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Xu L, Yang L, Li A, Guo J, Wang H, Qi H, Li M, Yang P, Song S. An AP2/ERF transcription factor confers chilling tolerance in rice. SCIENCE ADVANCES 2024; 10:eado4788. [PMID: 39196924 PMCID: PMC11352847 DOI: 10.1126/sciadv.ado4788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Accepted: 07/24/2024] [Indexed: 08/30/2024]
Abstract
Cold stress, a prominent adverse environmental factor, severely hinders rice growth and productivity. Unraveling the complex mechanisms governing chilling tolerance in rice is crucial for molecular breeding of cold-tolerant varieties. Here, we identify an APETALA2/Ethylene Responsive Factor (AP2/ERF) transcription factor, OsERF52, as a positive modulator in response to low temperatures. OsERF52 directly regulates the expression of C-Repeat Binding Factor (CBF) genes in rice. In addition, Osmotic Stress/ABA-Activated Protein Kinase 9-mediated phosphorylation of OsERF52 at S261 enhances its stability and interaction with Ideal Plant Architecture 1 and OsbHLH002/OsICE1. This collaborative activation leads to the expression of OsCBFs, thereby initiating the chilling response in rice. Notably, plants with base-edited OsERF52S261D-3HA exhibit enhanced chilling resistance without yield penalty. Our findings unveil the mechanism orchestrated by a regulatory framework involving a protein kinase and transcription factors from diverse families, offering potential genetic resources for developing chilling-tolerant rice varieties.
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Affiliation(s)
- Liang Xu
- State Key Laboratory of Rice Biology and Breeding, Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Lijia Yang
- State Key Laboratory of Rice Biology and Breeding, Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Aipeng Li
- State Key Laboratory of Rice Biology and Breeding, Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Jiazhuo Guo
- State Key Laboratory of Rice Biology and Breeding, Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Huanyu Wang
- State Key Laboratory of Rice Biology and Breeding, Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Haoyue Qi
- State Key Laboratory of Rice Biology and Breeding, Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Ming Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430026, China
| | - Pingfang Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430026, China
| | - Shiyong Song
- State Key Laboratory of Rice Biology and Breeding, Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
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2
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Han J, Yang X, Cai Y, Qiao F, Tao J, Zhu X, Mou Q, An J, Hu J, Li Z, Guan Y. MORN motif-containing protein OsMORN1 and OsMORN2 are crucial for rice pollen viability and cold tolerance. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:998-1013. [PMID: 38761113 DOI: 10.1111/tpj.16812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 04/23/2024] [Accepted: 05/03/2024] [Indexed: 05/20/2024]
Abstract
The pollen viability directly affects the pollination process and the ultimate grain yield of rice. Here, we identified that the MORN motif-containing proteins, OsMORN1 and OsMORN2, had a crucial role in maintaining pollen fertility. Compared with the wild type (WT), the pollen viability of the osmorn1 and osmorn2 mutants was reduced, and pollen germination was abnormal, resulting in significantly lower spikelet fertility, seed-setting rate, and grain yield per plant. Further investigation revealed that OsMORN1 was localized to the Golgi apparatus and lipid droplets. Lipids associated with pollen viability underwent alterations in osmorn mutants, such as the diacylglyceride (18:3_18:3) was 5.1-fold higher and digalactosyldiacylglycerol (18:2_18:2) was 5.2-fold lower in osmorn1, while the triacylglycerol (TG) (16:0_18:2_18:3) was 8.3-fold higher and TG (16:0_18:1_18:3) was 8.5-fold lower in osmorn2 than those in WT. Furthermore, the OsMORN1/2 was found to be associated with rice cold tolerance, as osmorn1 and osmorn2 mutants were more sensitive to chilling stress than WT. The mutants displayed increased hydrogen peroxide accumulation, reduced antioxidant enzyme activities, elevated malondialdehyde content, and a significantly decreased seedling survival rate. Lipidomics analysis revealed distinct alterations in lipids under low temperature, highlighting significant changes in TG (18:2_18:3_18:3) and TG (18:4_18:2_18:2) in osmorn1, TG (16:0_18:2_18:2) and PI (17:2_18:3) in osmorn2 compared to the WT. Therefore, it suggested that OsMORN1 and OsMORN2 regulate both pollen viability and cold tolerance through maintaining lipid homeostasis.
