1
|
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: 0] [Impact Index Per Article: 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.
Collapse
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
| |
Collapse
|
2
|
Jian C, Pan Y, Liu S, Guo M, Huang Y, Cao L, Zhang W, Yan L, Zhang X, Hou J, Hao C, Li T. The TaGW2-TaSPL14 module regulates the trade-off between tiller number and grain weight in wheat. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024. [PMID: 38924348 DOI: 10.1111/jipb.13723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 05/09/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024]
Abstract
IDEAL PLANT ARCHITECTURE1 (IPA1) is a pivotal gene controlling plant architecture and grain yield. However, little is known about the effects of Triticum aestivum SQUAMOSA PROMOTER-BINDING-LIKE 14 (TaSPL14), an IPA1 ortholog in wheat, on balancing yield traits and its regulatory mechanism in wheat (T. aestivum L.). Here, we determined that the T. aestivum GRAIN WIDTH2 (TaGW2)-TaSPL14 module influences the balance between tiller number and grain weight in wheat. Overexpression of TaSPL14 resulted in a reduced tiller number and increased grain weight, whereas its knockout had the opposite effect, indicating that TaSPL14 negatively regulates tillering while positively regulating grain weight. We further identified TaGW2 as a novel interacting protein of TaSPL14 and confirmed its ability to mediate the ubiquitination and degradation of TaSPL14. Based on our genetic evidence, TaGW2 acts as a positive regulator of tiller number, in addition to its known role as a negative regulator of grain weight, which is opposite to TaSPL14. Moreover, combinations of TaSPL14-7A and TaGW2-6A haplotypes exhibit significantly additive effects on tiller number and grain weight in wheat breeding. Our findings provide insight into how the TaGW2-TaSPL14 module regulates the trade-off between tiller number and grain weight and its potential application in improving wheat yield.
Collapse
Affiliation(s)
- Chao Jian
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciencesy, Beijing, 100081, China
| | - Yuxue Pan
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciencesy, Beijing, 100081, China
| | - Shujuan Liu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciencesy, Beijing, 100081, China
| | - Mengjiao Guo
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciencesy, Beijing, 100081, China
| | - Yilin Huang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciencesy, Beijing, 100081, China
| | - Lina Cao
- Crop Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China
| | - Weijun Zhang
- Crop Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China
| | - Liuling Yan
- Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, 74078, Oklahoma, USA
| | - Xueyong Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciencesy, Beijing, 100081, China
| | - Jian Hou
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciencesy, Beijing, 100081, China
| | - Chenyang Hao
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciencesy, Beijing, 100081, China
| | - Tian Li
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciencesy, Beijing, 100081, China
| |
Collapse
|
3
|
Cui Z, Wang X, Dai Y, Li Y, Ban Y, Tian W, Zhang X, Feng X, Zhang X, Jia L, He G, Sang X. Transcription factor OsNF-YC1 regulates grain size by coordinating the transcriptional activation of OsMADS1 in Oryza sativa L. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 38887937 DOI: 10.1111/tpj.16868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 04/23/2024] [Accepted: 05/23/2024] [Indexed: 06/20/2024]
Abstract
Grain weight, grain number per panicle, and the number of panicles are the three factors that determine rice (Oryza sativa L.) yield. Of these, grain weight, which not only directly determines rice yield but also influences appearance and quality, is often considered the most important for rice production. Here, we describe OsNF-YC1, a member of the NF-Y transcription factor family that regulates rice grain size. OsNF-YC1 knockout plants (osnf-yc1), obtained using CRISPR-Cas9 technology, showed reduced grain weight due to reduced width and thickness, with no change in grain length, leading to a slenderer grain shape. Downregulation of OsNF-YC1 using RNA interference resulted in similar grain phenotypes as osnf-yc1. OsNF-YC1 affects grain formation by regulating both cell proliferation and cell expansion. OsNF-YC1 localizes in both the nucleus and cytoplasm, has transcriptional activation activity at both the N-terminus and C-terminus, and is highly expressed in young panicles. OsNF-YC1 interacts with OsMADS1 both in vivo and in vitro. Further analysis showed that the histone-like structural CBFD-NFYB-HMF domain of OsNF-YC1 conserved in the OsNF-YC transcription factor family can directly interact with the MADS-box domain of OsMADS1 to enhance its transcriptional activation activity. This interaction positively regulates the expression of OsMADS55, the direct downstream target of OsMADS1. Therefore, this paper reveals a potential grain size regulation pathway controlled by an OsNF-YC1-OsMADS1-OsMADS55 module in rice.
Collapse
Affiliation(s)
- Zhibo Cui
- Chongqing Key Laboratory of Crop Molecular Improvement, Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Xiaowen Wang
- Chongqing Key Laboratory of Crop Molecular Improvement, Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Yongdong Dai
- Chongqing Key Laboratory of Crop Molecular Improvement, Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Yangyang Li
- Chongqing Key Laboratory of Crop Molecular Improvement, Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Yijie Ban
- Chongqing Key Laboratory of Crop Molecular Improvement, Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Weijiang Tian
- Chongqing Key Laboratory of Crop Molecular Improvement, Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Xiaobo Zhang
- Chongqing Key Laboratory of Crop Molecular Improvement, Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Xinyu Feng
- Chongqing Key Laboratory of Crop Molecular Improvement, Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Xuefei Zhang
- Chongqing Key Laboratory of Crop Molecular Improvement, Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Luqi Jia
- Chongqing Key Laboratory of Crop Molecular Improvement, Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Guanghua He
- Chongqing Key Laboratory of Crop Molecular Improvement, Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Xianchun Sang
- Chongqing Key Laboratory of Crop Molecular Improvement, Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, 400715, China
| |
Collapse
|
4
|
Wei M, Yan Q, Huang D, Ma Z, Chen S, Yin X, Liu C, Qin Y, Zhou X, Wu Z, Lu Y, Yan L, Qin G, Zhang Y. Integration of molecular breeding and multi-resistance screening for developing a promising restorer line Guihui5501 with heavy grain, good grain quality, and endurance to biotic and abiotic stresses. FRONTIERS IN PLANT SCIENCE 2024; 15:1390603. [PMID: 38911983 PMCID: PMC11190317 DOI: 10.3389/fpls.2024.1390603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 05/20/2024] [Indexed: 06/25/2024]
Abstract
Rice, a critical staple on a global scale, faces escalating challenges in yield preservation due to the rising prevalence of abiotic and biotic stressors, exacerbated by frequent climatic fluctuations in recent years. Moreover, the scorching climate prevalent in the rice-growing regions of South China poses obstacles to the cultivation of good-quality, heavy-grain varieties. Addressing this dilemma requires the development of resilient varieties capable of withstanding multiple stress factors. To achieve this objective, our study employed the broad-spectrum blast-resistant line Digu, the brown planthopper (BPH)-resistant line ASD7, and the heavy-grain backbone restorer lines Fuhui838 (FH838) and Shuhui527 (SH527) as parental materials for hybridization and multiple crossings. The incorporation of molecular markers facilitated the rapid pyramiding of six target genes (Pi5, Pita, Pid2, Pid3, Bph2, and Wxb ). Through a comprehensive evaluation encompassing blast resistance, BPH resistance, cold tolerance, grain appearance, and quality, alongside agronomic trait selection, a promising restorer line, Guihui5501 (GH5501), was successfully developed. It demonstrated broad-spectrum resistance to blast, exhibiting a resistance frequency of 77.33% against 75 artificially inoculated isolates, moderate resistance to BPH (3.78 grade), strong cold tolerance during the seedling stage (1.80 grade), and characteristics of heavy grains (1,000-grain weight reaching 35.64 g) with good grain quality. The primary rice quality parameters for GH5501, with the exception of alkali spreading value, either met or exceeded the second-grade national standard for premium edible rice varieties, signifying a significant advancement in the production of good-quality heavy-grain varieties in the southern rice-growing regions. Utilizing GH5501, a hybrid combination named Nayou5501, characterized by high yield, good quality, and resistance to multiple stresses, was bred and received approval as a rice variety in Guangxi in 2021. Furthermore, genomic analysis with gene chips revealed that GH5501 possessed an additional 20 exceptional alleles, such as NRT1.1B for efficient nitrogen utilization, SKC1 for salt tolerance, and STV11 for resistance to rice stripe virus. Consequently, the restorer line GH5501 could serve as a valuable resource for the subsequent breeding of high-yielding, good-quality, and stress-tolerant hybrid rice varieties.
Collapse
Affiliation(s)
- Minyi Wei
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding/State Key Laboratory for Conservation and Utillzation of Subtropical Agro-bioresources, Nanning, China
| | - Qun Yan
- Plant Protection Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Dahui Huang
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding/State Key Laboratory for Conservation and Utillzation of Subtropical Agro-bioresources, Nanning, China
| | - Zengfeng Ma
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding/State Key Laboratory for Conservation and Utillzation of Subtropical Agro-bioresources, Nanning, China
| | - Shen Chen
- Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou, China
| | | | - Chi Liu
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding/State Key Laboratory for Conservation and Utillzation of Subtropical Agro-bioresources, Nanning, China
| | - Yuanyuan Qin
- Agricultural Science and Technology Information Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Xiaolong Zhou
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding/State Key Laboratory for Conservation and Utillzation of Subtropical Agro-bioresources, Nanning, China
| | - Zishuai Wu
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding/State Key Laboratory for Conservation and Utillzation of Subtropical Agro-bioresources, Nanning, China
| | - Yingping Lu
- Liuzhou Branch, Guangxi Academy of Agricultural Sciences, Liuzhou Research Center of Agricultural Sciences, Liuzhou, China
| | - Liuhui Yan
- Liuzhou Branch, Guangxi Academy of Agricultural Sciences, Liuzhou Research Center of Agricultural Sciences, Liuzhou, China
| | - Gang Qin
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding/State Key Laboratory for Conservation and Utillzation of Subtropical Agro-bioresources, Nanning, China
| | - Yuexiong Zhang
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding/State Key Laboratory for Conservation and Utillzation of Subtropical Agro-bioresources, Nanning, China
| |
Collapse
|
5
|
Wang H, Wang X, Li Y, Cui Y, Yan X, Gao J, Ouyang J, Li S. Pleiotropic Effects of miR5504 Underlying Plant Height, Grain Yield and Quality in Rice. PLANT & CELL PHYSIOLOGY 2024; 65:781-789. [PMID: 38447119 DOI: 10.1093/pcp/pcae015] [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: 08/14/2023] [Accepted: 02/13/2024] [Indexed: 03/08/2024]
Abstract
MicroRNAs (miRNAs) are known to play critical roles in regulating rice agronomic traits through mRNA cleavage or translational repression. Our previous study indicated that miR5504 regulates plant height by affecting cell proliferation and expansion. Here, the two independent homozygous mir5504 mutants (CR1 and CR2) and overexpression lines (OE1 and OE2) were further used to investigate the functions of miR5504. The panicle length, 1000-grain weight and grain yield per plant of miR5504-OE lines were identical to those of Nipponbare (NIP), but the 1000-grain weight of mir5504 mutants was reduced by about 10% and 9%, respectively. Meanwhile, the grain width and thickness of mir5504 mutants decreased significantly by approximately 10% and 11%, respectively. Moreover, the cytological results revealed a significant decrease in cell number along grain width direction and cell width in spikelet in mir5504, compared with those in NIP. In addition, several major storage substances of the rice seeds were measured. Compared to NIP, the amylose content of the mir5504 seeds was noticeably decreased, leading to an increase of nearly 10 mm in gel consistency (GC) in mir5504 lines. Further investigation confirmed that LOC_Os08g16914 was the genuine target of miR5504: LOC_Os08g16914 over-expression plants phenocopied the mir5504 mutants. This study provides insights into the role of miR5504 in rice seed development.
Collapse
Affiliation(s)
- Huihui Wang
- Key Laboratory of Molecular Biology and Genetic Engineering of Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang 330031, China
| | - Xin Wang
- Key Laboratory of Molecular Biology and Genetic Engineering of Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang 330031, China
| | - Yangyang Li
- Key Laboratory of Molecular Biology and Genetic Engineering of Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang 330031, China
| | - Ying Cui
- Key Laboratory of Molecular Biology and Genetic Engineering of Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang 330031, China
| | - Xin Yan
- Key Laboratory of Molecular Biology and Genetic Engineering of Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang 330031, China
| | - Jiadong Gao
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Guangzhou 510640, China
- Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510555, China
| | - Jiexiu Ouyang
- Key Laboratory of Molecular Biology and Genetic Engineering of Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang 330031, China
| | - Shaobo Li
- Key Laboratory of Molecular Biology and Genetic Engineering of Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang 330031, China
| |
Collapse
|
6
|
Bai C, Wang GJ, Feng XH, Gao Q, Wang WQ, Xu R, Guo SJ, Shen SY, Ma M, Lin WH, Liu CM, Li Y, Song XJ. OsMAPK6 phosphorylation and CLG1 ubiquitylation of GW6a non-additively enhance rice grain size through stabilization of the substrate. Nat Commun 2024; 15:4300. [PMID: 38773134 PMCID: PMC11109111 DOI: 10.1038/s41467-024-48786-0] [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: 10/18/2023] [Accepted: 05/10/2024] [Indexed: 05/23/2024] Open
Abstract
The chromatin modifier GRAIN WEIGHT 6a (GW6a) enhances rice grain size and yield. However, little is known about its gene network determining grain size. Here, we report that MITOGEN-ACTIVED PROTEIN KINASE 6 (OsMAPK6) and E3 ligase CHANG LI GENG 1 (CLG1) interact with and target GW6a for phosphorylation and ubiquitylation, respectively. Unexpectedly, however, in vitro and in vivo assays reveal that both of the two post-translational modifications stabilize GW6a. Furthermore, we uncover two major GW6a phosphorylation sites (serine142 and threonine186) targeted by OsMAPK6 serving an important role in modulating grain size. In addition, our genetic and molecular results suggest that the OsMAPK6-GW6a and CLG1-GW6a axes are crucial and operate in a non-additive manner to control grain size. Overall, our findings identify a previously unknown mechanism by which phosphorylation and ubiquitylation non-additively stabilize GW6a to enhance grain size, and reveal correlations and interactions of these posttranslational modifications during rice grain development.
