1
|
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.
Collapse
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
| |
Collapse
|
2
|
Sun C, Zhang Z, Liu M, Ceretta S, Zhang S, Guo B, Li Y, Liu Z, Gu Y, Ao X, Qiu L. Comparison of grain traits and genetic diversity between Chinese and Uruguayan soybeans ( Glycine max L.). FRONTIERS IN PLANT SCIENCE 2024; 15:1435881. [PMID: 39114471 PMCID: PMC11303235 DOI: 10.3389/fpls.2024.1435881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Accepted: 07/09/2024] [Indexed: 08/10/2024]
Abstract
Soybeans (Glycine max L.), originating in China, were introduced to South America in the late 19th century after passing through North America. South America is now a major soybean-producing region, accounting for approximately 40% of the global soybean production. Crops like soybeans gradually adapt to the local climate and human-selected conditions, resulting in beneficial variations during cultivation in different regions. Comparing the phenotypic and genetic variations in soybeans across different regions is crucial to determining the variations that may enhance soybean productivity. This study identified seed-related traits and conducted a genetic diversity analysis using 46 breeding soybean varieties from China and Uruguay. Compared to the Chinese soybean germplasm, the Uruguayan equivalent had a lower 100-grain weight, higher oil content, lower protein content, and higher soluble sugar content. Using ZDX1 gene chips, genetic typing was performed on the 46 breeding varieties. Cluster analysis based on SNP sites revealed significant differences in the genetic basis of Sino-Uruguayan soybean germplasm. Selection analysis, including nucleotide polymorphism (π) and fixation indexes (Fst), identified several genomic regions under selection between Sino-Uruguayan soybean germplasm. The selected intervals significantly enriched gene ontology (GO) terms related to protein metabolism. Additionally, differentiation occurred in genes associated with the oil content, seed weight, and cyst nematodes between Sino-Uruguayan soybean germplasm, such as GmbZIP123 and GmSSS1. These findings highlight the differences in seed-related phenotypes between Sino-Uruguay soybean germplasm and provide genomic-level insights into the mechanisms behind phenotypic differences, offering valuable references for understanding soybean evolution and molecular breeding.
Collapse
Affiliation(s)
- Chang Sun
- College of Agronomy, Shenyang Agricultural University, Shenyang, China
| | - Zhihao Zhang
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/State Key Laboratory of Crop Gene Resources and Breeding/Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA)/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- 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, China
| | - Meiling Liu
- College of Agronomy, Shenyang Agricultural University, Shenyang, China
| | - Sergio Ceretta
- National Agricultural Research Institute (INIA), Soybean Breeding Program, Colonia, Uruguay
| | - Shengrui Zhang
- The National Engineering Research Center for Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs (MARA) Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Bingfu Guo
- Nanchang Branch of the National Center of Oilcrops Improvement, Jiangxi Province Key Laboratory for the Genetic Improvement of Oilcrops, Institute of Crops, Jiangxi Academy of Agricultural Sciences, Nanchang, China
| | - Yinghui Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/State Key Laboratory of Crop Gene Resources and Breeding/Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA)/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhangxiong Liu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/State Key Laboratory of Crop Gene Resources and Breeding/Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA)/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yongzhe Gu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/State Key Laboratory of Crop Gene Resources and Breeding/Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA)/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xue Ao
- College of Agronomy, Shenyang Agricultural University, Shenyang, China
| | - Lijuan Qiu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/State Key Laboratory of Crop Gene Resources and Breeding/Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA)/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| |
Collapse
|
3
|
Zhao JX, Wang S, Wen J, Zhou SZ, Jiang XD, Zhong MC, Liu J, Dong X, Deng Y, Hu JY, Li DZ. Evolution of FLOWERING LOCUS T-like genes in angiosperms: a core Lamiales-specific diversification. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:3946-3958. [PMID: 38642399 DOI: 10.1093/jxb/erae176] [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: 10/14/2023] [Accepted: 04/18/2024] [Indexed: 04/22/2024]
