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Xu B, Hao Y, Li S, Du D, Xiao D, Chen M, Song Y, Wei G, Zong W, Guo X, Sun K, Li W, Wu Z, Zhang K, Liao N, Liu YG, Guo J. Fine regulation of heading date by editing the untranslated regions of heading-related genes in rice. PLANT BIOTECHNOLOGY JOURNAL 2025. [PMID: 40448282 DOI: 10.1111/pbi.70114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2024] [Revised: 04/03/2025] [Accepted: 04/17/2025] [Indexed: 06/02/2025]
Affiliation(s)
- Bingqun Xu
- Guangdong Basic Research Center of Excellence for Precise Breeding of Future Crops, Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Yu Hao
- Guangdong Basic Research Center of Excellence for Precise Breeding of Future Crops, Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Shengting Li
- Guangdong Basic Research Center of Excellence for Precise Breeding of Future Crops, Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Duoduo Du
- Guangdong Basic Research Center of Excellence for Precise Breeding of Future Crops, Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Dongdong Xiao
- Guangdong Basic Research Center of Excellence for Precise Breeding of Future Crops, Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Miaomiao Chen
- Guangdong Basic Research Center of Excellence for Precise Breeding of Future Crops, Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Yingang Song
- Guangdong Basic Research Center of Excellence for Precise Breeding of Future Crops, Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Guangliang Wei
- Guangdong Basic Research Center of Excellence for Precise Breeding of Future Crops, Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Wubei Zong
- Guangdong Basic Research Center of Excellence for Precise Breeding of Future Crops, Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Xiaotong Guo
- Guangdong Basic Research Center of Excellence for Precise Breeding of Future Crops, Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Kangli Sun
- Guangdong Basic Research Center of Excellence for Precise Breeding of Future Crops, Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Weitao Li
- Guangdong Basic Research Center of Excellence for Precise Breeding of Future Crops, Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Zeqiang Wu
- Guangdong Basic Research Center of Excellence for Precise Breeding of Future Crops, Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Kai Zhang
- Guangdong Basic Research Center of Excellence for Precise Breeding of Future Crops, Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Nan Liao
- Guangdong Basic Research Center of Excellence for Precise Breeding of Future Crops, Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Yao-Guang Liu
- Guangdong Basic Research Center of Excellence for Precise Breeding of Future Crops, Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Jingxin Guo
- Guangdong Basic Research Center of Excellence for Precise Breeding of Future Crops, Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou, China
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Liu L, Hao J, Huang K, Duan P, Zhang B, Chi Z, Yao X, Li Y. Redox regulation of G protein oligomerization and signaling by the glutaredoxin WG1 controls grain size in rice. EMBO J 2025:10.1038/s44318-025-00462-9. [PMID: 40389777 DOI: 10.1038/s44318-025-00462-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2024] [Revised: 04/08/2025] [Accepted: 04/24/2025] [Indexed: 05/21/2025] Open
Abstract
Grain size is an important agronomic trait and influences both grain yield and quality in crops. The atypical heterotrimeric Gγ protein subunit GS3 is a central regulator of grain length in rice, and the loss-of-function allele of its corresponding gene has been widely utilized by breeders to improve grain length in rice. Here we report that the CC-type glutaredoxin WG1/OsGRX8 has disulfide oxidoreductase activity and regulates redox state of GS3, thereby determining grain length in rice. GS3 can form dimers and oligomers by intermolecular disulfide bonds, and the cysteine-rich C-terminal region of GS3 is predominantly required for its oligomerization. The oligomerization of GS3 alleviates its inhibitory effect on the interaction between RGB1 and DEP1/GGC2, resulting in an increase in grain length. WG1 interacts with GS3 and reduces the oligomerization of GS3 through redox mechanisms, which causes a decrease in grain length. Genetic analyses support WG1 and GS3 function in a common pathway to control grain length. Thus, our findings reveal a previously unrecognized mechanism, in which redox regulation of a Gγ subunit by a glutaredoxin controls grain length, opening a novel perspective for G protein signaling regulation.
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Affiliation(s)
- Lijie Liu
- State Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agriculture, University of Chinese Academy of Sciences, Beijing, China
| | - Jianqin Hao
- State Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Ke Huang
- State Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Penggen Duan
- State Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Baolan Zhang
- State Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Zhihai Chi
- State Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Xiaohong Yao
- State Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yunhai Li
- State Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
- College of Advanced Agriculture, University of Chinese Academy of Sciences, Beijing, China.
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3
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Li S, Zhao Z, Liu T, Zhang J, Xing X, Feng M, Liu X, Luo S, Dong K, Wang J, Wang Y, Zhang F, Miao R, Luo W, Lei C, Ren Y, Zhu S, Guo X, Wang X, Lin Q, Cheng Z, Wan J. The G-protein γ subunit DEP1 facilitates brassinosteroid signaling in rice via a MYB-bHLH-ARF module. THE PLANT CELL 2025; 37:koaf122. [PMID: 40398925 PMCID: PMC12124404 DOI: 10.1093/plcell/koaf122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/21/2025] [Revised: 04/13/2025] [Accepted: 04/16/2025] [Indexed: 05/23/2025]
Abstract
G-protein signaling and brassinosteroid (BR) phytohormones play important roles in regulating rice (Oryza sativa) yield-related plant architecture, such as leaf inclination and grain size. However, the relationship between G-proteins and BR signaling has not been fully elucidated in rice. The present study indicates that the G-protein Gγ subunit DENSE AND ERECT PANICLE 1 (DEP1) positively regulates BR signaling in rice and that BRs promote DEP1 nuclear entry through GRAIN NUMBER ASSOCIATED (GNA). Additionally, DEP1 interacts with and acts upstream of OsMYB86, an R2R3-MYB family transcription factor that positively regulates BR signaling by directly binding to the promoter of its downstream gene BRASSINOSTEROID UPREGULATED 1 (BU1), activating its expression in rice. In the nucleus, DEP1 interacts with OsMYB86 and GNA, significantly enhancing OsMYB86-mediated activation of BU1 expression. Furthermore, BU1 interacts with another HLH protein, INCREASED LEAF INCLINATION1 (ILI1), and a bHLH protein, ILI1 BINDING bHLH (IBH1). Interaction between ILI1 and BU1 facilitates translocation of BU1 from the cytoplasm to the nucleus, where they impede IBH1 binding to the promoter of the AUXIN RESPONSE FACTOR 11 (OsARF11) gene, which is involved in crosstalk between BR and auxin, thus effectively relieving the IBH1-repressed transcription of OsARF11. These findings reveal a DEP1-mediated signaling pathway that links G-proteins to the traditional BR signaling pathway, ensuring the efficient activation of BR responses in rice.
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Affiliation(s)
- Shuai Li
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhichao Zhao
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Tianzhen Liu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jinhui Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xinxin Xing
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Miao Feng
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xin Liu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Sheng Luo
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Kun Dong
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jian Wang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yupeng Wang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Feng Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Rong Miao
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Wenfan Luo
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Cailin Lei
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yulong Ren
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shanshan Zhu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiuping Guo
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xin Wang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qibing Lin
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhijun Cheng
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya 572025, China
| | - Jianmin Wan
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
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Sun S, Cheng J, Zhang Y, Wang Y, Wang L, Wang T, Wang Z, Li X, Zhou Y, Li X, Xiao J, Yan C, Zhang Q, Ouyang Y. Novel repetitive elements in plant-specific tails of Gγ proteins as the functional unit in G-protein signaling in crops. THE PLANT CELL 2025; 37:koaf052. [PMID: 40088466 PMCID: PMC12070394 DOI: 10.1093/plcell/koaf052] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/24/2025] [Accepted: 02/13/2025] [Indexed: 03/17/2025]
Abstract
Heterotrimeric G-proteins act as molecular switches in signal transduction in response to stimuli in all eukaryotes. However, what specifies G-protein signaling in plants and how the mechanism evolved and diverged remain unsolved. Here, we found that the recently evolved tails of three Gγ subunits, Dense and erect panicle 1 (DEP1), G-protein gamma subunit 2 of type C (GGC2), and Grain size 3 (GS3), determine their distinct functions and specify grain size in rice (Oryza sativa L.). These Gγ subunits originated and expanded by an ancestral σ duplication ∼130 million years ago (mya) and a pancereal ρ duplication ∼70 mya in monocots, increasing genome complexity and inspiring functional innovations. In particular, through the comprehensive creation of artificial chimeric Gγ proteins, we found that this signaling selectivity is driven by repetitive elements and a link region hidden in plant-specific Gγ tails, allowing crops to switch from positive regulation to negative control. Unlike the tails, the conserved Gγ heads did not bias the signaling specificity; however, the change in the interaction between the mutated Gβ and Gγ affected the subsequent downstream signal transduction and grain size. Manipulating G-protein signaling also affects organ size in maize (Zea mays) and is expected to constitute a general mechanism for crop improvement. Collectively, these findings reveal that plant-specific Gγ tails drive signaling selectivity and serve as valuable targets for optimizing crop traits through G-protein manipulation.
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Affiliation(s)
- Shengyuan Sun
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Zhongshan Biological Breeding Laboratory, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou 225009, China
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinliang Cheng
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Zhongshan Biological Breeding Laboratory, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
| | - Yiwen Zhang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Zhongshan Biological Breeding Laboratory, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
| | - Yifei Wang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Zhongshan Biological Breeding Laboratory, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
| | - Lei Wang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Tian Wang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhengji Wang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Xu Li
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Yong Zhou
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Zhongshan Biological Breeding Laboratory, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
| | - Xianghua Li
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinghua Xiao
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Changjie Yan
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Zhongshan Biological Breeding Laboratory, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
| | - Qifa Zhang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Yidan Ouyang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
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Zhuang L, Du L, Liu H, Liu H, Li H, Zhang Y, Liu Y, Hou J, Li T, Yang D, Zhang X, Hao C. Joint linkage and association analysis identifies genomic regions and candidate genes for yield-related traits in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2025; 138:107. [PMID: 40314838 PMCID: PMC12048430 DOI: 10.1007/s00122-025-04900-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2024] [Accepted: 04/04/2025] [Indexed: 05/03/2025]
Abstract
KEY MESSAGE Twenty-six QTLs associated with yield-related traits in wheat were identified through joint linkage and association analysis, with TraesCS5A03G0002500 being selected as a candidate gene for QGl.caas-5A.1. As a major staple crop worldwide, continuously increasing wheat yield is crucial for ensuring food security. Wheat yield is influenced by multiple traits, and elucidating the genetic basis of yield-related traits lays a foundation for future gene cloning and molecular mechanism studies. In this study, a recombinant inbred line (RIL) population derived from 292 lines of Hengguan 35/Zhoumai 18 was genotyped with the Affymetrix wheat 660 K SNP array. Combined with the phenotype of the RIL population in 13 environments, linkage analysis of six yield-related traits including plant height, grain number per spike, thousand-grain weight, grain length, grain width, and grain thickness was conducted. A total of 262 quantitative trait locus (QTLs) (logarithm of odds [LOD] > 3) were identified across 21 chromosomes, in which 50 QTLs were repeatedly detected in more than three environments. Numerous QTLs harbored cloned genes and overlapped with those reported in previous studies. Subsequently, joint analysis of genome-wide association study (GWAS) data from the advanced backcross-nested association mapping plus inter-crossed (AB-NAMIC) population and QTLs identified in the RIL population revealed 26 overlapping genomic regions. Notably, the QGl.caas-5A.1 associated with grain length on chromosome 5A was detected in both the RIL and AB-NAMIC populations, and TraesCS5A03G0002500 was selected as a candidate gene. A kompetitive allele-specific PCR (KASP) marker based on a variant [A/G] in TraesCS5A03G0002500 was developed and validated in a natural population containing 350 accessions. Taken together, these results provide valuable information for fine mapping and cloning of yield-related wheat genes in the future.
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Affiliation(s)
- Lei Zhuang
- State Key Laboratory of Crop Gene Resources and Breeding/National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Lifeng Du
- Jiaozuo Academy of Agricultural and Forestry Sciences, Jiaozuo, 454000, Henan, China
| | - Haixia Liu
- State Key Laboratory of Crop Gene Resources and Breeding/National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hongxia Liu
- State Key Laboratory of Crop Gene Resources and Breeding/National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Huifang Li
- State Key Laboratory of Wheat and Maize Crop Science, and Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Yinhui Zhang
- State Key Laboratory of Crop Gene Resources and Breeding/National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yunchuan Liu
- State Key Laboratory of Crop Gene Resources and Breeding/National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jian Hou
- State Key Laboratory of Crop Gene Resources and Breeding/National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Tian Li
- State Key Laboratory of Crop Gene Resources and Breeding/National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Delong Yang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China.
| | - Xueyong Zhang
- State Key Laboratory of Crop Gene Resources and Breeding/National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Chenyang Hao
- State Key Laboratory of Crop Gene Resources and Breeding/National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Du Y, Ye C, Han P, Sheng Y, Li F, Sun H, Zhang J, Li J. The molecular mechanism of transcription factor regulation of grain size in rice. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2025; 354:112434. [PMID: 40023197 DOI: 10.1016/j.plantsci.2025.112434] [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: 11/13/2024] [Revised: 02/14/2025] [Accepted: 02/17/2025] [Indexed: 03/04/2025]
Abstract
Rice is a crucial food crop in China, and the continuous and stable improvement of rice yield is of great significance for ensuring national food security. Grain size in rice is closely related to thousand-grain weight, making it a key factor influencing yield. Identifying genes associated with grain size and elucidating their molecular mechanisms are essential for breeding high-yield, high-quality rice varieties. Transcription factors play a vital role in regulating plant growth and development, and many transcription factor families are crucial in controlling grain size in rice. Here, we review the mechanisms by which transcription factors regulate rice grain size, summarize and evaluate the regulatory mechanisms of transcription factors that have been discovered in recent decades to regulate rice grain size, construct two possible super networks composed of transcription factors as links to regulate rice grain size, and points out the application of transcription factors regulating grain size in rice breeding. This review will provide a roadmap for understanding the regulatory mechanisms of rice grain size and applying these genes to rice breeding using molecular breeding techniques.
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Affiliation(s)
- Yanxiu Du
- Henan Agricultural University, College of Agronomy / Henan Provincial Key Laboratory of Rice Molecular Breeding and High-Efficiency Production, Zhengzhou 450046, China.
| | - Chun Ye
- Henan Agricultural University, College of Agronomy / Henan Provincial Key Laboratory of Rice Molecular Breeding and High-Efficiency Production, Zhengzhou 450046, China
| | - Peijie Han
- Henan Agricultural University, College of Agronomy / Henan Provincial Key Laboratory of Rice Molecular Breeding and High-Efficiency Production, Zhengzhou 450046, China
| | - Yile Sheng
- Henan Agricultural University, College of Agronomy / Henan Provincial Key Laboratory of Rice Molecular Breeding and High-Efficiency Production, Zhengzhou 450046, China
| | - Fei Li
- Henan Agricultural University, College of Agronomy / Henan Provincial Key Laboratory of Rice Molecular Breeding and High-Efficiency Production, Zhengzhou 450046, China
| | - Hongzheng Sun
- Henan Agricultural University, College of Agronomy / Henan Provincial Key Laboratory of Rice Molecular Breeding and High-Efficiency Production, Zhengzhou 450046, China
| | - Jing Zhang
- Henan Agricultural University, College of Agronomy / Henan Provincial Key Laboratory of Rice Molecular Breeding and High-Efficiency Production, Zhengzhou 450046, China
| | - Junzhou Li
- Henan Agricultural University, College of Agronomy / Henan Provincial Key Laboratory of Rice Molecular Breeding and High-Efficiency Production, Zhengzhou 450046, China.
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7
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Yaseen M, Tariq N, Kanwal R, Farooq A, Wang H, Yuan H. Rice grain size: current regulatory mechanisms and future perspectives. JOURNAL OF PLANT RESEARCH 2025; 138:403-417. [PMID: 40056359 DOI: 10.1007/s10265-025-01626-8] [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: 07/01/2024] [Accepted: 02/12/2025] [Indexed: 03/10/2025]
Abstract
Rice is a staple food for over half of the world's population. To feed the growing population, molecular breeders aim to increase grain yield. Grain size is an important factor for crop productivity, and it has been extensively studied. However, molecular breeders face a major challenge in further improving crop productivity in terms of grain yield and quality. Grain size is a complex trait controlled by multiple genes. Over the past few decades, genetic studies have identified various gene families involved in grain size development. The list of molecular mechanisms, and key regulators involved in grain size development is constantly expanding, making it difficult to understand the main regulators that play crucial roles in grain development. In this review, we focus on the major regulators of grain size, including G-protein signaling, the mitogen-activated protein kinase (MAPK) pathway, transcriptional regulation, the ubiquitin-proteasome degradation (UPD) pathway, and phytohormone signaling. These molecular mechanisms directly or indirectly regulate grain size. We provided a comprehensive understanding of the genes involved in these mechanisms and cross discussions about how these mechanisms are interlinked. This review serves as a valuable resource for understanding the molecular mechanisms that govern grain development and can aid in the development of molecular breeding strategies.