Collapse
Affiliation(s)
- Chen Bai
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Gao-Jie Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiao-Hui Feng
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qiong Gao
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
| | - Wei-Qing Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
| | - Ran Xu
- Sanya Nanfan Research, Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China
- College of Tropical Crops Hainan University, Hainan University, Haikou, 570288, China
| | - Su-Jie Guo
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shao-Yan Shen
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ming Ma
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wen-Hui Lin
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chun-Ming Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yunhai Li
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xian-Jun Song
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- China National Botanical Garden, Beijing, 100093, China.
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
| |
Collapse
|
7
|
Hu C, Li X, Zhang M, Jing C, Hai M, Shen J, Xu Q, Dang X, Shi Y, Liu E, Jiang J. Identifying the Quantitative Trait Locus and Candidate Genes of Traits Related to Milling Quality in Rice via a Genome-Wide Association Study. PLANTS (BASEL, SWITZERLAND) 2024; 13:1324. [PMID: 38794395 PMCID: PMC11124788 DOI: 10.3390/plants13101324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 05/08/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024]
Abstract
Milling quality directly affects production efficiency in rice, which is closely related to the brown rice recovery (BRR), the milled rice recovery (MRR) and the head milled rice recovery (HMRR). The present study investigated these three traits in 173 germplasms in two environments, finding abundant phenotypic variation. Three QTLs for BRR, two for MRR, and three for HMRR were identified in a genome-wide association study, five of these were identified in previously reported QTLs and three were newly identified. By combining the linkage disequilibrium (LD) analyses, the candidate gene LOC_Os05g08350 was identified. It had two haplotypes with significant differences and Hap 2 increased the BRR by 4.40%. The results of the qRT-PCR showed that the expression of LOC_Os05g08350 in small-BRR accessions was significantly higher than that in large-BRR accessions at Stages 4-5 of young panicle development, reaching the maximum value at Stage 5. The increase in thickness of the spikelet hulls of the accession carrying LOC_Os05g08350TT occurred due to an increase in the cell width and the cell numbers in cross-sections of spikelet hulls. These results help to further clarify the molecular genetic mechanism of milling-quality-related traits and provide genetic germplasm materials for high-quality breeding in rice.
Collapse
Affiliation(s)
- Changmin Hu
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
- Institute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Xinru Li
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
- Institute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Mengyuan Zhang
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
- Institute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Chunyu Jing
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
- Institute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Mei Hai
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
- Institute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Jiaming Shen
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
- Institute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Qing Xu
- Institute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Xiaojing Dang
- Institute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Yingyao Shi
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Erbao Liu
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Jianhua Jiang
- Institute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| |
Collapse
|
8
|
Hu Z, Huang X, Xia H, Zhang Z, Lu H, Wang X, Sun Y, Cui M, Yang S, Kant S, Xu G, Sun S. Transcription factor OsSHR2 regulates rice architecture and yield per plant in response to nitrogen. PLANTA 2024; 259:148. [PMID: 38717679 DOI: 10.1007/s00425-024-04400-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 03/28/2024] [Indexed: 05/23/2024]
Abstract
MAIN CONCLUSION Mutation of OsSHR2 adversely impacted root and shoot growth and impaired plant response to N conditions, further reducing the yield per plant. Nitrogen (N) is a crucial factor that regulates the plant architecture. There is still a lack of research on it. In our study, it was observed that the knockout of the SHORTROOT 2 (OsSHR2) which was induced by N deficiency, can significantly affect the regulation of plant architecture response to N in rice. Under N deficiency, the mutation of OsSHR2 significantly reduced root growth, and impaired the sensitivity of the root meristem length to N deficiency. The mutants were found to have approximately a 15% reduction in plant height compared to wild type. But mutants showed a significant increase in tillering at post-heading stage, approximately 26% more than the wild type, particularly in high N conditions. In addition, due to reduced seed setting rate and 1000-grain weight, mutant yield was significantly decreased by approximately 33% under low N fertilizer supply. The mutation also changed the distribution of N between the vegetative and reproductive organs. Our findings suggest that the transcription factor OsSHR2 plays a regulatory role in the response of plant architecture and yield per plant to N in rice.
Collapse
Affiliation(s)
- Zhi Hu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xu Huang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Huihuang Xia
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhantian Zhang
- Yantai Academy of Agricultural Sciences, Yantai, 265500, China
| | - Huixin Lu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaowen Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yafei Sun
- Institute of Eco-Environment and Plant Protection, Shanghai Academy of Agriculture Science, Shanghai, 201403, China
| | - Mengyuan Cui
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shanshan Yang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Surya Kant
- Agriculture Victoria, Grains Innovation Park, Horsham, VIC, 3400, Australia
| | - Guohua Xu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shubin Sun
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
| |
Collapse
|
9
|
Zhou Y, Yang H, Liu E, Liu R, Alam M, Gao H, Gao G, Zhang Q, Li Y, Xiong L, He Y. Fine Mapping of Five Grain Size QTLs Which Affect Grain Yield and Quality in Rice. Int J Mol Sci 2024; 25:4149. [PMID: 38673733 PMCID: PMC11050437 DOI: 10.3390/ijms25084149] [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: 02/23/2024] [Revised: 04/02/2024] [Accepted: 04/03/2024] [Indexed: 04/28/2024] Open
Abstract
Grain size is a quantitative trait with a complex genetic mechanism, characterized by the combination of grain length (GL), grain width (GW), length to width ration (LWR), and grain thickness (GT). In this study, we conducted quantitative trait loci (QTL) analysis to investigate the genetic basis of grain size using BC1F2 and BC1F2:3 populations derived from two indica lines, Guangzhan 63-4S (GZ63-4S) and TGMS29 (core germplasm number W240). A total of twenty-four QTLs for grain size were identified, among which, three QTLs (qGW1, qGW7, and qGW12) controlling GL and two QTLs (qGW5 and qGL9) controlling GW were validated and subsequently fine mapped to regions ranging from 128 kb to 624 kb. Scanning electron microscopic (SEM) analysis and expression analysis revealed that qGW7 influences cell expansion, while qGL9 affects cell division. Conversely, qGW1, qGW5, and qGW12 promoted both cell division and expansion. Furthermore, negative correlations were observed between grain yield and quality for both qGW7 and qGW12. Nevertheless, qGW5 exhibited the potential to enhance quality without compromising yield. Importantly, we identified two promising QTLs, qGW1 and qGL9, which simultaneously improved both grain yield and quality. In summary, our results laid the foundation for cloning these five QTLs and provided valuable resources for breeding rice varieties with high yield and superior quality.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Yuqing He
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (H.Y.); (E.L.); (R.L.); (M.A.); (H.G.); (G.G.); (Q.Z.); (Y.L.); (L.X.)
| |
Collapse
|
10
|
Xu F, Dong H, Guo W, Le L, Jing Y, Fletcher JC, Sun J, Pu L. The trxG protein ULT1 regulates Arabidopsis organ size by interacting with TCP14/15 to antagonize the LIM peptidase DA1 for H3K4me3 on target genes. PLANT COMMUNICATIONS 2024; 5:100819. [PMID: 38217289 PMCID: PMC11009162 DOI: 10.1016/j.xplc.2024.100819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 08/18/2023] [Accepted: 01/09/2024] [Indexed: 01/15/2024]
Abstract
Plant organ size is an important agronomic trait that makes a significant contribution to plant yield. Despite its central importance, the genetic and molecular mechanisms underlying organ size control remain to be fully clarified. Here, we report that the trithorax group protein ULTRAPETALA1 (ULT1) interacts with the TEOSINTE BRANCHED1/CYCLOIDEA/PCF14/15 (TCP14/15) transcription factors by antagonizing the LIN-11, ISL-1, and MEC-3 (LIM) peptidase DA1, thereby regulating organ size in Arabidopsis. Loss of ULT1 function significantly increases rosette leaf, petal, silique, and seed size, whereas overexpression of ULT1 results in reduced organ size. ULT1 associates with TCP14 and TCP15 to co-regulate cell size by affecting cellular endoreduplication. Transcriptome analysis revealed that ULT1 and TCP14/15 regulate common target genes involved in endoreduplication and leaf development. ULT1 can be recruited by TCP14/15 to promote lysine 4 of histone H3 trimethylation at target genes, activating their expression to determine final cell size. Furthermore, we found that ULT1 influences the interaction of DA1 and TCP14/15 and antagonizes the effect of DA1 on TCP14/15 degradation. Collectively, our findings reveal a novel epigenetic mechanism underlying the regulation of organ size in Arabidopsis.
Collapse
Affiliation(s)
- Fan Xu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Huixue Dong
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Weijun Guo
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Liang Le
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yexing Jing
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jennifer C Fletcher
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Plant Gene Expression Center, United States Department of Agriculture - Agricultural Research Service, Albany, CA 94710, USA
| | - Jiaqiang Sun
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Li Pu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| |
Collapse
|
11
|
Wen Y, Hu P, Fang Y, Tan Y, Wang Y, Wu H, Wang J, Wu K, Chai B, Zhu L, Zhang G, Gao Z, Ren D, Zeng D, Shen L, Dong G, Zhang Q, Li Q, Xiong G, Xue D, Qian Q, Hu J. GW9 determines grain size and floral organ identity in rice. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:915-928. [PMID: 37983630 PMCID: PMC10955487 DOI: 10.1111/pbi.14234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 09/22/2023] [Accepted: 11/04/2023] [Indexed: 11/22/2023]
Abstract
Grain weight is an important determinant of grain yield. However, the underlying regulatory mechanisms for grain size remain to be fully elucidated. Here, we identify a rice mutant grain weight 9 (gw9), which exhibits larger and heavier grains due to excessive cell proliferation and expansion in spikelet hull. GW9 encodes a nucleus-localized protein containing both C2H2 zinc finger (C2H2-ZnF) and VRN2-EMF2-FIS2-SUZ12 (VEFS) domains, serving as a negative regulator of grain size and weight. Interestingly, the non-frameshift mutations in C2H2-ZnF domain result in increased plant height and larger grain size, whereas frameshift mutations in both C2H2-ZnF and VEFS domains lead to dwarf and malformed spikelet. These observations indicated the dual functions of GW9 in regulating grain size and floral organ identity through the C2H2-ZnF and VEFS domains, respectively. Further investigation revealed the interaction between GW9 and the E3 ubiquitin ligase protein GW2, with GW9 being the target of ubiquitination by GW2. Genetic analyses suggest that GW9 and GW2 function in a coordinated pathway controlling grain size and weight. Our findings provide a novel insight into the functional role of GW9 in the regulation of grain size and weight, offering potential molecular strategies for improving rice yield.
Collapse
Affiliation(s)
- Yi Wen
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Peng Hu
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Yunxia Fang
- College of Life and Environmental SciencesHangzhou Normal UniversityHangzhouChina
| | - Yiqing Tan
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
- Plant Phenomics Research CenterNanjing Agricultural UniversityNanjingChina
| | - Yueying Wang
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Hao Wu
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Junge Wang
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Kaixiong Wu
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Bingze Chai
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Li Zhu
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Guangheng Zhang
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Zhenyu Gao
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Deyong Ren
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Dali Zeng
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Lan Shen
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Guojun Dong
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Qiang Zhang
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Qing Li
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Guosheng Xiong
- Plant Phenomics Research CenterNanjing Agricultural UniversityNanjingChina
| | - Dawei Xue
- College of Life and Environmental SciencesHangzhou Normal UniversityHangzhouChina
| | - Qian Qian
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Jiang Hu
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| |
Collapse
|
12
|
Shim KC, Luong NH, Tai TH, Lee GR, Ahn SN, Park I. T-DNA insertion mutants of Arabidopsis DA1 orthologous genes displayed altered plant height and yield-related traits in rice (O. Sativa L.). Genes Genomics 2024; 46:451-459. [PMID: 38436907 DOI: 10.1007/s13258-024-01501-1] [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: 10/07/2023] [Accepted: 02/01/2024] [Indexed: 03/05/2024]
Abstract
BACKGROUND The Arabidopsis DA1 gene is a key player in the regulation of organ and seed development. To extend our understanding of its functional counterparts in rice, this study investigates the roles of orthologous genes, namely DA1, HDR3, HDR3.1, and the DA2 ortholog GW2, through the analysis of T-DNA insertion mutants. OBJECTIVE The aim of this research is to elucidate the impact of T-DNA insertions in DA1, HDR3, HDR3.1, and GW2 on agronomic traits in rice. By evaluating homozygous plants, we specifically focus on key parameters such as plant height, tiller number, days to heading, and grain size. METHODS T-DNA insertion locations were validated using PCR, and subsequent analyses were conducted on homozygous plants. Agronomic traits, including plant height, tiller number, days to heading, and grain size, were assessed. Additionally, leaf senescence assays were performed under dark incubation conditions to gauge the impact of T-DNA insertions on this physiological aspect. RESULTS The study revealed distinctive phenotypic outcomes associated with T-DNA insertions in HDR3, HDR3.1, GW2, and DA1. Specifically, HDR3 and HDR3.1 mutants exhibited significantly reduced plant height and smaller grain size, while GW2 and DA1 mutants displayed a notable increase in both plant height and grain size compared to the wild type variety Dongjin. Leaf senescence assays further indicated delayed leaf senescence in hdr3.1 mutants, contrasting with slightly earlier leaf senescence observed in hdr3 mutants under dark incubation. CONCLUSIONS The findings underscore the pivotal roles of DA1 orthologous genes in rice, shedding light on their significance in regulating plant growth and development. The observed phenotypic variations highlight the potential of these genes as targets for crop improvement strategies, offering insights that could contribute to the enhancement of agronomic traits in rice and potentially other crops.
