06/28/2024] [Indexed: 07/13/2024] Open
Abstract
Zinc (Zn) is an essential micronutrient but can be cytotoxic when present in excess. Plants have evolved mechanisms to tolerate Zn toxicity. To identify genetic loci responsible for natural variation of plant tolerance to Zn toxicity, we conduct genome-wide association studies for root growth responses to high Zn and identify 21 significant associated loci. Among these loci, we identify Trichome Birefringence (TBR) allelic variation determining root growth variation in high Zn conditions. Natural alleles of TBR determine TBR transcript and protein levels which affect pectin methylesterification in root cell walls. Together with previously published data showing that pectin methylesterification increase goes along with decreased Zn binding to cell walls in TBR mutants, our findings lead to a model in which TBR allelic variation enables Zn tolerance through modulating root cell wall pectin methylesterification. The role of TBR in Zn tolerance is conserved across dicot and monocot plant species.
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Affiliation(s)
- Kaizhen Zhong
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, Zhejiang, China
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
- School of Agricultural Sciences, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Peng Zhang
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, Zhejiang, China
| | - Xiangjin Wei
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, Zhejiang, China
| | - Matthieu Pierre Platre
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Wenrong He
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Ling Zhang
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Anna Małolepszy
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Min Cao
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Shikai Hu
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, Zhejiang, China
| | - Shaoqing Tang
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, Zhejiang, China
| | - Baohai Li
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA.
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang, China.
| | - Peisong Hu
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, Zhejiang, China.
- School of Agricultural Sciences, Jiangxi Agricultural University, Nanchang, Jiangxi, China.
| | - Wolfgang Busch
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA.
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3
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Wang B, Bu Y, Zhang G, Liu N, Feng Z, Gong Y. Comparative transcriptome analysis of vegetable soybean grain discloses genes essential for grain quality. BMC PLANT BIOLOGY 2024; 24:491. [PMID: 38825702 PMCID: PMC11145879 DOI: 10.1186/s12870-024-05214-1] [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: 04/25/2023] [Accepted: 05/29/2024] [Indexed: 06/04/2024]
Abstract
BACKGROUND Vegetable soybean is an important vegetable crop in world. Seed size and soluble sugar content are considered crucial indicators of quality in vegetable soybean, and there is a lack of clarity on the molecular basis of grain quality in vegetable soybean. RESULTS In this context, we performed a comprehensive comparative transcriptome analysis of seeds between a high-sucrose content and large-grain variety (Zhenong 6, ZN6) and a low-sucrose content and small-grain variety (Williams 82, W82) at three developmental stages, i.e. stage R5 (Beginning Seed), stage R6 (Full Seed), and stage R7 (Beginning Maturity). The transcriptome analysis showed that 17,107 and 13,571 differentially expressed genes (DEGs) were identified in ZN6 at R6 (vs. R5) and R7 (vs. R6), respectively, whereas 16,203 and 16,032 were detected in W82. Gene expression pattern and DEGs functional enrichment proposed genotype-specific biological processes during seed development. The genes participating in soluble sugar biosynthesis such as FKGP were overexpressed in ZN6, whereas those responsible for lipid and protein metabolism such as ALDH3 were more enhanced in W82, exhibiting different dry material accumulation between two genotypes. Furthermore, hormone-associated transcriptional factors involved in seed size regulation such as BEH4 were overrepresented in ZN6, exhibiting different seed size regulation processes between two genotypes. CONCLUSIONS Herein, we not only discovered the differential expression of genes encoding metabolic enzymes involved in seed composition, but also identified a type of hormone-associated transcriptional factors overexpressed in ZN6, which may regulate seed size and soluble content. This study provides new insights into the underlying causes of differences in the soybean metabolites and appearance, and suggests that genetic data can be used to improve its appearance and textural quality.
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Affiliation(s)
- Bin Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, 198, Shiqiao Rd, Hangzhou, 310021, Zhejiang, China.
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China of Ministry of Agriculture and Rural Affairs, 198, Shiqiao Rd, Hangzhou, 310021, Zhejiang, China.
| | - Yuanpeng Bu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, 198, Shiqiao Rd, Hangzhou, 310021, Zhejiang, China
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China of Ministry of Agriculture and Rural Affairs, 198, Shiqiao Rd, Hangzhou, 310021, Zhejiang, China
| | - Guwen Zhang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, 198, Shiqiao Rd, Hangzhou, 310021, Zhejiang, China
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China of Ministry of Agriculture and Rural Affairs, 198, Shiqiao Rd, Hangzhou, 310021, Zhejiang, China
| | - Na Liu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, 198, Shiqiao Rd, Hangzhou, 310021, Zhejiang, China
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China of Ministry of Agriculture and Rural Affairs, 198, Shiqiao Rd, Hangzhou, 310021, Zhejiang, China
| | - Zhijuan Feng
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, 198, Shiqiao Rd, Hangzhou, 310021, Zhejiang, China
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China of Ministry of Agriculture and Rural Affairs, 198, Shiqiao Rd, Hangzhou, 310021, Zhejiang, China
| | - Yaming Gong
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, 198, Shiqiao Rd, Hangzhou, 310021, Zhejiang, China.
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China of Ministry of Agriculture and Rural Affairs, 198, Shiqiao Rd, Hangzhou, 310021, Zhejiang, China.
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4
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Yuan X, Jiang X, Zhang M, Wang L, Jiao W, Chen H, Mao J, Ye W, Song Q. Integrative omics analysis elucidates the genetic basis underlying seed weight and oil content in soybean. THE PLANT CELL 2024; 36:2160-2175. [PMID: 38412459 PMCID: PMC11132872 DOI: 10.1093/plcell/koae062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 01/29/2024] [Accepted: 02/22/2024] [Indexed: 02/29/2024]
Abstract
Synergistic optimization of key agronomic traits by traditional breeding has dramatically enhanced crop productivity in the past decades. However, the genetic basis underlying coordinated regulation of yield- and quality-related traits remains poorly understood. Here, we dissected the genetic architectures of seed weight and oil content by combining genome-wide association studies (GWAS) and transcriptome-wide association studies (TWAS) using 421 soybean (Glycine max) accessions. We identified 26 and 33 genetic loci significantly associated with seed weight and oil content by GWAS, respectively, and detected 5,276 expression quantitative trait loci (eQTLs) regulating expression of 3,347 genes based on population transcriptomes. Interestingly, a gene module (IC79), regulated by two eQTL hotspots, exhibited significant correlation with both seed weigh and oil content. Twenty-two candidate causal genes for seed traits were further prioritized by TWAS, including Regulator of Weight and Oil of Seed 1 (GmRWOS1), which encodes a sodium pump protein. GmRWOS1 was verified to pleiotropically regulate seed weight and oil content by gene knockout and overexpression. Notably, allelic variations of GmRWOS1 were strongly selected during domestication of soybean. This study uncovers the genetic basis and network underlying regulation of seed weight and oil content in soybean and provides a valuable resource for improving soybean yield and quality by molecular breeding.
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Affiliation(s)
- Xiaobo Yuan
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu 210095, China
| | - Xinyu Jiang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu 210095, China
| | - Mengzhu Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu 210095, China
| | - Longfei Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu 210095, China
| | - Wu Jiao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu 210095, China
| | - Huatao Chen
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, No. 50 Zhongling, Nanjing, Jiangsu 210014, China
| | - Junrong Mao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu 210095, China
| | - Wenxue Ye
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu 210095, China
| | - Qingxin Song
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu 210095, China
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5
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Zhao X, Zhang Y, Wang J, Zhao X, Li Y, Teng W, Han Y, Zhan Y. GWAS and WGCNA Analysis Uncover Candidate Genes Associated with Oil Content in Soybean. PLANTS (BASEL, SWITZERLAND) 2024; 13:1351. [PMID: 38794422 PMCID: PMC11125034 DOI: 10.3390/plants13101351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/10/2024] [Accepted: 05/02/2024] [Indexed: 05/26/2024]
Abstract
Soybean vegetable oil is an important source of the human diet. However, the analysis of the genetic mechanism leading to changes in soybean oil content is still incomplete. In this study, a total of 227 soybean materials were applied and analyzed by a genome-wide association study (GWAS). There are 44 quantitative trait nucleotides (QTNs) that were identified as associated with oil content. A total of six, four, and 34 significant QTN loci were identified in Xiangyang, Hulan, and Acheng, respectively. Of those, 26 QTNs overlapped with or were near the known oil content quantitative trait locus (QTL), and 18 new QTNs related to oil content were identified. A total of 594 genes were located near the peak single nucleotide polymorphism (SNP) from three tested environments. These candidate genes exhibited significant enrichment in tropane, piperidine, and pyridine alkaloid biosynthesiss (ko00960), ABC transporters (ko02010), photosynthesis-antenna proteins (ko00196), and betalain biosynthesis (ko00965). Combined with the GWAS and weighted gene co-expression network analysis (WGCNA), four candidate genes (Glyma.18G300100, Glyma.11G221100, Glyma.13G343300, and Glyma.02G166100) that may regulate oil content were identified. In addition, Glyma.18G300100 was divided into two main haplotypes in the studied accessions. The oil content of haplotype 1 is significantly lower than that of haplotype 2. Our research findings provide a theoretical basis for improving the regulatory mechanism of soybean oil content.
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Affiliation(s)
| | | | | | | | | | | | - Yingpeng Han
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin 150030, China; (X.Z.); (Y.Z.); (J.W.); (X.Z.); (Y.L.); (W.T.)
| | - Yuhang Zhan
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin 150030, China; (X.Z.); (Y.Z.); (J.W.); (X.Z.); (Y.L.); (W.T.)
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6
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Wu X, Hu Z, Zhang Y, Li M, Liao N, Dong J, Wang B, Wu J, Wu X, Wang Y, Wang J, Lu Z, Yang Y, Sun Y, Dong W, Zhang M, Li G. Differential selection of yield and quality traits has shaped genomic signatures of cowpea domestication and improvement. Nat Genet 2024; 56:992-1005. [PMID: 38649710 DOI: 10.1038/s41588-024-01722-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 03/19/2024] [Indexed: 04/25/2024]
Abstract
Cowpeas (tropical legumes) are important in ensuring food and nutritional security in developing countries, especially in sub-Saharan Africa. Herein, we report two high-quality genome assemblies of grain and vegetable cowpeas and we re-sequenced 344 accessions to characterize the genomic variations landscape. We identified 39 loci for ten important agronomic traits and more than 541 potential loci that underwent selection during cowpea domestication and improvement. In particular, the synchronous selections of the pod-shattering loci and their neighboring stress-relevant loci probably led to the enhancement of pod-shattering resistance and the compromise of stress resistance during the domestication from grain to vegetable cowpeas. Moreover, differential selections on multiple loci associated with pod length, grain number per pod, seed weight, pod and seed soluble sugars, and seed crude proteins shaped the yield and quality diversity in cowpeas. Our findings provide genomic insights into cowpea domestication and improvement footprints, enabling further genome-informed cultivar improvement of cowpeas.
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Affiliation(s)
- Xinyi Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
| | - Zhongyuan Hu
- Laboratory of Vegetable Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, P. R. China
| | - Yan Zhang
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, P. R. China
| | - Mao Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
| | - Nanqiao Liao
- Laboratory of Vegetable Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, P. R. China
| | - Junyang Dong
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
| | - Baogen Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
| | - Jian Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
| | - Xiaohua Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
| | - Ying Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
| | - Jian Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
| | - Zhongfu Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
| | - Yi Yang
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, P. R. China
| | - Yuyan Sun
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
| | - Wenqi Dong
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
| | - Mingfang Zhang
- Laboratory of Vegetable Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, P. R. China.
- Hainan Institute of Zhejiang University, Yazhou Bay Science and Technology City, Sanya, P. R. China.
- Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture and Rural Affairs, Hangzhou, P. R. China.
| | - Guojing Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China.
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China.