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Affiliation(s)
- Jiajun Han
- Seed Science Center, The Advanced Seed Institute, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Xiaoying 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, 510640, China
| | - Yibei Cai
- Seed Science Center, The Advanced Seed Institute, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Fengpei Qiao
- Seed Science Center, The Advanced Seed Institute, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Ji Tao
- Seed Science Center, The Advanced Seed Institute, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Xiaobo Zhu
- Hainan Research Institute, Zhejiang University, Sanya, 572025, China
| | - Qingshan Mou
- Hainan Research Institute, Zhejiang University, Sanya, 572025, China
| | - Jianyu An
- Seed Science Center, The Advanced Seed Institute, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Jin Hu
- Seed Science Center, The Advanced Seed Institute, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- Hainan Research Institute, Zhejiang University, Sanya, 572025, 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, 510640, China
| | - Yajing Guan
- Seed Science Center, The Advanced Seed Institute, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- Hainan Research Institute, Zhejiang University, Sanya, 572025, China
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3
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Zhong Y, Luo Y, Sun J, Qin X, Gan P, Zhou Z, Qian Y, Zhao R, Zhao Z, Cai W, Luo J, Chen LL, Song JM. Pan-transcriptomic analysis reveals alternative splicing control of cold tolerance in rice. THE PLANT CELL 2024; 36:2117-2139. [PMID: 38345423 PMCID: PMC11132889 DOI: 10.1093/plcell/koae039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 01/19/2024] [Indexed: 05/30/2024]
Abstract
Plants have evolved complex mechanisms to adapt to harsh environmental conditions. Rice (Oryza sativa) is a staple food crop that is sensitive to low temperatures. However, its cold stress responses remain poorly understood, thus limiting possibilities for crop engineering to achieve greater cold tolerance. In this study, we constructed a rice pan-transcriptome and characterized its transcriptional regulatory landscape in response to cold stress. We performed Iso-Seq and RNA-Seq of 11 rice cultivars subjected to a time-course cold treatment. Our analyses revealed that alternative splicing-regulated gene expression plays a significant role in the cold stress response. Moreover, we identified CATALASE C (OsCATC) and Os03g0701200 as candidate genes for engineering enhanced cold tolerance. Importantly, we uncovered central roles for the 2 serine-arginine-rich proteins OsRS33 and OsRS2Z38 in cold tolerance. Our analysis of cold tolerance and resequencing data from a diverse collection of 165 rice cultivars suggested that OsRS2Z38 may be a key selection gene in japonica domestication for cold adaptation, associated with the adaptive evolution of rice. This study systematically investigated the distribution, dynamic changes, and regulatory mechanisms of alternative splicing in rice under cold stress. Overall, our work generates a rich resource with broad implications for understanding the genetic basis of cold response mechanisms in plants.