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Affiliation(s)
- Muhammad Yaseen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, Sichuan, China
| | - Naveed Tariq
- State Key Laboratory of Hybrid Rice, Shanghai Jiao Tong University - University of Adelaide Joint Centre for Agriculture and Health, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Rida Kanwal
- College of Resource and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Akasha Farooq
- College of Resource and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Hao Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, Sichuan, China.
| | - Hua Yuan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, Sichuan, China.
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8
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Miao R, Lin Q, Cao P, Zhou C, Feng M, Lan J, Luo S, Zhang F, Wu H, Hao Q, Zheng H, Ma T, Huang Y, Mou C, Nguyen T, Cheng Z, Guo X, Liu S, Jiang L, Wan J. SMALL AND ROUND GRAIN is involved in the brassinosteroid signaling pathway which regulates grain size in rice. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2025; 67:1290-1306. [PMID: 39936852 DOI: 10.1111/jipb.13861] [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: 11/25/2024] [Accepted: 01/15/2025] [Indexed: 02/13/2025]
Abstract
Grain size is a key determinant of 1,000-grain weight, one of three factors determining grain yield. However, the complete regulatory network controlling grain size has not been fully clarified. Here, we identified a rice mutant, named small and round grain (srg) that exhibits semi-dwarf stature and small grain size. Cytological analysis showed that cell length and number of spikelet epidermal cells of the srg mutant are reduced, indicating that SRG controls grain size by promoting cell elongation and increasing cell number. SRG encodes a kinesin belonging to the kinesin-1 subfamily and is extensively expressed in different plant tissues with relatively high expression in young panicles. SRG protein is mainly located in the nucleus and cell membrane. Expression of the SRG gene was induced by brassinolide through the brassinosteroid (BR) responsive factor OsWRKY53 and SRG protein was phosphorylated by BR-activated kinase OsBSK3 to prevent its degradation. In addition, microtubule (MT) morphology was abnormal and disordered in the srg and cr-1 mutants. These findings suggest that BR likely stabilizes orderly assembly and arrangement of MTs by stabilizing SRG proteins, thus promoting grain size. SRG overexpression lines produced more tillers and significantly larger and heavier grains to increase 1,000-grain weight, suggesting that SRG has potential to increase grain yield. Our study indicated that SRG is a new BR responsive factor and BR might regulate grain size by influencing the expression of SRG.
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Affiliation(s)
- Rong Miao
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Nanjing National Field Scientific Observation and Research Station for Rice Germplasm, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qibing Lin
- State Key Laboratory of Crop Gene Resource and Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Penghui Cao
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Nanjing National Field Scientific Observation and Research Station for Rice Germplasm, Nanjing Agricultural University, Nanjing, 210095, China
- Suzhou Academy of Agricultural Sciences, Suzhou, 215105, China
| | - Chunlei Zhou
- State Key Laboratory of Crop Gene Resource and Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Miao Feng
- State Key Laboratory of Crop Gene Resource and Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jie Lan
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Nanjing National Field Scientific Observation and Research Station for Rice Germplasm, Nanjing Agricultural University, Nanjing, 210095, China
| | - Sheng Luo
- State Key Laboratory of Crop Gene Resource and Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Fulin Zhang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Nanjing National Field Scientific Observation and Research Station for Rice Germplasm, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hongmin Wu
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Nanjing National Field Scientific Observation and Research Station for Rice Germplasm, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qixian Hao
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Nanjing National Field Scientific Observation and Research Station for Rice Germplasm, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hai Zheng
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Nanjing National Field Scientific Observation and Research Station for Rice Germplasm, Nanjing Agricultural University, Nanjing, 210095, China
| | - Tengfei Ma
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Nanjing National Field Scientific Observation and Research Station for Rice Germplasm, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yunshuai Huang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Nanjing National Field Scientific Observation and Research Station for Rice Germplasm, Nanjing Agricultural University, Nanjing, 210095, China
| | - Changling Mou
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Nanjing National Field Scientific Observation and Research Station for Rice Germplasm, Nanjing Agricultural University, Nanjing, 210095, China
| | - Thanhliem Nguyen
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Nanjing National Field Scientific Observation and Research Station for Rice Germplasm, Nanjing Agricultural University, Nanjing, 210095, China
- Faculty of Natural Sciences, Quynhon University, Quynhon, 590000, Binhdinh, Vietnam
| | - Zhijun Cheng
- State Key Laboratory of Crop Gene Resource and Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiuping Guo
- State Key Laboratory of Crop Gene Resource and Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Shijia Liu
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Nanjing National Field Scientific Observation and Research Station for Rice Germplasm, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ling Jiang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Nanjing National Field Scientific Observation and Research Station for Rice Germplasm, Nanjing Agricultural University, Nanjing, 210095, China
- Zhongshan Biological Breeding Laboratory, Nanjing, 210095, China
| | - Jianmin Wan
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Nanjing National Field Scientific Observation and Research Station for Rice Germplasm, Nanjing Agricultural University, Nanjing, 210095, China
- State Key Laboratory of Crop Gene Resource and Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Zhongshan Biological Breeding Laboratory, Nanjing, 210095, China
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9
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Yan P, Wang Y, Cui J, Liu M, Zhu Y, Ma F, Liu Y, Lan D, Dong S, Hu Z, Niu F, Liu Y, Zhang X, He S, Hu J, Yuan X, Li Y, Yang J, Cao L, Luo X. OsMAPKKK5 affects brassinosteroid signal transduction via phosphorylating OsBSK1-1 and regulates rice plant architecture and yield. PLANT BIOTECHNOLOGY JOURNAL 2025; 23:1798-1813. [PMID: 39967024 PMCID: PMC12018843 DOI: 10.1111/pbi.70008] [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: 07/12/2024] [Revised: 01/23/2025] [Accepted: 01/24/2025] [Indexed: 02/20/2025]
Abstract
Improving plant architecture and increasing yields are the main goals of rice breeders. However, yield is a complex trait influenced by many yield-related traits. Identifying and characterizing important genes in the coordinated network regulating complex rice traits and their interactions is conducive to cultivating high-yielding rice varieties. In this study, we determined that the interaction between mitogen-activated protein kinase kinase kinase5 (OsMAPKKK5) and brassinosteroid-signalling kinase1-1 (OsBSK1-1) regulates yield-related traits in rice. Specifically, OsMAPKKK5 phosphorylates OsBSK1-1, which enhances the interaction between these two proteins, but adversely affects the OsBSK1-1-OsBRI1 (BR insensitive1) and OsBSK1-1-OsPPKL1 (protein phosphatase with two Kelch-like domains) interactions. Additionally, OsMAPKKK5 disrupts brassinosteroid signal transduction, which prevents OsBZR1 (brassinazole-resistant1) from efficiently entering the nucleus, thereby negatively modulating its function as a transcription factor regulating downstream effector genes, ultimately adversely affecting plant architecture and yield. This study revealed the relationship between the MAPK cascade and the regulatory effects of brassinosteroid on the rice grain yield involves OsMAPKKK5 and OsBSK1-1. The study data may be important for future investigations on the rice yield-regulating molecular network.
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Affiliation(s)
- Peiwen Yan
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life SciencesFudan UniversityShanghaiChina
| | - Ying Wang
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life SciencesFudan UniversityShanghaiChina
- State Key Laboratory of Wetland Conservation and Restoration, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, and Institute of Eco‐Chongming, School of Life SciencesFudan UniversityShanghaiChina
| | - Jinhao Cui
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life SciencesFudan UniversityShanghaiChina
| | - Mingyu Liu
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life SciencesFudan UniversityShanghaiChina
| | - Yu Zhu
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life SciencesFudan UniversityShanghaiChina
| | - Fuying Ma
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life SciencesFudan UniversityShanghaiChina
| | - Yahui Liu
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life SciencesFudan UniversityShanghaiChina
| | - Dengyong Lan
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life SciencesFudan UniversityShanghaiChina
| | - Shiqing Dong
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life SciencesFudan UniversityShanghaiChina
| | - Zejun Hu
- Key Laboratory of Germplasm Innovation and Genetic Improvement of Grain and Oil Crops (Co‐Construction by Ministry and Province)Ministry of Agriculture and Rural Affairs, Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural SciencesShanghaiChina
| | - Fuan Niu
- Key Laboratory of Germplasm Innovation and Genetic Improvement of Grain and Oil Crops (Co‐Construction by Ministry and Province)Ministry of Agriculture and Rural Affairs, Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural SciencesShanghaiChina
| | - Yang Liu
- MOE Key Laboratory of Crop Physiology, Ecology and Genetic Breeding College of AgronomyJiangxi Agricultural UniversityNanchangJiangxiChina
| | - Xinwei Zhang
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life SciencesFudan UniversityShanghaiChina
| | - Shicong He
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life SciencesFudan UniversityShanghaiChina
| | - Jian Hu
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life SciencesFudan UniversityShanghaiChina
| | - Xinyu Yuan
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life SciencesFudan UniversityShanghaiChina
| | - Yizhen Li
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life SciencesFudan UniversityShanghaiChina
| | - Jinshui Yang
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life SciencesFudan UniversityShanghaiChina
| | - Liming Cao
- Key Laboratory of Germplasm Innovation and Genetic Improvement of Grain and Oil Crops (Co‐Construction by Ministry and Province)Ministry of Agriculture and Rural Affairs, Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural SciencesShanghaiChina
| | - Xiaojin Luo
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life SciencesFudan UniversityShanghaiChina
- MOE Key Laboratory of Crop Physiology, Ecology and Genetic Breeding College of AgronomyJiangxi Agricultural UniversityNanchangJiangxiChina
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10
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Du L, Ye R, Liu X, He Q, Qiao J, Charrier L, Geisler M, Gao Z, Qian Q, Qi Y. The OsbHLH166-OsABCB4 module regulates grain length and weight via altering auxin efflux. Sci Bull (Beijing) 2025:S2095-9273(25)00457-8. [PMID: 40374475 DOI: 10.1016/j.scib.2025.04.053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2024] [Revised: 02/10/2025] [Accepted: 04/16/2025] [Indexed: 05/17/2025]
Abstract
Grain size is one of the key factors determining grain weight and yield. However, it remains largely unknown how the auxin signal regulates grain size in rice. Here, a quantitative trait locus qGL1 for grain length was identified with recombinant inbred lines 9311 and Nipponbare (NIP), and fine-mapped to the OsABCB4 gene, which encodes a member of the ATP Binding Cassette B (ABCB) subfamily. Compared to NIP, loss of OsABCB4 function leads to longer and heavier grains, while over-expression of OsABCB4 causes shorter and lighter grains, demonstrating a negative control of grain length and weight in rice. Haplotype analyses using 3024 rice-sequenced genomes indicated that SNP25 and SNP55 in OsABCB4 are correlated with grain length in rice. OsbHLH166, a basic helix-loop-helix transcription factor, was screened from a yeast one-hybrid library and confirmed to directly bind the promoter of OsABCB4 by electrophoretic mobility shift assay and yeast one hybridization validation and to activate the expression of OsABCB4 by dual-luciferase reporter assay. And OsbHLH166 expressions matching OsABCB4 were all higher expressed in stems and glumes. OsABCB4 was subcellularly localized on the plasma membrane, which was verified as an auxin efflux transporter. Histological analysis, IAA content measurement and DR5:GUS activity analyses demonstrated that OsbHLH166 and OsABCB4 control grain length by regulating cell expansion and auxin contents in glume cells and altering the expression of GL7, GS2, TGW3 and GS3 genes during rice grain development. This newly identified OsbHLH166-OsABCB4 module sheds light on our understanding of molecular mechanisms underlying the regulation of grain size and weight via auxin and provides a new gene resource for molecular design breeding of grain type.
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Affiliation(s)
- Lina Du
- Key Laboratory of Herbage & Endemic Crop Biology of Ministry of Education, Inner Mongolia Key Laboratory of Herbage & Endemic Crop Biotechnology, School of Life Sciences, Inner Mongolia University, Hohhot 010000, China; State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Rigui Ye
- Key Laboratory of Herbage & Endemic Crop Biology of Ministry of Education, Inner Mongolia Key Laboratory of Herbage & Endemic Crop Biotechnology, School of Life Sciences, Inner Mongolia University, Hohhot 010000, China
| | - Xin Liu
- Key Laboratory of Herbage & Endemic Crop Biology of Ministry of Education, Inner Mongolia Key Laboratory of Herbage & Endemic Crop Biotechnology, School of Life Sciences, Inner Mongolia University, Hohhot 010000, China
| | - Qianqian He
- Key Laboratory of Herbage & Endemic Crop Biology of Ministry of Education, Inner Mongolia Key Laboratory of Herbage & Endemic Crop Biotechnology, School of Life Sciences, Inner Mongolia University, Hohhot 010000, China
| | - Jiyue Qiao
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China; Yazhouwan National Laboratory, Sanya 572024, China
| | - Laurence Charrier
- Department of Biology, University of Fribourg, Fribourg 1700, Switzerland
| | - Markus Geisler
- Department of Biology, University of Fribourg, Fribourg 1700, Switzerland
| | - Zhenyu Gao
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China.
| | - Qian Qian
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China; Yazhouwan National Laboratory, Sanya 572024, China.
| | - Yanhua Qi
- Key Laboratory of Herbage & Endemic Crop Biology of Ministry of Education, Inner Mongolia Key Laboratory of Herbage & Endemic Crop Biotechnology, School of Life Sciences, Inner Mongolia University, Hohhot 010000, China.
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11
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Sonkar K, Singh A. Wax deposition is vital for thermotolerance in rice. PLANT COMMUNICATIONS 2025; 6:101317. [PMID: 40091348 PMCID: PMC12010369 DOI: 10.1016/j.xplc.2025.101317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2025] [Revised: 03/02/2025] [Accepted: 03/12/2025] [Indexed: 03/19/2025]
Affiliation(s)
- Kamankshi Sonkar
- National Institute of Plant Genome Research, New Delhi 110067, India
| | - Amarjeet Singh
- National Institute of Plant Genome Research, New Delhi 110067, India.
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12
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Jin T, Hao X, Huang Z, Zhang X, Li S, Yang Y, Long W. Genome-Wide Identification of the GS3 Gene Family and the Influence of Natural Variations in BnGS3-3 on Salt and Cold Stress Tolerance in Brassica napus. PLANTS (BASEL, SWITZERLAND) 2025; 14:1145. [PMID: 40219212 PMCID: PMC11991296 DOI: 10.3390/plants14071145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2025] [Revised: 03/29/2025] [Accepted: 04/02/2025] [Indexed: 04/14/2025]
Abstract
Saline-alkali stress and cold damage significantly impact the yield of Brassica napus. G proteins play a crucial role in plant resistance to abiotic stresses, and research on G proteins in Brassica napus (rapeseed) is still in its early stages. In this study, we employed bioinformatics tools to systematically investigate the basic physicochemical properties, phylogenetic relationships, distribution, gene structure, cis-regulatory elements, and expansion patterns of the GS3 gene family in Brassica napus. Additionally, reverse transcription polymerase chain reaction (RT-PCR) was used to analyze the response of the BnGS3-3 gene to salt and low-temperature stresses. Natural variations were found in the promoter region of BnGS3-3. By conducting a promoter-driven luciferase (LUC) assay, the relationship between natural variations in the BnGS3-3 promoter and salt and cold tolerance was analyzed. Furthermore, the impact of these natural variations on flowering time, root length, and yield was explored using phenotypic data from a population. Our research results aim to provide insights into the function and molecular mechanisms of BnGS3-3 in Brassica napus, and to offer valuable genetic resources for molecular breeding to improve salt and low-temperature tolerance in Brassica napus.