Collapse
Affiliation(s)
- Kyu-Chan Shim
- Department of Agronomy, College of Agriculture and Life Science, Chungnam National University, Daejeon, 34134, Republic of Korea.
- USDA-ARS Crops Pathology and Genetics Research Unit, Davis, CA, 95616, USA.
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
| | - Ngoc Ha Luong
- Department of Agronomy, College of Agriculture and Life Science, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Thomas H Tai
- USDA-ARS Crops Pathology and Genetics Research Unit, Davis, CA, 95616, USA
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Gyu-Ri Lee
- Department of Agronomy, College of Agriculture and Life Science, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Sang-Nag Ahn
- Department of Agronomy, College of Agriculture and Life Science, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Inkyu Park
- Department of Biology and Chemistry, Changwon National University, Changwon, 51140, Republic of Korea.
| |
Collapse
|
13
|
Chen Y, Vermeersch M, Van Leene J, De Jaeger G, Li Y, Vanhaeren H. A dynamic ubiquitination balance of cell proliferation and endoreduplication regulators determines plant organ size. SCIENCE ADVANCES 2024; 10:eadj2570. [PMID: 38478622 PMCID: PMC10936951 DOI: 10.1126/sciadv.adj2570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 02/08/2024] [Indexed: 03/17/2024]
Abstract
Ubiquitination plays a crucial role throughout plant growth and development. The E3 ligase DA2 has been reported to activate the peptidase DA1 by ubiquitination, hereby limiting cell proliferation. However, the molecular mechanisms that regulate DA2 remain elusive. Here, we demonstrate that DA2 has a very high turnover and auto-ubiquitinates with K48-linkage polyubiquitin chains, which is counteracted by two deubiquitinating enzymes, UBIQUITIN-SPECIFIC PROTEASE 12 (UBP12) and UBP13. Unexpectedly, we found that auto-ubiquitination of DA2 does not influence its stability but determines its E3 ligase activity. We also demonstrate that impairing the protease activity of DA1 abolishes the growth-reducing effect of DA2. Last, we show that synthetic, constitutively activated DA1-ubiquitin fusion proteins overrule this complex balance of ubiquitination and deubiquitination and strongly restrict growth and promote endoreduplication. Our findings highlight a nonproteolytic function of K48-linked polyubiquitination and reveal a mechanism by which DA2 auto-ubiquitination levels, in concert with UBP12 and UBP13, precisely monitor the activity of DA1 and fine-tune plant organ size.
Collapse
Affiliation(s)
- Ying Chen
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, B-9052 Ghent, Belgium
| | - Mattias Vermeersch
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, B-9052 Ghent, Belgium
| | - Jelle Van Leene
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, B-9052 Ghent, Belgium
| | - Geert De Jaeger
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, B-9052 Ghent, Belgium
| | - Yunhai Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant, Institute of Genetics and Development Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hannes Vanhaeren
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, B-9052 Ghent, Belgium
- Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Proeftuinstraat 86, 9000 Ghent, Belgium
| |
Collapse
|
14
|
Kis A, Polgári D, Dalmadi Á, Ahmad I, Rakszegi M, Sági L, Csorba T, Havelda Z. Targeted mutations in the GW2.1 gene modulate grain traits and induce yield loss in barley. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 340:111968. [PMID: 38157889 DOI: 10.1016/j.plantsci.2023.111968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/14/2023] [Accepted: 12/26/2023] [Indexed: 01/03/2024]
Abstract
Grain Width and Weight 2 (GW2) is an E3-ubiquitin ligase-encoding gene that negatively regulates the size and weight of the grain in cereal species. Therefore, disabling GW2 gene activity was suggested for enhancing crop productivity. We show here that CRISPR/Cas-mediated mutagenesis of the barley GW2.1 homologue results in the development of elongated grains and increased protein content. At the same time, GW2.1 loss of function induces a significant grain yield deficit caused by reduced spike numbers and low grain setting. We also show that the converse effect caused by GW2.1 absence on crop yield and protein content is largely independent of cultivation conditions. These findings indicate that the barley GW2.1 gene is necessary for the optimization between yield and grain traits. Altogether, our data show that the loss of GW2.1 gene activity in barley is associated with pleiotropic effects negatively affecting the development of generative organs and consequently the grain production. Our findings contribute to the better understanding of grain development and the utilisation of GW2.1 control in quantitative and qualitative genetic improvement of barley.
Collapse
Affiliation(s)
- András Kis
- Hungarian University of Agriculture and Life Sciences (MATE), Institute of Genetics and Biotechnology, Gödöllő, Hungary
| | - Dávid Polgári
- Hungarian University of Agriculture and Life Sciences (MATE), Institute of Genetics and Biotechnology, Gödöllő, Hungary; Agricultural Institute, Centre for Agricultural Research, Martonvásár, Hungary; Agribiotechnology and Precision Breeding for Food Security National Laboratory, Plant Biotechnology Section, Hungary
| | - Ágnes Dalmadi
- Hungarian University of Agriculture and Life Sciences (MATE), Institute of Genetics and Biotechnology, Gödöllő, Hungary; Agribiotechnology and Precision Breeding for Food Security National Laboratory, Plant Biotechnology Section, Hungary
| | - Imtiaz Ahmad
- Hungarian University of Agriculture and Life Sciences (MATE), Institute of Genetics and Biotechnology, Gödöllő, Hungary
| | - Marianna Rakszegi
- Agricultural Institute, Centre for Agricultural Research, Martonvásár, Hungary
| | - László Sági
- Agricultural Institute, Centre for Agricultural Research, Martonvásár, Hungary; Agribiotechnology and Precision Breeding for Food Security National Laboratory, Plant Biotechnology Section, Hungary
| | - Tibor Csorba
- Hungarian University of Agriculture and Life Sciences (MATE), Institute of Genetics and Biotechnology, Gödöllő, Hungary
| | - Zoltán Havelda
- Hungarian University of Agriculture and Life Sciences (MATE), Institute of Genetics and Biotechnology, Gödöllő, Hungary; Agribiotechnology and Precision Breeding for Food Security National Laboratory, Plant Biotechnology Section, Hungary.
| |
Collapse
|
15
|
Herrera-Ubaldo H. Less water, more seeds? The E3 ligase TaGW2 regulates drought resistance in wheat. THE PLANT CELL 2024; 36:495-496. [PMID: 38109462 PMCID: PMC10896284 DOI: 10.1093/plcell/koad311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 12/11/2023] [Accepted: 12/11/2023] [Indexed: 12/20/2023]
Affiliation(s)
- Humberto Herrera-Ubaldo
- Assistant Features Editor, The Plant Cell, American Society of Plant Biologists
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| |
Collapse
|
16
|
Li S, Zhang Y, Liu Y, Zhang P, Wang X, Chen B, Ding L, Nie Y, Li F, Ma Z, Kang Z, Mao H. The E3 ligase TaGW2 mediates transcription factor TaARR12 degradation to promote drought resistance in wheat. THE PLANT CELL 2024; 36:605-625. [PMID: 38079275 PMCID: PMC10896296 DOI: 10.1093/plcell/koad307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 11/07/2023] [Indexed: 02/27/2024]
Abstract
Drought stress limits crop yield, but the molecular modulators and their mechanisms underlying the trade-off between drought resistance and crop growth and development remain elusive. Here, a grain width and weight2 (GW2)-like really interesting new gene finger E3 ligase, TaGW2, was identified as a pivotal regulator of both kernel development and drought responses in wheat (Triticum aestivum). TaGW2 overexpression enhances drought resistance but leads to yield drag under full irrigation conditions. In contrast, TaGW2 knockdown or knockout attenuates drought resistance but remarkably increases kernel size and weight. Furthermore, TaGW2 directly interacts with and ubiquitinates the type-B Arabidopsis response regulator TaARR12, promoting its degradation via the 26S proteasome. Analysis of TaARR12 overexpression and knockdown lines indicated that TaARR12 represses the drought response but does not influence grain yield in wheat. Further DNA affinity purification sequencing combined with transcriptome analysis revealed that TaARR12 downregulates stress-responsive genes, especially group-A basic leucine zipper (bZIP) genes, resulting in impaired drought resistance. Notably, TaARR12 knockdown in the clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated nuclease 9 (Cas9)-mediated tagw2 knockout mutant leads to significantly higher drought resistance and grain yield compared to wild-type plants. Collectively, these findings show that the TaGW2-TaARR12 regulatory module is essential for drought responses, providing a strategy for improving stress resistance in high-yield wheat varieties.
Collapse
Affiliation(s)
- Shumin Li
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yifang Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yuling Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Peiyin Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xuemin Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Bin Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Li Ding
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yingxiong Nie
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Fangfang Li
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhenbing Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
- Yangling Seed Industry Innovation Center, Yangling, Shaanxi 712100, China
| | - Hude Mao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| |
Collapse
|
17
|
Bi C, Wei C, Li J, Wen S, Zhao H, Yu J, Shi X, Zhang Y, Liu Q, Zhang Y, Li B, You M. A novel variation of TaGW2-6B increases grain weight without penalty in grain protein content in wheat ( Triticum aestivum L.). MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2024; 44:15. [PMID: 38362529 PMCID: PMC10864231 DOI: 10.1007/s11032-024-01455-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 01/23/2024] [Indexed: 02/17/2024]
Abstract
Yield and quality are two crucial breeding objects of wheat therein grain weight and grain protein content (GPC) are two key relevant factors correspondingly. Investigations of their genetic mechanisms represent special significance for breeding. In this study, 199 F2 plants and corresponding F2:3 families derived from Nongda3753 (ND3753) and its EMS-generated mutant 564 (M564) were used to investigate the genetic basis of larger grain and higher GPC of M564. QTL analysis identified a total of 33 environmentally stable QTLs related to thousand grain weight (TGW), grain area (GA), grain circle (GC), grain length (GL), grain width (GW), and GPC on chromosomes 1B, 2A, 2B, 4D, 6B, and 7D, respectively, among which QGw.cau-6B.1, QTgw.cau-6B.1, QGa.cau-6B.1, and QGc.cau-6B.1 shared overlap confidence interval on chromosome 6B. This interval contained the TaGW2 gene playing the same role as the QTLs, so TaGW2-6B was cloned and sequenced. Sequence alignment revealed two G/A SNPs between two parents, among which the SNP in the seventh exon led to a premature termination in M564. A KASP marker was developed based on the SNP, and single-marker analysis on biparental populations showed that the mutant allele could significantly increase GW and TGW, but had no effect on GPC. Distribution detection of the mutant allele through KASP marker genotyping and sequence alignment against databases ascertained that no materials harbored this allele within natural populations. This allele was subsequently introduced into three different varieties through molecular marker-assisted backcrossing, and it was revealed that the allele had a significant effect on simultaneously increasing GW, TGW, and even GPC in all of three backgrounds. Summing up the above, it could be concluded that a novel elite allele of TaGW2-6B was artificially created and might play an important role in wheat breeding for high yield and quality. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-024-01455-y.
Collapse
Affiliation(s)
- Chan Bi
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Chaoxiong Wei
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Jinghui Li
- Wheat Center, Henan Institute of Science and Technology, Henan Provincial Key Laboratory of Hybrid Wheat, Xinxiang, 453003 China
| | - Shaozhe Wen
- Department of Landscape and Garden, Yangzhou Polytechnic College, Yangzhou, 225009 China
| | - Huanhuan Zhao
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Jiazheng Yu
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Xintian Shi
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Yuan Zhang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Qiaofeng Liu
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Yufeng Zhang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Baoyun Li
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Mingshan You
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| |
Collapse
|
18
|
Li L, Li J, Liu K, Jiang C, Jin W, Ye J, Qin T, Luo B, Chen Z, Li J, Lv F, Li X, Wang H, Jin J, Deng Q, Wang S, Zhu J, Zou T, Liu H, Li S, Li P, Liang Y. DGW1, encoding an hnRNP-like RNA binding protein, positively regulates grain size and weight by interacting with GW6 mRNA. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:512-526. [PMID: 37862261 PMCID: PMC10826988 DOI: 10.1111/pbi.14202] [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: 06/05/2023] [Revised: 09/13/2023] [Accepted: 10/03/2023] [Indexed: 10/22/2023]
Abstract
Grain size and weight determine rice yield. Although numerous genes and pathways involved in regulating grain size have been identified, our knowledge of post-transcriptional control of grain size remains elusive. In this study, we characterize a rice mutant, decreased grain width and weight 1 (dgw1), which produces small grains. We show that DGW1 encodes a member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family protein and preferentially expresses in developing panicles, positively regulating grain size by promoting cell expansion in spikelet hulls. Overexpression of DGW1 increases grain weight and grain numbers, leading to a significant rise in rice grain yield. We further demonstrate that DGW1 functions in grain size regulation by directly binding to the mRNA of Grain Width 6 (GW6), a critical grain size regulator in rice. Overexpression of GW6 restored the grain size phenotype of DGW1-knockout plants. DGW1 interacts with two oligouridylate binding proteins (OsUBP1a and OsUBP1b), which also bind the GW6 mRNA. In addition, the second RRM domain of DGW1 is indispensable for its mediated protein-RNA and protein-protein interactions. In summary, our findings identify a new regulatory module of DGW1-GW6 that regulates rice grain size and weight, providing important insights into the function of hnRNP-like proteins in the regulation of grain size.