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Affiliation(s)
- Yuanyuan Zhong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Yuhong Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Jinliang Sun
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Xuemei Qin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Ping Gan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Zuwen Zhou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Yongqing Qian
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Rupeng Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Zhiyuan Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Wenguo Cai
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Jijing Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Ling-Ling Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Jia-Ming Song
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
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Sar P, Gupta S, Behera M, Chakraborty K, Ngangkham U, Verma BC, Banerjee A, Hanjagi PS, Bhaduri D, Shil S, Kumar J, Mandal NP, Kole PC, Purugganan MD, Roy S. Exploring Genetic Diversity within aus Rice Germplasm: Insights into the Variations in Agro-morphological Traits. RICE (NEW YORK, N.Y.) 2024; 17:20. [PMID: 38526679 DOI: 10.1186/s12284-024-00700-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 03/12/2024] [Indexed: 03/27/2024]
Abstract
The aus (Oryza sativa L.) varietal group comprises of aus, boro, ashina and rayada seasonal and/or field ecotypes, and exhibits unique stress tolerance traits, making it valuable for rice breeding. Despite its importance, the agro-morphological diversity and genetic control of yield traits in aus rice remain poorly understood. To address this knowledge gap, we investigated the genetic structure of 181 aus accessions using 399,115 SNP markers and evaluated them for 11 morpho-agronomic traits. Through genome-wide association studies (GWAS), we aimed to identify key loci controlling yield and plant architectural traits.Our population genetic analysis unveiled six subpopulations with strong geographical patterns. Subpopulation-specific differences were observed in most phenotypic traits. Principal component analysis (PCA) of agronomic traits showed that principal component 1 (PC1) was primarily associated with panicle traits, plant height, and heading date, while PC2 and PC3 were linked to primary grain yield traits. GWAS using PC1 identified OsSAC1 on Chromosome 7 as a significant gene influencing multiple agronomic traits. PC2-based GWAS highlighted the importance of OsGLT1 and OsPUP4/ Big Grain 3 in determining grain yield. Haplotype analysis of these genes in the 3,000 Rice Genome Panel revealed distinct genetic variations in aus rice.In summary, this study offers valuable insights into the genetic structure and phenotypic diversity of aus rice accessions. We have identified significant loci associated with essential agronomic traits, with GLT1, PUP4, and SAC1 genes emerging as key players in yield determination.
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Affiliation(s)
- Puranjoy Sar
- Central Rainfed Upland Rice Research Station, ICAR-National Rice Research Institute, Hazaribag, Jharkhand, 825 301, India
| | - Sonal Gupta
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Motilal Behera
- Crop Physiology and Biochemistry Division, ICAR-National Rice Research Institute, Cuttack, Odisha, 753 006, India
| | - Koushik Chakraborty
- Crop Physiology and Biochemistry Division, ICAR-National Rice Research Institute, Cuttack, Odisha, 753 006, India
| | - Umakanta Ngangkham
- Manipur Center, ICAR Research Complex for NEH Region, Imphal, Manipur, 795 004, India
| | - Bibhash Chandra Verma
- Central Rainfed Upland Rice Research Station, ICAR-National Rice Research Institute, Hazaribag, Jharkhand, 825 301, India
| | - Amrita Banerjee
- Central Rainfed Upland Rice Research Station, ICAR-National Rice Research Institute, Hazaribag, Jharkhand, 825 301, India
| | - Prashantkumar S Hanjagi
- Crop Physiology and Biochemistry Division, ICAR-National Rice Research Institute, Cuttack, Odisha, 753 006, India
| | - Debarati Bhaduri
- Crop Production Division, ICAR-National Rice Research Institute, Cuttack, Odisha, 753 006, India
| | - Sandip Shil
- Research Centre - Mohitnagar, ICAR-Central Plantation Crops Research Institute, Jalpaiguri, West Bengal, 735 101, India
| | - Jitendra Kumar
- Central Rainfed Upland Rice Research Station, ICAR-National Rice Research Institute, Hazaribag, Jharkhand, 825 301, India
| | - Nimai Prasad Mandal
- Central Rainfed Upland Rice Research Station, ICAR-National Rice Research Institute, Hazaribag, Jharkhand, 825 301, India
| | - Paresh Chandra Kole
- Palli Siksha Bhavana (Institute of Agriculture), Visva-Bharati, Sriniketan, West Bengal, 731236, India
| | | | - Somnath Roy
- Central Rainfed Upland Rice Research Station, ICAR-National Rice Research Institute, Hazaribag, Jharkhand, 825 301, India.