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7
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Cao Y, Han Z, Zhang Z, He L, Huang C, Chen J, Dai F, Xuan L, Yan S, Si Z, Hu Y, Zhang T. UDP-glucosyltransferase 71C4 controls the flux of phenylpropanoid metabolism to shape cotton seed development. PLANT COMMUNICATIONS 2024:100938. [PMID: 38689494 DOI: 10.1016/j.xplc.2024.100938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 04/24/2024] [Accepted: 04/29/2024] [Indexed: 05/02/2024]
Abstract
Seeds play a crucial role in plant reproduction, making it essential to identify genes that affect seed development. In this study, we focused on UDP-glucosyltransferase 71C4 (UGT71C4) in cotton, a member of the glycosyltransferase family that shapes seed width and length, thereby influencing seed index and seed cotton yield. Overexpression of UGT71C4 results in seed enlargement owing to its glycosyltransferase activity on flavonoids, which redirects metabolic flux from lignin to flavonoid metabolism. This shift promotes cell proliferation in the ovule via accumulation of flavonoid glycosides, significantly enhancing seed cotton yield and increasing the seed index from 10.66 g to 11.91 g. By contrast, knockout of UGT71C4 leads to smaller seeds through activation of the lignin metabolism pathway and redirection of metabolic flux back to lignin synthesis. This redirection leads to increased ectopic lignin deposition in the ovule, inhibiting ovule growth and development, and alters yield components, increasing the lint percentage from 41.42% to 43.40% and reducing the seed index from 10.66 g to 8.60 g. Our research sheds new light on seed size development and reveals potential pathways for enhancing seed yield.
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Affiliation(s)
- Yiwen Cao
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China; Hainan Institute, Zhejiang University, Sanya, China
| | - Zegang Han
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | | | - Lu He
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Chujun Huang
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Jinwen Chen
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Fan Dai
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Lisha Xuan
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Sunyi Yan
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Zhanfeng Si
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yan Hu
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China; Hainan Institute, Zhejiang University, Sanya, China
| | - Tianzhen Zhang
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China; Hainan Institute, Zhejiang University, Sanya, China.
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8
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Zhao X, Zhu H, Liu F, Wang J, Zhou C, Yuan M, Zhao X, Li Y, Teng W, Han Y, Zhan Y. Integrating Genome-Wide Association Study, Transcriptome and Metabolome Reveal Novel QTL and Candidate Genes That Control Protein Content in Soybean. PLANTS (BASEL, SWITZERLAND) 2024; 13:1128. [PMID: 38674535 PMCID: PMC11054237 DOI: 10.3390/plants13081128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 04/11/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024]
Abstract
Protein content (PC) is crucial to the nutritional quality of soybean [Glycine max (L.) Merrill]. In this study, a total of 266 accessions were used to perform a genome-wide association study (GWAS) in three tested environments. A total of 23,131 high-quality SNP markers (MAF ≥ 0.02, missing data ≤ 10%) were identified. A total of 40 association signals were significantly associated with PC. Among them, five novel quantitative trait nucleotides (QTNs) were discovered, and another 32 QTNs were found to be overlapping with the genomic regions of known quantitative trait loci (QTL) related to soybean PC. Combined with GWAS, metabolome and transcriptome sequencing, 59 differentially expressed genes (DEGs) that might control the change in protein content were identified. Meantime, four commonly upregulated differentially abundant metabolites (DAMs) and 29 commonly downregulated DAMs were found. Remarkably, the soybean gene Glyma.08G136900, which is homologous with Arabidopsis hydroxyproline-rich glycoproteins (HRGPs), may play an important role in improving the PC. Additionally, Glyma.08G136900 was divided into two main haplotype in the tested accessions. The PC of haplotype 1 was significantly lower than that of haplotype 2. The results of this study provided insights into the genetic mechanisms regulating protein content in soybean.
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Affiliation(s)
- Xunchao Zhao
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin 150030, China; (X.Z.); (H.Z.); (F.L.); (J.W.); (X.Z.); (Y.L.); (W.T.)
| | - Hanhan Zhu
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin 150030, China; (X.Z.); (H.Z.); (F.L.); (J.W.); (X.Z.); (Y.L.); (W.T.)
| | - Fang Liu
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin 150030, China; (X.Z.); (H.Z.); (F.L.); (J.W.); (X.Z.); (Y.L.); (W.T.)
| | - Jie Wang
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin 150030, China; (X.Z.); (H.Z.); (F.L.); (J.W.); (X.Z.); (Y.L.); (W.T.)
| | - Changjun Zhou
- Daqing Branch, Heilongjiang Academy of Agricultural Science, Daqing 163711, China;
| | - Ming Yuan
- Qiqihar Branch, Heilongjiang Academy of Agricultural Science, Qiqihar 161006, China;
| | - Xue Zhao
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin 150030, China; (X.Z.); (H.Z.); (F.L.); (J.W.); (X.Z.); (Y.L.); (W.T.)
| | - Yongguang Li
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin 150030, China; (X.Z.); (H.Z.); (F.L.); (J.W.); (X.Z.); (Y.L.); (W.T.)
| | - Weili Teng
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin 150030, China; (X.Z.); (H.Z.); (F.L.); (J.W.); (X.Z.); (Y.L.); (W.T.)
| | - Yingpeng Han
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin 150030, China; (X.Z.); (H.Z.); (F.L.); (J.W.); (X.Z.); (Y.L.); (W.T.)
| | - Yuhang Zhan
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin 150030, China; (X.Z.); (H.Z.); (F.L.); (J.W.); (X.Z.); (Y.L.); (W.T.)
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9
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Zuo Y, Liu H, Li B, Zhao H, Li X, Chen J, Wang L, Zheng Q, He Y, Zhang J, Wang M, Liang C, Wang L. The Idesia polycarpa genome provides insights into its evolution and oil biosynthesis. Cell Rep 2024; 43:113909. [PMID: 38451814 DOI: 10.1016/j.celrep.2024.113909] [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: 06/29/2023] [Revised: 01/26/2024] [Accepted: 02/20/2024] [Indexed: 03/09/2024] Open
Abstract
The deciduous tree Idesia polycarpa can provide premium edible oil with high polyunsaturated fatty acid contents. Here, we generate its high-quality reference genome, which is ∼1.21 Gb, comprising 21 pseudochromosomes and 42,086 protein-coding genes. Phylogenetic and genomic synteny analyses show that it diverged with Populus trichocarpa about 16.28 million years ago. Notably, most fatty acid biosynthesis genes are not only increased in number in its genome but are also highly expressed in the fruits. Moreover, we identify, through genome-wide association analysis and RNA sequencing, the I. polycarpa SUGAR TRANSPORTER 5 (IpSTP5) gene as a positive regulator of high oil accumulation in the fruits. Silencing of IpSTP5 by virus-induced gene silencing causes a significant reduction of oil content in the fruits, suggesting it has the potential to be used as a molecular marker to breed the high-oil-content cultivars. Our results collectively lay the foundation for breeding the elite cultivars of I. polycarpa.
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Affiliation(s)
- Yi Zuo
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Science, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China
| | - Hongbing Liu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Bin Li
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Science, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China
| | - Hang Zhao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Xiuli Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Jiating Chen
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Science, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lu Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Science, Beijing 100093, China
| | - Qingbo Zheng
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Science, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China
| | - Yuqing He
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Science, Beijing 100093, China; Academician Workstation of Agricultural High-Tech Industrial Area of the Yellow River Delta, National Center of Technology Innovation for Comprehensive Utilization of Saline-Alkali Land, Dongying 257300, China
| | - Jiashuo Zhang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Science, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Minxian Wang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Chengzhi Liang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Lei Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Science, Beijing 100093, China; Academician Workstation of Agricultural High-Tech Industrial Area of the Yellow River Delta, National Center of Technology Innovation for Comprehensive Utilization of Saline-Alkali Land, Dongying 257300, China; China National Botanical Garden, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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10
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Wei S, Yu Z, Du F, Cao F, Yang M, Liu C, Qi Z, Chen Q, Zou J, Wang J. Integrated Transcriptomic and Proteomic Characterization of a Chromosome Segment Substitution Line Reveals the Regulatory Mechanism Controlling the Seed Weight in Soybean. PLANTS (BASEL, SWITZERLAND) 2024; 13:908. [PMID: 38592937 PMCID: PMC10975824 DOI: 10.3390/plants13060908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 03/13/2024] [Accepted: 03/18/2024] [Indexed: 04/11/2024]
Abstract
Soybean is the major global source of edible oils and vegetable proteins. Seed size and weight are crucial traits determining the soybean yield. Understanding the molecular regulatory mechanism underlying the seed weight and size is helpful for improving soybean genetic breeding. The molecular regulatory pathways controlling the seed weight and size were investigated in this study. The 100-seed weight, seed length, seed width, and seed weight per plant of a chromosome segment substitution line (CSSL) R217 increased compared with those of its recurrent parent 'Suinong14' (SN14). Transcriptomic and proteomic analyses of R217 and SN14 were performed at the seed developmental stages S15 and S20. In total, 2643 differentially expressed genes (DEGs) and 208 differentially accumulated proteins (DAPs) were detected at S15, and 1943 DEGs and 1248 DAPs were detected at S20. Furthermore, integrated transcriptomic and proteomic analyses revealed that mitogen-activated protein kinase signaling and cell wall biosynthesis and modification were potential pathways associated with seed weight and size control. Finally, 59 candidate genes that might control seed weight and size were identified. Among them, 25 genes were located on the substituted segments of R217. Two critical pathways controlling seed weight were uncovered in our work. These findings provided new insights into the seed weight-related regulatory network in soybean.
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Affiliation(s)
- Siming Wei
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (S.W.); (F.D.); (F.C.); (M.Y.); (C.L.); (Z.Q.)
| | - Zhenhai Yu
- Heilongjiang Province Green Food Science Institute, Harbin 150028, China;
| | - Fangfang Du
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (S.W.); (F.D.); (F.C.); (M.Y.); (C.L.); (Z.Q.)
| | - Fubin Cao
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (S.W.); (F.D.); (F.C.); (M.Y.); (C.L.); (Z.Q.)
| | - Mingliang Yang
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (S.W.); (F.D.); (F.C.); (M.Y.); (C.L.); (Z.Q.)
| | - Chunyan Liu
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (S.W.); (F.D.); (F.C.); (M.Y.); (C.L.); (Z.Q.)
| | - Zhaoming Qi
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (S.W.); (F.D.); (F.C.); (M.Y.); (C.L.); (Z.Q.)
| | - Qingshan Chen
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (S.W.); (F.D.); (F.C.); (M.Y.); (C.L.); (Z.Q.)
| | - Jianan Zou
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (S.W.); (F.D.); (F.C.); (M.Y.); (C.L.); (Z.Q.)
| | - Jinhui Wang
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (S.W.); (F.D.); (F.C.); (M.Y.); (C.L.); (Z.Q.)
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11
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Qi Z, Guo C, Li H, Qiu H, Li H, Jong C, Yu G, Zhang Y, Hu L, Wu X, Xin D, Yang M, Liu C, Lv J, Wang X, Kong F, Chen Q. Natural variation in Fatty Acid 9 is a determinant of fatty acid and protein content. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:759-773. [PMID: 37937736 PMCID: PMC10893952 DOI: 10.1111/pbi.14222] [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: 04/19/2023] [Revised: 10/12/2023] [Accepted: 10/20/2023] [Indexed: 11/09/2023]
Abstract
Soybean is one of the most economically important crops worldwide and an important source of unsaturated fatty acids and protein for the human diet. Consumer demand for healthy fats and oils is increasing, and the global demand for vegetable oil is expected to double by 2050. Identification of key genes that regulate seed fatty acid content can facilitate molecular breeding of high-quality soybean varieties with enhanced fatty acid profiles. Here, we analysed the genetic architecture underlying variations in soybean seed fatty acid content using 547 accessions, including mainly landraces and cultivars from northeastern China. Through fatty acid profiling, genome re-sequencing, population genomics analyses, and GWAS, we identified a SEIPIN homologue at the FA9 locus as an important contributor to seed fatty acid content. Transgenic and multiomics analyses confirmed that FA9 was a key regulator of seed fatty acid content with pleiotropic effects on seed protein and seed size. We identified two major FA9 haplotypes in 1295 resequenced soybean accessions and assessed their phenotypic effects in a field planting of 424 accessions. Soybean accessions carrying FA9H2 had significantly higher total fatty acid contents and lower protein contents than those carrying FA9H1 . FA9H2 was absent in wild soybeans but present in 13% of landraces and 26% of cultivars, suggesting that it may have been selected during soybean post-domestication improvement. FA9 therefore represents a useful genetic resource for molecular breeding of high-quality soybean varieties with specific seed storage profiles.