Collapse
Affiliation(s)
- Lingfeng Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduChina
- Rice Research Institute, Sichuan Agricultural UniversityChengduChina
| | - Jijin Li
- Rice Research Institute, Sichuan Agricultural UniversityChengduChina
| | - Keke Liu
- Rice Research Institute, Sichuan Agricultural UniversityChengduChina
| | - Chenglong Jiang
- Rice Research Institute, Sichuan Agricultural UniversityChengduChina
| | - Wenhu Jin
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduChina
| | - Jiangkun Ye
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduChina
| | - Tierui Qin
- Rice Research Institute, Sichuan Agricultural UniversityChengduChina
| | - Binjiu Luo
- Rice Research Institute, Sichuan Agricultural UniversityChengduChina
| | - Zeyu Chen
- Rice Research Institute, Sichuan Agricultural UniversityChengduChina
| | - Jinzhao Li
- Rice Research Institute, Sichuan Agricultural UniversityChengduChina
| | - Fuxiang Lv
- Rice Research Institute, Sichuan Agricultural UniversityChengduChina
| | - Xiaojun Li
- Rice Research Institute, Sichuan Agricultural UniversityChengduChina
| | - Haipeng Wang
- Neijiang Academy of Agricultural Science in Sichuan ProvinceNeijiangChina
| | - Jinghua Jin
- Rice Research Institute, Sichuan Agricultural UniversityChengduChina
| | - Qiming Deng
- Rice Research Institute, Sichuan Agricultural UniversityChengduChina
| | - Shiquan Wang
- Rice Research Institute, Sichuan Agricultural UniversityChengduChina
| | - Jun Zhu
- Rice Research Institute, Sichuan Agricultural UniversityChengduChina
| | - Ting Zou
- Rice Research Institute, Sichuan Agricultural UniversityChengduChina
| | - Huainian Liu
- Rice Research Institute, Sichuan Agricultural UniversityChengduChina
| | - Shuangcheng Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduChina
| | - Ping Li
- Rice Research Institute, Sichuan Agricultural UniversityChengduChina
| | - Yueyang Liang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduChina
| |
Collapse
|
19
|
Li H, Peng L, Yin F, Fang J, Cai L, Zhang C, Xiang Z, Zhao Y, Zhang S, Sheng H, Wang D, Zhang X, Liang Z. Research on Coix seed as a food and medicinal resource, it's chemical components and their pharmacological activities: A review. JOURNAL OF ETHNOPHARMACOLOGY 2024; 319:117309. [PMID: 37858750 DOI: 10.1016/j.jep.2023.117309] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 10/21/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Coix lacryma-jobi var. ma-yuen (Romanet du Caillaud) Stapf is a plant of the genus Coix in the Gramineae family. Coix seed is cultivated in various regions throughout China. In recent years, with the research on the medicinal value of Coix seed, it has received more and more widespread attention from people. Numerous pharmacological effects of Coix seed have been demonstrated through modern pharmacological studies, such as hypoglycemia, improving liver function, anti-tumor, regulating intestinal microbiota, improving spleen function, and anti-inflammatory effects. AIMS OF THE STUDY This article is a literature review. In recent years, despite the extensive research on Coix seed, there has yet to be a comprehensive review of its traditional usage, medicinal resources, chemical components, and pharmacological effects is still lacking. To fill this gap, the paper provides an overview of the latest research progress on Coix seed, aiming to offer guidance and references for its further development and comprehensive utilization. MATERIAL AND METHODS To gather information on the traditional usage, phytochemical ingredients, and pharmacological properties of Coix seed, we conducted a literature search using both Chinese and English languages in five databases: PubMed, Web of Science, China National Knowledge Infrastructure (CNKI), and Springer. RESULTS This article is a literature review. The chemical constituents of Coix seed include various fatty acids, esters, polysaccharides, sterols, alkaloids, triterpenes, tocopherols, lactams, lignans, phenols, flavonoids and other constituents. Modern pharmacological research has indeed shown that Coix seed has many pharmacological effects and is a natural anti-tumor drug. In addition to its anti-tumor effect, it also has pharmacological effects such as hypoglycemia, improving liver function, regulating intestinal microbiota, improving spleen function, and anti-inflammatory effects. CONCLUSIONS This article provides a brief overview of the traditional uses, biotechnological applications, chemical components, and pharmacological effects of Coix seed. It highlights the importance of establishing quality standards, discovering new active ingredients, and exploring pharmacological mechanisms in Coix seed research. The article also emphasizes the significance of clinical trials, toxicology studies, pharmacokinetics data, and multidisciplinary collaboration for further advancements in this field. Overall, it aims to enhance understanding of Coix seed and its potential in pharmaceutical development and wellness products.
Collapse
Affiliation(s)
- Hongju Li
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Lingxia Peng
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Feng Yin
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Jiahao Fang
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Lietao Cai
- R&D Center of Kanglaite, Hangzhou, 310018, China
| | | | - Zheng Xiang
- Medical School, Hangzhou City University, Hangzhou, 310015, China
| | - Yuyang Zhao
- State Key Lab Breeding Base Dao-Di Herbs, National Resource Center Chinese Materia Medica, Beijing, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Shuifeng Zhang
- Food Safety Key Laboratory of Zhejiang Province, Zhejiang Fangyuan Test Group Co., LTD, Hanghzou, 310018, China
| | - Huadong Sheng
- Food Safety Key Laboratory of Zhejiang Province, Zhejiang Fangyuan Test Group Co., LTD, Hanghzou, 310018, China
| | - Dekai Wang
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Xiaodan Zhang
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
| | - Zongsuo Liang
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
| |
Collapse
|
20
|
Wang Y, Lv Y, Yu H, Hu P, Wen Y, Wang J, Tan Y, Wu H, Zhu L, Wu K, Chai B, Liu J, Zeng D, Zhang G, Zhu L, Gao Z, Dong G, Ren D, Shen L, Zhang Q, Li Q, Guo L, Xiong G, Qian Q, Hu J. GR5 acts in the G protein pathway to regulate grain size in rice. PLANT COMMUNICATIONS 2024; 5:100673. [PMID: 37596786 PMCID: PMC10811372 DOI: 10.1016/j.xplc.2023.100673] [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: 02/24/2023] [Revised: 08/09/2023] [Accepted: 08/14/2023] [Indexed: 08/20/2023]
Abstract
Grain size is an important determinant of grain yield in rice. Although dozens of grain size genes have been reported, the molecular mechanisms that control grain size remain to be fully clarified. Here, we report the cloning and characterization of GR5 (GRAIN ROUND 5), which is allelic to SMOS1/SHB/RLA1/NGR5 and encodes an AP2 transcription factor. GR5 acts as a transcriptional activator and determines grain size by influencing cell proliferation and expansion. We demonstrated that GR5 physically interacts with five Gγ subunit proteins (RGG1, RGG2, DEP1, GS3, and GGC2) and acts downstream of the G protein complex. Four downstream target genes of GR5 in grain development (DEP2, DEP3, DRW1, and CyCD5;2) were revealed and their core T/CGCAC motif identified by yeast one-hybrid, EMSA, and ChIP-PCR experiments. Our results revealed that GR5 interacts with Gγ subunits and cooperatively determines grain size by regulating the expression of downstream target genes. These findings provide new insight into the genetic regulatory network of the G protein signaling pathway in the control of grain size and provide a potential target for high-yield rice breeding.
Collapse
Affiliation(s)
- Yueying Wang
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Yang Lv
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Haiping Yu
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Peng Hu
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Yi Wen
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Junge Wang
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Yiqing Tan
- Nanjing Agricultural University, Nan Jing 210000, Jiangsu, China
| | - Hao Wu
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Lixin Zhu
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Kaixiong Wu
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Bingze Chai
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Jialong Liu
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Dali Zeng
- 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
| | - Zhenyu Gao
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Guojun Dong
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Deyong Ren
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Lan Shen
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Qiang Zhang
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Qing Li
- 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
| | - Guosheng Xiong
- Nanjing Agricultural University, Nan Jing 210000, Jiangsu, China.
| | - Qian Qian
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China; Hainan Yazhou Bay Seed Laboratory, Sanya 572024, Hainan, China; National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China.
| | - Jiang Hu
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China; Hainan Yazhou Bay Seed Laboratory, Sanya 572024, Hainan, China; National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China.
| |
Collapse
|
21
|
Zhang Y, Shen C, Li G, Shi J, Yuan Y, Ye L, Song Q, Shi J, Zhang D. MADS1-regulated lemma and awn development benefits barley yield. Nat Commun 2024; 15:301. [PMID: 38182608 PMCID: PMC10770128 DOI: 10.1038/s41467-023-44457-8] [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: 04/19/2023] [Accepted: 12/14/2023] [Indexed: 01/07/2024] Open
Abstract
Floral organ shape and size in cereal crops can affect grain size and yield, so genes that regulate their development are promising breeding targets. The lemma, which protects inner floral organs, can physically constrain grain growth; while the awn, a needle-like extension of the lemma, creates photosynthate to developing grain. Although several genes and modules controlling grain size and awn/lemma growth in rice have been characterized, these processes, and the relationships between them, are not well understood for barley and wheat. Here, we demonstrate that the barley E-class gene HvMADS1 positively regulates awn length and lemma width, affecting grain size and weight. Cytological data indicates that HvMADS1 promotes awn and lemma growth by promoting cell proliferation, while multi-omics data reveals that HvMADS1 target genes are associated with cell cycle, phytohormone signaling, and developmental processes. We define two potential targets of HvMADS1 regulation, HvSHI and HvDL, whose knockout mutants mimic awn and/or lemma phenotypes of mads1 mutants. Additionally, we demonstrate that HvMADS1 interacts with APETALA2 (A-class) to synergistically activate downstream genes in awn/lemma development in barley. Notably, we find that MADS1 function remains conserved in wheat, promoting cell proliferation to increase awn length. These findings extend our understanding of MADS1 function in floral organ development and provide insights for Triticeae crop improvement strategies.
Collapse
Affiliation(s)
- Yueya Zhang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Chaoqun Shen
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- School of Agriculture, Food and Wine, The University of Adelaide, Waite Campus, Adelaide, SA, 5064, Australia
| | - Gang Li
- School of Agriculture, Food and Wine, The University of Adelaide, Waite Campus, Adelaide, SA, 5064, Australia.
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Jin Shi
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yajing Yuan
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Lingzhen Ye
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Qingfeng Song
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Jianxin Shi
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, 572025, China.
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- School of Agriculture, Food and Wine, The University of Adelaide, Waite Campus, Adelaide, SA, 5064, Australia
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, 572025, China
| |
Collapse
|
22
|
He L, Chen T, Liang W, Zhao C, Zhao L, Yao S, Zhou L, Zhu Z, Zhao Q, Lu K, Wang C, Zhu L, Zhang Y. The RING-Type Domain-Containing Protein GNL44 Is Essential for Grain Size and Quality in Rice ( Oryza sativa L.). Int J Mol Sci 2024; 25:589. [PMID: 38203760 PMCID: PMC10779214 DOI: 10.3390/ijms25010589] [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: 11/22/2023] [Revised: 12/15/2023] [Accepted: 12/23/2023] [Indexed: 01/12/2024] Open
Abstract
Grain size in rice (Oryza sativa L.) shapes yield and quality, but the underlying molecular mechanism is not fully understood. We functionally characterized GRAIN NUMBER AND LARGE GRAIN SIZE 44 (GNL44), encoding a RING-type protein that localizes to the cytoplasm. The gnl44 mutant has fewer but enlarged grains compared to the wild type. GNL44 is mainly expressed in panicles and developing grains. Grain chalkiness was higher in the gnl44 mutant than in the wild type, short-chain amylopectin content was lower, middle-chain amylopectin content was higher, and appearance quality was worse. The amylose content and gel consistency of gnl44 were lower, and protein content was higher compared to the wild type. Rapid Visco Analyzer results showed that the texture of cooked gnl44 rice changed, and that the taste value of gnl44 was lower, making the eating and cooking quality of gnl44 worse than that of the wild type. We used gnl44, qgl3, and gs3 monogenic and two-gene near-isogenic lines to study the effects of different combinations of genes affecting grain size on rice quality-related traits. Our results revealed additive effects for these three genes on grain quality. These findings enrich the genetic resources available for rice breeders.
Collapse
Affiliation(s)
- Lei He
- Institute of Food Crops, Key Laboratory of Jiangsu Province for Agrobiology, East China Branch of National Center of Technology Innovation for Saline-Alkali Tolerant Rice, Jiangsu Academy of Agricultural Science, Nanjing 210014, China (C.W.)
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
| | - Tao Chen
- Institute of Food Crops, Key Laboratory of Jiangsu Province for Agrobiology, East China Branch of National Center of Technology Innovation for Saline-Alkali Tolerant Rice, Jiangsu Academy of Agricultural Science, Nanjing 210014, China (C.W.)
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
| | - Wenhua Liang
- Institute of Food Crops, Key Laboratory of Jiangsu Province for Agrobiology, East China Branch of National Center of Technology Innovation for Saline-Alkali Tolerant Rice, Jiangsu Academy of Agricultural Science, Nanjing 210014, China (C.W.)
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
| | - Chunfang Zhao
- Institute of Food Crops, Key Laboratory of Jiangsu Province for Agrobiology, East China Branch of National Center of Technology Innovation for Saline-Alkali Tolerant Rice, Jiangsu Academy of Agricultural Science, Nanjing 210014, China (C.W.)
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
| | - Ling Zhao
- Institute of Food Crops, Key Laboratory of Jiangsu Province for Agrobiology, East China Branch of National Center of Technology Innovation for Saline-Alkali Tolerant Rice, Jiangsu Academy of Agricultural Science, Nanjing 210014, China (C.W.)
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
| | - Shu Yao
- Institute of Food Crops, Key Laboratory of Jiangsu Province for Agrobiology, East China Branch of National Center of Technology Innovation for Saline-Alkali Tolerant Rice, Jiangsu Academy of Agricultural Science, Nanjing 210014, China (C.W.)
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
| | - Lihui Zhou
- Institute of Food Crops, Key Laboratory of Jiangsu Province for Agrobiology, East China Branch of National Center of Technology Innovation for Saline-Alkali Tolerant Rice, Jiangsu Academy of Agricultural Science, Nanjing 210014, China (C.W.)
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
| | - Zhen Zhu
- Institute of Food Crops, Key Laboratory of Jiangsu Province for Agrobiology, East China Branch of National Center of Technology Innovation for Saline-Alkali Tolerant Rice, Jiangsu Academy of Agricultural Science, Nanjing 210014, China (C.W.)
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
| | - Qingyong Zhao
- Institute of Food Crops, Key Laboratory of Jiangsu Province for Agrobiology, East China Branch of National Center of Technology Innovation for Saline-Alkali Tolerant Rice, Jiangsu Academy of Agricultural Science, Nanjing 210014, China (C.W.)