Abstract
Plant life history is determined by two transitions, germination and flowering time, in which the phosphatidylethanolamine-binding proteins (PEBPs) FLOWERING LOCUS T (FT) and TERMINAL FLOWER1 (TFL1) play key regulatory roles. Compared with the highly conserved TFL1-like genes, FT-like genes vary significantly in copy numbers in gymnosperms, and monocots within the angiosperms, while sporadic duplications can be observed in eudicots. Here, via a systematic analysis of the PEBPs in angiosperms with a special focus on 12 representative species featuring high-quality genomes in the order Lamiales, we identified a successive lineage-specific but systematic expansion of FT-like genes in the families of core Lamiales. The first expansion event generated FT1-like genes mainly via a core Lamiales-specific whole-genome duplication (cL-WGD), while a likely random duplication produced the FT2-like genes in the lineages containing Scrophulariaceae and the rest of the core Lamiales. Both FT1- and FT2-like genes were further amplified tandemly in some families. These expanded FT-like genes featured highly diverged expression patterns and structural variation, indicating functional diversification. Intriguingly, some core Lamiales contained the relict MOTHER OF FT AND TFL1 like 2 (MFT2) that probably expanded in the common ancestor of angiosperms. Our data showcase the highly dynamic lineage-specific expansion of the FT-like genes, and thus provide important and fresh evolutionary insights into the gene regulatory network underpinning flowering time diversity in Lamiales and, more generally, in angiosperms.
Collapse
Affiliation(s)
- Jiu-Xia Zhao
- Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Shu Wang
- State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong 510650, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
- Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, Guangzhou 510650, China
| | - Jing Wen
- Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Shi-Zhao Zhou
- Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Xiao-Dong Jiang
- Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Mi-Cai Zhong
- Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Jie Liu
- Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Xue Dong
- Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Yunfei Deng
- State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong 510650, China
- Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, Guangzhou 510650, China
| | - Jin-Yong Hu
- Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - De-Zhu Li
- Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| |
Collapse
|
4
|
Xie H, Su F, Niu Q, Geng L, Cao X, Song M, Dong J, Zheng Z, Guo R, Zhang Y, Deng Y, Ji Z, Pang K, Zhu JK, Zhu J. Knockout of miR396 genes increases seed size and yield in soybean. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:1148-1157. [PMID: 38597776 DOI: 10.1111/jipb.13660] [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: 01/28/2024] [Accepted: 03/22/2024] [Indexed: 04/11/2024]
Abstract
Yield improvement has long been an important task for soybean breeding in the world in order to meet the increasing demand for food and animal feed. miR396 genes have been shown to negatively regulate grain size in rice, but whether miR396 family members may function in a similar manner in soybean is unknown. Here, we generated eight soybean mutants harboring different combinations of homozygous mutations in the six soybean miR396 genes through genome editing with clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated nuclease (Cas)12SF01 in the elite soybean cultivar Zhonghuang 302 (ZH302). Four triple mutants (mir396aci, mir396acd, mir396adf, and mir396cdf), two quadruple mutants (mir396abcd and mir396acfi), and two quintuple mutants (mir396abcdf and mir396bcdfi) were characterized. We found that plants of all the mir396 mutants produced larger seeds compared to ZH302 plants. Field tests showed that mir396adf and mir396cdf plants have significantly increased yield in growth zones with relatively high latitude which are suited for ZH302 and moderately increased yield in lower latitude. In contrast, mir396abcdf and mir396bcdfi plants have increased plant height and decreased yield in growth zones with relatively high latitude due to lodging issues, but they are suited for low latitude growth zones with increased yield without lodging problems. Taken together, our study demonstrated that loss-of-function of miR396 genes leads to significantly enlarged seed size and increased yield in soybean, providing valuable germplasms for breeding high-yield soybean.