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Affiliation(s)
- Ting Jin
- College of Rural Revitalization, Jiangsu Open University, Nanjing 210036, China; (T.J.); (Y.Y.)
| | - Xiaoshuai Hao
- College of Agronomy, Nanjing Agricultural University, Nanjing 211800, China;
| | - Zhen Huang
- College of Agronomy, Northwest A&F University, Yangling 712100, China;
| | - Xingguo Zhang
- College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China;
| | - Shimeng Li
- Institute of Agriculture, Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa 850032, China;
| | - Ying Yang
- College of Rural Revitalization, Jiangsu Open University, Nanjing 210036, China; (T.J.); (Y.Y.)
| | - Weihua Long
- College of Rural Revitalization, Jiangsu Open University, Nanjing 210036, China; (T.J.); (Y.Y.)
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13
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Robinson J. Using chimeric rice proteins to make heads or tails of the function of repetitive elements in Gγ subunits. THE PLANT CELL 2025; 37:koaf080. [PMID: 40179254 PMCID: PMC12012680 DOI: 10.1093/plcell/koaf080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2025] [Accepted: 03/31/2025] [Indexed: 04/05/2025]
Affiliation(s)
- Julie Robinson
- Assistant Features Editor, The Plant Cell, American Society of Plant Biologists
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
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14
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Chen S, Li F, Ouyang W, Chen S, Luo S, Liu J, Li G, Lin Z, Liu YG, Xie X. Time-course transcriptome and chromatin accessibility analyses reveal the dynamic transcriptional regulation shaping spikelet hull size. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2025; 122:e70141. [PMID: 40204676 DOI: 10.1111/tpj.70141] [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: 10/28/2024] [Revised: 02/24/2025] [Accepted: 03/25/2025] [Indexed: 04/11/2025]
Abstract
The grains of rice (Oryza sativa) are enclosed by a spikelet hull comprising the lemma and palea. Development of the spikelet hull determines the storage capacity of the grain, thus affecting grain yield and quality. Although multiple signaling pathways controlling grain size have been identified, the transcriptional regulatory mechanisms underlying grain development remain limited. Here, we used RNA-seq and ATAC-seq to characterize the transcription and chromatin accessibility dynamics during the development of spikelet hulls. A time-course analysis showed that more than half of the genes were sequentially expressed during hull development and that the accessibility of most open chromatin regions (OCRs) changed moderately, although some regions positively or negatively affected the expression of their closest genes. We revealed a crucial role of GROWTH-REGULATING FACTORs in shaping grain size by influencing multiple metabolic and signaling pathways, and a coordinated transcriptional regulation in response to auxin and cytokinin signaling. We also demonstrated the function of SCL6-IIb, a member of the GRAS family transcription factors, in regulating grain size, with SCL6-IIb expression being activated by SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 18 (OsSPL18). When we edited the DNA sequences within OCRs upstream of the start codon of BRASSINAZOLE-RESISTANT 1 (BZR1) and SCL6-IIb, we generated multiple mutant lines with longer grains. These findings offer a comprehensive overview of the cis-regulatory landscape involved in forming grain capacity and a valuable resource for exploring the regulatory network behind grain development.
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Affiliation(s)
- Shaotong Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Basic Research Center of Excellence for Precise Breeding of Future Crops, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Fuquan Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Basic Research Center of Excellence for Precise Breeding of Future Crops, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Weizhi Ouyang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shuifu Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Basic Research Center of Excellence for Precise Breeding of Future Crops, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Sanyang Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Basic Research Center of Excellence for Precise Breeding of Future Crops, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Jianhong Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Basic Research Center of Excellence for Precise Breeding of Future Crops, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Gufeng Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Basic Research Center of Excellence for Precise Breeding of Future Crops, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Zhansheng Lin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Basic Research Center of Excellence for Precise Breeding of Future Crops, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Yao-Guang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Basic Research Center of Excellence for Precise Breeding of Future Crops, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Xianrong Xie
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Basic Research Center of Excellence for Precise Breeding of Future Crops, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
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15
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Liu L, Sheng Y, Zhang Y, Xie X, Chen J, Wang J, Pan H, Huang H, Cao X, Xu J, Zhuo R, Yao X. Phenotype and transcriptome analysis identify the key genes controlling seed size and oil accumulation in oil-Camellia. PLANT CELL REPORTS 2025; 44:78. [PMID: 40111505 DOI: 10.1007/s00299-025-03454-5] [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: 11/05/2024] [Accepted: 02/07/2025] [Indexed: 03/22/2025]
Abstract
KEY MESSAGE Phenotypic analysis of an F1 oil-Camellia population, combined with transcriptome sequencing of its parental lines, identifies pivotal genes controlling seed size and oil accumulation. Oil - Camellia is a major oil-producing tree, known for its high nutritional value and health benefits. Improving seed size and oil content is the key breeding objective, governed by intricate genetic networks. However, the molecular mechanism underlying these traits in oil-Camellia has been rarely reported. In this study, an F1 population was developed from two parental genotypes, CL4 (hexaploid with high oil content and large seed size) and XG (tetraploid with low oil content and small seed size), which exhibited significant variation in yield-related traits. Ploidy analysis of progenies of F1 population showed that most individuals were tetraploids and hexaploids, with a smaller number of diploids and octoploids present. Additionally, the analysis identified progeny individuals exhibiting both large seed and high oil content although no clear correlation with ploidy was observed. Comparative RNA sequencing (RNA seq) of developing seeds at four developmental stages revealed dynamic expression patterns, associated with seed size and oil content in the two parents. Co-expression regulatory network and differentially expressed genes of fatty acid biosynthesis pathway indicated that genes, such as Oleosin5 and ACCase α-subunit, displayed central roles in controlling seed size and oil content with notable expression peaks in S3 and S4. Additionally, the ABA signaling pathway, along with expansin proteins and transcription factors, showed co-expression with these genes, suggesting a regulatory pathway centered around Oleosin5 and ACCase α-subunit. This study identifies essential genes linked to oil seed yield traits, enhancing the understanding of oil-Camellia's molecular breeding targets.
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Affiliation(s)
- Linxiu Liu
- Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
- Faculty of Forestry, Nanjing Forestry University, Nanjing, 210000, Jiangsu, China
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
| | - Yu Sheng
- Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
| | - Yunbin Zhang
- Mount Huangshan Forestry Research Institute, Huangshan, 245099, China
| | - Xinru Xie
- Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
| | - Juanjuan Chen
- Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
| | - Jingfei Wang
- Mount Huangshan Forestry Research Institute, Huangshan, 245099, China
| | - Huanhuan Pan
- Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
| | - Hu Huang
- Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
| | - Xun Cao
- Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
| | - Jing Xu
- Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China.
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China.
| | - Renying Zhuo
- Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China.
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China.
| | - Xiaohua Yao
- Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China.
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China.
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16
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Wang X, Wang Y, Zheng Z, Cui Y. GPA1 is a determinant of leaf width and fruit size in tomato. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2025; 352:112336. [PMID: 39622387 DOI: 10.1016/j.plantsci.2024.112336] [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: 09/27/2024] [Revised: 11/06/2024] [Accepted: 11/23/2024] [Indexed: 12/08/2024]
Abstract
The identification and dissection of the genetic foundations underlying natural variations in crop species are critical for understanding their phenotypic diversity and for subsequent application in selective breeding. In this research, we identify a natural polymorphism in the promoter region of the G protein α subunit 1 (GPA1) gene, which is associated with the width of the tomato leaves. This may be an evolutionary consequence resulting from the domestication processes aimed at increasing fruit size. A functional disruption of the GPA1 gene resulted in a significant reduction in both the leaf size and the fruit mass in tomatoes compared to the wild type. Further exploration revealed that the intrinsic variation present in the GPA1 promoter region is responsible for the differential expression of the GPA1 gene. Distinct GPA1 haplotypes show a significant correlation with geographic distribution, suggesting that the polymorphisms within the GPA1 locus confer adaptive advantages for modulating leaf morphology in tomatoes, reflecting evolutionary responses to regional environmental pressures. Consequently, our findings provide new insights into the genetic diversity underlying leaf morphology and offer a valuable genetic resource for the selective breeding of cultivated tomato varieties.
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Affiliation(s)
- Xiang Wang
- The State Key Laboratory of Subtropical Silviculture, Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China.
| | - Youwei Wang
- The State Key Laboratory of Subtropical Silviculture, Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Ziyi Zheng
- The State Key Laboratory of Subtropical Silviculture, Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Yongmei Cui
- Academy of Agricultural and Forestry Sciences, Qinghai University, Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining 810016, China
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17
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Shao Z, Ding C, Liu H, Zhang G, Zhu L, Hu J, Gao Z, Guo L, Qian Q, Ren D. A zinc metalloproteinase controls rice grain zinc content and weight. PLANT COMMUNICATIONS 2025:101295. [PMID: 40023765 DOI: 10.1016/j.xplc.2025.101295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2024] [Revised: 02/13/2025] [Accepted: 02/28/2025] [Indexed: 03/04/2025]
Abstract
This study identifies of a zinc metalloproteinase, ZG, that positively regulates both zinc content and grain size in rice. ZG's proteolytic activity increases with higher zinc ion concentrations. These findings, along with haplotype analysis in global rice cultivars, highlight its strong potential for enhancing both yield and nutritional value in rice breeding.
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Affiliation(s)
- Zhengji Shao
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Chaoqing Ding
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - He Liu
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Guangheng Zhang
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Li Zhu
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Jiang Hu
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Zhenyu Gao
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Longbiao Guo
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Qian Qian
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China; National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya 572024, China; Yazhouwan National Laboratory, Sanya 572024, China.
| | - Deyong Ren
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China; National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya 572024, China.
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18
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Jiang Y, Xue R, Chang Y, Cao D, Liu B, Li Y. The knockout of Gγ subunit HvGS3 by CRISPR/Cas9 gene editing improves the lodging resistance of barley through dwarfing and stem strengthening. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2025; 138:61. [PMID: 40014102 DOI: 10.1007/s00122-025-04853-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2024] [Accepted: 02/09/2025] [Indexed: 02/28/2025]
Abstract
Gγ subunits participate in multiple biological processes, but their biological function in barley is unknown. Here, CRISPR/Cas9 gene editing was used to knockout HvGS3 in barley. The height of hvgs3 plants were reduced by 37.8 ~ 43.1% compared to wild type, and the culm lodging resistance index (CLRI) of the second internode of stems was increased by 76.6%. The decrease in cell length of the second internode was similar to its node length. The shorter cells may be the main reason for the declines in the internode length and plant height. The number and area of vascular bundles, the epidermal thickness, and the mechanical tissue thickness were significantly higher in hvgs3 due to the higher lignin content. Transcriptome analysis showed higher expression of structural genes related to lignin biosynthesis. Gibberellin (GA) biosynthesis was suppressed through the down-regulation of the GA3ox gene, and the application of gibberellin restored the plant height of hvgs3, indicating that plant height was altered by hindering gibberellin biosynthesis. These results shed new light on the functions of the Gγ subunit GS3 and provide a resource for breeding new lodging-resistant barley cultivars.
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Affiliation(s)
- Yanyan Jiang
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, 810016, Qinghai, China
- Key Laboratory of Crop Molecular Breeding, Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, Qinghai, China
| | - Ruiyin Xue
- Key Laboratory of Crop Molecular Breeding, Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, Qinghai, China
- Qinghai Normal University, No. 38 Wusi West Road, Xining, Qinghai, China
| | - Yanzi Chang
- Key Laboratory of Crop Molecular Breeding, Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, Qinghai, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dong Cao
- Key Laboratory of Crop Molecular Breeding, Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, Qinghai, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Baolong Liu
- Key Laboratory of Crop Molecular Breeding, Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, Qinghai, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Yun Li
- Key Laboratory of Crop Molecular Breeding, Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, Qinghai, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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19
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Ueda T, Taniguchi Y, Adachi S, Shenton M, Hori K, Tanaka J. Gene Pyramiding Strategies for Sink Size and Source Capacity for High-Yield Japonica Rice Breeding. RICE (NEW YORK, N.Y.) 2025; 18:6. [PMID: 39945924 PMCID: PMC11825427 DOI: 10.1186/s12284-025-00756-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Accepted: 01/13/2025] [Indexed: 02/16/2025]
Abstract
In Japan, high-yielding indica rice cultivars such as 'Habataki', 'Takanari', and 'Hokuriku 193' have been bred, and many genes related to the high-yield traits have been isolated from these and other indica cultivars. Many such genes are expected to be effective in increasing the yield of japonica rice, including those that increase sink size. It has been expected that high-yielding japonica rice could be bred by introducing sink-size genes into the genetic background of japonica cultivars such as 'Koshihikari', which show strong cold tolerance, have good taste characteristics, and fetch a high price. However, the corresponding near-isogenic lines did not necessarily produce high yields when tested in the field. In this review, we summarize information on the major high-yield-related rice genes and discuss pyramiding strategies to further increase the yield of japonica rice. In parallel with increasing sink size, source capacity needs to be increased by increasing photosynthetic rate per unit leaf area (single leaf photosynthesis), improving canopy structure, and increasing translocation capacity during the ripening stage. To implement these strategies, innovative breeding methodologies that efficiently produce the combinations of desired alleles are required.
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Affiliation(s)
- Tadamasa Ueda
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Yojiro Taniguchi
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Shunsuke Adachi
- Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan
| | - Matthew Shenton
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Kiyosumi Hori
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Junichi Tanaka
- NARO Headquarters, 3-1-1 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan.
- Graduate School of Science and Technology, University of Tsukuba, Tsukuba, Ibaraki, 305-8577, Japan.
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20
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He X, Liu J, Ren X, Wei S, Zhu Z, Zhang F, Hu S, Ding Y, Sun F, Han D, Bai G, Ni Z, Sun Q, Su Z. Mapping and validation of QTkw.cau-3DL, a major QTL controlling thousand-kernel weight in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2025; 138:46. [PMID: 39907799 DOI: 10.1007/s00122-025-04824-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2024] [Accepted: 01/15/2025] [Indexed: 02/06/2025]
Abstract
KEY MESSAGE A novel major QTL, QTkw.cau-3DL, for thousand-kernel weight has been identified on the wheat chromosome arm 3DL and enhances grain yield by 6.2% under field conditions. Increasing kernel weight is an effective way to improve yield potential in wheat. The identification of major quantitative trait loci (QTL) for kernel weight, without negative effects on other yield-related traits, is crucial for continuous yield improvement. We developed a population of F6 recombinant inbred lines from Jimai 120 × Jimai 325 and identified eight QTL for thousand-kernel weight, kernel length, and kernel width across five environments. The population was genotyped using Wheat15K SNP arrays and QTL analysis found that one QTL, QTkw.cau-3DL, on the chromosome arm 3DL consistently showed major effects on TKW and KL in five field experiments. This QTL accounted for up to 16.43% and 13.87% of phenotypic variation, respectively. QTkw.cau-3DL was confined to a 5.72-Mb (3.48 cM) interval between 554.39 Mb and 560.11 Mb. This QTL was validated in a pair of NILs and in a new population. QTkw.cau-3DL increased kernel weight per spike without any negative effect on heading data, plant height, spike length, spikelet number per spike, or kernels number per spike. It increased grain yield by 6.2% under regular field production conditions. Haplotype analysis and geographical distribution in a nationwide collection of 630 wheat cultivars showed that QTkw.cau-3DL has not been widely deployed in Chinese wheat breeding programs. QTkw.cau-3DL is a novel QTL for increasing TKW through increasing KL; therefore, it is an important locus for enhancing wheat grain yield. The tightly linked, user-friendly markers developed in this study should facilitate map-based cloning and marker-assisted selection of the QTL in wheat breeding programs.
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Affiliation(s)
- Xi He
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100083, China
| | - Jilu Liu
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100083, China
| | - Xiaomeng Ren
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100083, China
| | - Shurong Wei
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100083, China
| | - Zhenzhen Zhu
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100083, China
| | - Fuping Zhang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100083, China
| | - Sijia Hu
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100083, China
| | - Yanpeng Ding
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100083, China
| | - Fangyao Sun
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100083, China
| | - Dong Han
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100083, China
| | - Guihua Bai
- US Department of Agriculture, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, 66506, USA
| | - Zhongfu Ni
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100083, China
| | - Qixin Sun
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100083, China
| | - Zhenqi Su
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100083, China.