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
| | - Kai Lu
- Institute of Food Crops, Key Laboratory of Jiangsu Province for Agrobiology, East China Branch of National Center of Technology Innovation for Saline-Alkali Tolerant Rice, Jiangsu Academy of Agricultural Science, Nanjing 210014, China (C.W.)
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
| | - Cailin Wang
- Institute of Food Crops, Key Laboratory of Jiangsu Province for Agrobiology, East China Branch of National Center of Technology Innovation for Saline-Alkali Tolerant Rice, Jiangsu Academy of Agricultural Science, Nanjing 210014, China (C.W.)
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
| | - Li Zhu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China
| | - Yadong Zhang
- Institute of Food Crops, Key Laboratory of Jiangsu Province for Agrobiology, East China Branch of National Center of Technology Innovation for Saline-Alkali Tolerant Rice, Jiangsu Academy of Agricultural Science, Nanjing 210014, China (C.W.)
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
| |
Collapse
|
23
|
Deng K, Zhang H, Wu J, Zhao Z, Wang D, Xu G, Yu J, Ling Y, Zhao F. Development of Single-Segment Substitution Lines and Fine-Mapping of qSPP4 for Spikelets Per Panicle and qGW9 for Grain Width Based on Rice Dual-Segment Substitution Line Z783. Int J Mol Sci 2023; 24:17305. [PMID: 38139135 PMCID: PMC10744095 DOI: 10.3390/ijms242417305] [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: 11/03/2023] [Revised: 12/05/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023] Open
Abstract
Single segment substitution line (SSSL) libraries are an ideal platform for breeding by design. To develop SSSLs-Xihui18 covering the whole genome, a novel rice chromosome segment substitution line (CSSL), Z783, carrying two substitution segments (average length of 6.55 Mb) on Chr.4 and Chr.9 was identified, which was a gap in the library previously. Z783 was developed from the progeny of recipient "Xihui18" (an indica restorer line) and donor "Huhan3" (a japonica cultivar) by advanced backcross combined molecular marker-assisted selection (MAS). It displayed multiple panicles and less spikelets and wide grains. Then, a F2 population derived from Xihui18/Z783 was used to map quantitative trait loci (QTLs) for yield-related traits by the mixed linear model method. Nine QTLs were detected (p < 0.05). Furthermore, three SSSLs were constructed by MAS, and all 9 QTLs could be validated, and 15 novel QTLs could be detected by these SSSLs by a one-way ANOVA analysis. The genetic analysis showed that qSSP4 for less spikelets and qGW9 for wide grain all displayed dominant gene action in their SSSLs. Finally, qSSP4 and qGW9 were fine-mapped to intervals of 2.75 Mb and 1.84 Mb, on Chromosomes 4 and 9, respectively. The results lay a solid foundation for their map cloning and molecular breeding by design.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Fangming Zhao
- Rice Research Institute, Academy of Agricultural Science, Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing 400715, China; (K.D.); (H.Z.); (J.W.); (Z.Z.); (D.W.); (G.X.); (J.Y.); (Y.L.)
| |
Collapse
|
24
|
Zhai R, Ye S, Ye J, Wu M, Zhu G, Yu F, Wang X, Feng Y, Zhang X. Glutaredoxin in Rice Growth, Development, and Stress Resistance: Mechanisms and Research Advances. Int J Mol Sci 2023; 24:16968. [PMID: 38069292 PMCID: PMC10707574 DOI: 10.3390/ijms242316968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 11/26/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
Rice (Oryza sativa L.) is a staple food for more than half of the global population. Various abiotic and biotic stresses lead to accumulation of reactive oxygen species in rice, which damage macromolecules and signaling pathways. Rice has evolved a variety of antioxidant systems, including glutaredoxin (GRX), that protect against various stressors. A total of 48 GRX gene loci have been identified on 11 of the 12 chromosomes of the rice genome; none were found on chromosome 9. GRX proteins were classified into four categories according to their active sites: CPYC, CGFS, CC, and GRL. In this paper, we summarized the recent research advances regarding the roles of GRX in rice development regulation and response to stresses, and discussed future research perspectives related to rice production. This review could provide information for rice researchers on the current status of the GRX and serve as guidance for breeding superior varieties.
Collapse
Affiliation(s)
- Rongrong Zhai
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Shenghai Ye
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Jing Ye
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Mingming Wu
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Guofu Zhu
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Faming Yu
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Xingyu Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Yue Feng
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Xiaoming Zhang
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| |
Collapse
|
25
|
Gasparis S, Miłoszewski MM. Genetic Basis of Grain Size and Weight in Rice, Wheat, and Barley. Int J Mol Sci 2023; 24:16921. [PMID: 38069243 PMCID: PMC10706642 DOI: 10.3390/ijms242316921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/27/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
Grain size is a key component of grain yield in cereals. It is a complex quantitative trait controlled by multiple genes. Grain size is determined via several factors in different plant development stages, beginning with early tillering, spikelet formation, and assimilates accumulation during the pre-anthesis phase, up to grain filling and maturation. Understanding the genetic and molecular mechanisms that control grain size is a prerequisite for improving grain yield potential. The last decade has brought significant progress in genomic studies of grain size control. Several genes underlying grain size and weight were identified and characterized in rice, which is a model plant for cereal crops. A molecular function analysis revealed most genes are involved in different cell signaling pathways, including phytohormone signaling, transcriptional regulation, ubiquitin-proteasome pathway, and other physiological processes. Compared to rice, the genetic background of grain size in other important cereal crops, such as wheat and barley, remains largely unexplored. However, the high level of conservation of genomic structure and sequences between closely related cereal crops should facilitate the identification of functional orthologs in other species. This review provides a comprehensive overview of the genetic and molecular bases of grain size and weight in wheat, barley, and rice, focusing on the latest discoveries in the field. We also present possibly the most updated list of experimentally validated genes that have a strong effect on grain size and discuss their molecular function.
Collapse
Affiliation(s)
- Sebastian Gasparis
- Plant Breeding and Acclimatization Institute—National Research Institute in Radzików, 05-870 Błonie, Poland;
| | | |
Collapse
|
26
|
Lin Z, Chen L, Tang S, Zhao M, Li T, You J, You C, Li B, Zhao Q, Zhang D, Wang J, Shen Z, Song X, Zhang S, Cao X. Efficient CRISPR/Cas9-mediated genome editing in sheepgrass (Leymus chinensis). JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:2416-2420. [PMID: 37698072 DOI: 10.1111/jipb.13567] [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: 04/26/2023] [Accepted: 09/11/2023] [Indexed: 09/13/2023]
Abstract
The lack of genome editing platforms has hampered efforts to study and improve forage crops that can be grown on lands not suited to other crops. Here, we established efficient Agrobacterium-mediated clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated nuclease 9 (Cas9) genome editing in a perennial, stress-tolerant forage grass, sheepgrass (Leymus chinensis). By screening for active single-guide RNAs (sgRNAs), accessions that regenerate well, suitable Agrobacterium strains, and optimal culture media, and co-expressing the morphogenic factor TaWOX5, we achieved 11% transformation and 5.83% editing efficiency in sheepgrass. Knocking out Teosinte Branched1 (TB1) significantly increased tiller number and biomass. This study opens avenues for studying gene function and breeding in sheepgrass.
Collapse
Affiliation(s)
- Zhelong Lin
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, The Chinese Academy of Sciences, Beijing, 100101, China
| | - Lei Chen
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, The Chinese Academy of Sciences, Beijing, 100101, China
| | - Shanjie Tang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, The Chinese Academy of Sciences, Beijing, 100101, China
| | - Mengjie Zhao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, The Chinese Academy of Sciences, Beijing, 100101, China
| | - Tong Li
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, The Chinese Academy of Sciences, Beijing, 100101, China
| | - Jia You
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Changqing You
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, The Chinese Academy of Sciences, Beijing, 100101, China
| | - Boshu Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, The Chinese Academy of Sciences, Beijing, 100101, China
| | - Qinghua Zhao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, The Chinese Academy of Sciences, Beijing, 100101, China
| | - Dongmei Zhang
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Jianli Wang
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Zhongbao Shen
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Xianwei Song
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, The Chinese Academy of Sciences, Beijing, 100101, China
| | - Shuaibin Zhang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, The Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, The Chinese Academy of Sciences, Beijing, 100101, China
| |
Collapse
|
27
|
Wang Y, Liang X, Gong G, Zhang G, Zhao H, Zheng Z, Wang C, Zhu H, Huang J, Li Z, Bu S, Liu G, Wang S, Liu Z. qGLF5 from Oryza rufipogon Griff. improves kernel shape, plant architecture, and yield in rice. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:225. [PMID: 37847396 DOI: 10.1007/s00122-023-04478-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 10/04/2023] [Indexed: 10/18/2023]
Abstract
KEY MESSAGE A novel QTL qGLF5 from Oryza rufipogon Griff. improves yield per plant and plant architecture in rice. Kernel size and plant architecture are critical agronomic traits that are key targets for improving crop yield. From the single-segment substitution lines of Oryza rufipogon Griff. in the indica cultivar Huajingxian74 (HJX74) background, we identified a novel quantitative trait locus (QTL), named qGLF5, which improves kernel shape, plant architecture, and yield per plant in rice. Compared with the control HJX74, the plant height, panicles per plant, panicle length, primary branches per panicle, secondary branches per panicle, and kernels per plant of the near-isogenic line-qGLF5 (NIL-qGLF5) are significantly increased. NIL-qGLF5 has long and narrow kernels by regulating cell number, cell length and width in the spikelet hulls. Yield per plant of NIL-qGLF5 is increased by 35.02% compared with that of HJX74. In addition, qGLF5 significantly improves yield per plant and plant architecture of NIL-gw5 and NIL-GW7. These results indicate that qGLF5 might be beneficial for improving plant architecture and kernel yield in rice breeding by molecular design.
Collapse
Affiliation(s)
- Yijun Wang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510630, Guangdong, China
| | - Xiaoya Liang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510630, Guangdong, China
| | - Gaoyang Gong
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510630, Guangdong, China
| | - Guiquan Zhang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510630, Guangdong, China
| | - Hongyuan Zhao
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510630, Guangdong, China
| | - Zhenwu Zheng
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510630, Guangdong, China
| | - Chihang Wang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510630, Guangdong, China
| | - Haitao Zhu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510630, Guangdong, China
| | - Jinyan Huang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510630, Guangdong, China
| | - Zhan Li
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510630, Guangdong, China
| | - Suhong Bu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510630, Guangdong, China
| | - Guifu Liu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510630, Guangdong, China
| | - Shaokui Wang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510630, Guangdong, China.
| | - Zupei Liu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510630, Guangdong, China.
| |
Collapse
|
28
|
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 2023:S2090-1232(23)00265-5. [PMID: 37739122 DOI: 10.1016/j.jare.2023.09.016] [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: 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.
Collapse
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.
| |
Collapse
|
29
|
Mao Y, Zhou S, Yang J, Wen J, Wang D, Zhou X, Wu X, He L, Liu M, Wu H, Yang L, Zhao B, Tadege M, Liu Y, Liu C, Chen J. The MIO1-MtKIX8 module regulates the organ size in Medicago truncatula. PHYSIOLOGIA PLANTARUM 2023; 175:e14046. [PMID: 37882293 DOI: 10.1111/ppl.14046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/19/2023] [Accepted: 10/04/2023] [Indexed: 10/27/2023]
Abstract
Plant organ size is an important agronomic trait tightly related to crop yield. However, the molecular mechanisms underlying organ size regulation remain largely unexplored in legumes. We previously characterized a key regulator F-box protein MINI ORGAN1 (MIO1)/SMALL LEAF AND BUSHY1 (SLB1), which controls plant organ size in the model legume Medicago truncatula. In order to further dissect the molecular mechanism, MIO1 was used as the bait to screen its interacting proteins from a yeast library. Subsequently, a KIX protein, designated MtKIX8, was identified from the candidate list. The interaction between MIO1 and MtKIX8 was confirmed further by Y2H, BiFC, split-luciferase complementation and pull-down assays. Phylogenetic analyses indicated that MtKIX8 is highly homologous to Arabidopsis KIX8, which negatively regulates organ size. Moreover, loss-of-function of MtKIX8 led to enlarged leaves and seeds, while ectopic expression of MtKIX8 in Arabidopsis resulted in decreased cotyledon area and seed weight. Quantitative reverse-transcription PCR and in situ hybridization showed that MtKIX8 is expressed in most developing organs. We also found that MtKIX8 serves as a crucial molecular adaptor, facilitating interactions with BIG SEEDS1 (BS1) and MtTOPLESS (MtTPL) proteins in M. truncatula. Overall, our results suggest that the MIO1-MtKIX8 module plays a significant and conserved role in the regulation of plant organ size. This module could be a good target for molecular breeding in legume crops and forages.