Collapse
Affiliation(s)
- Hongtao Xie
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
- Research Center for Biological Breeding Technology, Research Institute of Frontier Science, Anhui Agricultural University, Hefei, 230036, China
- Bellagen Biotechnology Co. Ltd, Jinan, 250000, China
| | - Fei Su
- Institute of Crop Sciences/National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Sanya, 572025, China
| | - Qingfeng Niu
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
- Research Center for Biological Breeding Technology, Research Institute of Frontier Science, Anhui Agricultural University, Hefei, 230036, China
| | - Leping Geng
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
- Research Center for Biological Breeding Technology, Research Institute of Frontier Science, Anhui Agricultural University, Hefei, 230036, China
| | - Xuesong Cao
- Southern University of Science, and Technology, Shenzhen, 518055, China
| | - Minglei Song
- Southern University of Science, and Technology, Shenzhen, 518055, China
| | - Jinsong Dong
- Institute of Crop Sciences/National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Sanya, 572025, China
| | - Zai Zheng
- Hainan Yazhou Bay Seed Laboratory, Sanya, 572024, China
| | - Rui Guo
- Institute of Crop Sciences/National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Sanya, 572025, China
| | - Yang Zhang
- Institute of Crop Sciences/National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Sanya, 572025, China
| | - Yuanwei Deng
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
- Research Center for Biological Breeding Technology, Research Institute of Frontier Science, Anhui Agricultural University, Hefei, 230036, China
| | - Zhanbo Ji
- Bellagen Biotechnology Co. Ltd, Jinan, 250000, China
| | - Kang Pang
- Bellagen Biotechnology Co. Ltd, Jinan, 250000, China
| | - Jian-Kang Zhu
- Southern University of Science, and Technology, Shenzhen, 518055, China
| | - Jianhua Zhu
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
- Research Center for Biological Breeding Technology, Research Institute of Frontier Science, Anhui Agricultural University, Hefei, 230036, China
| |
Collapse
|
5
|
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.
Collapse
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.)
| |
Collapse
|
6
|
Yang Z, Luo C, Pei X, Wang S, Huang Y, Li J, Liu B, Kong F, Yang QY, Fang C. SoyMD: a platform combining multi-omics data with various tools for soybean research and breeding. Nucleic Acids Res 2024; 52:D1639-D1650. [PMID: 37811889 PMCID: PMC10767819 DOI: 10.1093/nar/gkad786] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/13/2023] [Accepted: 09/15/2023] [Indexed: 10/10/2023] Open
Abstract
Advanced multi-omics technologies offer much information that can uncover the regulatory mechanisms from genotype to phenotype. In soybean, numerous multi-omics databases have been published. Although they cover multiple omics, there are still limitations when it comes to the types and scales of omics datasets and analysis methods utilized. This study aims to address these limitations by collecting and integrating a comprehensive set of multi-omics datasets. This includes 38 genomes, transcriptomes from 435 tissue samples, 125 phenotypes from 6686 accessions, epigenome data involving histone modification, transcription factor binding, chromosomal accessibility and chromosomal interaction, as well as genetic variation data from 24 501 soybean accessions. Then, common analysis pipelines and statistical methods were applied to mine information from these multi-omics datasets, resulting in the successful establishment of a user-friendly multi-omics database called SoyMD (https://yanglab.hzau.edu.cn/SoyMD/#/). SoyMD provides researchers with efficient query options and analysis tools, allowing them to swiftly access relevant omics information and conduct comprehensive multi-omics data analyses. Another notable feature of SoyMD is its capability to facilitate the analysis of candidate genes, as demonstrated in the case study on seed oil content. This highlights the immense potential of SoyMD in soybean genetic breeding and functional genomics research.