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5
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Xie L, Wu D, Fang Y, Ye C, Zhu QH, Wei X, Fan L. Population genomic analysis unravels the evolutionary roadmap of pericarp color in rice. PLANT COMMUNICATIONS 2024; 5:100778. [PMID: 38062703 PMCID: PMC10943583 DOI: 10.1016/j.xplc.2023.100778] [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: 10/31/2023] [Revised: 11/29/2023] [Accepted: 12/04/2023] [Indexed: 01/13/2024]
Abstract
Pigmented rice stands out for its nutritional value and is gaining more and more attention. Wild rice, domesticated red rice, and weedy rice all have a red pericarp and a comprehensive genetic background in terms of the red-pericarp phenotype. We performed population genetic analyses using 5104 worldwide rice accessions, including 2794 accessions with red or black pericarps, 85 of which were newly sequenced in this study. The results suggested an evolutionary trajectory of red landraces originating from wild rice, and the split times of cultivated red and white rice populations were estimated to be within the past 3500 years. Cultivated red rice was found to feralize to weedy rice, and weedy rice could be further re-domesticated to cultivated red rice. A genome-wide association study based on the 2794 accessions with pigmented pericarps revealed several new candidate genes associated with the red-pericarp trait for further functional characterization. Our results provide genomic evidence for the origin of pigmented rice and a valuable genomic resource for genetic investigation and breeding of pigmented rice.
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Affiliation(s)
- Lingjuan Xie
- Institute of Crop Sciences & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China; Shandong (Linyi) Institute of Modern Agriculture, Zhejiang University, Linyi 310014, China
| | - Dongya Wu
- Institute of Crop Sciences & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Yu Fang
- Institute of Crop Sciences & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China; Shanghai ZKW Molecular Breeding Technology Co., Ltd., Shanghai 200234, China
| | - Chuyu Ye
- Institute of Crop Sciences & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Qian-Hao Zhu
- CSIRO Agriculture and Food, Black Mountain Laboratories, Canberra, ACT 2601, Australia
| | - Xinghua Wei
- China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 311401, China
| | - Longjiang Fan
- Institute of Crop Sciences & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China; Shandong (Linyi) Institute of Modern Agriculture, Zhejiang University, Linyi 310014, China.
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6
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Guo N, Tang S, Wang Y, Chen W, An R, Ren Z, Hu S, Tang S, Wei X, Shao G, Jiao G, Xie L, Wang L, Chen Y, Zhao F, Sheng Z, Hu P. A mediator of OsbZIP46 deactivation and degradation negatively regulates seed dormancy in rice. Nat Commun 2024; 15:1134. [PMID: 38326370 PMCID: PMC10850359 DOI: 10.1038/s41467-024-45402-z] [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: 11/27/2022] [Accepted: 01/22/2024] [Indexed: 02/09/2024] Open
Abstract
Preharvest sprouting (PHS) is a deleterious phenotype that occurs frequently in rice-growing regions where the temperature and precipitation are high. It negatively affects yield, quality, and downstream grain processing. Seed dormancy is a trait related to PHS. Longer seed dormancy is preferred for rice production as it can prevent PHS. Here, we map QTLs associated with rice seed dormancy and clone Seed Dormancy 3.1 (SDR3.1) underlying one major QTL. SDR3.1 encodes a mediator of OsbZIP46 deactivation and degradation (MODD). We show that SDR3.1 negatively regulates seed dormancy by inhibiting the transcriptional activity of ABIs. In addition, we reveal two critical amino acids of SDR3.1 that are critical for the differences in seed dormancy between the Xian/indica and Geng/japonica cultivars. Further, SDR3.1 has been artificially selected during rice domestication. We propose a two-line model for the process of rice seed dormancy domestication from wild rice to modern cultivars. We believe the candidate gene and germplasm studied in this study would be beneficial for the genetic improvement of rice seed dormancy.
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Affiliation(s)
- Naihui Guo
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
- Rice Research Institute, Shenyang Agricultural University, Shenyang, 110866, P. R. China
| | - Shengjia Tang
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Yakun Wang
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
- National Nanfan Research Academy (Sanya), Chinese Academy of Agricultural Sciences, Sanya, 572024, P. R. China
| | - Wei Chen
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Ruihu An
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Zongliang Ren
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Shikai Hu
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Shaoqing Tang
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Xiangjin Wei
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Gaoneng Shao
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Guiai Jiao
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Lihong Xie
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Ling Wang
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Ying Chen
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Fengli Zhao
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Zhonghua Sheng
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China.
- Jiangxi Early-season Rice Research Center, Pingxiang, Jiangxi Province, 337000, P. R. China.
| | - Peisong Hu
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China.
- Rice Research Institute, Shenyang Agricultural University, Shenyang, 110866, P. R. China.