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Affiliation(s)
- Zhaoming Qi
- College of AgricultureNortheast Agricultural UniversityHarbinHeilongjiangChina
| | - Chaocheng Guo
- Shanghai Collaborative Innovation Center of Agri‐Seeds, Joint Center for Single Cell Biology, School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | - Haiyang Li
- Guangdong Provincial 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 SciencesGuangzhou UniversityGuangzhouChina
| | - Hongmei Qiu
- Soybean Research InstituteJilin Academy of Agricultural Sciences/National Soybean Engineering CenterChangchunChina
| | - Hui Li
- College of AgricultureNortheast Agricultural UniversityHarbinHeilongjiangChina
| | - CholNam Jong
- College of AgricultureNortheast Agricultural UniversityHarbinHeilongjiangChina
| | - Guolong Yu
- Shanghai Collaborative Innovation Center of Agri‐Seeds, Joint Center for Single Cell Biology, School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | - Yu Zhang
- College of AgricultureNortheast Agricultural UniversityHarbinHeilongjiangChina
| | - Limin Hu
- College of AgricultureNortheast Agricultural UniversityHarbinHeilongjiangChina
| | - Xiaoxia Wu
- College of AgricultureNortheast Agricultural UniversityHarbinHeilongjiangChina
| | - Dawei Xin
- College of AgricultureNortheast Agricultural UniversityHarbinHeilongjiangChina
| | - Mingliang Yang
- College of AgricultureNortheast Agricultural UniversityHarbinHeilongjiangChina
| | - Chunyan Liu
- College of AgricultureNortheast Agricultural UniversityHarbinHeilongjiangChina
| | - Jian Lv
- Department of InnovationSyngenta Biotechnology ChinaBeijingChina
| | - Xu Wang
- Shanghai Collaborative Innovation Center of Agri‐Seeds, Joint Center for Single Cell Biology, School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | - Fanjiang Kong
- Guangdong Provincial 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 SciencesGuangzhou UniversityGuangzhouChina
| | - Qingshan Chen
- College of AgricultureNortheast Agricultural UniversityHarbinHeilongjiangChina
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12
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Li Y, Zhao W, Tang J, Yue X, Gu J, Zhao B, Li C, Chen Y, Yuan J, Lin Y, Li Y, Kong F, He J, Wang D, Zhao TJ, Wang ZY. Identification of the domestication gene GmCYP82C4 underlying the major quantitative trait locus for the seed weight in soybean. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:62. [PMID: 38418640 DOI: 10.1007/s00122-024-04571-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 01/30/2024] [Indexed: 03/02/2024]
Abstract
KEY MESSAGE A major quantitative trait locus (QTL) for the hundred-seed weight (HSW) was identified and confirmed in the two distinct soybean populations, and the target gene GmCYP82C4 underlying this locus was identified that significantly associated with soybean seed weight, and it was selected during the soybean domestication and improvement process. Soybean is a major oil crop for human beings and the seed weight is a crucial goal of soybean breeding. However, only a limited number of target genes underlying the quantitative trait loci (QTLs) controlling seed weight in soybean are known so far. In the present study, six loci associated with hundred-seed weight (HSW) were detected in the first population of 573 soybean breeding lines by genome-wide association study (GWAS), and 64 gene models were predicted in these candidate QTL regions. The QTL qHSW_1 exhibits continuous association signals on chromosome four and was also validated by region association study (RAS) in the second soybean population (409 accessions) with wild, landrace, and cultivar soybean accessions. There were seven genes in qHSW_1 candidate region by linkage disequilibrium (LD) block analysis, and only Glyma.04G035500 (GmCYP82C4) showed specifically higher expression in flowers, pods, and seeds, indicating its crucial role in the soybean seed development. Significant differences in HSW trait were detected when the association panels are genotyped by single-nucleotide polymorphisms (SNPs) in putative GmCYP82C4 promoter region. Eight haplotypes were generated by six SNPs in GmCYP82C4 in the second soybean population, and two superior haplotypes (Hap2 and Hap4) of GmCYP82C4 were detected with average HSW of 18.27 g and 18.38 g, respectively. The genetic diversity of GmCYP82C4 was analyzed in the second soybean population, and GmCYP82C4 was most likely selected during the soybean domestication and improvement process, leading to the highest proportion of Hap2 of GmCYP82C4 both in landrace and cultivar subpopulations. The QTLs and GmCYP82C4 identified in this study provide novel genetic resources for soybean seed weight trait, and the GmCYP82C4 could be used for soybean molecular breeding to develop desirable seed weight in the future.
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Affiliation(s)
- Yang Li
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, 510316, China
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Wenqian Zhao
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Jiajun Tang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Xiuli Yue
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Jinbao Gu
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, 510316, China
| | - Biyao Zhao
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, 510316, China
| | - Cong Li
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, 510316, China
| | - Yanhang Chen
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, 510316, China
| | - Jianbo Yuan
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, 510316, China
| | - Yan Lin
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, 510316, China
| | - Yan Li
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Fanjiang Kong
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Jin He
- College of Agriculture, Guizhou University, Guiyang, China
| | - Dong Wang
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Nanchang, China
| | - Tuan-Jie Zhao
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China.
| | - Zhen-Yu Wang
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, 510316, China.
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13
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Wang L, Niu F, Wang J, Zhang H, Zhang D, Hu Z. Genome-Wide Association Studies Prioritize Genes Controlling Seed Size and Reproductive Period Length in Soybean. PLANTS (BASEL, SWITZERLAND) 2024; 13:615. [PMID: 38475461 DOI: 10.3390/plants13050615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 02/12/2024] [Accepted: 02/14/2024] [Indexed: 03/14/2024]
Abstract
Hundred-seed weight (HSW) and reproductive period length (RPL) are two major agronomic traits critical for soybean production and adaptation. However, both traits are quantitatively controlled by multiple genes that have yet to be comprehensively elucidated due to the lack of major genes; thereby, the genetic basis is largely unknown. In the present study, we conducted comprehensive genome-wide association analyses (GWAS) of HSW and RPL with multiple sets of accessions that were phenotyped across different environments. The large-scale analysis led to the identification of sixty-one and seventy-four significant QTLs for HSW and RPL, respectively. An ortholog-based search analysis prioritized the most promising candidate genes for the QTLs, including nine genes (TTG2, BZR1, BRI1, ANT, KLU, EOD1/BB, GPA1, ABA2, and ABI5) for HSW QTLs and nine genes (such as AGL8, AGL9, TOC1, and COL4) and six known soybean flowering time genes (E2, E3, E4, Tof11, Tof12, and FT2b) for RPL QTLs. We also demonstrated that some QTLs were targeted during domestication to drive the artificial selection of both traits towards human-favored traits. Local adaptation likely contributes to the increased genomic diversity of the QTLs underlying RPL. The results provide additional insight into the genetic basis of HSW and RPL and prioritize a valuable resource of candidate genes that merits further investigation to reveal the complex molecular mechanism and facilitate soybean improvement.
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Affiliation(s)
- Le Wang
- State Key Laboratory of Black Soils Conservation and Utilization, Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Fu'an Niu
- Institute of Crop Breeding and Cultivation, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Jinshe Wang
- National Innovation Centre for Bio-Breeding Industry, Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Hengyou Zhang
- State Key Laboratory of Black Soils Conservation and Utilization, Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Dan Zhang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Zhenbin Hu
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD 20705, USA
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14
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Li Y, Ye H, Vuong TD, Zhou L, Do TD, Satish Chhapekar S, Zhao W, Li B, Jin T, Gu J, Li C, Chen Y, Li Y, Wang ZY, Nguyen HT. A novel natural variation in the promoter of GmCHX1 regulates conditional gene expression to improve salt tolerance in soybean. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1051-1062. [PMID: 37864556 PMCID: PMC10837011 DOI: 10.1093/jxb/erad404] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 10/20/2023] [Indexed: 10/23/2023]
Abstract
Identification and characterization of soybean germplasm and gene(s)/allele(s) for salt tolerance is an effective way to develop improved varieties for saline soils. Previous studies identified GmCHX1 (Glyma03g32900) as a major salt tolerance gene in soybean, and two main functional variations were found in the promoter region (148/150 bp insertion) and the third exon with a retrotransposon insertion (3.78 kb). In the current study, we identified four salt-tolerant soybean lines, including PI 483460B (Glycine soja), carrying the previously identified salt-sensitive variations at GmCHX1, suggesting new gene(s) or new functional allele(s) of GmCHX1 in these soybean lines. Subsequently, we conducted quantitative trait locus (QTL) mapping in a recombinant-inbred line population (Williams 82 (salt-sensitive) × PI 483460B) to identify the new salt tolerance loci/alleles. A new locus, qSalt_Gm18, was mapped on chromosome 18 associated with leaf scorch score. Another major QTL, qSalt_Gm03, was identified to be associated with chlorophyll content ratio and leaf scorch score in the same chromosomal region of GmCHX1 on chromosome 3. Novel variations in a STRE (stress response element) cis-element in the promoter region of GmCHX1 were found to regulate the salt-inducible expression of the gene in these four newly identified salt-tolerant lines including PI 483460B. This new allele of GmCHX1 with salt-inducible expression pattern provides an energy cost efficient (conditional gene expression) strategy to protect soybean yield in saline soils without yield penalty under non-stress conditions. Our results suggest that there might be no other major salt tolerance locus similar to GmCHX1 in soybean germplasm, and further improvement of salt tolerance in soybean may rely on gene-editing techniques instead of looking for natural variations.
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Affiliation(s)
- Yang Li
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, 510316, China
- Division of Plant Science and Technology, University of Missouri, Columbia, MO 65211, USA
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Heng Ye
- Division of Plant Science and Technology, University of Missouri, Columbia, MO 65211, USA
| | - Tri D Vuong
- Division of Plant Science and Technology, University of Missouri, Columbia, MO 65211, USA
| | - Lijuan Zhou
- Division of Plant Science and Technology, University of Missouri, Columbia, MO 65211, USA
| | - Tuyen D Do
- Division of Plant Science and Technology, University of Missouri, Columbia, MO 65211, USA
| | | | - Wenqian Zhao
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Bin Li
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ting Jin
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jinbao Gu
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, 510316, China
| | - Cong Li
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, 510316, China
| | - Yanhang Chen
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, 510316, China
| | - Yan Li
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhen-Yu Wang
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, 510316, China
| | - Henry T Nguyen
- Division of Plant Science and Technology, University of Missouri, Columbia, MO 65211, USA
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15
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Zhang Y, Bhat JA, Zhang Y, Yang S. Understanding the Molecular Regulatory Networks of Seed Size in Soybean. Int J Mol Sci 2024; 25:1441. [PMID: 38338719 PMCID: PMC10855573 DOI: 10.3390/ijms25031441] [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: 12/27/2023] [Revised: 01/22/2024] [Accepted: 01/23/2024] [Indexed: 02/12/2024] Open
Abstract
Soybean being a major cash crop provides half of the vegetable oil and a quarter of the plant proteins to the global population. Seed size traits are the most important agronomic traits determining the soybean yield. These are complex traits governed by polygenes with low heritability as well as are highly influenced by the environment as well as by genotype x environment interactions. Although, extensive efforts have been made to unravel the genetic basis and molecular mechanism of seed size in soybean. But most of these efforts were majorly limited to QTL identification, and only a few genes for seed size were isolated and their molecular mechanism was elucidated. Hence, elucidating the detailed molecular regulatory networks controlling seed size in soybeans has been an important area of research in soybeans from the past decades. This paper describes the current progress of genetic architecture, molecular mechanisms, and regulatory networks for seed sizes of soybeans. Additionally, the main problems and bottlenecks/challenges soybean researchers currently face in seed size research are also discussed. This review summarizes the comprehensive and systematic information to the soybean researchers regarding the molecular understanding of seed size in soybeans and will help future research work on seed size in soybeans.
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Affiliation(s)
- Ye Zhang
- 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, Changchun 130102, China; (Y.Z.); (Y.Z.)
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 101408, China
| | | | - Yaohua Zhang
- 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, Changchun 130102, China; (Y.Z.); (Y.Z.)
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 101408, China
| | - Suxin Yang
- 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, Changchun 130102, China; (Y.Z.); (Y.Z.)