Collapse
Affiliation(s)
- Yawen Mao
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shaoli Zhou
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jing Yang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
- School of Ecology and Environmental Science, Yunnan University, Kunming, China
| | - Jiangqi Wen
- Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, Oklahoma, USA
| | - Dongfa Wang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Xuan Zhou
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xinyuan Wu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Liangliang He
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
| | - Mingli Liu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
- Southwest Forestry University, Kunming, China
| | - Huan Wu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Liling Yang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
| | - Baolin Zhao
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
| | - Million Tadege
- Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, Oklahoma, USA
| | - Yu Liu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
| | - Changning Liu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
| | - Jianghua Chen
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
- School of Ecology and Environmental Science, Yunnan University, Kunming, China
| |
Collapse
|
30
|
Zheng L, Wu H, Wang A, Zhang Y, Liu Z, Ling HQ, Song XJ, Li Y. The SOD7/DPA4-GIF1 module coordinates organ growth and iron uptake in Arabidopsis. NATURE PLANTS 2023; 9:1318-1332. [PMID: 37550368 DOI: 10.1038/s41477-023-01475-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 07/03/2023] [Indexed: 08/09/2023]
Abstract
Organ growth is controlled by both intrinsic genetic factors and external environmental signals. However, the molecular mechanisms that coordinate plant organ growth and nutrient supply remain largely unknown. We have previously reported that the B3 domain transcriptional repressor SOD7 (NGAL2) and its closest homologue DPA4 (NGAL3) act redundantly to limit organ and seed growth in Arabidopsis. Here we report that SOD7 represses the interaction between the transcriptional coactivator GRF-INTERACTING FACTOR 1 (GIF1) and growth-regulating factors (GRFs) by competitively interacting with GIF1, thereby limiting organ and seed growth. We further reveal that GIF1 physically interacts with FER-LIKE IRON DEFICIENCY-INDUCED TRANSCRIPTION FACTOR (FIT), which acts as a central regulator of iron uptake and homeostasis. SOD7 can competitively repress the interaction of GIF1 with FIT to influence iron uptake and responses. The sod7-2 dpa4-3 mutant enhances the expression of genes involved in iron uptake and displays high iron accumulation. Genetic analyses support that GIF1 functions downstream of SOD7 to regulate organ and seed growth as well as iron uptake and responses. Thus, our findings define a previously unrecognized mechanism that the SOD7/DPA4-GIF1 module coordinates organ growth and iron uptake by targeting key regulators of growth and iron uptake.
Collapse
Affiliation(s)
- Leiying Zheng
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Huilan Wu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Anbin Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yueying Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zupei Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Hong-Qing Ling
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China.
- Hainan Yazhou Bay Seed Laboratory, Sanya, China.
| | - Xian-Jun Song
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China.
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China.
| | - Yunhai Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China.
| |
Collapse
|
31
|
Zhao H, Fu Y, Zhang G, Luo Y, Yang W, Liang X, Yin L, Zheng Z, Wang Y, Li Z, Zhu H, Huang J, Tan Q, Bu S, Liu G, Wang S, Liu Z. GS6.1 controls kernel size and plant architecture in rice. PLANTA 2023; 258:42. [PMID: 37432475 DOI: 10.1007/s00425-023-04201-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 07/06/2023] [Indexed: 07/12/2023]
Abstract
MAIN CONCLUSION A novel QTL GS6.1 increases yield per plant by controlling kernel size, plant architecture, and kernel filling in rice. Kernel size and plant architecture are critical agronomic traits that greatly influence kernel yield in rice. Using the single-segment substitution lines (SSSLs) with an indica cultivar Huajingxian74 as a recipient parent and American Jasmine as a donor parent, we identified a novel quantitative trait locus (QTL), named GS6.1. Near isogenic line-GS6.1 (NIL-GS6.1) produces long and narrow kernels by regulating cell length and width in the spikelet hulls, thus increasing the 1000-kernel weight. Compared with the control, the plant height, panicles per plant, panicle length, kernels per plant, secondary branches per panicle, and yield per plant of NIL-GS6.1 are increased. In addition, GS6.1 regulates the kernel filling rate. GS6.1 controls kernel size by modulating the transcription levels of part of EXPANSINs, kernel filling-related genes, and kernel size-related genes. These results indicate that GS6.1 might be beneficial for improving kernel yield and plant architecture in rice breeding by molecular design.
Collapse
Affiliation(s)
- Hongyuan Zhao
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510630, Guangdong, China
| | - Yu Fu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510630, Guangdong, China
| | - Guiquan Zhang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510630, Guangdong, China
| | - Yingqin Luo
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510630, Guangdong, China
| | - Weifeng Yang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510630, Guangdong, China
| | - Xiaoya Liang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510630, Guangdong, China
| | - Lin Yin
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510630, Guangdong, China
| | - Zhenwu Zheng
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510630, Guangdong, China
| | - Yijun Wang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510630, Guangdong, China
| | - Zhan Li
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510630, Guangdong, China
| | - Haitao Zhu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510630, Guangdong, China
| | - Jinyan Huang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510630, Guangdong, China
| | - Quanya Tan
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510630, Guangdong, China
| | - Suhong Bu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510630, Guangdong, China
| | - Guifu Liu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510630, Guangdong, China
| | - Shaokui Wang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510630, Guangdong, China.
| | - Zupei Liu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510630, Guangdong, China.
| |
Collapse
|
32
|
Zhong Q, Jia Q, Yin W, Wang Y, Rao Y, Mao Y. Advances in cloning functional genes for rice yield traits and molecular design breeding in China. FRONTIERS IN PLANT SCIENCE 2023; 14:1206165. [PMID: 37404533 PMCID: PMC10317195 DOI: 10.3389/fpls.2023.1206165] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 05/31/2023] [Indexed: 07/06/2023]
Abstract
Rice, a major food crop in China, contributes significantly to international food stability. Advances in rice genome sequencing, bioinformatics, and transgenic techniques have catalyzed Chinese researchers' discovery of novel genes that control rice yield. These breakthroughs in research also encompass the analysis of genetic regulatory networks and the establishment of a new framework for molecular design breeding, leading to numerous transformative findings in this field. In this review, some breakthroughs in rice yield traits and a series of achievements in molecular design breeding in China in recent years are presented; the identification and cloning of functional genes related to yield traits and the development of molecular markers of rice functional genes are summarized, with the intention of playing a reference role in the following molecular design breeding work and how to further improve rice yield.
Collapse
Affiliation(s)
- Qianqian Zhong
- College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Qiwei Jia
- College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Wenjing Yin
- College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Yuexing Wang
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, China
| | - Yuchun Rao
- College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Yijian Mao
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, China
| |
Collapse
|
33
|
Li F, Wang K, Zhang X, Han P, Liu Y, Zhang J, Peng T, Li J, Zhao Y, Sun H, Du Y. BPB1 regulates rice ( Oryza sative L.) panicle length and panicle branch development by promoting lignin and inhibiting cellulose accumulation. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:41. [PMID: 37312745 PMCID: PMC10248638 DOI: 10.1007/s11032-023-01389-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 04/24/2023] [Indexed: 06/15/2023]
Abstract
Panicle structure is one of the most important agronomic traits directly related to rice yield. This study identified a rice mutant basal primary branch 1 (bpb1), which exhibited a phenotype of reduced panicle length and arrested basal primary branch development. In addition, lignin content was found to be increased while cellulose content was decreased in bpb1 young panicles. Map-based cloning methods characterized the gene BPB1, which encodes a peptide transporter (PTR) family transporter. Phylogenetic tree analysis showed that the BPB1 family is highly conserved in plants, especially the PTR2 domain. It is worth noting that BPB1 is divided into two categories based on monocotyledonous and dicotyledonous plants. Transcriptome analysis showed that BPB1 mutation can promote lignin synthesis and inhibit cellulose synthesis, starch and sucrose metabolism, cell cycle, expression of various plant hormones, and some star genes, thereby inhibiting rice panicle length, resulting in basal primary branch development stagnant phenotypes. In this study, BPB1 provides new insights into the molecular mechanism of rice panicle structure regulation by BPB1 by regulating lignin and cellulose content and several transcriptional metabolic pathways. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01389-x.
Collapse
Affiliation(s)
- Fei Li
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450046 Henan Province China
| | - Ke Wang
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450046 Henan Province China
| | - Xiaohua Zhang
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450046 Henan Province China
| | - Peijie Han
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450046 Henan Province China
| | - Ye Liu
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450046 Henan Province China
| | - Jing Zhang
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450046 Henan Province China
| | - Ting Peng
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450046 Henan Province China
| | - Junzhou Li
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450046 Henan Province China
| | - Yafan Zhao
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450046 Henan Province China
| | - Hongzheng Sun
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450046 Henan Province China
| | - Yanxiu Du
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450046 Henan Province China
| |
Collapse
|
34
|
Wang S, Wang T, Xuan Q, Qu X, Xu Q, Jiang Q, Pu Z, Li Y, Jiang Y, Chen G, Deng M, Liu Y, Tang H, Chen G, He Y, Gou L, Wei Y, Zheng Y, Ma J. Major and stably expressed QTL for traits related to the mature wheat embryo independent of kernel size. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:90. [PMID: 37000252 DOI: 10.1007/s00122-023-04346-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 03/14/2023] [Indexed: 06/19/2023]
Abstract
Two major and stably expressed QTL for traits related to mature wheat embryo independent of kernel size were identified and validated in a natural population that contained 171 Sichuan wheat accessions and 49 Sichuan wheat landraces. As the juvenile of a highly differentiated plant, mature wheat (Triticum aestivum L.) embryos are highly significant to agricultural production. To understand the genetic basis of traits related to wheat embryo size, the embryo of mature kernels in a recombination inbred line that contained 126 lines from four environments was measured. The genetic loci of embryo size, including embryo length (EL), embryo width (EW), embryo area (EA), embryo length/kernel length (EL/KL), embryo width/kernel width (EW/KW), and EL/EW, were identified based on a genetic linkage map constructed based on PCR markers and the Wheat 55 K single nucleotide polymorphism (SNP) array. A total of 50 quantitative trait loci (QTL) for traits related to wheat embryo size were detected. Among them, QEL.sicau-2SY-4A for EL and QEW.sicau-2SY-7B for EW were major and stably expressed and were genetically independent of KL and KW, respectively. Their effects were further verified in a natural population that contained 171 Sichuan wheat accessions and 49 Sichuan wheat landraces. Further analysis showed that TraesCS4A02G343300 and TraesCS7B02G006800 could be candidate genes for QEL.sicau-2SY-4A and QEW.sicau-2SY-7B, respectively. In addition, significant positive correlations between EL and kernel-related traits and the 1,000-grain weight were detected. Collectively, this study broadens our understanding of the genetic basis of wheat embryo size and will be helpful for the further fine-mapping of interesting loci in the future.
Collapse
Affiliation(s)
- Surong Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Tianyu Wang
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qijing Xuan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiangru Qu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qiang Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qiantao Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zhien Pu
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yang Li
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yunfeng Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guoyue Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Mei Deng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yanling Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Huaping Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guangdeng Chen
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yuanjiang He
- Mianyang Academy of Agricultural Science/Crop Characteristic Resources Creation and Utilization Key Laboratory of Sichuan Providence, Mianyang, 621000, China
| | - Lulu Gou
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yuming Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Youliang Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jian Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China.
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
| |
Collapse
|
35
|
Li J, Zhang B, Duan P, Yan L, Yu H, Zhang L, Li N, Zheng L, Chai T, Xu R, Li Y. An endoplasmic reticulum-associated degradation-related E2-E3 enzyme pair controls grain size and weight through the brassinosteroid signaling pathway in rice. THE PLANT CELL 2023; 35:1076-1091. [PMID: 36519262 PMCID: PMC10015164 DOI: 10.1093/plcell/koac364] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 11/08/2022] [Accepted: 12/12/2022] [Indexed: 05/16/2023]
Abstract
Grain size is an important agronomic trait, but our knowledge about grain size determination in crops is still limited. Endoplasmic reticulum (ER)-associated degradation (ERAD) is a special ubiquitin proteasome system that is involved in degrading misfolded or incompletely folded proteins in the ER. Here, we report that SMALL GRAIN 3 (SMG3) and DECREASED GRAIN SIZE 1 (DGS1), an ERAD-related E2-E3 enzyme pair, regulate grain size and weight through the brassinosteroid (BR) signaling pathway in rice (Oryza sativa). SMG3 encodes a homolog of Arabidopsis (Arabidopsis thaliana) UBIQUITIN CONJUGATING ENZYME 32, which is a conserved ERAD-associated E2 ubiquitin conjugating enzyme. SMG3 interacts with another grain size regulator, DGS1. Loss of function of SMG3 or DGS1 results in small grains, while overexpression of SMG3 or DGS1 leads to long grains. Further analyses showed that DGS1 is an active E3 ubiquitin ligase and colocates with SMG3 in the ER. SMG3 and DGS1 are involved in BR signaling. DGS1 ubiquitinates the BR receptor BRASSINOSTEROID INSENSITIVE 1 (BRI1) and affects its accumulation. Genetic analysis suggests that SMG3, DGS1, and BRI1 act together to regulate grain size and weight. In summary, our findings identify an ERAD-related E2-E3 pair that regulates grain size and weight, which gives insight into the function of ERAD in grain size control and BR signaling.
Collapse
Affiliation(s)
- Jing Li
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Baolan Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Penggen Duan
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Li Yan
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Haiyue Yu
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Limin Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Na Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Leiying Zheng
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Tuanyao Chai
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ran Xu
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya 572025, China
- College of Tropical Crops Hainan University, Hainan University, Haikou 570288, China
| | - Yunhai Li
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- The Innovative of Seed Design, Chinese Academy of Sciences, Sanya 572025, China
| |
Collapse
|
36
|
Molecular bases of rice grain size and quality for optimized productivity. Sci Bull (Beijing) 2023; 68:314-350. [PMID: 36710151 DOI: 10.1016/j.scib.2023.01.026] [Citation(s) in RCA: 39] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/30/2022] [Accepted: 01/16/2023] [Indexed: 01/19/2023]
Abstract
The accomplishment of further optimization of crop productivity in grain yield and quality is a great challenge. Grain size is one of the crucial determinants of rice yield and quality; all of these traits are typical quantitative traits controlled by multiple genes. Research advances have revealed several molecular and developmental pathways that govern these traits of agronomical importance. This review provides a comprehensive summary of these pathways, including those mediated by G-protein, the ubiquitin-proteasome system, mitogen-activated protein kinase, phytohormone, transcriptional regulators, and storage product biosynthesis and accumulation. We also generalize the excellent precedents for rice variety improvement of grain size and quality, which utilize newly developed gene editing and conventional gene pyramiding capabilities. In addition, we discuss the rational and accurate breeding strategies, with the aim of better applying molecular design to breed high-yield and superior-quality varieties.