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21
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Jin X, Lu Y, Liu J, Liu H, Wu N, Li M, Zhou W. Unraveling the role of OsSCL26 in transcriptional regulation in rice: Insights into grain shape, heading date, and carbohydrates. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2025; 121:e17268. [PMID: 39968609 DOI: 10.1111/tpj.17268] [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: 04/07/2024] [Revised: 12/27/2024] [Accepted: 12/30/2024] [Indexed: 02/20/2025]
Abstract
Grain shape, heading date, and amylase content are pivotal traits influencing rice yield, quality, distribution, and regional adaptability. Through our investigation, we identified a mutant, characterized by slender grains, elevated amylose content, and early heading date. Histocytologic scrutiny unveiled heightened cell proliferation in the spikelet hull contributing to the slender grain morphology. The OsSCL26 gene, governing these significant traits, was meticulously cloned via fine-mapping. Phenotypic scrutiny of OsSCL26 knockout and overexpression lines validated its pivotal role in trait regulation. Further analysis disclosed a substitution in the OsSCL26 promoter region, creating a novel binding site for the transcript factor OsbZIP47, thereby modulating its expression in the osscl26 mutant. Functionally, OsSCL26, acting as a serine/arginine-rich SC35-like protein, interacted with U1-70K in vivo and in vitro. OsSCL26 exhibited direct binding to genes implicated in grain shape and carbohydrates, thereby regulating their splicing. Moreover, OsSCL26 showed direct and indirect associations with target RNAs involved in circadian rhythm. Overall, our findings elucidate the mechanism of OsSCL26, an RNA binding protein interacting with splicing factor, as a crucial member of the spliceosome, thereby impacting post-transcriptional splicing and regulating grain shape, heading date, and carbohydrates in rice.
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Affiliation(s)
- Xiaoli Jin
- The Advanced Seed Institute, Zhejiang Key Laboratory of Crop Germplasm Innovation and Utilization, Zhejiang University, Hangzhou, 310058, China
| | - Yingying Lu
- The Advanced Seed Institute, Zhejiang Key Laboratory of Crop Germplasm Innovation and Utilization, Zhejiang University, Hangzhou, 310058, China
| | - Jialin Liu
- The Advanced Seed Institute, Zhejiang Key Laboratory of Crop Germplasm Innovation and Utilization, Zhejiang University, Hangzhou, 310058, China
| | - Hui Liu
- The Advanced Seed Institute, Zhejiang Key Laboratory of Crop Germplasm Innovation and Utilization, Zhejiang University, Hangzhou, 310058, China
| | - Nan Wu
- The Advanced Seed Institute, Zhejiang Key Laboratory of Crop Germplasm Innovation and Utilization, Zhejiang University, Hangzhou, 310058, China
| | - Mei Li
- Analysis Center of Agrobiology and Environmental Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Weijun Zhou
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
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22
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Wang W, Pan Q, Tian B, Yu Z, Davidson D, Bai G, Akhunova A, Trick H, Akhunov E. Non-additive dosage-dependent effects of TaGS3 gene editing on grain size and weight in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2025; 138:38. [PMID: 39880939 PMCID: PMC11779757 DOI: 10.1007/s00122-025-04827-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Accepted: 01/16/2025] [Indexed: 01/31/2025]
Abstract
KEY MESSAGE Loss-of-function mutations induced by CRISPR-Cas9 in the TaGS3 gene homoeologs show non-additive dosage-dependent effects on grain size and weight and have potential utility for increasing grain yield in wheat. The grain size in cereals is one of the component traits contributing to yield. Previous studies showed that loss-of-function (LOF) mutations in GS3, encoding Gγ subunit of the multimeric G protein complex, increase grain size and weight in rice. While an association between allelic variation in the GS3 homologs of wheat and grain weight/size has been detected previously, the effects of LOF alleles at TaGS3 on these traits remain unknown. We used genome editing to create TaGS3 mutant lines with varying LOF homeo-allele dosages. Contrary to the results obtained in rice, editing all three TaGS3 homoeologous copies resulted in a significant decrease in grain length (4.4%), width (3.4%), grain area (7.3%) and weight (7.5%), without affecting the number of grains per spike. Compared to the wild type, the highest increase in grain weight (up to 9.6%) and area (up to 5.0%) was observed in homozygous mutants with one or two genomes carrying LOF homeo-alleles, suggesting non-additive suppressive effects of TaGS3 on grain size and weight in wheat. Our results suggest that the regulatory effects of GS3 homologs in wheat and rice have diverged. The newly developed LOF homeo-alleles of TaGS3 expand the set of CRISPR-Cas9-induced variants of yield component genes that have potential to increase grain weight in wheat.
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Affiliation(s)
- Wei Wang
- Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA
- Nanjing Agricultural University, Nanjing, China
| | - Qianli Pan
- Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA
| | - Bin Tian
- Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA
| | - Zitong Yu
- Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA
| | - Dwight Davidson
- Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA
| | - Guihua Bai
- USDA-ARS Hard Winter Wheat Genetics Research Unit, Manhattan, KS, USA
| | - Alina Akhunova
- Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA
- Integrated Genomics Facility, Kansas State University, Manhattan, KS, USA
| | - Harold Trick
- Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA
| | - Eduard Akhunov
- Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA.
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23
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Liu R, Zhao D, Li P, Xia D, Feng Q, Wang L, Wang Y, Shi H, Zhou Y, Chen F, Lou G, Yang H, Gao H, Wu B, Chen J, Gao G, Zhang Q, Xiao J, Li X, Xiong L, Li Y, Li Z, You A, He Y. Natural variation in OsMADS1 transcript splicing affects rice grain thickness and quality by influencing monosaccharide loading to the endosperm. PLANT COMMUNICATIONS 2025; 6:101178. [PMID: 39489992 PMCID: PMC11783882 DOI: 10.1016/j.xplc.2024.101178] [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: 03/05/2024] [Revised: 04/30/2024] [Accepted: 10/23/2024] [Indexed: 11/05/2024]
Abstract
Grain size, which encompasses grain length, width, and thickness, is a critical determinant of both grain weight and quality in rice. Despite the extensive regulatory networks known to determine grain length and width, the pathway(s) that regulate grain thickness remain to be clarified. Here, we present the map-based cloning and characterization of qGT3, a major quantitative trait locus for grain thickness in rice that encodes the MADS-domain transcription factor OsMADS1. Our findings demonstrate that OsMADS1 regulates grain thickness by affecting sugar delivery during grain filling, and we show that OsMADS1 modulates expression of the downstream monosaccharide transporter gene MST4. A natural variant leads to alternative splicing and thus to a truncated OsMADS1 protein with attenuated transcriptional repressor activity. The truncated OsMADS1 protein results in increased expression of MST4, leading to enhanced loading of monosaccharides into the developing endosperm and thereby increasing grain thickness and improving grain quality. In addition, our results reveal that NF-YB1 and NF-YC12 interact directly with OsMADS1, acting as cofactors to enhance its transcriptional activity toward MST4. Collectively, these findings reveal a novel molecular mechanism underlying grain thickness regulation that is controlled by the OsMADS1-NF-YB1-YC12 complex and has great potential for synergistic improvement of grain yield and quality in rice.
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Affiliation(s)
- Rongjia Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Da Zhao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Pingbo Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Duo Xia
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Qingfei Feng
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Lu Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Yipei Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Huan Shi
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Yin Zhou
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Fangying Chen
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Guangming Lou
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Hanyuan Yang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Haozhou Gao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Bian Wu
- Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wuhan 430070, China
| | - Junxiao Chen
- Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wuhan 430070, China
| | - Guanjun Gao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Qinglu Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinghua Xiao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Xianghua Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Lizhong Xiong
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Yibo Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Zichao Li
- Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100000, China
| | - Aiqing You
- Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wuhan 430070, China.
| | - Yuqing He
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China.
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24
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Whisnant ED, Keith C, Smieska L, Chia JC, Bekele-Alemu A, Vatamaniuk OK, VanBuren R, Ligaba-Osena A. Biggest of tinies: natural variation in seed size and mineral distribution in the ancient crop tef [ Eragrostis tef (Zucc.) Trotter]. FRONTIERS IN PLANT SCIENCE 2024; 15:1485819. [PMID: 39726428 PMCID: PMC11669528 DOI: 10.3389/fpls.2024.1485819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2024] [Accepted: 11/18/2024] [Indexed: 12/28/2024]
Abstract
Tef [Eragrostis tef (Zucc.) Trotter] is the major staple crop for millions of people in Ethiopia and Eritrea and is believed to have been domesticated several thousand years ago. Tef has the smallest grains of all the cereals, which directly impacts its productivity and presents numerous challenges to its cultivation. In this study, we assessed the natural variation in seed size of 189 tef and 11 accessions of its wild progenitor Indian lovegrass (Eragrostis pilosa (L.) P. Beauv.) and explored the mineral distribution of representative accessions. Our findings revealed significant natural variation in seed size and mineral concentration among both the tef and E. pilosa accessions. We observed significant variation in seed length, seed width, and seed area among the accessions of both Eragrostis spp. we analyzed. Using representative accessions of both species, we also found significant variation in 1000-grain weight. The observed variation in seed size attributes prompted us to use comparative genomics to identify seed size regulating genes based on the well-studied and closely related monocot cereal rice [Oryza sativa (L.)]. Using this approach, we identified putative orthologous genes in the tef genome that belong to a number of key pathways known to regulate seed size in rice. Phylogenetic analysis of putative tef orthologs of ubiquitin-proteasome, G-protein, MAPK, and brassinosteroid (BR)-family genes indicate significant similarity to seed size regulating genes in rice and other cereals. Because tef is known to be more nutrient-dense than other more common cereals such as rice, wheat, and maize, we also studied the mineral concentration of selected accessions using ICP-OES and explored their distribution within the seeds using synchrotron-based X-ray fluorescence (SXRF) microscopy. The findings showed significant variation in seed mineral concentration and mineral distribution among the selected accessions of both Eragrostis spp. This study highlights the natural variation in seed size attributes, mineral concentration, and distribution, while establishing the basis for understanding the genetic mechanisms regulating these traits. We hope our findings will lead to a better understanding of the evolution of tef at the genetic level and for the development of elite tef cultivars to improve seed size, yield, and quality of the grains.
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Affiliation(s)
- Eric D. Whisnant
- Laboratory of Plant Molecular Biology and Biotechnology, Department of Biology, The University of North Carolina at Greensboro, Greensboro, NC, United States
| | - Christian Keith
- Laboratory of Plant Molecular Biology and Biotechnology, Department of Biology, The University of North Carolina at Greensboro, Greensboro, NC, United States
| | - Louisa Smieska
- Cornell High Energy Synchrotron Source, Cornell University, Ithaca, NY, United States
| | - Ju-Chen Chia
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Abreham Bekele-Alemu
- Laboratory of Plant Molecular Biology and Biotechnology, Department of Biology, The University of North Carolina at Greensboro, Greensboro, NC, United States
| | - Olena K. Vatamaniuk
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Robert VanBuren
- Department of Horticulture, Michigan State University, East Lansing, MI, United States
| | - Ayalew Ligaba-Osena
- Laboratory of Plant Molecular Biology and Biotechnology, Department of Biology, The University of North Carolina at Greensboro, Greensboro, NC, United States
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25
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Chen J, Wen Y, Pan Y, He Y, Gong X, Yang W, Chen W, Zhou F, Jiang D. Analysis of the role of the rice metallothionein gene OsMT2b in grain size regulation. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 349:112272. [PMID: 39321878 DOI: 10.1016/j.plantsci.2024.112272] [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: 06/05/2024] [Revised: 09/19/2024] [Accepted: 09/21/2024] [Indexed: 09/27/2024]
Abstract
Seed size is one of the three main characteristics determining rice yield. Clarification of the mechanisms regulating seed size in rice has implications for improving rice yield. Although several genes have been reported to regulate seed size, most of the reports are fragmentary. The role of metallothioneins (MTs) in regulating seed size remains unknown. Here, we found that OsMT2b was expressed in both spikelets and developing seeds. OsMT2b-overexpression lines had large and heavy seeds, and RNAi (RNA interference) lines had small and light seeds. Scanning electron microscopy (SEM) observations revealed that OsMT2b regulated spikelet hull size by affecting cell expansion in the outer epidermis. Histological analysis indicated that OsMT2b affected the number of cells in the cross-section of spikelet hulls, which affected seed size. The fresh weight of seeds was consistently higher in OsMT2b-overexpression lines than in seeds of the wild-type (WT) and RNAi lines from 6 DAP (days after pollination) until maturity, indicating that OsMT2b affected seed filling. Reverse transcription-quantitative PCR (RT-qPCR) analyses revealed that OsMT2b regulates the expression of reactive oxygen species scavenging-related genes involved in seed size regulation. In conclusion, our results indicated that OsMT2b positively regulates seed size, which provides a novel approach for regulating seed size with genetic engineering technology.
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Affiliation(s)
- Jian Chen
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Yunyi Wen
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Yibin Pan
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Ying He
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Xiaoting Gong
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Wenli Yang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Weiting Chen
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Feng Zhou
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Dagang Jiang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China.
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26
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Qi Y, Xie Y, Ge M, Shen W, He Y, Zhang X, Qiao F, Xu X, Qiu QS. Alkaline tolerance in plants: The AT1 gene and beyond. JOURNAL OF PLANT PHYSIOLOGY 2024; 303:154373. [PMID: 39454297 DOI: 10.1016/j.jplph.2024.154373] [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: 08/30/2024] [Revised: 10/20/2024] [Accepted: 10/20/2024] [Indexed: 10/28/2024]
Abstract
Salt stress poses a serious challenge to crop production and a significant threat to global food security and ecosystem sustainability. Soil salinization commonly occurs in conjunction with alkalization, which causes combined saline-alkaline stress. Alkaline soil predominantly comprises NaHCO3 and Na2CO3 and is characterized by a high pH. The combined saline-alkaline stress is more harmful to crop production than neutral salt stress owing to the effects of both elevated salinity and high pH stress. Through genome association analysis of sorghum, a recent study has identified Alkaline tolerance 1 (AT1) as a contributor to alkaline sensitivity in crops. AT1, which is the first gene to be identified as being specifically associated with alkaline tolerance, encodes a G protein γ-subunit (Gγ). Editing of AT1 enhances the yields of sorghum, rice, maize, and millet grown in alkaline soils, indicating that AT1 has potential for generating alkaline-resistant crops. In this review, we summarize the role of AT1 in alkaline tolerance in plants and present a phylogenetic analysis along with a motif comparison of Gγ subunits of monocot and dicot plants across various species.
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Affiliation(s)
- Yuting Qi
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, 730000, China
| | - Yujie Xie
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, 730000, China
| | - Mingrui Ge
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, 730000, China
| | - Wei Shen
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, 730000, China
| | - Yu He
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, 730000, China
| | - Xiao Zhang
- College of Life Science and Technology, Tarim University, Alar, Xinjiang, 843300, China
| | - Feng Qiao
- Academy of Plateau Science and Sustainability, School of Life Sciences, Qinghai Normal University, Xining, Qinghai, 810000, China
| | - Xing Xu
- School of Agriculture, Ningxia University, Yinchuan, 750021, China
| | - Quan-Sheng Qiu
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, 730000, China.
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Fan M, Li J, Zhang T, Huo H, Lü S, He Z, Wang X, Zhang J. Genome-wide identification of heterotrimeric G protein genes in castor (Ricinus communis L.) and expression patterns under salt stress. BMC Genomics 2024; 25:1115. [PMID: 39567878 PMCID: PMC11577925 DOI: 10.1186/s12864-024-11027-1] [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: 05/18/2024] [Accepted: 11/11/2024] [Indexed: 11/22/2024] Open
Abstract
BACKGROUND Heterotrimeric G proteins are crucial signaling molecules involved in cell signaling, plant development, and stress response. However, the genome-wide identification and analysis of G proteins in castor (Ricinus communis L.) have not been researched. RESULTS In this study, RcG-protein genes were identified using a sequence alignment method and analyzed by bioinformatics and expression analysis in response to salt stress. The results showed that a total of 9 G-protein family members were identified in the castor genome, which were classified into three subgroups, with the majority of RcG-proteins showing homology to soybean G-protein members. The promoter regions of all RcG-protein genes contained antioxidant response elements and ABA-responsive elements. Go enrichment analysis displayed that RcG-protein genes were involved in the G protein-coupled receptor signaling pathway, regulation of root development, and response to the bacterium. Real-time PCR showed varying responses of all RcG-protein genes to salt stress. RcGB1 was notably expressed in both roots and leaves under salt treatment, suggesting that it may be an essential gene associated with salt tolerance in the castor. CONCLUSIONS This study offers a theoretical framework for exploring G-protein function and presents potential genetic assets for improving crop resilience through genetic enhancement.