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 101408, China
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16
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Hu Y, Liu Y, Wei JJ, Zhang WK, Chen SY, Zhang JS. Regulation of seed traits in soybean. ABIOTECH 2023; 4:372-385. [PMID: 38106437 PMCID: PMC10721594 DOI: 10.1007/s42994-023-00122-8] [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: 08/01/2023] [Accepted: 10/18/2023] [Indexed: 12/19/2023]
Abstract
Soybean (Glycine max) is an essential economic crop that provides vegetative oil and protein for humans, worldwide. Increasing soybean yield as well as improving seed quality is of great importance. Seed weight/size, oil and protein content are the three major traits determining seed quality, and seed weight also influences soybean yield. In recent years, the availability of soybean omics data and the development of related techniques have paved the way for better research on soybean functional genomics, providing a comprehensive understanding of gene functions. This review summarizes the regulatory genes that influence seed size/weight, oil content and protein content in soybean. We also provided a general overview of the pleiotropic effect for the genes in controlling seed traits and environmental stresses. Ultimately, it is expected that this review will be beneficial in breeding improved traits in soybean.
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Affiliation(s)
- Yang Hu
- State Key Lab of Plant Genomics, 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
| | - Yue Liu
- State Key Lab of Plant Genomics, 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
| | - Jun-Jie Wei
- State Key Lab of Plant Genomics, 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
| | - Wan-Ke Zhang
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101 China
| | - Shou-Yi Chen
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101 China
| | - Jin-Song Zhang
- State Key Lab of Plant Genomics, 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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17
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Hu Y, Liu Y, Lu L, Tao JJ, Cheng T, Jin M, Wang ZY, Wei JJ, Jiang ZH, Sun WC, Liu CL, Gao F, Zhang Y, Li W, Bi YD, Lai YC, Zhou B, Yu DY, Yin CC, Wei W, Zhang WK, Chen SY, Zhang JS. Global analysis of seed transcriptomes reveals a novel PLATZ regulator for seed size and weight control in soybean. THE NEW PHYTOLOGIST 2023; 240:2436-2454. [PMID: 37840365 DOI: 10.1111/nph.19316] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 09/20/2023] [Indexed: 10/17/2023]
Abstract
Seed size and weight are important factors that influence soybean yield. Combining the weighted gene co-expression network analysis (WGCNA) of 45 soybean accessions and gene dynamic changes in seeds at seven developmental stages, we identified candidate genes that may control the seed size/weight. Among these, a PLATZ-type regulator overlapping with 10 seed weight QTLs was further investigated. This zinc-finger transcriptional regulator, named as GmPLATZ, is required for the promotion of seed size and weight in soybean. The GmPLATZ may exert its functions through direct binding to the promoters and activation of the expression of cyclin genes and GmGA20OX for cell proliferation. Overexpression of the GmGA20OX enhanced seed size/weight in soybean. We further found that the GmPLATZ binds to a 32-bp sequence containing a core palindromic element AATGCGCATT. Spacing of the flanking sequences beyond the core element facilitated GmPLATZ binding. An elite haplotype Hap3 was also identified to have higher promoter activity and correlated with higher gene expression and higher seed weight. Orthologues of the GmPLATZ from rice and Arabidopsis play similar roles in seeds. Our study reveals a novel module of GmPLATZ-GmGA20OX/cyclins in regulating seed size and weight and provides valuable targets for breeding of crops with desirable agronomic traits.
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Affiliation(s)
- Yang Hu
- State Key Lab of Plant Genomics, 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
| | - Yue Liu
- State Key Lab of Plant Genomics, 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
| | - Long Lu
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jian-Jun Tao
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Tong Cheng
- State Key Lab of Plant Genomics, 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
| | - Meng Jin
- State Key Lab of Plant Genomics, 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
| | - Zhou-Ya Wang
- State Key Lab of Plant Genomics, 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
| | - Jun-Jie Wei
- State Key Lab of Plant Genomics, 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
| | - Zhi-Hao Jiang
- State Key Lab of Plant Genomics, 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
| | - Wan-Cai Sun
- Qilu Zhongke Academy of Modern Microbiology Technology, Jinan, 250018, China
| | - Cheng-Lan Liu
- Qilu Zhongke Academy of Modern Microbiology Technology, Jinan, 250018, China
| | - Feng Gao
- Qilu Zhongke Academy of Modern Microbiology Technology, Jinan, 250018, China
| | - Yong Zhang
- Keshan Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihar, 161000, China
| | - Wei Li
- Crop Tillage and Cultivation Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Ying-Dong Bi
- Crop Tillage and Cultivation Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Yong-Cai Lai
- Crop Tillage and Cultivation Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Bin Zhou
- Crop Research Institute of Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - De-Yue 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
| | - Cui-Cui Yin
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wei Wei
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wan-Ke Zhang
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Shou-Yi Chen
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- Qilu Zhongke Academy of Modern Microbiology Technology, Jinan, 250018, China
| | - Jin-Song Zhang
- State Key Lab of Plant Genomics, 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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18
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Di Q, Dong L, Jiang L, Liu X, Cheng P, Liu B, Yu G. Genome-wide association study and RNA-seq identifies GmWRI1-like transcription factor related to the seed weight in soybean. FRONTIERS IN PLANT SCIENCE 2023; 14:1268511. [PMID: 38046612 PMCID: PMC10691256 DOI: 10.3389/fpls.2023.1268511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 10/30/2023] [Indexed: 12/05/2023]
Abstract
The cultivated soybean (Glycine max (L.) Merrill) is domesticated from wild soybean (Glycine soja) and has heavier seeds with a higher oil content than the wild soybean. In this study, we identified a novel candidate gene associated with SW using a genome-wide association study (GWAS). The candidate gene GmWRI14-like was detected by GWAS analysis in three consecutive years. By constructing transgenic soybeans overexpressing the GmWRI14-like gene and gmwri14-like soybean mutants, we found that overexpression of GmWRI14-like increased the SW and increased total fatty acid content. We then used RNA-seq and qRT-PCR to identify the target genes directly or indirectly regulated by GmWRI14-like. Transgenic soyabeans overexpressing GmWRI14-like showed increased accumulation of GmCYP78A50 and GmCYP78A69 than non-transgenic soybean lines. Interestingly, we also found that GmWRI14-like proteins could interact with GmCYP78A69/GmCYP78A50 using yeast two-hybrid and bimolecular fluorescence complementation. Our results not only shed light on the genetic architecture of cultivated soybean SW, but also lays a theoretical foundation for improving the SW and oil content of soybeans.
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Affiliation(s)
- Qin Di
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, China
- Innovative Center of Molecular Genetics and Evolution, College of Life Sciences, Guangzhou University, Guangzhou, Guangdong, China
| | - Lidong Dong
- Innovative Center of Molecular Genetics and Evolution, College of Life Sciences, Guangzhou University, Guangzhou, Guangdong, China
| | - Li Jiang
- Innovative Center of Molecular Genetics and Evolution, College of Life Sciences, Guangzhou University, Guangzhou, Guangdong, China
| | - Xiaoyi Liu
- Research Center of Integrative Medicine, School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Ping Cheng
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Baohui Liu
- Innovative Center of Molecular Genetics and Evolution, College of Life Sciences, Guangzhou University, Guangzhou, Guangdong, China
| | - Guohui Yu
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, China
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19
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Tayade R, Imran M, Ghimire A, Khan W, Nabi RBS, Kim Y. Molecular, genetic, and genomic basis of seed size and yield characteristics in soybean. FRONTIERS IN PLANT SCIENCE 2023; 14:1195210. [PMID: 38034572 PMCID: PMC10684784 DOI: 10.3389/fpls.2023.1195210] [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: 03/28/2023] [Accepted: 10/30/2023] [Indexed: 12/02/2023]
Abstract
Soybean (Glycine max L. Merr.) is a crucial oilseed cash crop grown worldwide and consumed as oil, protein, and food by humans and feed by animals. Comparatively, soybean seed yield is lower than cereal crops, such as maize, rice, and wheat, and the demand for soybean production does not keep up with the increasing consumption level. Therefore, increasing soybean yield per unit area is the most crucial breeding objective and is challenging for the scientific community. Moreover, yield and associated traits are extensively researched in cereal crops, but little is known about soybeans' genetics, genomics, and molecular regulation of yield traits. Soybean seed yield is a complex quantitative trait governed by multiple genes. Understanding the genetic and molecular processes governing closely related attributes to seed yield is crucial to increasing soybean yield. Advances in sequencing technologies have made it possible to conduct functional genomic research to understand yield traits' genetic and molecular underpinnings. Here, we provide an overview of recent progress in the genetic regulation of seed size in soybean, molecular, genetics, and genomic bases of yield, and related key seed yield traits. In addition, phytohormones, such as auxin, gibberellins, cytokinins, and abscisic acid, regulate seed size and yield. Hence, we also highlight the implications of these factors, challenges in soybean yield, and seed trait improvement. The information reviewed in this study will help expand the knowledge base and may provide the way forward for developing high-yielding soybean cultivars for future food demands.
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Affiliation(s)
- Rupesh Tayade
- Upland Field Machinery Research Center, Kyungpook National University, Daegu, Republic of Korea
| | - Muhammad Imran
- Division of Biosafety, National Institute of Agriculture Science, Rural Development Administration, Jeonju, Jeollabul-do, Republic of Korea
| | - Amit Ghimire
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
- Department of Integrative Biology, Kyungpook National University, Daegu, Republic of Korea
| | - Waleed Khan
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
- Department of Integrative Biology, Kyungpook National University, Daegu, Republic of Korea
| | - Rizwana Begum Syed Nabi
- Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang, Republic of Korea
| | - Yoonha Kim
- Upland Field Machinery Research Center, Kyungpook National University, Daegu, Republic of Korea
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
- Department of Integrative Biology, Kyungpook National University, Daegu, Republic of Korea
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20
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Wei S, Yong B, Jiang H, An Z, Wang Y, Li B, Yang C, Zhu W, Chen Q, He C. A loss-of-function mutant allele of a glycosyl hydrolase gene has been co-opted for seed weight control during soybean domestication. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:2469-2489. [PMID: 37635359 DOI: 10.1111/jipb.13559] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 08/28/2023] [Indexed: 08/29/2023]
Abstract
The resultant DNA from loss-of-function mutation can be recruited in biological evolution and development. Here, we present such a rare and potential case of "to gain by loss" as a neomorphic mutation during soybean domestication for increasing seed weight. Using a population derived from a chromosome segment substitution line of Glycine max (SN14) and Glycine soja (ZYD06), a quantitative trait locus (QTL) of 100-seed weight (qHSW) was mapped on chromosome 11, corresponding to a truncated β-1, 3-glucosidase (βGlu) gene. The novel gene hsw results from a 14-bp deletion, causing a frameshift mutation and a premature stop codon in the βGlu. In contrast to HSW, the hsw completely lost βGlu activity and function but acquired a novel function to promote cell expansion, thus increasing seed weight. Overexpressing hsw instead of HSW produced large soybean seeds, and surprisingly, truncating hsw via gene editing further increased the seed size. We further found that the core 21-aa peptide of hsw and its variants acted as a promoter of seed size. Transcriptomic variation in these transgenic soybean lines substantiated the integration hsw into cell and seed size control. Moreover, the hsw allele underwent selection and expansion during soybean domestication and improvement. Our work cloned a likely domesticated QTL controlling soybean seed weight, revealed a novel genetic variation and mechanism in soybean domestication, and provided new insight into crop domestication and breeding, and plant evolution.