Collapse
|
37
|
Wang N, Chen H, Qian Y, Liang Z, Zheng G, Xiang J, Feng T, Li M, Zeng W, Bao Y, Liu E, Zhang C, Xu J, Shi Y. Genome-Wide Association Study of Rice Grain Shape and Chalkiness in a Worldwide Collection of Xian Accessions. PLANTS (BASEL, SWITZERLAND) 2023; 12:419. [PMID: 36771503 PMCID: PMC9919668 DOI: 10.3390/plants12030419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/11/2023] [Accepted: 01/13/2023] [Indexed: 06/18/2023]
Abstract
Rice (Oryza sativa L.) appearance quality, which is mainly defined by grain shape and chalkiness, is an important target in rice breeding. In this study, we first re-sequenced 137 indica accessions and then conducted a genome-wide association study (GWAS) for six agronomic traits with the 2,998,034 derived single nucleotide polymorphisms (SNPs) by using the best linear unbiased prediction (BLUP) values for each trait. The results revealed that 195 SNPs had significant associations with the six agronomic traits. Based on the genome-wide linkage disequilibrium (LD) blocks, candidate genes for the target traits were detected within 100 kb upstream and downstream of the relevant SNP loci. Results indicate that six quantitative trait loci (QTLs) significantly associated with six traits (qTGW4.1, qTGW4.2, qGL4.1, qGL12.1, qGL12.2, qGW2.1, qGW4.1, qGW6.1, qGW8.1, qGW8.2, qGW9.1, qGW11.1, qGLWR2.1, qGLWR2.2, qGLWR4.2, qPGWC5.1 and qDEC6.1) were identified for haplotype analysis. Among these QTLs, two (qTGW4.2 and qGW6.1), were overlapped with FLO19 and OsbZIP47, respectively, and the remaining four were novel QTLs. These candidate genes were further validated by haplotype block construction.
Collapse
Affiliation(s)
- Nansheng Wang
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Huguang Chen
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yingzhi Qian
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Zhaojie Liang
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Guiqiang Zheng
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Jun Xiang
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Ting Feng
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Min Li
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Wei Zeng
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Yaling Bao
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Erbao Liu
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Chaopu Zhang
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Jianlong Xu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yingyao Shi
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| |
Collapse
|
38
|
Comparative Ubiquitination Proteomics Revealed the Salt Tolerance Mechanism in Sugar Beet Monomeric Additional Line M14. Int J Mol Sci 2022; 23:ijms232416088. [PMID: 36555729 PMCID: PMC9782053 DOI: 10.3390/ijms232416088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/04/2022] [Accepted: 12/06/2022] [Indexed: 12/23/2022] Open
Abstract
Post-translational modifications (PTMs) are important molecular processes that regulate organismal responses to different stresses. Ubiquitination modification is not only involved in human health but also plays crucial roles in plant growth, development, and responses to environmental stresses. In this study, we investigated the ubiquitination proteome changes in the salt-tolerant sugar beet monomeric additional line M14 under salt stress treatments. Based on the expression of the key genes of the ubiquitination system and the ubiquitination-modified proteins before and after salt stress, 30 min of 200 mM NaCl treatment and 6 h of 400 mM NaCl treatment were selected as time points. Through label-free proteomics, 4711 and 3607 proteins were identified in plants treated with 200 mM NaCl and 400 mM NaCl, respectively. Among them, 611 and 380 proteins were ubiquitinated, with 1085 and 625 ubiquitination sites, in the two salt stress conditions, respectively. A quantitative analysis revealed that 70 ubiquitinated proteins increased and 47 ubiquitinated proteins decreased. At the total protein level, 42 were induced and 20 were repressed with 200 mM NaCl, while 28 were induced and 27 were repressed with 400 mM NaCl. Gene ontology, KEGG pathway, protein interaction, and PTM crosstalk analyses were performed using the differentially ubiquitinated proteins. The differentially ubiquitinated proteins were mainly involved in cellular transcription and translation processes, signal transduction, metabolic pathways, and the ubiquitin/26S proteasome pathway. The uncovered ubiquitinated proteins constitute an important resource of the plant stress ubiquitinome, and they provide a theoretical basis for the marker-based molecular breeding of crops for enhanced stress tolerance.
Collapse
|
39
|
Mao Z, Di X, Xia S, Chen Q, Ma X, Chen M, Yang Z, Zhao F, Ling Y. Detecting and pyramiding target QTL for plant- and grain-related traits via chromosomal segment substitution line of rice. FRONTIERS IN PLANT SCIENCE 2022; 13:1020847. [PMID: 36589042 PMCID: PMC9800928 DOI: 10.3389/fpls.2022.1020847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 10/26/2022] [Indexed: 06/17/2023]
Abstract
INTRODUCTION Plant height and grain length are important agronomic traits in rice, exhibiting a strong effect on plant architecture and grain quality of rice varieties. METHODS Methods: A novel rice chromosomal segment substitution line (CSSL), i.e., CSSL-Z1357, with significantly increased plant height (PH) and grain length (GL) was identified from CSSLs constructed by using Nipponbare as a receptor and a restorer line Xihui 18 as a donor. Seven agronomic traits of PH, PL, GL, GW, GPP, SPP, and TGW were phenotyped, and REML implemented in HPMIXED of SAS were used to detect the QTL for these traits. Secondary CSSLs were screened out via marker-assisted selection (MAS) to estimate the additive and epistatic effects of detected QTLs, evaluating the potential utilization of pyramiding the target QTLs for yield and quality improvement of rice varieties. RESULTS AND DISCUSSION Results and Discussion: CSSL-Z1357 carried nine segments from Xihui 18 with an average segment length of 4.13 Mb. The results show that the long grain of CSSL-Z1357 was caused by the increased number of surface cells and the length of the inner glume. Thirteen quantitative trait loci were identified via the F2 population of Nipponbare/CSSL-Z1357, including three each for GL (qGL-3, qGL-6, and qGL-7) and PH (qPH-1, qPH-7, and qPH-12I), among which qGL-3 increased GL by 0.23 mm with synergistic allele from CSSL-Z1357. Additionally, three single (S1 to S3), two double (D1, D2), and one triple segment (T1) substitution lines were developed in F3 via MAS. Results show that pyramiding the segments from Chr.3 (qGL-3 and qPH-3), Chr.6 (qGL-6 and qPH-6), and Chr.7 (Null and qPH-7) tended to result in better phenotype of increased GL and PH and decreased grain width, providing a potential basis for enhancing grain yield and quality in rice breeding.
Collapse
|
40
|
Huang J, Chen Z, Lin J, Guan B, Chen J, Zhang Z, Chen F, Jiang L, Zheng J, Wang T, Chen H, Xie W, Huang S, Wang H, Huang Y, Huang R. gw2.1, a new allele of GW2, improves grain weight and grain yield in rice. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 325:111495. [PMID: 36240912 DOI: 10.1016/j.plantsci.2022.111495] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 10/04/2022] [Accepted: 10/08/2022] [Indexed: 06/16/2023]
Abstract
Grain weight is an important characteristic of grain shape and a key contributing factor to the grain yield in rice. Here, we report that gw2.1, a new allele of the Grain Width and Weight 2 (GW2) gene, regulates grain size and grain weight. A single nucleotide substitution in the coding sequence (CDS) of gw2.1 resulted in the change of glutamate to lysine (E128K) in GW2.1 protein. Complementation tests and GW2 overexpression experiments demonstrated that the missense mutation in gw2.1 was responsible for the phenotype of enlarged grain size in the mutant line jf42. The large grain trait of the near-isogenic line NIL-gw2.1 was found to result from increased cell proliferation during flower development. Meanwhile, NIL-gw2.1 was shown to increase grain yield without compromising the grain quality. The GW2 protein was localized to the cell nucleus and membrane, and interacted with CHB705, a subunit of the chromatin remodeling complex. Finally, the F1 hybrids from crosses of NIL-gw2.1 with 7 cytoplasmic male-sterile lines exhibited large grains and desirable grain appearance. Thus, gw2.1 is a promising allele that could be applied to improve grain yield and grain appearance in rice. AVAILABILITY OF DATA AND MATERIALS: The datasets generated and/or analyzed in the study are available from the corresponding author on reasonable request.
Collapse
Affiliation(s)
- Jinpeng Huang
- School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Zhiming Chen
- School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Jiajia Lin
- School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Binbin Guan
- School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Jinwen Chen
- Quanzhou Agricultural Science Institute, Quanzhou 362212, China
| | - Zesen Zhang
- School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Fangyu Chen
- Key Laboratory of Ministry of Education for Genetic Improvement and Comprehensive Utilization of Crops, Fujian Provincial Key Laboratory of Crop Breeding by Design, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Liangrong Jiang
- School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Jingsheng Zheng
- School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Tiansheng Wang
- Quanzhou Agricultural Science Institute, Quanzhou 362212, China
| | - Huiqing Chen
- Quanzhou Agricultural Science Institute, Quanzhou 362212, China
| | - Wangyou Xie
- Quanzhou Agricultural Science Institute, Quanzhou 362212, China
| | - Senhao Huang
- Key Laboratory of Ministry of Education for Genetic Improvement and Comprehensive Utilization of Crops, Fujian Provincial Key Laboratory of Crop Breeding by Design, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Houcong Wang
- School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Yumin Huang
- School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Rongyu Huang
- School of Life Sciences, Xiamen University, Xiamen 361102, China.
| |
Collapse
|
41
|
Profile of Dr. Qian Qian. SCIENCE CHINA. LIFE SCIENCES 2022; 65:2145-2147. [PMID: 35997918 DOI: 10.1007/s11427-022-2162-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
|
42
|
Ren D, Xie W, Xu Q, Hu J, Zhu L, Zhang G, Zeng D, Qian Q. LSL1 controls cell death and grain production by stabilizing chloroplast in rice. SCIENCE CHINA. LIFE SCIENCES 2022; 65:2148-2161. [PMID: 35960419 DOI: 10.1007/s11427-022-2152-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 06/22/2022] [Indexed: 06/15/2023]
Abstract
Lesion mutants can be valuable tools to reveal the interactions between genetic factors and environmental signals and to improve grain production. Here we identified a rice (Oryza sativa) mutant, lesion spotleaf1 (lsl1), which produces necrotic leaf lesions throughout its life cycle. LSL1 encodes a protein of unknown function and belongs to a grass-specific clade. The lesion phenotype of the lsl1 mutant was sharply induced by shading, and its detached leaves incubated in 6-benzylamino purine similarly formed lesions in the dark. In addition, the lsl1 mutant exhibited reactive oxygen species accumulation and cell death. The terminal deoxynucleotidyl transferase dUTP nick end-labeling (TUNEL) and comet assays revealed that the lsl1 mutant contained severe DNA damage, resulting in reduced grain yield and quality. RNA sequencing, gene expression, and protein activity analyses indicate that LSL1 is required for chloroplast function. Furthermore, LSL1 interacts with PsaD and PAP10 to form a regulatory module that functions in chlorophyll synthesis and chloroplast development to maintain redox balance. Our results reveal that LSL1 maintains chloroplast structure, redox homeostasis, and DNA stability, and plays important roles in the interaction between genetic factors and environmental signals and in regulating grain size and quality.
Collapse
Affiliation(s)
- Deyong Ren
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.
| | - Wei Xie
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Qiankun Xu
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
- College of Modern Agriculture, Zhejiang A&F University, Hangzhou, 310006, China
| | - Jiang Hu
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Li Zhu
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Guangheng Zhang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
- National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya, 572024, China
| | - Dali Zeng
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
- College of Modern Agriculture, Zhejiang A&F University, Hangzhou, 310006, China
| | - Qian Qian
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.
| |
Collapse
|
43
|
Jiang H, Guo D, Liu Y, Zhu L, Xie F, Xie L. RNA-Seq combined with population-level analysis reveals important candidate genes related to seed size in flax ( Linum usitatissimum L.). FRONTIERS IN PLANT SCIENCE 2022; 13:1015399. [PMID: 36388602 PMCID: PMC9641021 DOI: 10.3389/fpls.2022.1015399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
Seed size is a key determinant of crop yields. Understanding the regulatory mechanisms of seed size is beneficial for improving flax seed yield. In this study, the development of large flax seeds lagged behind that of small seeds, and 1,751 protein-coding genes were differentially expressed in early seeds, torpedo-stage embryos, and endosperms of CIli2719 and Z11637 using RNA sequencing. Homologous alignment revealed that 129 differentially expressed genes (DEGs) in flax were homologous with 71 known seed size-related genes in Arabidopsis thaliana and rice (Oryza sativa L.). These DEGs controlled seed size through multiple processes and factors, among which phytohormone pathways and transcription factors were the most important. Moreover, 54 DEGs were found to be associated with seed size and weight in a DEG-based association study. Nucleotide diversity (π) analysis of seed size-related candidate DEGs by homologous alignment and association analysis showed that the π values decreased significantly during flax acclimation from oil to fiber flax, suggesting that some seed size-related candidate genes were selected in this acclimation process. These results provide important resources and genetic foundation for further research on seed size regulation and seed improvement in flax.
Collapse
|
44
|
Hu Y, Peng X, Shen S. Identification and Investigation of the Genetic Variations and Candidate Genes Responsible for Seed Weight via GWAS in Paper Mulberry. Int J Mol Sci 2022; 23:ijms232012520. [PMID: 36293375 PMCID: PMC9604540 DOI: 10.3390/ijms232012520] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/30/2022] [Accepted: 10/17/2022] [Indexed: 11/17/2022] Open
Abstract
Seeds directly determine the survival and population size of woody plants, but the genetic basis of seed weight in woody plants remain poorly explored. To identify genetic variations and candidate genes responsible for seed weight in natural woody populations, we investigated the hundred-seed weight of 198 paper mulberry individuals from different areas. Our results showed that the hundred-seed weight of paper mulberry was significantly associated with the bioclimatic variables of sampling sites, which increased from south to north along the latitudinal-temperature gradient. Using 2,414,978 high-quality SNPs from re-sequencing data, the genome-wide association analysis of the hundred-seed weight was performed under three models, which identified 148, 19 and 12 associated genes, respectively. Among them, 25 candidate genes were directly hit by the significant SNPs, including the WRKY transcription factor, fatty acid desaturase, F-box protein, etc. Most importantly, we identified three crucial genetic variations in the coding regions of candidate genes (Bp02g2123, Bp01g3291 and Bp10g1642), and significant differences in the hundred-seed weight were detected among the individuals carrying different genotypes. Further analysis revealed that Bp02g2123 encoding a fatty acid desaturase (FAD) might be a key factor affecting the seed weight and local climate adaptation of woody plants. Furthermore, the genome-wide investigation and expression analysis of FAD genes were performed, and the results suggested that BpFADs widely expressed in various tissues and responded to multiple phytohormone and stress treatments. Overall, our study identifies valuable genetic variations and candidate genes, and provides a better understanding of the genetic basis of seed weight in woody plants.