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Affiliation(s)
- Mubo Fan
- College of Life Science and Food Engineering, Inner Mongolia Minzu University, Tongliao, 028000, China
- Inner Mongolia Collaborative Innovation Center for Castor Industry, Tongliao, 028000, China
| | - Jiayu Li
- College of Life Science and Food Engineering, Inner Mongolia Minzu University, Tongliao, 028000, China
- Inner Mongolia Collaborative Innovation Center for Castor Industry, Tongliao, 028000, China
| | - Tongjie Zhang
- Inner Mongolia Collaborative Innovation Center for Castor Industry, Tongliao, 028000, China
- College of Agronomy, Inner Mongolia Minzu University, Tongliao, 028000, China
| | - Hongyan Huo
- College of Life Science and Food Engineering, Inner Mongolia Minzu University, Tongliao, 028000, China
- Inner Mongolia Collaborative Innovation Center for Castor Industry, Tongliao, 028000, China
| | - Shiyou Lü
- Inner Mongolia Collaborative Innovation Center for Castor Industry, Tongliao, 028000, China
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Zhibiao He
- Inner Mongolia Collaborative Innovation Center for Castor Industry, Tongliao, 028000, China
- Tongliao Academy of Agricultural and Animal Husbandry Sciences, Tongliao, 028015, China
| | - Xiaoyu Wang
- College of Life Science and Food Engineering, Inner Mongolia Minzu University, Tongliao, 028000, China
- Inner Mongolia Collaborative Innovation Center for Castor Industry, Tongliao, 028000, China
| | - Jixing Zhang
- College of Life Science and Food Engineering, Inner Mongolia Minzu University, Tongliao, 028000, China.
- Inner Mongolia Collaborative Innovation Center for Castor Industry, Tongliao, 028000, China.
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28
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Lee H. Trade-Off Regulation in Plant Growth and Stress Responses Through the Role of Heterotrimeric G Protein Signaling. PLANTS (BASEL, SWITZERLAND) 2024; 13:3239. [PMID: 39599448 PMCID: PMC11598323 DOI: 10.3390/plants13223239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2024] [Revised: 11/16/2024] [Accepted: 11/18/2024] [Indexed: 11/29/2024]
Abstract
Unlike animals, plants are sessile organisms that cannot migrate to more favorable conditions and must constantly adapt to a variety of biotic and abiotic stresses. Therefore, plants exhibit developmental plasticity to cope, which is probably based on the underlying trade-off mechanism that allocates energy expenditure between growth and stress responses to achieve appropriate growth and development under different environmental conditions. Plant heterotrimeric G protein signaling plays a crucial role in the trade-off involved in the regulation of normal growth and stress adaptation. This review examines the composition and signaling processes of heterotrimeric G proteins in plants, detailing how they balance growth and adaptive responses in plant immunity and thermomorphogenesis through recent advances in the field. Understanding the trade-offs associated with plant G protein signaling will have significant implications for agricultural innovation, particularly in the development of crops with improved resilience and minimal growth penalties under environmental stress.
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Affiliation(s)
- Horim Lee
- Department of Biotechnology, Duksung Women's University, Seoul 01369, Republic of Korea
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29
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Zhang L, Lu Z, Pan Z, Chen T, Wang S, Liu W, Wang X, Wu H, Chen H, Zhan Y, He X. Genetic Dissection of Milled Rice Grain Shape by Using a Recombinant Inbred Line Population and Validation of qMLWR11.1 and qMLWR11.2. PLANTS (BASEL, SWITZERLAND) 2024; 13:3178. [PMID: 39599386 PMCID: PMC11597858 DOI: 10.3390/plants13223178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2024] [Revised: 10/10/2024] [Accepted: 11/07/2024] [Indexed: 11/29/2024]
Abstract
Grain shape in rice (Oryza sativa L.) is a complex trait governed by multiple quantitative trait loci (QTLs). To dissect the genetic basis of rice shape, QTL analysis was conducted for milled rice grain width (MGW), milled rice grain length (MGL), and milled rice length-to-width ratio (MLWR) using a recombinant inbred line (RIL) population of F10 and F11 generations derived from a cross between Yuexiangzhan and Shengbasimiao. A high-density genetic map consisting of 2412 bins was constructed by sequencing 184 RILs, spanning a total length of 2376.46 cM. A total of 19 QTLs related to MGL, MGW, and MLWR were detected under two environments. The range of phenotypic variation attributed to individual QTL ranged from 1.67% to 32.08%. Among those, a novel locus for MGL, MGW and MLWR, designated as qMLWR3.2, was pinpointed within a specific ~0.96-Mb region. Two novel loci for MGW and MLWR, qMLWR11.1 and qMLWR11.2, were verified within ~1.22-Mb and ~0.52-Mb regions using three RIL-developed populations, respectively. These findings lay the foundation for further map-based cloning and molecular design breeding in rice.
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Affiliation(s)
- Liting Zhang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (L.Z.); (Z.L.); (Z.P.); (T.C.); (S.W.); (W.L.); (X.W.); (H.W.); (H.C.); (Y.Z.)
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
| | - Zhanhua Lu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (L.Z.); (Z.L.); (Z.P.); (T.C.); (S.W.); (W.L.); (X.W.); (H.W.); (H.C.); (Y.Z.)
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
| | - Zhaoyang Pan
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (L.Z.); (Z.L.); (Z.P.); (T.C.); (S.W.); (W.L.); (X.W.); (H.W.); (H.C.); (Y.Z.)
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
| | - Tengkui Chen
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (L.Z.); (Z.L.); (Z.P.); (T.C.); (S.W.); (W.L.); (X.W.); (H.W.); (H.C.); (Y.Z.)
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
| | - Shiguang Wang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (L.Z.); (Z.L.); (Z.P.); (T.C.); (S.W.); (W.L.); (X.W.); (H.W.); (H.C.); (Y.Z.)
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
| | - Wei Liu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (L.Z.); (Z.L.); (Z.P.); (T.C.); (S.W.); (W.L.); (X.W.); (H.W.); (H.C.); (Y.Z.)
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
| | - Xiaofei Wang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (L.Z.); (Z.L.); (Z.P.); (T.C.); (S.W.); (W.L.); (X.W.); (H.W.); (H.C.); (Y.Z.)
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
| | - Haoxiang Wu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (L.Z.); (Z.L.); (Z.P.); (T.C.); (S.W.); (W.L.); (X.W.); (H.W.); (H.C.); (Y.Z.)
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
| | - Hao Chen
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (L.Z.); (Z.L.); (Z.P.); (T.C.); (S.W.); (W.L.); (X.W.); (H.W.); (H.C.); (Y.Z.)
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
| | - Yunyi Zhan
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (L.Z.); (Z.L.); (Z.P.); (T.C.); (S.W.); (W.L.); (X.W.); (H.W.); (H.C.); (Y.Z.)
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
| | - Xiuying He
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (L.Z.); (Z.L.); (Z.P.); (T.C.); (S.W.); (W.L.); (X.W.); (H.W.); (H.C.); (Y.Z.)
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
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30
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Wang Y, Chen W, Xing M, Sun J, Wang S, Yang Z, Huang J, Nie Y, Zhao M, Li Y, Guo W, Wang Y, Chen Z, Zhang Q, Hu J, Li Y, Huang K, Zheng X, Zhou L, Zhang L, Cheng Y, Qian Q, Yang Q, Qiao W. Wild rice GL12 synergistically improves grain length and salt tolerance in cultivated rice. Nat Commun 2024; 15:9453. [PMID: 39487109 PMCID: PMC11530696 DOI: 10.1038/s41467-024-53611-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Accepted: 10/16/2024] [Indexed: 11/04/2024] Open
Abstract
The abounding variations in wild rice provided potential reservoirs of beneficial genes for rice breeding. Maintaining stable and high yields under environmental stresses is a long-standing goal of rice breeding but is challenging due to internal trade-off mechanisms. Here, we report wild rice GL12W improves grain length and salt tolerance in both indica and japonica genetic backgrounds. GL12W alters cell length by regulating grain size related genes including GS2, and positively regulates the salt tolerance related genes, such as NAC5, NCED3, under salt stresses. We find that a G/T variation in GL12 promoter determined its binding to coactivator GIF1 and transcription factor WRKY53. GIF1 promotes GL12W expression in young panicle and WRKY53 represses GL12W expression under salt stresses. The G/T variation also contributes to the divergence of indica and japonica subspecies. Our results provide useful resources for modern rice breeding and shed insights for understanding yield and salt tolerance trade-off mechanism.
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Affiliation(s)
- Yanyan Wang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, 572024, China
- Nanjing Institute of Agricultural Sciences in Jiangsu Hilly Area, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Wenxi Chen
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, 572024, China
| | - Meng Xing
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, 572024, China
| | - Jiaqiang Sun
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shizhuang Wang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ziyi Yang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jingfen Huang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, 572024, China
| | - Yamin Nie
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mingchao Zhao
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, 572024, China
- Cereal Crop Institute, Hainan Agricultural Academy Sciences, Haikou, China
| | - Yapeng Li
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, 572024, China
- Cereal Crop Institute, Hainan Agricultural Academy Sciences, Haikou, China
| | - Wenlong Guo
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, 572024, China
| | - Yinting Wang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ziyi Chen
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qiaoling Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, 572024, China
| | - Jiang Hu
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, 572024, China
- China National Rice Research Institute, Hangzhou, 310006, China
| | - Yunhai Li
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Ke Huang
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Xiaoming Zheng
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, 572024, China
| | - Leina Zhou
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lifang Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yunlian Cheng
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qian Qian
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
- China National Rice Research Institute, Hangzhou, 310006, China.
- Yazhouwan National Laboratory, Sanya, China.
| | - Qingwen Yang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, 572024, China.
| | - Weihua Qiao
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, 572024, China.
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Yang Q, Tang X, Wu Y, Zhu W, Zhang T, Zhang Y. CRISPR-Based Modulation of uORFs in DEP1 and GIF1 for Enhanced Rice Yield Traits. RICE (NEW YORK, N.Y.) 2024; 17:67. [PMID: 39455475 PMCID: PMC11511795 DOI: 10.1186/s12284-024-00743-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2024] [Accepted: 10/08/2024] [Indexed: 10/28/2024]
Affiliation(s)
- Qingqing Yang
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009, China
| | - Xu Tang
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Chongqing Key Laboratory of Tree Germplasm Innovation and Utilization, School of Life Sciences, Southwest University, Chongqing, 400715, China
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 311400, Zhejiang, China
| | - Yuechao Wu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009, China
| | - Wenjie Zhu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009, China
| | - Tao Zhang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College, Yangzhou University, Yangzhou, 225009, China.
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009, China.
| | - Yong Zhang
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Chongqing Key Laboratory of Tree Germplasm Innovation and Utilization, School of Life Sciences, Southwest University, Chongqing, 400715, China.
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Thiruppathi A, Salunkhe SR, Ramasamy SP, Palaniswamy R, Rajagopalan VR, Rathnasamy SA, Alagarswamy S, Swaminathan M, Manickam S, Muthurajan R. Unleashing the Potential of CRISPR/Cas9 Genome Editing for Yield-Related Traits in Rice. PLANTS (BASEL, SWITZERLAND) 2024; 13:2972. [PMID: 39519891 PMCID: PMC11547960 DOI: 10.3390/plants13212972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2024] [Revised: 10/18/2024] [Accepted: 10/22/2024] [Indexed: 11/16/2024]
Abstract
Strategies to enhance rice productivity in response to global demand have been the paramount focus of breeders worldwide. Multiple factors, including agronomical traits such as plant architecture and grain formation and physiological traits such as photosynthetic efficiency and NUE (nitrogen use efficiency), as well as factors such as phytohormone perception and homeostasis and transcriptional regulation, indirectly influence rice grain yield. Advances in genetic analysis methodologies and functional genomics, numerous genes, QTLs (Quantitative Trait Loci), and SNPs (Single-Nucleotide Polymorphisms), linked to yield traits, have been identified and analyzed in rice. Genome editing allows for the targeted modification of identified genes to create novel mutations in rice, avoiding the unintended mutations often caused by random mutagenesis. Genome editing technologies, notably the CRISPR/Cas9 system, present a promising tool to generate precise and rapid modifications in the plant genome. Advancements in CRISPR have further enabled researchers to modify a larger number of genes with higher efficiency. This paper reviews recent research on genome editing of yield-related genes in rice, discusses available gene editing tools, and highlights their potential to expedite rice breeding programs.
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Affiliation(s)
- Archana Thiruppathi
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641003, India; (A.T.); (S.R.S.); (R.P.); (V.R.R.); (S.A.R.)
| | - Shubham Rajaram Salunkhe
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641003, India; (A.T.); (S.R.S.); (R.P.); (V.R.R.); (S.A.R.)
| | - Shobica Priya Ramasamy
- Department of Plant Breeding and Genetics, Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore 641003, India;
| | - Rakshana Palaniswamy
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641003, India; (A.T.); (S.R.S.); (R.P.); (V.R.R.); (S.A.R.)
| | - Veera Ranjani Rajagopalan
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641003, India; (A.T.); (S.R.S.); (R.P.); (V.R.R.); (S.A.R.)
| | - Sakthi Ambothi Rathnasamy
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641003, India; (A.T.); (S.R.S.); (R.P.); (V.R.R.); (S.A.R.)
| | - Senthil Alagarswamy
- Department of Crop Physiology, Tamil Nadu Agricultural University, Coimbatore 641003, India;
| | - Manonmani Swaminathan
- Department of Rice, Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore 641003, India;
| | - Sudha Manickam
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641003, India; (A.T.); (S.R.S.); (R.P.); (V.R.R.); (S.A.R.)
| | - Raveendran Muthurajan
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641003, India; (A.T.); (S.R.S.); (R.P.); (V.R.R.); (S.A.R.)
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Sun LQ, Bai Y, Wu J, Fan SJ, Chen SY, Zhang ZY, Xia JQ, Wang SM, Wang YP, Qin P, Li SG, Xu P, Zhao Z, Xiang CB, Zhang ZS. OsNLP3 enhances grain weight and reduces grain chalkiness in rice. PLANT COMMUNICATIONS 2024; 5:100999. [PMID: 38853433 PMCID: PMC11574284 DOI: 10.1016/j.xplc.2024.100999] [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: 01/22/2024] [Revised: 05/29/2024] [Accepted: 06/07/2024] [Indexed: 06/11/2024]
Abstract
Grain weight, a key determinant of yield in rice (Oryza sativa L.), is governed primarily by genetic factors, whereas grain chalkiness, a detriment to grain quality, is intertwined with environmental factors such as mineral nutrients. Nitrogen (N) is recognized for its effect on grain chalkiness, but the underlying molecular mechanisms remain to be clarified. This study revealed the pivotal role of rice NODULE INCEPTION-LIKE PROTEIN 3 (OsNLP3) in simultaneously regulating grain weight and grain chalkiness. Our investigation showed that loss of OsNLP3 leads to a reduction in both grain weight and dimension, in contrast to the enhancement observed with OsNLP3 overexpression. OsNLP3 directly suppresses the expression of OsCEP6.1 and OsNF-YA8, which were identified as negative regulators associated with grain weight. Consequently, two novel regulatory modules, OsNLP3-OsCEP6.1 and OsNLP3-OsNF-YA8, were identified as key players in grain weight regulation. Notably, the OsNLP3-OsNF-YA8 module not only increases grain weight but also mitigates grain chalkiness in response to N. This research clarifies the molecular mechanisms that orchestrate grain weight through the OsNLP3-OsCEP6.1 and OsNLP3-OsNF-YA8 modules, highlighting the pivotal role of the OsNLP3-OsNF-YA8 module in alleviating grain chalkiness. These findings reveal potential targets for simultaneous enhancement of rice yield and quality.
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Affiliation(s)
- Liang-Qi Sun
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province 230027, China
| | - Yu Bai
- Experimental Center of Engineering and Materials Science, University of Science and Technology of China, Hefei 230027, China
| | - Jie Wu
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province 230027, China
| | - Shi-Jun Fan
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province 230027, China
| | - Si-Yan Chen
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province 230027, China
| | - Zheng-Yi Zhang
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province 230027, China
| | - Jin-Qiu Xia
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province 230027, China
| | - Shi-Mei Wang
- Rice Research Institute, Anhui Academy of Agricultural Science, Hefei, China
| | - Yu-Ping Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Peng Qin
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Shi-Gui Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Ping Xu
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
| | - Zhong Zhao
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province 230027, China
| | - Cheng-Bin Xiang
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province 230027, China.
| | - Zi-Sheng Zhang
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province 230027, China.