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Affiliation(s)
- Siming Wei
- State Key Laboratory of Plant Diversity and Specialty Crops/State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bin Yong
- State Key Laboratory of Plant Diversity and Specialty Crops/State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hongwei Jiang
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, China
- Jilin Academy of Agricultural Sciences, Changchun, 130022, China
| | - Zhenghong An
- State Key Laboratory of Plant Diversity and Specialty Crops/State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yan Wang
- State Key Laboratory of Plant Diversity and Specialty Crops/State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
| | - Bingbing Li
- State Key Laboratory of Plant Diversity and Specialty Crops/State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ce Yang
- State Key Laboratory of Plant Diversity and Specialty Crops/State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Weiwei Zhu
- State Key Laboratory of Plant Diversity and Specialty Crops/State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qingshan Chen
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, China
| | - Chaoying He
- State Key Laboratory of Plant Diversity and Specialty Crops/State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- The Innovative Academy of Seed Design, the Chinese Academy of Sciences, Beijing, 100101, China
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21
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Zhao K, Wang L, Qiu D, Cao Z, Wang K, Li Z, Wang X, Wang J, Ma Q, Cao D, Qi Y, Zhao K, Gong F, Li Z, Ren R, Ma X, Zhang X, Yu F, Yin D. PSW1, an LRR receptor kinase, regulates pod size in peanut. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:2113-2124. [PMID: 37431286 PMCID: PMC10502750 DOI: 10.1111/pbi.14117] [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: 02/07/2023] [Revised: 05/30/2023] [Accepted: 06/15/2023] [Indexed: 07/12/2023]
Abstract
Pod size is a key agronomic trait that greatly determines peanut yield, the regulatory genes and molecular mechanisms that controlling peanut pod size are still unclear. Here, we used quantitative trait locus analysis to identify a peanut pod size regulator, POD SIZE/WEIGHT1 (PSW1), and characterized the associated gene and protein. PSW1 encoded leucine-rich repeat receptor-like kinase (LRR-RLK) and positively regulated pod stemness. Mechanistically, this allele harbouring a 12-bp insertion in the promoter and a point mutation in the coding region of PSW1 causing a serine-to-isoleucine (S618I) substitution substantially increased mRNA abundance and the binding affinity of PSW1 for BRASSINOSTEROID INSENSITIVE1-ASSOCIATED RECEPTOR KINASE 1 (BAK1). Notably, PSW1HapII (super-large pod allele of PSW1) expression led to up-regulation of a positive regulator of pod stemness PLETHORA 1 (PLT1), thereby resulting in larger pod size. Moreover, overexpression of PSW1HapII increased seed/fruit size in multiple plant species. Our work thus discovers a conserved function of PSW1 that controls pod size and provides a valuable genetic resource for breeding high-yield crops.
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Affiliation(s)
- Kunkun Zhao
- College of Agronomy & Peanut Functional Genome and Molecular Breeding Engineering, Henan Agricultural UniversityZhengzhouChina
| | - Long Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Key Laboratory of Plant Functional Genomics and Developmental RegulationHunan UniversityChangshaChina
| | - Ding Qiu
- College of Agronomy & Peanut Functional Genome and Molecular Breeding Engineering, Henan Agricultural UniversityZhengzhouChina
| | - Zenghui Cao
- College of Agronomy & Peanut Functional Genome and Molecular Breeding Engineering, Henan Agricultural UniversityZhengzhouChina
| | - Kuopeng Wang
- College of Agronomy & Peanut Functional Genome and Molecular Breeding Engineering, Henan Agricultural UniversityZhengzhouChina
| | - Zhan Li
- College of Agronomy & Peanut Functional Genome and Molecular Breeding Engineering, Henan Agricultural UniversityZhengzhouChina
| | - Xiaoxuan Wang
- College of Agronomy & Peanut Functional Genome and Molecular Breeding Engineering, Henan Agricultural UniversityZhengzhouChina
| | - Jinzhi Wang
- College of Agronomy & Peanut Functional Genome and Molecular Breeding Engineering, Henan Agricultural UniversityZhengzhouChina
| | - Qian Ma
- College of Agronomy & Peanut Functional Genome and Molecular Breeding Engineering, Henan Agricultural UniversityZhengzhouChina
| | - Di Cao
- College of Agronomy & Peanut Functional Genome and Molecular Breeding Engineering, Henan Agricultural UniversityZhengzhouChina
| | - Yinyao Qi
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Key Laboratory of Plant Functional Genomics and Developmental RegulationHunan UniversityChangshaChina
| | - Kai Zhao
- College of Agronomy & Peanut Functional Genome and Molecular Breeding Engineering, Henan Agricultural UniversityZhengzhouChina
| | - Fangping Gong
- College of Agronomy & Peanut Functional Genome and Molecular Breeding Engineering, Henan Agricultural UniversityZhengzhouChina
| | - Zhongfeng Li
- College of Agronomy & Peanut Functional Genome and Molecular Breeding Engineering, Henan Agricultural UniversityZhengzhouChina
| | - Rui Ren
- College of Agronomy & Peanut Functional Genome and Molecular Breeding Engineering, Henan Agricultural UniversityZhengzhouChina
| | - Xingli Ma
- College of Agronomy & Peanut Functional Genome and Molecular Breeding Engineering, Henan Agricultural UniversityZhengzhouChina
| | - Xingguo Zhang
- College of Agronomy & Peanut Functional Genome and Molecular Breeding Engineering, Henan Agricultural UniversityZhengzhouChina
| | - Feng Yu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Key Laboratory of Plant Functional Genomics and Developmental RegulationHunan UniversityChangshaChina
| | - Dongmei Yin
- College of Agronomy & Peanut Functional Genome and Molecular Breeding Engineering, Henan Agricultural UniversityZhengzhouChina
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22
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Cai Z, Xian P, Cheng Y, Yang Y, Zhang Y, He Z, Xiong C, Guo Z, Chen Z, Jiang H, Ma Q, Nian H, Ge L. Natural variation of GmFATA1B regulates seed oil content and composition in soybean. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:2368-2379. [PMID: 37655952 DOI: 10.1111/jipb.13561] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 08/30/2023] [Indexed: 09/02/2023]
Abstract
Soybean (Glycine max) produces seeds that are rich in unsaturated fatty acids and is an important oilseed crop worldwide. Seed oil content and composition largely determine the economic value of soybean. Due to natural genetic variation, seed oil content varies substantially across soybean cultivars. Although much progress has been made in elucidating the genetic trajectory underlying fatty acid metabolism and oil biosynthesis in plants, the causal genes for many quantitative trait loci (QTLs) regulating seed oil content in soybean remain to be revealed. In this study, we identified GmFATA1B as the gene underlying a QTL that regulates seed oil content and composition, as well as seed size in soybean. Nine extra amino acids in the conserved region of GmFATA1B impair its function as a fatty acyl-acyl carrier protein thioesterase, thereby affecting seed oil content and composition. Heterogeneously overexpressing the functional GmFATA1B allele in Arabidopsis thaliana increased both the total oil content and the oleic acid and linoleic acid contents of seeds. Our findings uncover a previously unknown locus underlying variation in seed oil content in soybean and lay the foundation for improving seed oil content and composition in soybean.
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Affiliation(s)
- Zhandong Cai
- Guangdong Sub-center of National Center for Soybean Improvement, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, Shaoguan University, Shaoguan, 512000, China
- Department of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Peiqi Xian
- Guangdong Sub-center of National Center for Soybean Improvement, South China Agricultural University, Guangzhou, 510642, China
| | - Yanbo Cheng
- Guangdong Sub-center of National Center for Soybean Improvement, South China Agricultural University, Guangzhou, 510642, China
| | - Yuan Yang
- Guangdong Sub-center of National Center for Soybean Improvement, South China Agricultural University, Guangzhou, 510642, China
| | - Yakun Zhang
- Guangdong Sub-center of National Center for Soybean Improvement, South China Agricultural University, Guangzhou, 510642, China
| | - Zihang He
- Guangdong Sub-center of National Center for Soybean Improvement, South China Agricultural University, Guangzhou, 510642, China
| | - Chuwen Xiong
- Guangdong Sub-center of National Center for Soybean Improvement, South China Agricultural University, Guangzhou, 510642, China
| | - Zhibin Guo
- Guangdong Sub-center of National Center for Soybean Improvement, South China Agricultural University, Guangzhou, 510642, China
| | - Zhicheng Chen
- Guangdong Sub-center of National Center for Soybean Improvement, South China Agricultural University, Guangzhou, 510642, China
| | - Huiqian Jiang
- Guangdong Sub-center of National Center for Soybean Improvement, South China Agricultural University, Guangzhou, 510642, China
| | - Qibin Ma
- Guangdong Sub-center of National Center for Soybean Improvement, South China Agricultural University, Guangzhou, 510642, China
| | - Hai Nian
- Guangdong Sub-center of National Center for Soybean Improvement, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Liangfa Ge
- Guangdong Sub-center of National Center for Soybean Improvement, South China Agricultural University, Guangzhou, 510642, China
- Department of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
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23
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Yao Y, Xiong E, Qu X, Li J, Liu H, Quan L, Lu W, Zhu X, Chen M, Li K, Chen X, Lian Y, Lu W, Zhang D, Zhou X, Chu S, Jiao Y. WGCNA and transcriptome profiling reveal hub genes for key development stage seed size/oil content between wild and cultivated soybean. BMC Genomics 2023; 24:494. [PMID: 37641045 PMCID: PMC10463976 DOI: 10.1186/s12864-023-09617-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 08/22/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND Soybean is one of the most important oil crops in the world. The domestication of wild soybean has resulted in significant changes in the seed oil content and seed size of cultivated soybeans. To better understand the molecular mechanisms of seed formation and oil content accumulation, WDD01514 (E1), ZYD00463 (E2), and two extreme progenies (E23 and E171) derived from RILs were used for weighted gene coexpression network analysis (WGCNA) combined with transcriptome analysis. RESULTS In this study, both seed weight and oil content in E1 and E171 were significantly higher than those in E2 and E23, and 20 DAF and 30 DAF may be key stages of soybean seed oil content accumulation and weight increase. Pathways such as "Photosynthesis", "Carbon metabolism", and "Fatty acid metabolism", were involved in oil content accumulation and grain formation between wild and cultivated soybeans at 20 and 30 DAF according to RNA-seq analysis. A total of 121 oil content accumulation and 189 seed formation candidate genes were screened from differentially expressed genes. WGCNA identified six modules related to seed oil content and seed weight, and 76 candidate genes were screened from modules and network. Among them, 16 genes were used for qRT-PCR and tissue specific expression pattern analysis, and their expression-levels in 33-wild and 23-cultivated soybean varieties were subjected to correlation analysis; some key genes were verified as likely to be involved in oil content accumulation and grain formation. CONCLUSIONS Overall, these results contribute to an understanding of seed lipid metabolism and seed size during seed development, and identify potential functional genes for improving soybean yield and seed oil quantity.
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Affiliation(s)
- Yanjie Yao
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
- Chongqing Academy of Agricultural Sciences, Chongqing, 401329, China
| | - Erhui Xiong
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China.
| | - Xuelian Qu
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Junfeng Li
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Hongli Liu
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Leipo Quan
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Wenyan Lu
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Xuling Zhu
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Meiling Chen
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Ke Li
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Xiaoming Chen
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Yun Lian
- Zhengzhou Subcenter of National Soybean Improvement Center, Key Laboratory of Oil Crops in Huang-Huai Valleys of Ministry of Agriculture, Institute of Industrial Crops, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Weiguo Lu
- Zhengzhou Subcenter of National Soybean Improvement Center, Key Laboratory of Oil Crops in Huang-Huai Valleys of Ministry of Agriculture, Institute of Industrial Crops, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Dan Zhang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Xinan Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, 430062, China.
| | - Shanshan Chu
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China.
| | - Yongqing Jiao
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China.
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, 430062, China.
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24
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Li H, Song K, Zhang X, Wang D, Dong S, Liu Y, Yang L. Application of Multi-Perspectives in Tea Breeding and the Main Directions. Int J Mol Sci 2023; 24:12643. [PMID: 37628823 PMCID: PMC10454712 DOI: 10.3390/ijms241612643] [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: 07/03/2023] [Revised: 07/29/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023] Open
Abstract
Tea plants are an economically important crop and conducting research on tea breeding contributes to enhancing the yield and quality of tea leaves as well as breeding traits that satisfy the requirements of the public. This study reviews the current status of tea plants germplasm resources and their utilization, which has provided genetic material for the application of multi-omics, including genomics and transcriptomics in breeding. Various molecular markers for breeding were designed based on multi-omics, and available approaches in the direction of high yield, quality and resistance in tea plants breeding are proposed. Additionally, future breeding of tea plants based on single-cellomics, pangenomics, plant-microbe interactions and epigenetics are proposed and provided as references. This study aims to provide inspiration and guidance for advancing the development of genetic breeding in tea plants, as well as providing implications for breeding research in other crops.