Collapse
|
45
|
Liu J, Lin Y, Chen J, Yan Q, Xue C, Wu R, Chen X, Yuan X. Genome-wide association studies provide genetic insights into natural variation of seed-size-related traits in mungbean. FRONTIERS IN PLANT SCIENCE 2022; 13:997988. [PMID: 36311130 PMCID: PMC9608654 DOI: 10.3389/fpls.2022.997988] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 08/15/2022] [Indexed: 05/24/2023]
Abstract
Although mungbean (Vigna radiata (L.) R. Wilczek) is an important legume crop, its seed yield is relatively low. To address this issue, here 196 accessions with 3,607,508 SNP markers were used to identify quantitative trait nucleotides (QTNs), QTN-by-environment interactions (QEIs), and their candidate genes for seed length (SL), seed width, and 100-seed weight (HSW) in two environments. As a result, 98 QTNs and 20 QEIs were identified using 3VmrMLM, while 95, >10,000, and 15 QTNs were identified using EMMAX, GEMMA, and CMLM, respectively. Among 809 genes around these QTNs, 12 were homologous to known seed-development genes in rice and Arabidopsis thaliana, in which 10, 2, 1, and 0 genes were found, respectively, by the above four methods to be associated with the three traits, such as VrEmp24/25 for SL and VrKIX8 for HSW. Eight of the 12 genes were significantly differentially expressed between two large-seed and two small-seed accessions, and VrKIX8, VrPAT14, VrEmp24/25, VrIAR1, VrBEE3, VrSUC4, and Vrflo2 were further verified by RT-qPCR. Among 65 genes around these QEIs, VrFATB, VrGSO1, VrLACS2, and VrPAT14 were homologous to known seed-development genes in A. thaliana, although new experiments are necessary to explore these novel GEI-trait associations. In addition, 54 genes were identified in comparative genomics analysis to be associated with seed development pathway, in which VrKIX8, VrABA2, VrABI5, VrSHB1, and VrIKU2 were also identified in genome-wide association studies. This result provided a reliable approach for identifying seed-size-related genes in mungbean and a solid foundation for further molecular biology research on seed-size-related genes.
Collapse
|
46
|
Hu B, Chen W, Wan L, Li T, Wang H, Wang Y, Pu Z, Tu B, Yuan H, Wang Y, Ma B, Qin P, Li S. Short grain 5 controls grain length in rice by regulating cell expansion. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 323:111412. [PMID: 35961516 DOI: 10.1016/j.plantsci.2022.111412] [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: 05/19/2022] [Revised: 07/22/2022] [Accepted: 08/07/2022] [Indexed: 06/15/2023]
Abstract
Grain shape is a crucial determinant of grain weight and quality and plays a vital role in rice breeding. Although many grain shape-related genes have been reported, the regulatory relationship between them has not been well characterized in rice. In this study, we report the isolation of a short-grain-length mutant called sg5 from the heavy-panicle-type hybrid rice elite restorer line 'ShuhuiR498' (R498) after ethyl methanesulfonate (EMS) treatment. MutMap cloning revealed that SG5 encodes a Myb-like transcription factor. A missense mutation in the first exon of SG5 was found to cause an amino acid change from leucine to proline at position 197 in the mutant SG5 protein. Gene knockout and genetic complementation experiments confirmed that the point mutation in SG5 was responsible for the sg5 mutant phenotype. SG5 is mainly expressed in young panicles and hulls. In addition, the SG5 protein is found in the nucleus and does not affect subcellular localization. Histochemical observation and gene expression analysis indicated that SG5 regulates spikelet hull development by mediating cell expansion. Moreover, the expression levels of BG1, GS2, and DEP1 were reduced in sg5 plants, and dual-luciferase (LUC) assays showed that SG5 can bind to the BG1 gene promoter. The effect of pyramiding sg5 and GS3 suggests that sg5 and GS3 regulate grain length independently. The results of our study show that the missense mutation in sg5 is essential for the molecular function of SG5 and SG5 is involved in regulating cell expansion and expression of grain-shape-related genes to regulate grain length. This work provides new data to help study and understand the molecular function of SG5.
Collapse
Affiliation(s)
- Binhua Hu
- Institute of Biotechnology and Nuclear Technology, Sichuan Academy of Agricultural Sciences, Chengdu 610061, China; Rice Research Institute, State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Weilan Chen
- Rice Research Institute, State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Li Wan
- Rice Research Institute, State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Ting Li
- Rice Research Institute, State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Hao Wang
- Rice Research Institute, State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yangkai Wang
- Rice Research Institute, State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Zhigang Pu
- Institute of Biotechnology and Nuclear Technology, Sichuan Academy of Agricultural Sciences, Chengdu 610061, China
| | - Bin Tu
- Rice Research Institute, State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Hua Yuan
- Rice Research Institute, State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yuping Wang
- Rice Research Institute, State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Bingtian Ma
- Rice Research Institute, State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Peng Qin
- Rice Research Institute, State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, China.
| | - Shigui Li
- Rice Research Institute, State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, China.
| |
Collapse
|
47
|
Zhang Y, Han E, Peng Y, Wang Y, Wang Y, Geng Z, Xu Y, Geng H, Qian Y, Ma S. Rice co-expression network analysis identifies gene modules associated with agronomic traits. PLANT PHYSIOLOGY 2022; 190:1526-1542. [PMID: 35866684 PMCID: PMC9516743 DOI: 10.1093/plphys/kiac339] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 06/28/2022] [Indexed: 06/15/2023]
Abstract
Identifying trait-associated genes is critical for rice (Oryza sativa) improvement, which usually relies on map-based cloning, quantitative trait locus analysis, or genome-wide association studies. Here we show that trait-associated genes tend to form modules within rice gene co-expression networks, a feature that can be exploited to discover additional trait-associated genes using reverse genetics. We constructed a rice gene co-expression network based on the graphical Gaussian model using 8,456 RNA-seq transcriptomes, which assembled into 1,286 gene co-expression modules functioning in diverse pathways. A number of the modules were enriched with genes associated with agronomic traits, such as grain size, grain number, tiller number, grain quality, leaf angle, stem strength, and anthocyanin content, and these modules are considered to be trait-associated gene modules. These trait-associated gene modules can be used to dissect the genetic basis of rice agronomic traits and to facilitate the identification of trait genes. As an example, we identified a candidate gene, OCTOPUS-LIKE 1 (OsOPL1), a homolog of the Arabidopsis (Arabidopsis thaliana) OCTOPUS gene, from a grain size module and verified it as a regulator of grain size via functional studies. Thus, our network represents a valuable resource for studying trait-associated genes in rice.
Collapse
Affiliation(s)
- Yu Zhang
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei, China
| | - Ershang Han
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei, China
| | - Yuming Peng
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei, China
| | - Yuzhou Wang
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei, China
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Yifan Wang
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei, China
| | - Zhenxing Geng
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei, China
| | - Yupu Xu
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei, China
| | - Haiying Geng
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei, China
| | | | | |
Collapse
|
48
|
He Y, Li L, Shi W, Tan J, Luo X, Zheng S, Chen W, Li J, Zhuang C, Jiang D. Florigen repression complexes involving rice CENTRORADIALIS2 regulate grain size. PLANT PHYSIOLOGY 2022; 190:1260-1274. [PMID: 35861433 PMCID: PMC9516737 DOI: 10.1093/plphys/kiac338] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 06/14/2022] [Indexed: 06/15/2023]
Abstract
Grain size is one of the crucial factors determining grain yield. However, the genetic and molecular mechanisms of florigen repression complexes (FRCs) underlying grain size in rice (Oryza sativa L.) have not been reported. Here, we report that the rice CENTRORADIALIS (CEN) family member OsCEN2 (also known as Rice TFL1/CEN homolog, RCN1), a phosphatidylethanolamine-binding protein (PEBP) family protein, negatively controls grain size in rice. Overexpression of OsCEN2 led to small grains, and knockout of OsCEN2 resulted in large, heavy grains. OsCEN2 influenced grain size by restricting cell expansion in the spikelet hull and seed filling. In in vivo and in vitro experiments, OsCEN2 physically interacted with a G-box factor 14-3-3 homolog, GF14f, which negatively regulates grain size. Bimolecular fluorescence complementation and yeast two-hybrid assays revealed that GF14f directly interacts with the basic leucine zipper (bZIP) transcription factor, OsFD2. Plants overexpressing OsFD2 produced smaller and lighter grains than wild-type plants. We found that OsFD2 also influences grain size by controlling cell expansion and division in the spikelet hull. Our results reveal the molecular mechanisms of the OsCEN2-GF14f-OsFD2 regulatory module in controlling grain size. Additionally, our study provides insight into the functions of the FRC in rice and suggests a strategy for improving seed size and weight.
Collapse
Affiliation(s)
- Ying He
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Liuyu Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Weibiao Shi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Juhong Tan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Xixiu Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Shaoyan Zheng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Weiting Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Jing Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | | | | |
Collapse
|
49
|
Wu X, Cai X, Zhang B, Wu S, Wang R, Li N, Li Y, Sun Y, Tang W. ERECTA regulates seed size independently of its intracellular domain via MAPK-DA1-UBP15 signaling. THE PLANT CELL 2022; 34:3773-3789. [PMID: 35848951 PMCID: PMC9516062 DOI: 10.1093/plcell/koac194] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 06/09/2022] [Indexed: 06/15/2023]
Abstract
Seed size is determined by the coordinated growth of the embryo, endosperm, and integument. Growth of the integument is initiated by signal molecules released from the developing endosperm or embryo. Although recent studies have identified many components that regulate seed size by controlling integument growth, the upstream signals and the signal transduction pathway that activate these components after double fertilization are unclear. Here, we report that the receptor-like kinase ERECTA (ER) controls seed size by regulating outer integument cell proliferation in Arabidopsis thaliana. Seeds from er mutants were smaller, while those from ER-overexpressing plants were larger, than those of control plants. Different from its role in regulating the development of other organs, ER regulates seed size via a novel mechanism that is independent of its intracellular domain. Our genetic and biochemical data show that a MITOGEN-ACTIVATED PROTEIN KINASE (MAPK) signaling pathway comprising MAPK-KINASE 4/5, MAPK 3/6 (MPK3/6), DA1, and UBIQUITIN SPECIFIC PROTEASE 15 (UBP15) functions downstream of ER and modulates seed size. MPK3/6 phosphorylation inactivates and destabilizes DA1 to increase the abundance of UBP15, promoting outer integument cell proliferation and increasing seed size. Our study illustrates a nearly completed ER-mediated signaling pathway that regulates seed size and will help uncover the mechanism that coordinates embryo, endosperm, and integument growth after double fertilization.
Collapse
Affiliation(s)
| | | | - Baowen Zhang
- Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Collaboration Innovation Center for Cell Signaling, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Shuting Wu
- Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Collaboration Innovation Center for Cell Signaling, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Ruiju Wang
- Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Collaboration Innovation Center for Cell Signaling, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Na Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant, Institute of Genetics and Development Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yunhai Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant, Institute of Genetics and Development Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yu Sun
- Author for correspondence: (Y.S.), (W.T.)
| | | |
Collapse
|
50
|
Li ZH, Wang SL, Zhu YJ, Fan YY, Huang DR, Zhu AK, Zhuang JY, Liang Y, Zhang ZH. Control of Grain Shape and Size in Rice by Two Functional Alleles of OsPUB3 in Varied Genetic Background. PLANTS (BASEL, SWITZERLAND) 2022; 11:2530. [PMID: 36235396 PMCID: PMC9571118 DOI: 10.3390/plants11192530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/20/2022] [Accepted: 09/23/2022] [Indexed: 06/16/2023]
Abstract
Grain shape and size are key determinants of grain appearance quality and yield in rice. In our previous study, a grain shape QTL, qGS1-35.2, was fine-mapped using near-isogenic lines (NILs) derived from a cross between Zhenshan 97 (ZS97) and Milyang 46 (MY46). One annotated gene, OsPUB3, was found to be the most likely candidate gene. Here, knockout and overexpression experiments were performed to investigate the effects of OsPUB3 on grain shape and size. Four traits were tested, including grain length, grain width, grain weight, and the ratio of grain length to width. Knockout of OsPUB3 in NILZS97, NILMY46, and another rice cultivar carrying the OsPUB3MY46 allele all caused decreases in grain width and weight and increases in the ratio of grain length to width. Results also showed that the magnitude of the mutational effects varied depending on the target allele and the genetic background. Moreover, it was found that NILZS97 and NILMY46 carried different functional alleles of OsPUB3, causing differences in grain shape rather than grain weight. In the overexpression experiment, significant differences between transgenic-positive and transgenic-negative plants were detected in all four traits. These results indicate that OsPUB3 regulates grain shape and size through a complex mechanism and is a good target for deciphering the regulatory network of grain shape. This gene could be used to improve grain appearance quality through molecular breeding as well.
Collapse
Affiliation(s)
- Zhu-Hao Li
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Shi-Lin Wang
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Yu-Jun Zhu
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Ye-Yang Fan
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - De-Run Huang
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Ai-Ke Zhu
- Nanchong Academy of Agricultural Sciences, Nanchong 637000, China
| | - Jie-Yun Zhuang
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Yan Liang
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Zhen-Hua Zhang
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| |
Collapse
|