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Zhang Q, Wu R, Hong T, Wang D, Li Q, Wu J, Zhang H, Zhou K, Yang H, Zhang T, Liu J, Wang N, Ling Y, Yang Z, He G, Zhao F. Natural variation in the promoter of qRBG1/OsBZR5 underlies enhanced rice yield. Nat Commun 2024; 15:8565. [PMID: 39362889 PMCID: PMC11449933 DOI: 10.1038/s41467-024-52928-9] [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: 12/19/2023] [Accepted: 09/24/2024] [Indexed: 10/05/2024] Open
Abstract
Seed size, a key determinant of rice yield, is regulated by brassinosteroid (BR); however, the BR pathway in rice has not been fully elucidated. Here, we report the cloning and characterization of the quantitative trait locus Rice Big Grain 1 (qRBG1) from single-segment substitution line Z499. Our data show that qRBG1Z is an unselected rare promoter variation that reduces qRBG1 expression to increase cell number and size, resulting in larger grains, whereas qRBG1 overexpression causes smaller grains in recipient Nipponbare. We demonstrate that qRBG1 encodes a non-canonical BES1 (Bri1-EMS-Suppressor1)/BZR1(Brassinazole-Resistant1) family member, OsBZR5, that regulates grain size upon phosphorylation by OsGSK2 (GSK3-like Kinase2) and binding to D2 (DWARF2) and OFP1 (Ovate-Family-Protein1) promoters. qRBG1 interacts with OsBZR1 to synergistically repress D2, and to antagonistically mediate OFP1 for grain size. Our results reveal a regulatory network controlling grain size via OsGSK2-qRBG1-OsBZR1-D2-OFP1 module, providing a target for improving rice yield.
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Affiliation(s)
- Qiuli Zhang
- Rice Research Institute, Key Laboratory of Crop Molecular Improvement, Academy of Agricultural Sciences, Ministry of Education, Southwest University, Chongqing, 400715, China
| | - Renhong Wu
- Rice Research Institute, Key Laboratory of Crop Molecular Improvement, Academy of Agricultural Sciences, Ministry of Education, Southwest University, Chongqing, 400715, China
| | - Tao Hong
- Rice Research Institute, Key Laboratory of Crop Molecular Improvement, Academy of Agricultural Sciences, Ministry of Education, Southwest University, Chongqing, 400715, China
| | - Dachuan Wang
- Rice Research Institute, Key Laboratory of Crop Molecular Improvement, Academy of Agricultural Sciences, Ministry of Education, Southwest University, Chongqing, 400715, China
| | - Qiaolong Li
- Rice Research Institute, Key Laboratory of Crop Molecular Improvement, Academy of Agricultural Sciences, Ministry of Education, Southwest University, Chongqing, 400715, China
| | - Jiayi Wu
- Rice Research Institute, Key Laboratory of Crop Molecular Improvement, Academy of Agricultural Sciences, Ministry of Education, Southwest University, Chongqing, 400715, China
| | - Han Zhang
- Rice Research Institute, Key Laboratory of Crop Molecular Improvement, Academy of Agricultural Sciences, Ministry of Education, Southwest University, Chongqing, 400715, China
| | - Kai Zhou
- Rice Research Institute, Key Laboratory of Crop Molecular Improvement, Academy of Agricultural Sciences, Ministry of Education, Southwest University, Chongqing, 400715, China
| | - Hongxia Yang
- Rice Research Institute, Key Laboratory of Crop Molecular Improvement, Academy of Agricultural Sciences, Ministry of Education, Southwest University, Chongqing, 400715, China
| | - Ting Zhang
- Rice Research Institute, Key Laboratory of Crop Molecular Improvement, Academy of Agricultural Sciences, Ministry of Education, Southwest University, Chongqing, 400715, China
| | - JinXiang Liu
- Rice Research Institute, Key Laboratory of Crop Molecular Improvement, Academy of Agricultural Sciences, Ministry of Education, Southwest University, Chongqing, 400715, China
| | - Nan Wang
- Rice Research Institute, Key Laboratory of Crop Molecular Improvement, Academy of Agricultural Sciences, Ministry of Education, Southwest University, Chongqing, 400715, China
| | - Yinghua Ling
- Rice Research Institute, Key Laboratory of Crop Molecular Improvement, Academy of Agricultural Sciences, Ministry of Education, Southwest University, Chongqing, 400715, China
| | - Zhenglin Yang
- Rice Research Institute, Key Laboratory of Crop Molecular Improvement, Academy of Agricultural Sciences, Ministry of Education, Southwest University, Chongqing, 400715, China
| | - Guanghua He
- Rice Research Institute, Key Laboratory of Crop Molecular Improvement, Academy of Agricultural Sciences, Ministry of Education, Southwest University, Chongqing, 400715, China.
| | - Fangming Zhao
- Rice Research Institute, Key Laboratory of Crop Molecular Improvement, Academy of Agricultural Sciences, Ministry of Education, Southwest University, Chongqing, 400715, China.
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Hao Q, Zhu X, Huang Y, Song J, Mou C, Zhang F, Miao R, Ma T, Wang P, Zhu Z, Chen C, Tong Q, Hu C, Chen Y, Dong H, Liu X, Jiang L, Wan J. E3 ligase DECREASED GRAIN SIZE 1 promotes degradation of a G-protein subunit and positively regulates grain size in rice. PLANT PHYSIOLOGY 2024; 196:948-960. [PMID: 38888990 DOI: 10.1093/plphys/kiae331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 03/22/2024] [Accepted: 05/01/2024] [Indexed: 06/20/2024]
Abstract
Grain size is one of the most important traits determining crop yield. However, the mechanism controlling grain size remains unclear. Here, we confirmed the E3 ligase activity of DECREASED GRAIN SIZE 1 (DGS1) in positive regulation of grain size in rice (Oryza sativa) suggested in a previous study. Rice G-protein subunit gamma 2 (RGG2), which negatively regulates grain size, was identified as an interacting protein of DGS1. Biochemical analysis suggested that DGS1 specifically interacts with canonical Gγ subunits (rice G-protein subunit gamma 1 [RGG1] and rice G-protein subunit gamma 2 [RGG2]) rather than non-canonical Gγ subunits (DENSE AND ERECT PANICLE 1 [DEP1], rice G-protein gamma subunit type C 2 [GCC2], GRAIN SIZE 3 [GS3]). We also identified the necessary domains for interaction between DGS1 and RGG2. As an E3 ligase, DGS1 ubiquitinated and degraded RGG2 via a proteasome pathway in several experiments. DGS1 also ubiquitinated RGG2 by its K140, K145, and S147 residues. Thus, this work identified a substrate of the E3 ligase DGS1 and elucidated the post-transcriptional regulatory mechanism of the G-protein signaling pathway in the control of grain size.
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Affiliation(s)
- Qixian Hao
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Nanjing National Field Scientific Observation and Research Station for Rice Germplasm, Nanjing Agricultural University, Nanjing 210095, China
| | - Xingjie Zhu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Nanjing National Field Scientific Observation and Research Station for Rice Germplasm, Nanjing Agricultural University, Nanjing 210095, China
| | - Yunshuai Huang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Nanjing National Field Scientific Observation and Research Station for Rice Germplasm, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiawei Song
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Nanjing National Field Scientific Observation and Research Station for Rice Germplasm, Nanjing Agricultural University, Nanjing 210095, China
| | - Changling Mou
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Nanjing National Field Scientific Observation and Research Station for Rice Germplasm, Nanjing Agricultural University, Nanjing 210095, China
| | - Fulin Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Nanjing National Field Scientific Observation and Research Station for Rice Germplasm, Nanjing Agricultural University, Nanjing 210095, China
| | - Rong Miao
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Nanjing National Field Scientific Observation and Research Station for Rice Germplasm, Nanjing Agricultural University, Nanjing 210095, China
| | - Tengfei Ma
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Nanjing National Field Scientific Observation and Research Station for Rice Germplasm, Nanjing Agricultural University, Nanjing 210095, China
| | - Ping Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Nanjing National Field Scientific Observation and Research Station for Rice Germplasm, Nanjing Agricultural University, Nanjing 210095, China
| | - Ziyan Zhu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Nanjing National Field Scientific Observation and Research Station for Rice Germplasm, Nanjing Agricultural University, Nanjing 210095, China
| | - Cheng Chen
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Nanjing National Field Scientific Observation and Research Station for Rice Germplasm, Nanjing Agricultural University, Nanjing 210095, China
| | - Qikai Tong
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Nanjing National Field Scientific Observation and Research Station for Rice Germplasm, Nanjing Agricultural University, Nanjing 210095, China
| | - Chen Hu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Nanjing National Field Scientific Observation and Research Station for Rice Germplasm, Nanjing Agricultural University, Nanjing 210095, China
| | - Yingying Chen
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Nanjing National Field Scientific Observation and Research Station for Rice Germplasm, Nanjing Agricultural University, Nanjing 210095, China
| | - Hui Dong
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Nanjing National Field Scientific Observation and Research Station for Rice Germplasm, Nanjing Agricultural University, Nanjing 210095, China
- Zhongshan Biological Breeding Laboratory, No. 50 Zhongling Street, Nanjing 210095, China
| | - Xi Liu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Nanjing National Field Scientific Observation and Research Station for Rice Germplasm, Nanjing Agricultural University, Nanjing 210095, China
- Zhongshan Biological Breeding Laboratory, No. 50 Zhongling Street, Nanjing 210095, China
| | - Ling Jiang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Nanjing National Field Scientific Observation and Research Station for Rice Germplasm, Nanjing Agricultural University, Nanjing 210095, China
- Zhongshan Biological Breeding Laboratory, No. 50 Zhongling Street, Nanjing 210095, China
| | - Jianmin Wan
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Nanjing National Field Scientific Observation and Research Station for Rice Germplasm, Nanjing Agricultural University, Nanjing 210095, China
- Zhongshan Biological Breeding Laboratory, No. 50 Zhongling Street, Nanjing 210095, China
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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Xin W, Chen N, Wang J, Liu Y, Sun Y, Han B, Wang X, Liu Z, Liu H, Zheng H, Yang L, Zou D, Wang J. Candidate gene analysis of rice grain shape based on genome-wide association study. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:241. [PMID: 39342533 DOI: 10.1007/s00122-024-04724-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Accepted: 08/21/2024] [Indexed: 10/01/2024]
Abstract
KEY MESSAGE Thirteen QTLs associated with rice grain shape were localized by genome-wide association study. LOC_Os01g74020, the putative candidate gene in the co-localized QTL-qGSE1.2 interval, was identified and validated. Grain shape (GS) is a key trait that affects yield and quality of rice. Identifying and analyzing GS-related genes and elucidating the physiological, biochemical and molecular mechanisms are important for rice breeding. In this study, genome-wide association studies (GWAS) were conducted based on 1, 795, 076 single-nucleotide polymorphisms (SNPs) and three GS-related traits, grain length (GL), grain width (GW) and thousand-grain weight (TGW), in a natural population which comprised 374 rice varieties. A total of 13 quantitative trait locus (QTLs) related to GL, GW and TGW were identified, respectively, of which two QTLs (qGSE1.2 and qGSE5.3) were associated with both GL and TGW. A known key GS regulatory gene, GW5, was present in the interval of qGSE5.3. Based on the qRT-PCR results, LOC_Os01g74020 (OsGSE1.2) was identified as a GS candidate gene. Functional analysis of OsGSE1.2 showed that glume cell width and GW were significantly reduced, and that glume cell length, GL, TGW and single-plant yield were significantly increased in OsGSE1.2 knockout lines than those of wild type. OsGSE1.2 affects rice grain length by suppressing the elongation of glume cell and is a novel GS regulatory gene. These findings laid the foundation for molecular breeding to improve rice GS and increase rice yield and profitability.
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Affiliation(s)
- Wei Xin
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Northeast Agricultural University, Ministry of Education, Harbin, 150030, China
| | - Ning Chen
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Northeast Agricultural University, Ministry of Education, Harbin, 150030, China
| | - Jiaqi Wang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Northeast Agricultural University, Ministry of Education, Harbin, 150030, China
| | - Yilei Liu
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Northeast Agricultural University, Ministry of Education, Harbin, 150030, China
| | - Yifeng Sun
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Northeast Agricultural University, Ministry of Education, Harbin, 150030, China
| | - Baojia Han
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Northeast Agricultural University, Ministry of Education, Harbin, 150030, China
| | - Xinghua Wang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Northeast Agricultural University, Ministry of Education, Harbin, 150030, China
| | - Zijie Liu
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Northeast Agricultural University, Ministry of Education, Harbin, 150030, China
| | - Hualong Liu
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Northeast Agricultural University, Ministry of Education, Harbin, 150030, China
| | - Hongliang Zheng
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Northeast Agricultural University, Ministry of Education, Harbin, 150030, China
| | - Luomiao Yang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Northeast Agricultural University, Ministry of Education, Harbin, 150030, China
| | - Detang Zou
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Northeast Agricultural University, Ministry of Education, Harbin, 150030, China
| | - Jingguo Wang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Northeast Agricultural University, Ministry of Education, Harbin, 150030, China.
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Li X, Sun M, Cui Z, Jiang Y, Yang L, Jiang Y. Transcription factor ZmNAC19 promotes embryo development in Arabidopsis thaliana. PLANT CELL REPORTS 2024; 43:244. [PMID: 39340665 DOI: 10.1007/s00299-024-03335-3] [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: 08/21/2024] [Accepted: 09/17/2024] [Indexed: 09/30/2024]
Abstract
KEY MESSAGE Overexpression of ZmNAC19, a NAC transcription factor gene from maize, improves embryo development in transgenic Arabidopsis. NAC proteins are plant-specific transcription factors that are involved in multiple aspects of plant growth, development and stress response. Although functions of many NAC transcription factors have been elucidated, little is known about their roles in seed development. In this study, we report the function of a maize NAC transcription factor ZmNAC19 in seed development. ZmNAC19 is highly expressed in embryos of developing maize seeds. ZmNAC19 localizes to nucleus and exhibits transactivation activity in yeast cells. Overexpression of ZmNAC19 in Arabidopsis significantly increases seed size and seed yield. During 3 to 7 days after flowering, embryos of ZmNAC19-overexpression Arabidopsis lines developed faster compared to Col-0, while no visible differences were detected for their endosperms. Furthermore, overexpression of ZmNAC19 in Arabidopsis leads to increased transcription levels of two embryo development-related genes YUC1 and RGE1, and several elements proven to be binding sites of NAC transcription factors were observed in promoters of these two genes. Taken together, these results suggest that ZmNAC19 acts as a positive regulator in plant embryo development.
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Affiliation(s)
- Xiulan Li
- School of Life Sciences, Qufu Normal University, Qufu, 273165, China.
| | - Mengdi Sun
- School of Life Sciences, Qufu Normal University, Qufu, 273165, China
| | - Zhenhao Cui
- School of Life Sciences, Qufu Normal University, Qufu, 273165, China
| | - Yuhan Jiang
- School of Life Sciences, Qufu Normal University, Qufu, 273165, China
| | - Lingkun Yang
- School of Life Sciences, Qufu Normal University, Qufu, 273165, China
| | - Yueshui Jiang
- School of Life Sciences, Qufu Normal University, Qufu, 273165, China.
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Liu F, Wodajo B, Xie P. Decoding the genetic blueprint: regulation of key agricultural traits in sorghum. ADVANCED BIOTECHNOLOGY 2024; 2:31. [PMID: 39883247 PMCID: PMC11709141 DOI: 10.1007/s44307-024-00039-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2024] [Revised: 09/04/2024] [Accepted: 09/05/2024] [Indexed: 01/31/2025]
Abstract
Sorghum, the fifth most important crop globally, thrives in challenging environments such as arid, saline-alkaline, and infertile regions. This remarkable crop, one of the earliest crops domesticated by humans, offers high biomass and stress-specific properties that render it suitable for a variety of uses including food, feed, bioenergy, and biomaterials. What's truly exciting is the extensive phenotypic variation in sorghum, particularly in traits related to growth, development, and stress resistance. This inherent adaptability makes sorghum a game-changer in agriculture. However, tapping into sorghum's full potential requires unraveling the complex genetic networks that govern its key agricultural traits. Understanding these genetic mechanisms is paramount for improving traits such as yield, quality, and tolerance to drought and saline-alkaline conditions. This review provides a comprehensive overview of functionally characterized genes and regulatory networks associated with plant and panicle architectures, as well as stress resistance in sorghum. Armed with this knowledge, we can develop more resilient and productive sorghum varieties through cutting-edge breeding techniques like genome-wide selection, gene editing, and synthetic biology. These approaches facilitate the identification and manipulation of specific genes responsible for desirable traits, ultimately enhancing agricultural performance and adaptability in sorghum.