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Affiliation(s)
| | | | | | | | | | | | - Long Yang
- College of Plant Protection and Agricultural Big-Data Research Center, Shandong Agricultural University, Tai’an 271018, China
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25
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Hu Y, Liu Y, Tao JJ, Lu L, Jiang ZH, Wei JJ, Wu CM, Yin CC, Li W, Bi YD, Lai YC, Wei W, Zhang WK, Chen SY, Zhang JS. GmJAZ3 interacts with GmRR18a and GmMYC2a to regulate seed traits in soybean. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:1983-2000. [PMID: 37066995 DOI: 10.1111/jipb.13494] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Accepted: 04/12/2023] [Indexed: 05/18/2023]
Abstract
Seed weight is usually associated with seed size and is one of the important agronomic traits that determine yield. Understanding of seed weight control is limited, especially in soybean plants. Here we show that Glycine max JASMONATE-ZIM DOMAIN 3 (GmJAZ3), a gene identified through gene co-expression network analysis, regulates seed-related traits in soybean. Overexpression of GmJAZ3 promotes seed size/weight and other organ sizes in stable transgenic soybean plants likely by increasing cell proliferation. GmJAZ3 interacted with both G. max RESPONSE REGULATOR 18a (GmRR18a) and GmMYC2a to inhibit their transcriptional activation of cytokinin oxidase gene G. max CYTOKININ OXIDASE 3-4 (GmCKX3-4), which usually affects seed traits. Meanwhile, the GmRR18a binds to the promoter of GmMYC2a and activates GmMYC2a gene expression. In GmJAZ3-overexpressing soybean seeds, the protein contents were increased while the fatty acid contents were reduced compared to those in the control seeds, indicating that the GmJAZ3 affects seed size/weight and compositions. Natural variation in JAZ3 promoter region was further analyzed and Hap3 promoter correlates with higher promoter activity, higher gene expression and higher seed weight. The Hap3 promoter may be selected and fixed during soybean domestication. JAZ3 orthologs from other plants/crops may also control seed size and weight. Taken together, our study reveals a novel molecular module GmJAZ3-GmRR18a/GmMYC2a-GmCKXs for seed size and weight control, providing promising targets during soybean molecular breeding for better seed traits.
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Affiliation(s)
- Yang Hu
- State Key Laboratory of Plant Genomics, 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
| | - Yue Liu
- State Key Laboratory of Plant Genomics, 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
| | - Jian-Jun Tao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Long Lu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhi-Hao Jiang
- State Key Laboratory of Plant Genomics, 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
| | - Jun-Jie Wei
- State Key Laboratory of Plant Genomics, 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
| | - Chun-Mei Wu
- State Key Laboratory of Plant Genomics, 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
| | - Cui-Cui Yin
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wei Li
- Crop Tillage and Cultivation Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Ying-Dong Bi
- Crop Tillage and Cultivation Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Yong-Cai Lai
- Crop Tillage and Cultivation Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Wei Wei
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wan-Ke Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Shou-Yi Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- Qilu Zhongke Academy of Modern Microbiology Technology, Jinan, 250000, China
| | - Jin-Song Zhang
- State Key Laboratory of Plant Genomics, 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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26
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Yuan B, Qi G, Yuan C, Wang Y, Zhao H, Li Y, Wang Y, Dong L, Dong Y, Liu X. Major genetic locus with pleiotropism determined seed-related traits in cultivated and wild soybeans. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:125. [PMID: 37165285 DOI: 10.1007/s00122-023-04358-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 04/04/2023] [Indexed: 05/12/2023]
Abstract
KEY MESSAGE Here, a novel pleiotropic QTL qSS14 simultaneously regulating four seed size traits and two consistently detected QTLs qSW17 and qSLW02 were identified across multiple years. Seed-related traits were the key agronomic traits that have been artificially selected during the domestication of wild soybean. Identifying the genetic loci and genes that regulate seed size could clarify the genetic variations in seed-related traits and provide novel insights into high-yield soybean breeding. In this study, we used a high-density genetic map constructed by F10 RIL populations from a cross between Glycine max and Glycine soja to detect additive QTLs for seven seed-related traits over the last three years. As a result, we identified one novel pleiotropic QTL, qSS14, that simultaneously controlled four seed size traits (100-seed weight, seed length, seed width, and seed thickness) and two consistently detected QTLs, qSW17, and qSLW02, in multiple years of phenotypic data. Furthermore, we predicted two, two and three candidate genes within these three critical loci based on the parental resequencing data and gene function annotations. And the relative expression of four candidate genes GLYMA_14G155100, GLYMA_17G061000, GLYMA_02G273100, and GLYMA_02G273300 showed significant differences among parents and the extreme materials through qRT-PCR analysis. These findings could facilitate the determination of beneficial genes in wild soybean and contribute to our understanding of the soybean domestication process.
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Affiliation(s)
- Baoqi Yuan
- Soybean Research Institute, Jilin Academy of Agricultural Sciences/National Engineering Research Center for Soybean, Changchun, Jilin, China
- College of Agronomy, Jilin Agricultural University, Changchun, Jilin, China
| | - Guangxun Qi
- Soybean Research Institute, Jilin Academy of Agricultural Sciences/National Engineering Research Center for Soybean, Changchun, Jilin, China
| | - Cuiping Yuan
- Soybean Research Institute, Jilin Academy of Agricultural Sciences/National Engineering Research Center for Soybean, Changchun, Jilin, China
| | - Yumin Wang
- Soybean Research Institute, Jilin Academy of Agricultural Sciences/National Engineering Research Center for Soybean, Changchun, Jilin, China
| | - Hongkun Zhao
- Soybean Research Institute, Jilin Academy of Agricultural Sciences/National Engineering Research Center for Soybean, Changchun, Jilin, China
| | - Yuqiu Li
- Soybean Research Institute, Jilin Academy of Agricultural Sciences/National Engineering Research Center for Soybean, Changchun, Jilin, China
| | - Yingnan Wang
- Soybean Research Institute, Jilin Academy of Agricultural Sciences/National Engineering Research Center for Soybean, Changchun, Jilin, China
| | - Lingchao Dong
- Soybean Research Institute, Jilin Academy of Agricultural Sciences/National Engineering Research Center for Soybean, Changchun, Jilin, China
| | - Yingshan Dong
- Soybean Research Institute, Jilin Academy of Agricultural Sciences/National Engineering Research Center for Soybean, Changchun, Jilin, China.
- College of Agronomy, Jilin Agricultural University, Changchun, Jilin, China.
| | - Xiaodong Liu
- College of Agronomy, Jilin Agricultural University, Changchun, Jilin, China.
- Crop Germplasm Institute, Jilin Academy of Agricultural Sciences, Changchun, Jilin, China.
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27
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Li D, Zhang Z, Gao X, Zhang H, Bai D, Wang Q, Zheng T, Li YH, Qiu LJ. The elite variations in germplasms for soybean breeding. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:37. [PMID: 37312749 PMCID: PMC10248635 DOI: 10.1007/s11032-023-01378-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 04/03/2023] [Indexed: 06/15/2023]
Abstract
The genetic base of soybean cultivars (Glycine max (L.) Merr.) has been narrowed through selective domestication and specific breeding improvement, similar to other crops. This presents challenges in breeding new cultivars with improved yield and quality, reduced adaptability to climate change, and increased susceptibility to diseases. On the other hand, the vast collection of soybean germplasms offers a potential source of genetic variations to address those challenges, but it has yet to be fully leveraged. In recent decades, rapidly improved high-throughput genotyping technologies have accelerated the harness of elite variations in soybean germplasm and provided the important information for solving the problem of a narrowed genetic base in breeding. In this review, we will overview the situation of maintenance and utilization of soybean germplasms, various solutions provided for different needs in terms of the number of molecular markers, and the omics-based high-throughput strategies that have been used or can be used to identify elite alleles. We will also provide an overall genetic information generated from soybean germplasms in yield, quality traits, and pest resistance for molecular breeding.
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Affiliation(s)
- Delin Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Zhengwei Zhang
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Xinyue Gao
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Hao Zhang
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Dong Bai
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Qi Wang
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
- College of Agriculture, Northeast Agricultural University, Harbin, 150030 China
| | - Tianqing Zheng
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Ying-Hui Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Li-Juan Qiu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
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28
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Ni L, Tian Z. Toward cis-regulation in soybean: a 3D genome scope. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:28. [PMID: 37313524 PMCID: PMC10248674 DOI: 10.1007/s11032-023-01374-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 03/25/2023] [Indexed: 06/15/2023]
Abstract
In eukaryotic cells, 3D genome plays an important role in the regulation of gene spatiotemporal expression, which is essential for the biological and developmental processes in a life cycle. In the past decade, the development of high-throughput technologies greatly enhances our ability to map the 3D genome organization, identifies multiple 3D genome structures, and investigates the functional role of 3D genome organization in gene regulation, which facilitates our understandings of cis-regulatory landscape and biological development. Comparing with the comprehensive analyses of 3D genome in mammals and model plants, the progress in soybean is much less. Future development and application of tools to precisely manipulate 3D genome structure at different levels will significantly strengthen the functional genome study and molecular breeding in soybean. Here, we review the recent progresses in 3D genome study and discuss future directions, which may help to improve soybean 3D functional genome study and molecular breeding.
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Affiliation(s)
- Lingbin Ni
- 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 Agriculture 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 Agriculture Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
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29
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Liu S, Liu Z, Hou X, Li X. Genetic mapping and functional genomics of soybean seed protein. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:29. [PMID: 37313523 PMCID: PMC10248706 DOI: 10.1007/s11032-023-01373-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 03/25/2023] [Indexed: 06/15/2023]
Abstract
Soybean is an utterly important crop for high-quality meal protein and vegetative oil. Soybean seed protein content has become a key factor in nutrients for livestock feed as well as human dietary consumption. Genetic improvement of soybean seed protein is highly desired to meet the demands of rapidly growing world population. Molecular mapping and genomic analysis in soybean have identified many quantitative trait loci (QTL) underlying seed protein content control. Exploring the mechanisms of seed storage protein regulation will be helpful to achieve the improvement of protein content. However, the practice of breeding higher protein soybean is challenging because soybean seed protein is negatively correlated with seed oil content and yield. To overcome the limitation of such inverse relationship, deeper insights into the property and genetic control of seed protein are required. Recent advances of soybean genomics have strongly enhanced the understandings for molecular mechanisms of soybean with better seed quality. Here, we review the research progress in the genetic characteristics of soybean storage protein, and up-to-date advances of molecular mappings and genomics of soybean protein. The key factors underlying the mechanisms of the negative correlation between protein and oil in soybean seeds are elaborated. We also briefly discuss the future prospects of breaking the bottleneck of the negative correlation to develop high protein soybean without penalty of oil and yield. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01373-5.
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Affiliation(s)
- Shu Liu
- Guangdong Provincial Key Laboratory of Applied Botany & Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Zhaojun Liu
- Heilongjiang Academy of Agricultural Sciences, Harbin, 150086 China
| | - Xingliang Hou
- Guangdong Provincial Key Laboratory of Applied Botany & Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 China
- Hainan Yazhou Bay Seed Laboratory, Sanya, 572025 China
| | - Xiaoming Li
- Guangdong Provincial Key Laboratory of Applied Botany & Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 China
- Hainan Yazhou Bay Seed Laboratory, Sanya, 572025 China
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30
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Tian Y, Li D, Wang X, Zhang H, Wang J, Yu L, Guo C, Luan X, Liu X, Li H, Reif JC, Li YH, Qiu LJ. Deciphering the genetic basis of resistance to soybean cyst nematode combining IBD and association mapping. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:50. [PMID: 36912956 PMCID: PMC10011322 DOI: 10.1007/s00122-023-04268-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 12/07/2022] [Indexed: 06/18/2023]
Abstract
IBD analysis clarified the dynamics of chromosomal recombination during the ZP pedigree breeding process and identified ten genomic regions resistant to SCN race3 combining association mapping. Soybean cyst nematode (SCN, Heterodera glycines Ichinohe) is one of the most devastating pathogens for soybean production worldwide. The cultivar Zhongpin03-5373 (ZP), derived from SCN-resistant progenitor parents, Peking, PI 437654 and Huipizhi Heidou, is an elite line with high resistance to SCN race3. In the current study, a pedigree variation map was generated for ZP and its ten progenitors using 3,025,264 high-quality SNPs identified from an average of 16.2 × re-sequencing for each genome. Through identity by decent (IBD) tracking, we showed the dynamic change of genome and detected important IBD fragments, which revealed the comprehensively artificial selection of important traits during ZP breeding process. A total of 2,353 IBD fragments related to SCN resistance including SCN-resistant genes rhg1, rhg4 and NSFRAN07 were identified based on the resistant-related genetic paths. Moreover, 23 genomic regions underlying resistance to SCN race3 were identified by genome-wide association study (GWAS) in 481 re-sequenced cultivated soybeans. Ten common loci were found by both IBD tracking and GWAS analysis. Haplotype analysis of 16 potential candidate genes suggested a causative SNP (C/T, - 1065) located in the promoter of Glyma.08G096500 and encoding a predicted TIFY5b-related protein on chr8 was highly correlated with SCN race3 resistance. Our results more thoroughly elucidated the dynamics of genomic fragments during ZP pedigree breeding and the genetic basis of SCN resistance, which will provide useful information for gene cloning and the development of resistant soybean cultivars using a marker-assisted selection approach.