Collapse
Affiliation(s)
- Zhiquan Yang
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510405, China
| | - Chengfang Luo
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Xinxin Pei
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510405, China
| | - Shengbo Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Yiming Huang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiawei Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Baohui Liu
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510405, China
| | - Fanjiang Kong
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510405, China
| | - Qing-Yong Yang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural Reclamation Sciences, Shihezi 832000, China
| | - Chao Fang
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510405, China
| |
Collapse
|
7
|
Rauf S, Fatima S, Ortiz R. Modification of Fatty Acid Profile and Oil Contents Using Gene Editing in Oilseed Crops for a Changing Climate. GM CROPS & FOOD 2023; 14:1-12. [PMID: 37551783 PMCID: PMC10761075 DOI: 10.1080/21645698.2023.2243041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 07/27/2023] [Indexed: 08/09/2023]
Abstract
Mutation breeding based on various chemical and physical mutagens induces and disrupts non-target loci. Hence, large populations were required for visual screening, but desired plants were rare and it was a further laborious task to identify desirable mutants. Generated mutant had high defect due to non-targeted mutation, with poor agronomic performance. Mutation techniques were augmented by targeted induced local lesions in genome (TILLING) facilitating the selection of desirable germplasm. On the other hand, gene editing through CRISPR/Cas9 allows knocking down genes for site-directed mutation. This handy technique has been exploited for the modification of fatty acid profile. High oleic acid genetic stocks were obtained in a broad range of crops. Moreover, genes involved in the accumulation of undesirable seed components such as starch, polysaccharide, and flavors were knocked down to enhance seed quality, which helps to improve oil contents and reduces the anti-nutritional component.
Collapse
Affiliation(s)
- Saeed Rauf
- Department of Plant Breeding & Genetics, College of Agriculture, University of Sargodha, Sargodha, Pakistan
| | - Seerat Fatima
- Department of Plant Breeding & Genetics, College of Agriculture, University of Sargodha, Sargodha, Pakistan
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| |
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
Shelake RM, Jadhav AM, Bhosale PB, Kim JY. Unlocking secrets of nature's chemists: Potential of CRISPR/Cas-based tools in plant metabolic engineering for customized nutraceutical and medicinal profiles. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 203:108070. [PMID: 37816270 DOI: 10.1016/j.plaphy.2023.108070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 10/12/2023]
Abstract
Plant species have evolved diverse metabolic pathways to effectively respond to internal and external signals throughout their life cycle, allowing adaptation to their sessile and phototropic nature. These pathways selectively activate specific metabolic processes, producing plant secondary metabolites (PSMs) governed by genetic and environmental factors. Humans have utilized PSM-enriched plant sources for millennia in medicine and nutraceuticals. Recent technological advances have significantly contributed to discovering metabolic pathways and related genes involved in the biosynthesis of specific PSM in different food crops and medicinal plants. Consequently, there is a growing demand for plant materials rich in nutrients and bioactive compounds, marketed as "superfoods". To meet the industrial demand for superfoods and therapeutic PSMs, modern methods such as system biology, omics, synthetic biology, and genome editing (GE) play a crucial role in identifying the molecular players, limiting steps, and regulatory circuitry involved in PSM production. Among these methods, clustered regularly interspaced short palindromic repeats-CRISPR associated protein (CRISPR/Cas) is the most widely used system for plant GE due to its simple design, flexibility, precision, and multiplexing capabilities. Utilizing the CRISPR-based toolbox for metabolic engineering (ME) offers an ideal solution for developing plants with tailored preventive (nutraceuticals) and curative (therapeutic) metabolic profiles in an ecofriendly way. This review discusses recent advances in understanding the multifactorial regulation of metabolic pathways, the application of CRISPR-based tools for plant ME, and the potential research areas for enhancing plant metabolic profiles.
Collapse
Affiliation(s)
- Rahul Mahadev Shelake
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 52828, Republic of Korea.
| | - Amol Maruti Jadhav
- Research Institute of Green Energy Convergence Technology (RIGET), Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea
| | - Pritam Bhagwan Bhosale
- Department of Veterinary Medicine, Research Institute of Life Science, Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea
| | - Jae-Yean Kim
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 52828, Republic of Korea; Division of Life Science, Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea; Nulla Bio Inc, 501 Jinju-daero, Jinju, 52828, Republic of Korea.
| |
Collapse
|