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Affiliation(s)
- Fangyuan Liu
- School of Agriculture and Biotechnology, Sun Yat-sen University, Shenzhen, 518107, P. R. China
| | - Baye Wodajo
- College of Natural and Computational Science, Woldia University, Po.box-400, Woldia, Ethiopia
| | - Peng Xie
- School of Agriculture and Biotechnology, Sun Yat-sen University, Shenzhen, 518107, P. R. China.
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39
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Yan Z, Deng R, Tang H, Zhu S. Genetic Diversity and Divergence between Southern Japonica and Northern Japonica Rice Varieties in China. Genes (Basel) 2024; 15:1182. [PMID: 39336773 PMCID: PMC11431492 DOI: 10.3390/genes15091182] [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: 08/20/2024] [Revised: 08/29/2024] [Accepted: 09/03/2024] [Indexed: 09/30/2024] Open
Abstract
Given the notable ecological and breeding disparities between southern and northern rice regions, delving into the genetic diversity and divergence between southern and northern japonica rice contributes to enhancing the genetic pool for japonica rice breeding. In this study, we analyzed 90 southern and 51 northern japonica rice varieties, focusing on nucleotide diversity (Pi), agronomic trait variations, population structure, genetic divergence, and a neutral test. For genetic diversity, the results demonstrated higher Pi in northern japonica rice varieties (NJRVs) on Chr2, Chr5, Chr6, Chr8, and Chr10, whereas in southern japonica rice varieties (SJRVs) on Chr7 and Chr9. In addition, SJRVs exhibited higher grain width and thickness, whereas NJRVs featured a higher grain aspect ratio, filled grain number, and grain number per panicle. Regarding genetic divergence, geographic differentiation existed between NJRVs and SJRVs, with Chr5 exhibiting numerous higher genetic differentiation windows, including cloned grain shape-controlling genes RGA1 and SFD5, stemming from intensified selection pressure on SJRVs. In summary, SJRVs and NJRVs exhibited diversity differences and genetic differentiation. Hence, it was suggested to conduct genetic introgression between NJRVs and SJRVs to broaden the genetic basis of the local japonica rice germplasm. By exploiting their heterotic advantage, new japonica rice cultivars with superior comprehensive traits could be developed.
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Affiliation(s)
- Zhiqiang Yan
- Guizhou Provincial Academy of Agricultural Sciences, Guiyang 550000, China
| | - Ruyue Deng
- Guizhou Provincial Academy of Agricultural Sciences, Guiyang 550000, China
| | - Huihui Tang
- Guizhou Provincial Academy of Agricultural Sciences, Guiyang 550000, China
| | - Susong Zhu
- Guizhou Provincial Academy of Agricultural Sciences, Guiyang 550000, China
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40
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Zhu L, Shen Y, Dai Z, Miao X, Shi Z. Gγ-protein GS3 Function in Tight Genetic Relation with OsmiR396/GS2 to Regulate Grain Size in Rice. RICE (NEW YORK, N.Y.) 2024; 17:59. [PMID: 39249660 PMCID: PMC11384671 DOI: 10.1186/s12284-024-00736-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Accepted: 08/27/2024] [Indexed: 09/10/2024]
Abstract
Manipulating grain size demonstrates great potential for yield promotion in cereals since it is tightly associated with grain weight. Several pathways modulating grain size have been elaborated in rice, but possible crosstalk between the ingredients is rarely studied. OsmiR396 negatively regulates grain size through targeting OsGRF4 (GS2) and OsGRF8, and proves to be multi-functioning. Here we showed that expression of GS3 gene, a Gγ-protein encoding gene, that negatively regulates grain size, was greatly down-regulated in the young embryos of MIM396, GRF8OE and GS2OE plants, indicating possible regulation of GS3 gene by OsmiR396/GRF module. Meanwhile, multiple biochemical assays proved possible transcriptional regulation of OsGRF4 and OsGRF8 proteins on GS3 gene. Further genetic relation analysis revealed tight genetic association between not only OsmiR396 and GS3 gene, but also GS2 and GS3 gene. Moreover, we revealed possible regulation of GS2 on four other grain size-regulating G protein encoding genes. Thus, the OsmiR396 pathway and the G protein pathway cross talks to regulate grain size. Therefore, we established a bridge linking the miRNA-transcription factors pathway and the G-protein signaling pathway that regulates grain size in rice.
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Affiliation(s)
- Lin Zhu
- Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences Shanghai, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanjie Shen
- Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences Shanghai, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhengyan Dai
- Translational Medical Center for Stem Cell Therapy, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Xuexia Miao
- Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences Shanghai, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Zhenying Shi
- Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences Shanghai, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.
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Yue Z, Wang Z, Yao Y, Liang Y, Li J, Yin K, Li R, Li Y, Ouyang Y, Xiong L, Hu H. Variation in WIDTH OF LEAF AND GRAIN contributes to grain and leaf size by controlling LARGE2 stability in rice. THE PLANT CELL 2024; 36:3201-3218. [PMID: 38701330 PMCID: PMC11371194 DOI: 10.1093/plcell/koae136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 03/22/2024] [Accepted: 04/12/2024] [Indexed: 05/05/2024]
Abstract
Grain and flag leaf size are two important agronomic traits that influence grain yield in rice (Oryza sativa). Many quantitative trait loci (QTLs) and genes that regulate these traits individually have been identified, however, few QTLs and genes that simultaneously control these two traits have been identified. In this study, we conducted a genome-wide association analysis in rice and detected a major locus, WIDTH OF LEAF AND GRAIN (WLG), that was associated with both grain and flag leaf width. WLG encodes a RING-domain E3 ubiquitin ligase. WLGhap.B, which possesses five single nucleotide polymophysim (SNP) variations compared to WLGhap.A, encodes a protein with enhanced ubiquitination activity that confers increased rice leaf width and grain size, whereas mutation of WLG leads to narrower leaves and smaller grains. Both WLGhap.A and WLGhap.B interact with LARGE2, a HETC-type E3 ligase, however, WLGhap.B exhibits stronger interaction with LARGE2, thus higher ubiquitination activity toward LARGE2 compared with WLGhap.A. Lysine1021 is crucial for the ubiquitination of LARGE2 by WLG. Loss-of-function of LARGE2 in wlg-1 phenocopies large2-c in grain and leaf width, suggesting that WLG acts upstream of LARGE2. These findings reveal the genetic and molecular mechanism by which the WLG-LARGE2 module mediates grain and leaf size in rice and suggest the potential of WLGhap.B in improving rice yield.
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Affiliation(s)
- Zhichuang Yue
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhipeng Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Yilong Yao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuanlin Liang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiaying Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Kaili Yin
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Ruiying Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Yibo Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Yidan Ouyang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Lizhong Xiong
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Honghong Hu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
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Zheng Y, Li M, Sun P, Gao G, Zhang Q, Li Y, Lou G, Wu B, He Y. QTL detection for grain shape and fine mapping of two novel locus qGL4 and qGL6 in rice. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2024; 44:62. [PMID: 39290202 PMCID: PMC11402885 DOI: 10.1007/s11032-024-01502-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Accepted: 09/05/2024] [Indexed: 09/19/2024]
Abstract
Rice grain size and grain weight, which have a great influence on rice quality and yield, are complex quantitative traits that are mediated by grain length (GL), grain width (GW), length-to-width ratio (LWR), and grain thickness (GT). In this study, the BC1F2 and BC1F2:3 populations derived from a cross between two indica rice varieties, Guangzhan 63-4S (GZ63-4S) and Dodda, were used to locate quantitative trait loci (QTL) related to grain size. A total of 30 QTL associated with GL, GW and LWR were detected, of which six QTL were scanned repeatedly in both populations. Two QTL, qGL4 and qGL6, were selected for genetic effect validation and were subsequently fine mapped to 2.359 kb and 176 kb, respectively. LOC_Os04g52240 (known as OsKS2/OsKSL2), which encoding an ent-beyerene synthase and as the only gene found in 2.359 kb interval, was proposed to be the candidate for qGL4. Moreover, the grains of qGL4 homozygous mutant plants generated by the CRISPR-Cas9 system became shorter and wider. In addition, the qGL4 allele from GZ63-4S contributes to the increase of yield per plant. Our study not only laid the foundation for further functional study of qGL4 and map-based cloning of qGL6, but also provided genetic resources for the development of high yield and good quality rice varieties. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-024-01502-8.
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Affiliation(s)
- Yuanyuan Zheng
- National Key Laboratory of Crop Genetic Improvementand, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 China
| | - Minqi Li
- National Key Laboratory of Crop Genetic Improvementand, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 China
| | - Ping Sun
- National Key Laboratory of Crop Genetic Improvementand, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 China
| | - Guanjun Gao
- National Key Laboratory of Crop Genetic Improvementand, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 China
| | - Qinglu Zhang
- National Key Laboratory of Crop Genetic Improvementand, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 China
| | - Yanhua Li
- National Key Laboratory of Crop Genetic Improvementand, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 China
| | - Guangming Lou
- National Key Laboratory of Crop Genetic Improvementand, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 China
| | - Bian Wu
- National Key Laboratory of Crop Genetic Improvementand, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 China
- Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs, Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, 430070 China
| | - Yuqing He
- National Key Laboratory of Crop Genetic Improvementand, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 China
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Li F, Wu L, Li X, Chai Y, Ruan N, Wang Y, Xu N, Yu Z, Wang X, Chen H, Lu J, Xu H, Xu Z, Chen W, Xu Q. Dissecting the molecular basis of the ultra-large grain formation in rice. THE NEW PHYTOLOGIST 2024; 243:2251-2264. [PMID: 39073105 DOI: 10.1111/nph.20001] [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: 06/15/2024] [Accepted: 07/05/2024] [Indexed: 07/30/2024]
Abstract
The shape of rice grains not only determines the thousand-grain weight but also correlates closely with the grain quality. Here we identified an ultra-large grain accession (ULG) with a thousand-grain weight exceeding 60 g. The integrated analysis of QTL, BSA, de novo genome assembled, transcription sequencing, and gene editing was conducted to dissect the molecular basis of the ULG formation. The ULG pyramided advantageous alleles from at least four known grain-shaping genes, OsLG3, OsMADS1, GS3, GL3.1, and one novel locus, qULG2-b, which encoded a leucine-rich repeat receptor-like kinase. The collective impacts of OsLG3, OsMADS1, GS3, and GL3.1 on grain size were confirmed in transgenic plants and near-isogenic lines. The transcriptome analysis identified 112 genes cooperatively regulated by these four genes that were prominently involved in photosynthesis and carbon metabolism. By leveraging the pleiotropy of these genes, we enhanced the grain yield, appearance, and stress tolerance of rice var. SN265. Beyond showcasing the pyramiding of multiple grain size regulation genes that can produce ULG, our study provides a theoretical framework and valuable genomic resources for improving rice variety by leveraging the pleiotropy of grain size regulated genes.
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Affiliation(s)
- Fengcheng Li
- Rice Research Institute of Shenyang Agricultural University, Shenyang, 110866, China
| | - Lian Wu
- Rice Research Institute of Shenyang Agricultural University, Shenyang, 110866, China
| | - Xiang Li
- Rice Research Institute of Shenyang Agricultural University, Shenyang, 110866, China
| | - Yanan Chai
- Rice Research Institute of Shenyang Agricultural University, Shenyang, 110866, China
| | - Nan Ruan
- Rice Research Institute of Shenyang Agricultural University, Shenyang, 110866, China
| | - Ye Wang
- Rice Research Institute of Shenyang Agricultural University, Shenyang, 110866, China
| | - Na Xu
- Rice Research Institute of Shenyang Agricultural University, Shenyang, 110866, China
| | - Zhiwen Yu
- Rice Research Institute of Shenyang Agricultural University, Shenyang, 110866, China
| | - Xiaoche Wang
- Rice Research Institute of Shenyang Agricultural University, Shenyang, 110866, China
| | - Hao Chen
- Rice Research Institute of Shenyang Agricultural University, Shenyang, 110866, China
| | - Jiahao Lu
- Rice Research Institute of Shenyang Agricultural University, Shenyang, 110866, China
| | - Hai Xu
- Rice Research Institute of Shenyang Agricultural University, Shenyang, 110866, China
| | - Zhengjin Xu
- Rice Research Institute of Shenyang Agricultural University, Shenyang, 110866, China
| | - Wenfu Chen
- Rice Research Institute of Shenyang Agricultural University, Shenyang, 110866, China
| | - Quan Xu
- Rice Research Institute of Shenyang Agricultural University, Shenyang, 110866, China
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Alam M, Lou G, Abbas W, Osti R, Ahmad A, Bista S, Ahiakpa JK, He Y. Improving Rice Grain Quality Through Ecotype Breeding for Enhancing Food and Nutritional Security in Asia-Pacific Region. RICE (NEW YORK, N.Y.) 2024; 17:47. [PMID: 39102064 DOI: 10.1186/s12284-024-00725-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 07/28/2024] [Indexed: 08/06/2024]
Abstract
Rice grain is widely consumed as a staple food, providing essential nutrition for households, particularly marginalized families. It plays a crucial role in ensuring food security, promoting human nutrition, supporting good health, and contributing to global food and nutritional security. Addressing the diverse quality demands of emerging diverse and climate-risked population dietary needs requires the development of a single variety of rice grain that can meet the various dietary and nutritional requirements. However, there is a lack of concrete definition for rice grain quality, making it challenging to cater to the different demands. The lack of sufficient genetic study and development in improving rice grain quality has resulted in widespread malnutrition, hidden hunger, and micronutrient deficiencies affecting a significant portion of the global population. Therefore, it is crucial to identify genetically evolved varieties with marked qualities that can help address these issues. Various factors account for the declining quality of rice grain and requires further study to improve their quality for healthier diets. We characterized rice grain quality using Lancastrians descriptor and a multitude of intrinsic and extrinsic quality traits. Next, we examined various components of rice grain quality favored in the Asia-Pacific region. This includes preferences by different communities, rice industry stakeholders, and value chain actors. We also explored the biological aspects of rice grain quality in the region, as well as specific genetic improvements that have been made in these traits. Additionally, we evaluated the factors that can influence rice grain quality and discussed the future directions for ensuring food and nutritional security and meeting consumer demands for grain quality. We explored the diverse consumer bases and their varied preferences in Asian-Pacific countries including India, China, Nepal, Bhutan, Vietnam, Sri Lanka, Pakistan, Thailand, Cambodia, Philippines, Bangladesh, Indonesia, Korea, Myanmar and Japan. The quality preferences encompassed a range of factors, including rice head recovery, grain shape, uniform size before cooking, gelatinization, chalkiness, texture, amylose content, aroma, red-coloration of grain, soft and shine when cooked, unbroken when cooked, gelatinization, less water required for cooking, gelatinization temperature (less cooking time), aged rice, firm and dry when cooked (gel consistency), extreme white, soft when chewed, easy-to-cook rice (parboiled rice), vitamins, and minerals. These preferences were evaluated across high, low, and medium categories. A comprehensive analysis is provided on the enhancement of grain quality traits, including brown rice recovery, recovery rate of milled rice, head rice recovery, as well as morphological traits such as grain length, grain width, grain length-width ratio, and grain chalkiness. We also explored the characteristics of amylose, gel consistency, gelatinization temperature, viscosity, as well as the nutritional qualities of rice grains such as starch, protein, lipids, vitamins, minerals, phytochemicals, and bio-fortification potential. The various factors that impact the quality of rice grains, including pre-harvest, post-harvest, and genotype considerations were explored. Additionally, we discussed the future direction and genetic strategies to effectively tackle these challenges. These qualitative characteristics represent the fundamental focus of regional and national breeding strategies employed by different countries to meet consumer preference. Given the significance of rice as a staple food in Asia-Pacific countries, it is primarily consumed domestically, with only a small portion being exported internationally. All the important attributes must be clearly defined within specific parameters. It is crucial for geneticists and breeders to develop a rice variety that can meet the diverse demands of consumers worldwide by incorporating multiple desirable traits. Thus, the goal of addressing global food and nutritional security, and human healthy can be achieved.