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Affiliation(s)
- Yu Tian
- The National Key Facility for Gene Resources and Genetic Improvement/Key Laboratory of Crop Germplasm Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Science, Beijing, 100081, People's Republic of China
| | - Delin Li
- The National Key Facility for Gene Resources and Genetic Improvement/Key Laboratory of Crop Germplasm Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Science, Beijing, 100081, People's Republic of China
| | - Xueqing Wang
- The National Key Facility for Gene Resources and Genetic Improvement/Key Laboratory of Crop Germplasm Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Science, Beijing, 100081, People's Republic of China
| | - Hao Zhang
- The National Key Facility for Gene Resources and Genetic Improvement/Key Laboratory of Crop Germplasm Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Science, Beijing, 100081, People's Republic of China
| | - Jiajun Wang
- Soybean Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Lijie Yu
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding, College of Life Science and Technology, Harbin Normal University, Heilongjiang Province, Harbin, China
| | - Changhong Guo
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding, College of Life Science and Technology, Harbin Normal University, Heilongjiang Province, Harbin, China
| | - Xiaoyan Luan
- Soybean Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Xinlei Liu
- Soybean Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Hongjie Li
- The National Key Facility for Gene Resources and Genetic Improvement/Key Laboratory of Crop Germplasm Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Science, Beijing, 100081, People's Republic of China
| | - Jochen C Reif
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Ying-Hui Li
- The National Key Facility for Gene Resources and Genetic Improvement/Key Laboratory of Crop Germplasm Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Science, Beijing, 100081, People's Republic of China.
| | - Li-Juan Qiu
- The National Key Facility for Gene Resources and Genetic Improvement/Key Laboratory of Crop Germplasm Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Science, Beijing, 100081, People's Republic of China.
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Duan Z, Li Q, Wang H, He X, Zhang M. Genetic regulatory networks of soybean seed size, oil and protein contents. FRONTIERS IN PLANT SCIENCE 2023; 14:1160418. [PMID: 36959925 PMCID: PMC10028097 DOI: 10.3389/fpls.2023.1160418] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 02/24/2023] [Indexed: 06/18/2023]
Abstract
As a leading oilseed crop that supplies plant oil and protein for daily human life, increasing yield and improving nutritional quality (high oil or protein) are the top two fundamental goals of soybean breeding. Seed size is one of the most critical factors determining soybean yield. Seed size, oil and protein contents are complex quantitative traits governed by genetic and environmental factors during seed development. The composition and quantity of seed storage reserves directly affect seed size. In general, oil and protein make up almost 60% of the total storage of soybean seed. Therefore, soybean's seed size, oil, or protein content are highly correlated agronomical traits. Increasing seed size helps increase soybean yield and probably improves seed quality. Similarly, rising oil and protein contents improves the soybean's nutritional quality and will likely increase soybean yield. Due to the importance of these three seed traits in soybean breeding, extensive studies have been conducted on their underlying quantitative trait locus (QTLs) or genes and the dissection of their molecular regulatory pathways. This review summarized the progress in functional genome controlling soybean seed size, oil and protein contents in recent decades, and presented the challenges and prospects for developing high-yield soybean cultivars with high oil or protein content. In the end, we hope this review will be helpful to the improvement of soybean yield and quality in the future breeding process.
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Affiliation(s)
- Zongbiao Duan
- Hainan Yazhou Bay Seed Laboratory, Sanya, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Qing Li
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Hong Wang
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Xuemei He
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Min Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
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Novel Seed Size: A Novel Seed-Developing Gene in Glycine max. Int J Mol Sci 2023; 24:ijms24044189. [PMID: 36835599 PMCID: PMC9967547 DOI: 10.3390/ijms24044189] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/09/2023] [Accepted: 02/13/2023] [Indexed: 02/22/2023] Open
Abstract
Soybean-seed development is controlled in multiple ways, as in many known regulating genes. Here, we identify a novel gene, Novel Seed Size (NSS), involved in seed development, by analyzing a T-DNA mutant (S006). The S006 mutant is a random mutant of the GmFTL4pro:GUS transgenic line, with phenotypes with small and brown seed coats. An analysis of the metabolomics and transcriptome combined with RT-qPCR in the S006 seeds revealed that the brown coat may result from the increased expression of chalcone synthase 7/8 genes, while the down-regulated expression of NSS leads to small seed size. The seed phenotypes and a microscopic observation of the seed-coat integument cells in a CRISPR/Cas9-edited mutant nss1 confirmed that the NSS gene conferred small phenotypes of the S006 seeds. As mentioned in an annotation on the Phytozome website, NSS encodes a potential DNA helicase RuvA subunit, and no such genes were previously reported to be involved in seed development. Therefore, we identify a novel gene in a new pathway controlling seed development in soybeans.
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Azam M, Zhang S, Li J, Ahsan M, Agyenim-Boateng KG, Qi J, Feng Y, Liu Y, Li B, Qiu L, Sun J. Identification of hub genes regulating isoflavone accumulation in soybean seeds via GWAS and WGCNA approaches. FRONTIERS IN PLANT SCIENCE 2023; 14:1120498. [PMID: 36866374 PMCID: PMC9971994 DOI: 10.3389/fpls.2023.1120498] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 02/01/2023] [Indexed: 06/18/2023]
Abstract
INTRODUCTION Isoflavones are the secondary metabolites synthesized by the phenylpropanoid biosynthesis pathway in soybean that benefits human and plant health. METHODS In this study, we have profiled seed isoflavone content by HPLC in 1551 soybean accessions grown in Beijing and Hainan for two consecutive years (2017 and 2018) and in Anhui for one year (2017). RESULTS A broad range of phenotypic variations was observed for individual and total isoflavone (TIF) content. The TIF content ranged from 677.25 to 5823.29 µg g-1 in the soybean natural population. Using a genome-wide association study (GWAS) based on 6,149,599 single nucleotide polymorphisms (SNPs), we identified 11,704 SNPs significantly associated with isoflavone contents; 75% of them were located within previously reported QTL regions for isoflavone. Two significant regions on chromosomes 5 and 11 were associated with TIF and malonylglycitin across more than 3 environments. Furthermore, the WGCNA identified eight key modules: black, blue, brown, green, magenta, pink, purple, and turquoise. Of the eight co-expressed modules, brown (r = 0.68***), magenta (r = 0.64***), and green (r = 0.51**) showed a significant positive association with TIF, as well as with individual isoflavone contents. By combining the gene significance, functional annotation, and enrichment analysis information, four hub genes Glyma.11G108100, Glyma.11G107100, Glyma.11G106900, and Glyma.11G109100 encoding, basic-leucine zipper (bZIP) transcription factor, MYB4 transcription factor, early responsive to dehydration, and PLATZ transcription factor respectively were identified in brown and green modules. The allelic variation in Glyma.11G108100 significantly influenced individual and TIF accumulation. DISCUSSION The present study demonstrated that the GWAS approach, combined with WGCNA, could efficiently identify isoflavone candidate genes in the natural soybean population.
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Affiliation(s)
- Muhammad Azam
- The National Engineering Research Center of Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shengrui Zhang
- The National Engineering Research Center of Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jing Li
- The National Engineering Research Center of Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Muhammad Ahsan
- The National Engineering Research Center of Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Kwadwo Gyapong Agyenim-Boateng
- The National Engineering Research Center of Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jie Qi
- The National Engineering Research Center of Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yue Feng
- The National Engineering Research Center of Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yitian Liu
- The National Engineering Research Center of Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Bin Li
- Ministry of Agriculture and Rural Affairs (MARA) Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lijuan Qiu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Germplasm and Biotechnology Ministry of Agriculture and Rural Affairs (MARA), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Junming Sun
- The National Engineering Research Center of Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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Cai Z, Xian P, Cheng Y, Zhong Y, Yang Y, Zhou Q, Lian T, Ma Q, Nian H, Ge L. MOTHER-OF-FT-AND-TFL1 regulates the seed oil and protein content in soybean. THE NEW PHYTOLOGIST 2023. [PMID: 36740575 DOI: 10.1111/nph.18792] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
Soybean is a major crop that produces valuable seed oil and protein for global consumption. Seed oil and protein are regulated by complex quantitative trait loci (QTLs) and have undergone intensive selections during the domestication of soybean. It is essential to identify the major genetic components and understand their mechanism behind seed oil and protein in soybean. We report that MOTHER-OF-FT-AND-TFL1 (GmMFT) is the gene of a classical QTL that has been reported to regulate seed oil and protein content in many studies. Mutation of MFT decreased seeds oil content and weight in both Arabidopsis and soybean, whereas increased expression of GmMFT enhanced seeds oil content and weight. Haplotype analysis showed that GmMFT has undergone selection, which resulted in the extended haplotype homozygosity in the cultivated soybean and the enriching of the oil-favorable allele in modern soybean cultivars. This work unraveled the GmMFT-mediated mechanism regulating seed oil and protein content and seed weight, and revealed a previously unknown function of MFT that provides new insights into targeted soybean improvement and breeding.
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Affiliation(s)
- Zhandong Cai
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, 510642, China
- Department of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Peiqi Xian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, 510642, China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Yanbo Cheng
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, 510642, China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Yiwang Zhong
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, 510642, China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Yuan Yang
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, 510642, China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Qianghua Zhou
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, 510642, China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Tengxiang Lian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, 510642, China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Qibin Ma
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, 510642, China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Hai Nian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, 510642, China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, Guangdong, China
| | - Liangfa Ge
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, 510642, China
- Department of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, Guangdong, China
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Du H, Fang C, Li Y, Kong F, Liu B. Understandings and future challenges in soybean functional genomics and molecular breeding. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:468-495. [PMID: 36511121 DOI: 10.1111/jipb.13433] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 12/11/2022] [Indexed: 06/17/2023]
Abstract
Soybean (Glycine max) is a major source of plant protein and oil. Soybean breeding has benefited from advances in functional genomics. In particular, the release of soybean reference genomes has advanced our understanding of soybean adaptation to soil nutrient deficiencies, the molecular mechanism of symbiotic nitrogen (N) fixation, biotic and abiotic stress tolerance, and the roles of flowering time in regional adaptation, plant architecture, and seed yield and quality. Nevertheless, many challenges remain for soybean functional genomics and molecular breeding, mainly related to improving grain yield through high-density planting, maize-soybean intercropping, taking advantage of wild resources, utilization of heterosis, genomic prediction and selection breeding, and precise breeding through genome editing. This review summarizes the current progress in soybean functional genomics and directs future challenges for molecular breeding of soybean.
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Affiliation(s)
- Haiping Du
- 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, 510006, China
| | - Chao Fang
- 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, 510006, China
| | - Yaru Li
- 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, 510006, 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, 510006, 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, 510006, China
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Bioengineering of Soybean Oil and Its Impact on Agronomic Traits. Int J Mol Sci 2023; 24:ijms24032256. [PMID: 36768578 PMCID: PMC9916542 DOI: 10.3390/ijms24032256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 01/26/2023] Open
Abstract
Soybean is a major oil crop and is also a dominant source of nutritional protein. The 20% seed oil content (SOC) of soybean is much lower than that in most oil crops and the fatty acid composition of its native oil cannot meet the specifications for some applications in the food and industrial sectors. Considerable effort has been expended on soybean bioengineering to tailor fatty acid profiles and improve SOC. Although significant advancements have been made, such as the creation of high-oleic acid soybean oil and high-SOC soybean, those genetic modifications have some negative impacts on soybean production, for instance, impaired germination or low protein content. In this review, we focus on recent advances in the bioengineering of soybean oil and its effects on agronomic traits.