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Affiliation(s)
- Mufid Alam
- National Key Laboratory of Crop Genetic Improvement and National Center of Crop Molecular Breeding, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Guangming Lou
- National Key Laboratory of Crop Genetic Improvement and National Center of Crop Molecular Breeding, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Waseem Abbas
- National Key Laboratory of Crop Genetic Improvement and National Center of Crop Molecular Breeding, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Rajani Osti
- College of Humanities and Social Sciences, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Aqeel Ahmad
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Science and Natural Resource Research, Chinese Academy of Science (CAS), Beijing, China
| | - Sunita Bista
- Sichuan Agricultural University, Chengdu, Sichuan, China
| | - John K Ahiakpa
- National Key Laboratory of Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Yuqing He
- National Key Laboratory of Crop Genetic Improvement and National Center of Crop Molecular Breeding, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
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Long Y, Wang C, Liu C, Li H, Pu A, Dong Z, Wei X, Wan X. Molecular mechanisms controlling grain size and weight and their biotechnological breeding applications in maize and other cereal crops. J Adv Res 2024; 62:27-46. [PMID: 37739122 PMCID: PMC11331183 DOI: 10.1016/j.jare.2023.09.016] [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: 06/17/2023] [Revised: 09/03/2023] [Accepted: 09/18/2023] [Indexed: 09/24/2023] Open
Abstract
BACKGROUND Cereal crops are a primary energy source for humans. Grain size and weight affect both evolutionary fitness and grain yield of cereals. Although studies on gene mining and molecular mechanisms controlling grain size and weight are constantly emerging in cereal crops, only a few systematic reviews on the underlying molecular mechanisms and their breeding applications are available so far. AIM OF REVIEW This review provides a general state-of-the-art overview of molecular mechanisms and targeted strategies for improving grain size and weight of cereals as well as insights for future yield-improving biotechnology-assisted breeding. KEY SCIENTIFIC CONCEPTS OF REVIEW In this review, the evolution of research on grain size and weight over the last 20 years is traced based on a bibliometric analysis of 1158 publications and the main signaling pathways and transcriptional factors involved are summarized. In addition, the roles of post-transcriptional regulation and photosynthetic product accumulation affecting grain size and weight in maize and rice are outlined. State-of-the-art strategies for discovering novel genes related to grain size and weight in maize and other cereal crops as well as advanced breeding biotechnology strategies being used for improving yield including marker-assisted selection, genomic selection, transgenic breeding, and genome editing are also discussed.
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Affiliation(s)
- Yan Long
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100083, China; Industry Research Institute of Biotechnology Breeding, Yili Normal University, Yining 835000, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Cheng Wang
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100083, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Chang Liu
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100083, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Huangai Li
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100083, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Aqing Pu
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100083, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Zhenying Dong
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100083, China; Industry Research Institute of Biotechnology Breeding, Yili Normal University, Yining 835000, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Xun Wei
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100083, China; Industry Research Institute of Biotechnology Breeding, Yili Normal University, Yining 835000, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Xiangyuan Wan
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100083, China; Industry Research Institute of Biotechnology Breeding, Yili Normal University, Yining 835000, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China.
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Zhang X, Yang M, Liu Z, Yang F, Zhang L, Guo Y, Huo D. Genetic analysis of yield components in buckwheat using high-throughput sequencing analysis and wild resource populations. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:1313-1328. [PMID: 39184561 PMCID: PMC11341512 DOI: 10.1007/s12298-024-01491-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 06/06/2024] [Accepted: 07/15/2024] [Indexed: 08/27/2024]
Abstract
Fagopyrum tataricum, an important medicinal and edible crop, possesses significant agricultural and economic value. However, the development of buckwheat varieties and yields has been hindered by the delayed breeding progress despite the abundant material resources in China. Current research indicates that quantitative trait loci (QTLs) play a crucial role in controlling plant seed type and yield. To address these limitations, this study constructed recombinant inbred lines (RILs) utilizing both cultivated species and wild buckwheat as raw materials. In total, 84,521 Single Nucleotide Polymorphism (SNP) markers were identified through Genotyping-by-Sequencing (GBS) technology, and high-resolution and high-density SNP genetic maps were developed, which had significant value for QTL mapping, gene cloning and comparative mapping of buckwheat. In this study, we successfully identified 5 QTLs related to thousand grain weight (TGW), 9 for grain length (GL), and 1 for grain width (GW) by combining seed type and TGW data from 202 RIL populations in four different environments, within which one co-located QTL for TGW were discovered on the first chromosome. Transcriptome analysis during different grain development stages revealed 59 significant expression differences between the two materials, which can serve as candidate genes for further investigation into the regulation of grain weight and yield enhancement. The mapped major loci controlling TGW, GL and GW will be valuable for gene cloning and reveal the mechanism underlying grain development and marker-assisted selection in Tartary buckwheat.
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Affiliation(s)
- Xiao Zhang
- College of Biological Sciences and Technology, Taiyuan Normal University, Jinzhong, 030619 China
| | - Miao Yang
- College of Biological Sciences and Technology, Taiyuan Normal University, Jinzhong, 030619 China
| | - Zhang Liu
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Taiyuan, 030031 China
| | - Fan Yang
- College of Biological Sciences and Technology, Taiyuan Normal University, Jinzhong, 030619 China
| | - Lei Zhang
- College of Biological Sciences and Technology, Taiyuan Normal University, Jinzhong, 030619 China
| | - Yajing Guo
- College of Biological Sciences and Technology, Taiyuan Normal University, Jinzhong, 030619 China
| | - Dongao Huo
- College of Biological Sciences and Technology, Taiyuan Normal University, Jinzhong, 030619 China
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Chen G, Gao J, Wu S, Chang Y, Chen Z, Sun J, Zhang L, Wu J, Sun X, Quick WP, Cui X, Zhang Z, Lu T. The OsMOB1A-OsSTK38 kinase complex phosphorylates CYCLIN C, controlling grain size and weight in rice. THE PLANT CELL 2024; 36:2873-2892. [PMID: 38723594 PMCID: PMC11289633 DOI: 10.1093/plcell/koae146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 04/12/2024] [Indexed: 08/02/2024]
Abstract
Grain size and weight are crucial yield-related traits in rice (Oryza sativa). Although certain key genes associated with rice grain size and weight have been successfully cloned, the molecular mechanisms underlying grain size and weight regulation remain elusive. Here, we identified a molecular pathway regulating grain size and weight in rice involving the MPS ONE BINDER KINASE ACTIVATOR-LIKE 1A-SERINE/THREONINE-PROTEIN KINASE 38-CYCLIN C (OsMOB1A-OsSTK38-OsCycC) module. OsSTK38 is a nuclear Dbf2-related kinase that positively regulates grain size and weight by coordinating cell proliferation and expansion in the spikelet hull. OsMOB1A interacts with and enhances the autophosphorylation of OsSTK38. Specifically, the critical role of the OsSTK38 S322 site in its kinase activity is highlighted. Furthermore, OsCycC, a component of the Mediator complex, was identified as a substrate of OsSTK38, with enhancement by OsMOB1A. Notably, OsSTK38 phosphorylates the T33 site of OsCycC. The phosphorylation of OsCycC by OsSTK38 influenced its interaction with the transcription factor KNOTTED-LIKE HOMEOBOX OF ARABIDOPSIS THALIANA 7 (OsKNAT7). Genetic analysis confirmed that OsMOB1A, OsSTK38, and OsCycC function in a common pathway to regulate grain size and weight. Taken together, our findings revealed a connection between the Hippo signaling pathway and the cyclin-dependent kinase module in eukaryotes. Moreover, they provide insights into the molecular mechanisms linked to yield-related traits and propose innovative breeding strategies for high-yielding varieties.
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Affiliation(s)
- Guoxin Chen
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, P. R. China
| | - Jiabei Gao
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, P. R. China
| | - Suting Wu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, P. R. China
| | - Yuan Chang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, P. R. China
| | - Zhenhua Chen
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, P. R. China
| | - Jing Sun
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, P. R. China
| | - Liying Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, P. R. China
| | - Jinxia Wu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, P. R. China
| | - Xuehui Sun
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, P. R. China
| | - William Paul Quick
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, P. R. China
- School of Biosciences, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - Xuean Cui
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, P. R. China
| | - Zhiguo Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, P. R. China
| | - Tiegang Lu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, P. R. China
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48
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Liu F, Wodajo B, Zhao K, Tang S, Xie Q, Xie P. Unravelling sorghum functional genomics and molecular breeding: past achievements and future prospects. J Genet Genomics 2024:S1673-8527(24)00194-2. [PMID: 39053846 DOI: 10.1016/j.jgg.2024.07.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 07/15/2024] [Accepted: 07/16/2024] [Indexed: 07/27/2024]
Abstract
Sorghum, renowned for its substantial biomass production and remarkable tolerance to various stresses, possesses extensive gene resources and phenotypic variations. A comprehensive understanding of the genetic basis underlying complex agronomic traits is essential for unlocking the potential of sorghum in addressing food and feed security and utilizing marginal lands. In this context, we provide an overview of the major trends in genomic resource studies focusing on key agronomic traits over the past decade, accompanied by a summary of functional genomic platforms. We also delve into the molecular functions and regulatory networks of impactful genes for important agricultural traits. Lastly, we discuss and synthesize the current challenges and prospects for advancing molecular design breeding by gene-editing and polymerization of the excellent alleles, with the aim of accelerating the development of desired sorghum varieties.
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Affiliation(s)
- Fangyuan Liu
- School of Agriculture and Biotechnology, Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Baye Wodajo
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Natural and Computational Science, Woldia University, Woldia, Po.box-400, Ethiopia.
| | - Kangxu Zhao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Sanyuan Tang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Qi Xie
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Peng Xie
- School of Agriculture and Biotechnology, Sun Yat-sen University, Shenzhen, Guangdong 518107, China.
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49
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Wang X, Yan W, Real N, Jia Y, Fu Y, Zhang X, You H, Cai Y, Liu B. Metabolic, transcriptomic, and genetic analyses of candidate genes for seed size in watermelon. FRONTIERS IN PLANT SCIENCE 2024; 15:1394724. [PMID: 39081518 PMCID: PMC11286464 DOI: 10.3389/fpls.2024.1394724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Accepted: 06/25/2024] [Indexed: 08/02/2024]
Abstract
Seed size (SS) constitutes a pivotal trait in watermelon breeding. In this study, we present findings from an examination of two watermelon accessions, namely, BW85 and F211. Seeds from BW85 exhibited a significant enlargement compared to those of F211 at 13 days after pollination (DAP), with the maximal disparity in seed length and width manifesting at 17 DAP. A comprehensive study involving both metabolic and transcriptomic analyses indicated a significant enrichment of the ubiquinone and other terpenoid-quinone biosynthesis KEGG pathways. To detect the genetic region governing seed size, a BSA-seq analysis was conducted utilizing the F2 (BW85 × F211) population, which resulted in the identification of two adjacent QTLs, namely, SS6.1 and SS6.2, located on chromosomes 6. SS6.1 spanned from Chr06:4847169 to Chr06:5163486, encompassing 33 genes, while SS6.2 ranged from Chr06:5379337 to Chr06:5419136, which included only one gene. Among these genes, 11 exhibited a significant differential expression between BW85 and F211 according to transcriptomic analysis. Notably, three genes (Cla97C06G113960, Cla97C06G114180, and Cla97C06G114000) presented a differential expression at both 13 and 17 DAP. Through annotation, Cla97C06G113960 was identified as a ubiquitin-conjugating enzyme E2, playing a role in the ubiquitin pathway that mediates seed size control. Taken together, our results provide a novel candidate gene influencing the seed size in watermelon, shedding light on the mechanism underlying seed development.
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Affiliation(s)
- Xiqing Wang
- Horticultural Branch of Heilongjiang Academy of Agricultural Sciences, Harbin, China
- Center for Research in Vegetable Engineering Technology of Heilongjiang, Harbin, China
| | - Wen Yan
- Horticultural Branch of Heilongjiang Academy of Agricultural Sciences, Harbin, China
- Center for Research in Vegetable Engineering Technology of Heilongjiang, Harbin, China
| | - Núria Real
- Plant Pathology, IRTA Cabrils, Cabrils, Spain
| | - Yunhe Jia
- Horticultural Branch of Heilongjiang Academy of Agricultural Sciences, Harbin, China
- Center for Research in Vegetable Engineering Technology of Heilongjiang, Harbin, China
| | - Yongkai Fu
- Horticultural Branch of Heilongjiang Academy of Agricultural Sciences, Harbin, China
- Center for Research in Vegetable Engineering Technology of Heilongjiang, Harbin, China
| | - Xuejun Zhang
- Hainan Sanya Crops Breeding Trial Center of Xinjiang Academy Agricultural Sciences, Sanya, China
| | - Haibo You
- Horticultural Branch of Heilongjiang Academy of Agricultural Sciences, Harbin, China
- Center for Research in Vegetable Engineering Technology of Heilongjiang, Harbin, China
| | - Yi Cai
- Horticultural Branch of Heilongjiang Academy of Agricultural Sciences, Harbin, China
- Center for Research in Vegetable Engineering Technology of Heilongjiang, Harbin, China
| | - Bin Liu
- Hami-Melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi, China
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50
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Lyu J, Wang D, Sun N, Yang F, Li X, Mu J, Zhou R, Zheng G, Yang X, Zhang C, Han C, Xia G, Li G, Fan M, Xiao J, Bai M. The TaSnRK1-TabHLH489 module integrates brassinosteroid and sugar signalling to regulate the grain length in bread wheat. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1989-2006. [PMID: 38412139 PMCID: PMC11182588 DOI: 10.1111/pbi.14319] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 02/06/2024] [Accepted: 02/15/2024] [Indexed: 02/29/2024]
Abstract
Regulation of grain size is a crucial strategy for improving the crop yield and is also a fundamental aspect of developmental biology. However, the underlying molecular mechanisms governing grain development in wheat remain largely unknown. In this study, we identified a wheat atypical basic helix-loop-helix (bHLH) transcription factor, TabHLH489, which is tightly associated with grain length through genome-wide association study and map-based cloning. Knockout of TabHLH489 and its homologous genes resulted in increased grain length and weight, whereas the overexpression led to decreased grain length and weight. TaSnRK1α1, the α-catalytic subunit of plant energy sensor SnRK1, interacted with and phosphorylated TabHLH489 to induce its degradation, thereby promoting wheat grain development. Sugar treatment induced TaSnRK1α1 protein accumulation while reducing TabHLH489 protein levels. Moreover, brassinosteroid (BR) promotes grain development by decreasing TabHLH489 expression through the transcription factor BRASSINAZOLE RESISTANT1 (BZR1). Importantly, natural variations in the promoter region of TabHLH489 affect the TaBZR1 binding ability, thereby influencing TabHLH489 expression. Taken together, our findings reveal that the TaSnRK1α1-TabHLH489 regulatory module integrates BR and sugar signalling to regulate grain length, presenting potential targets for enhancing grain size in wheat.
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Affiliation(s)
- Jinyang Lyu
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life SciencesShandong UniversityQingdaoChina
| | - Dongzhi Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Na Sun
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life SciencesShandong UniversityQingdaoChina
| | - Fan Yang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life SciencesShandong UniversityQingdaoChina
| | - Xuepeng Li
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life SciencesShandong UniversityQingdaoChina
| | - Junyi Mu
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life SciencesShandong UniversityQingdaoChina
| | - Runxiang Zhou
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life SciencesShandong UniversityQingdaoChina
| | - Guolan Zheng
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life SciencesShandong UniversityQingdaoChina
| | - Xin Yang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life SciencesShandong UniversityQingdaoChina
| | - Chenxuan Zhang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life SciencesShandong UniversityQingdaoChina
| | - Chao Han
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life SciencesShandong UniversityQingdaoChina
| | - Guang‐Min Xia
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life SciencesShandong UniversityQingdaoChina
| | - Genying Li
- Crop Research InstituteShandong Academy of Agricultural SciencesJinanChina
| | - Min Fan
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life SciencesShandong UniversityQingdaoChina
| | - Jun Xiao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
- Centre of Excellence for Plant and Microbial Science (CEPAMS)JIC‐CASBeijingChina
| | - Ming‐Yi Bai
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life SciencesShandong UniversityQingdaoChina
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