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Xu M, Kong K, Miao L, He J, Liu T, Zhang K, Yue X, Jin T, Gai J, Li Y. Identification of major quantitative trait loci and candidate genes for seed weight in soybean. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:22. [PMID: 36688967 PMCID: PMC9870841 DOI: 10.1007/s00122-023-04299-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 01/09/2023] [Indexed: 06/17/2023]
Abstract
Four major quantitative trait loci for 100-seed weight were identified in a soybean RIL population under five environments, and the most likely candidate genes underlying these loci were identified. Seed weight is an important target of soybean breeding. However, the genes underlying the major quantitative trait loci (QTL) controlling seed weight remain largely unknown. In this study, a soybean population of 300 recombinant inbred lines (RILs) derived from a cross between PI595843 (PI) and WH was used to map the QTL and identify candidate genes for seed weight. The RIL population was genotyped through whole genome resequencing, and phenotyped for 100-seed weight under five environments. A total of 38 QTL were detected, and four major QTL, each explained at least 10% of the variation in 100-seed weight, were identified. Six candidate genes within these four major QTL regions were identified by analyses of their tissue expression patterns, gene annotations, and differential gene expression levels in soybean seeds during four developmental stages between two parental lines. Further sequence variation analyses revealed a C to T substitution in the first exon of the Glyma.19G143300, resulting in an amino acid change between PI and WH, and thus leading to a different predicted kinase domain, which might affect its protein function. Glyma.19G143300 is highly expressed in soybean seeds and encodes a leucine-rich repeat receptor-like protein kinase (LRR-RLK). Its predicted protein has typical domains of LRR-RLK family, and phylogenetic analyses reveled its similarity with the known LRR-RLK protein XIAO (LOC_Os04g48760), which is involved in controlling seed size. The major QTL and candidate genes identified in this study provide useful information for molecular breeding of new soybean cultivars with desirable seed weight.
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Affiliation(s)
- Mengge Xu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Keke Kong
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Long Miao
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Jianbo He
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Tengfei Liu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Kai Zhang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Xiuli Yue
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Ting Jin
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Junyi Gai
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Yan Li
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China.
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Xu C, Wu T, Yuan S, Sun S, Han T, Song W, Wu C. Can Soybean Cultivars with Larger Seed Size Produce More Protein, Lipids, and Seed Yield? A Meta-Analysis. Foods 2022; 11:foods11244059. [PMID: 36553799 PMCID: PMC9777928 DOI: 10.3390/foods11244059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/09/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Increasing soybean production and ensuring greater access to soybean protein and lipids is critical for global food security and human health. Seed size (i.e., seed weight) is one of the most important agronomic traits of soybean, which not only determines the seed yield, but can also affect the yield of protein and lipids. In China, farmers favor soybean cultivars with large seeds, which they believe produce more protein and lipids; however, experimental evidence supporting this belief is lacking. Therefore, we conducted field experiments from 2017 to 2020 at 35 locations across the Huang-Huai-Hai region (HHH) of China with 64 soybean cultivars. The seed yield, seed protein content, and seed lipids content of soybean, and their relationship with seed size were investigated. The highest seed yield (i.e., seed weight per unit area) was 2996.5 kg ha−1 in the north of HHH. However, the highest seed protein content was found in the south of HHH (42.5%) for the higher temperature, which was significantly higher than that of the middle (41.7%) and north of HHH (40.2%). In contrast, the highest seed lipids content was 20.7% in the north of HHH. Temperature, which had a path coefficient on seed yield of 0.519, can promote soybean seed yield. The correlation analysis indicated that the selection of the large seed size cultivar did not increase seed yield, and even led to a reduction of seed yield under high-yield environmental conditions. The seed protein content of soybean was not increased in the cultivars with large seed sizes. In addition, under different levels of seed lipids content (<20.30% or >20.30%), a significantly negative relationship was found between seed lipids content and hundred seed weight. Therefore, it is recommended that farmers choose to plant cultivars with smaller soybean seed sizes, so as to ensure high and stable soybean seed yield and obtain more vegetable protein and lipids per unit area.
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GmWRI1c Increases Palmitic Acid Content to Regulate Seed Oil Content and Nodulation in Soybean ( Glycine max). Int J Mol Sci 2022; 23:ijms232213793. [PMID: 36430287 PMCID: PMC9694093 DOI: 10.3390/ijms232213793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/06/2022] [Accepted: 11/07/2022] [Indexed: 11/11/2022] Open
Abstract
Soybean (Glycine max) is an important oil crop, but the regulatory mechanisms underlying seed oil accumulation remain unclear. We identified a member of the GmWRI1s transcription factor family, GmWRI1c, that is involved in regulating soybean oil content and nodulation. Overexpression of GmWRI1c in soybean hairy roots increased the expression of genes involved in glycolysis and de novo lipogenesis, the proportion of palmitic acid (16:0), and the number of root nodules. The effect of GmWRI1c in increasing the number of root nodules via regulating the proportion of palmitic acid was confirmed in a recombinant inbred line (RIL) population. GmWRI1c shows abundant sequence diversity and has likely undergone artificial selection during domestication. An association analysis revealed a correlation between seed oil content and five linked natural variations (Hap1/Hap2) in the GmWRI1c promoter region. Natural variations in the GmWRI1c promoter were strongly associated with the GmWRI1c transcript level, with higher GmWRI1c transcript levels in lines carrying GmWRI1cHap1 than in those carrying GmWRI1cHap2. The effects of GmWRI1c alleles on seed oil content were confirmed in natural and RIL populations. We identified a favourable GmWRI1c allele that can be used to breed new varieties with increased seed oil content and nodulation.
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Promoter of Vegetable Soybean GmTIP1;6 Responds to Diverse Abiotic Stresses and Hormone Signals in Transgenic Arabidopsis. Int J Mol Sci 2022; 23:ijms232012684. [PMID: 36293538 PMCID: PMC9604487 DOI: 10.3390/ijms232012684] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 09/30/2022] [Accepted: 10/18/2022] [Indexed: 11/17/2022] Open
Abstract
Tonoplast intrinsic proteins (TIPs), a sub-family of aquaporins (AQPs), are known to play important roles in plant abiotic stress responses. However, evidence for the promoters of TIPs involvement in abiotic stress processes remains scarce. In this study, the promoter of the vegetable soybean GmTIP1;6 gene, which had the highest similarity to TIP1-type AQPs from other plants, was cloned. Expression pattern analyses indicated that the GmTIP1;6 gene was dramatically induced by drought, salt, abscisic acid (ABA), and methyl jasmonate (MeJA) stimuli. Promoter analyses revealed that the GmTIP1;6 promoter contained drought, ABA, and MeJA cis-acting elements. Histochemical staining of the GmTIP1;6 promoter in transgenic Arabidopsis corroborated that it was strongly expressed in the vascular bundles of leaves, stems, and roots. Beta-glucuronidase (GUS) activity assays showed that the activities of the GmTIP1;6 promoter were enhanced by different concentrations of polyethylene glycol 6000 (PEG 6000), NaCl, ABA, and MEJA treatments. Integrating these results revealed that the GmTIP1;6 promoter could be applied for improving the tolerance to abiotic stresses of the transgenic plants by promoting the expression of vegetable soybean AQPs.
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Liu J, Lin Y, Chen J, Yan Q, Xue C, Wu R, Chen X, Yuan X. Genome-wide association studies provide genetic insights into natural variation of seed-size-related traits in mungbean. FRONTIERS IN PLANT SCIENCE 2022; 13:997988. [PMID: 36311130 PMCID: PMC9608654 DOI: 10.3389/fpls.2022.997988] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 08/15/2022] [Indexed: 05/24/2023]
Abstract
Although mungbean (Vigna radiata (L.) R. Wilczek) is an important legume crop, its seed yield is relatively low. To address this issue, here 196 accessions with 3,607,508 SNP markers were used to identify quantitative trait nucleotides (QTNs), QTN-by-environment interactions (QEIs), and their candidate genes for seed length (SL), seed width, and 100-seed weight (HSW) in two environments. As a result, 98 QTNs and 20 QEIs were identified using 3VmrMLM, while 95, >10,000, and 15 QTNs were identified using EMMAX, GEMMA, and CMLM, respectively. Among 809 genes around these QTNs, 12 were homologous to known seed-development genes in rice and Arabidopsis thaliana, in which 10, 2, 1, and 0 genes were found, respectively, by the above four methods to be associated with the three traits, such as VrEmp24/25 for SL and VrKIX8 for HSW. Eight of the 12 genes were significantly differentially expressed between two large-seed and two small-seed accessions, and VrKIX8, VrPAT14, VrEmp24/25, VrIAR1, VrBEE3, VrSUC4, and Vrflo2 were further verified by RT-qPCR. Among 65 genes around these QEIs, VrFATB, VrGSO1, VrLACS2, and VrPAT14 were homologous to known seed-development genes in A. thaliana, although new experiments are necessary to explore these novel GEI-trait associations. In addition, 54 genes were identified in comparative genomics analysis to be associated with seed development pathway, in which VrKIX8, VrABA2, VrABI5, VrSHB1, and VrIKU2 were also identified in genome-wide association studies. This result provided a reliable approach for identifying seed-size-related genes in mungbean and a solid foundation for further molecular biology research on seed-size-related genes.
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Hooker JC, Nissan N, Luckert D, Zapata G, Hou A, Mohr RM, Glenn AJ, Barlow B, Daba KA, Warkentin TD, Lefebvre F, Golshani A, Cober ER, Samanfar B. GmSWEET29 and Paralog GmSWEET34 Are Differentially Expressed between Soybeans Grown in Eastern and Western Canada. PLANTS 2022; 11:plants11182337. [PMID: 36145738 PMCID: PMC9502396 DOI: 10.3390/plants11182337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 08/31/2022] [Accepted: 09/01/2022] [Indexed: 11/16/2022]
Abstract
Over the past two decades soybeans grown in western Canada have persistently had lower seed protein than those grown in eastern Canada. To understand the discrepancy in seed protein content between eastern- and western-grown soybeans, RNA-seq and differential expression analysis have been investigated. Ten soybean genotypes, ranging from low to high in seed protein content, were grown in four locations across eastern (Ottawa) and western (Morden, Brandon, and Saskatoon) Canada. Differential expression analysis revealed 34 differentially expressed genes encoding Glycine max Sugars Will Eventually be Exported Transporters (GmSWEETs), including paralogs GmSWEET29 and GmSWEET34 (AtSWEET2 homologs) that were consistently upregulated across all ten genotypes in each of the western locations over three years. GmSWEET29 and GmSWEET34 are likely candidates underlying the lower seed protein content of western soybeans. GmSWEET20 (AtSWEET12 homolog) was downregulated in the western locations and may also play a role in lower seed protein content. These findings are valuable for improving soybean agriculture in western growing regions, establishing more strategic and efficient agricultural practices.
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Affiliation(s)
- Julia C. Hooker
- Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Nour Nissan
- Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Doris Luckert
- Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
| | - Gerardo Zapata
- Canadian Centre for Computational Genomics, Montréal, QC H3A 0G1, Canada
| | - Anfu Hou
- Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada
| | - Ramona M. Mohr
- Agriculture and Agri-Food Canada, Brandon, MB R7A 5Y3, Canada
| | - Aaron J. Glenn
- Agriculture and Agri-Food Canada, Brandon, MB R7A 5Y3, Canada
| | - Brent Barlow
- Crop Development Centre, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
| | - Ketema A. Daba
- Crop Development Centre, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
| | - Thomas D. Warkentin
- Crop Development Centre, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
| | - François Lefebvre
- Canadian Centre for Computational Genomics, Montréal, QC H3A 0G1, Canada
| | - Ashkan Golshani
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Elroy R. Cober
- Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
| | - Bahram Samanfar
- Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
- Correspondence:
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