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7
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Huang G, Zeng Y. Increased stomatal conductance and leaf biochemical capacity, not mesophyll conductance, contributing to the enhanced photosynthesis in Oryza plants during domestication. PLANTA 2023; 259:28. [PMID: 38127197 DOI: 10.1007/s00425-023-04305-x] [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: 10/08/2023] [Accepted: 11/28/2023] [Indexed: 12/23/2023]
Abstract
MAIN CONCLUSION Leaf biochemical capacity and the ratio of leaf biochemical capacity to stomatal conductance are promising to enhance leaf photosynthetic rate and water use efficiency in rice plants, respectively. Domestication may have great impact on crop photosynthetic rate, which has not been fully understood, especially from the perspective of stomatal conductance, mesophyll conductance, and leaf biochemical capacity simultaneously. In this study, we constructed a database consisting of 141 and 92 sets of data from wild and cultivated rice, respectively, including leaf gas exchange parameters, hydraulic conductance, structural traits, and nitrogen content. We found that, compared to wild rice, enhanced leaf photosynthetic rate in cultivated rice was mainly resulted by the increased stomatal conductance and leaf biochemical capacity, rather than mesophyll conductance. The unchanged mesophyll conductance observed during domestication suggested that it might have been optimized during plant evolution in wild rice. Additionally, the positive relationship between stomatal density and stomatal conductance disappeared in Oryza plants during domestication, suggesting that stomatal conductance in cultivated rice is less restricted by stomatal density, compared to wild rice. Moreover, in both wild and cultivated rice, leaf photosynthetic rate was mainly determined by leaf biochemical capacity, rather than stomatal conductance and mesophyll conductance. This study highlighted the important role of stomatal conductance and leaf biochemical capacity in improvement of leaf photosynthetic rate in rice during domestication. Leaf biochemical capacity and the ratio of leaf biochemical capacity to stomatal conductance should be further investigated to enhance leaf photosynthetic rate and water use efficiency in rice plants, respectively.
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Affiliation(s)
- Guanjun Huang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, School of Agricultural Sciences, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi, China.
| | - Yongjun Zeng
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, School of Agricultural Sciences, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi, China
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8
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Li X, Zhang S, Lowey D, Hissam C, Clevenger J, Perera S, Jia Y, Caicedo AL. A derived weedy rice × ancestral cultivar cross identifies evolutionarily relevant weediness QTLs. Mol Ecol 2023; 32:5971-5985. [PMID: 37861465 DOI: 10.1111/mec.17172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 09/02/2023] [Accepted: 10/06/2023] [Indexed: 10/21/2023]
Abstract
Weedy rice (Oryza spp.) is a weedy relative of the cultivated rice that competes with the crop and causes significant production loss. The BHA (blackhull awned) US weedy rice group has evolved from aus cultivated rice and differs from its ancestors in several important weediness traits, including flowering time, plant height and seed shattering. Prior attempts to determine the genetic basis of weediness traits in plants using linkage mapping approaches have not often considered weed origins. However, the timing of divergence between crossed parents can affect the detection of quantitative trait loci (QTL) relevant to the evolution of weediness. Here, we used a QTL-seq approach that combines bulked segregant analysis and high-throughput whole genome resequencing to map the three important weediness traits in an F2 population derived from a cross between BHA weedy rice with an ancestral aus cultivar. We compared these QTLs with those previously detected in a cross of BHA with a more distantly related crop, indica. We identified multiple QTLs that overlapped with regions under selection during the evolution of weedy BHA rice and some candidate genes possibly underlying the evolution weediness traits in BHA. We showed that QTLs detected with ancestor-descendant crosses are more likely to be involved in the evolution of weediness traits than those detected from crosses of more diverged taxa.
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Affiliation(s)
- Xiang Li
- Plant Biology Graduate Program and Department of Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Shulin Zhang
- College of Biology and Food Engineering, Innovation and Practice Base for Postdoctors, Anyang Institute of Technology, Anyang, China
| | - Daniel Lowey
- Plant Biology Graduate Program and Department of Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Carter Hissam
- Plant Biology Graduate Program and Department of Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Josh Clevenger
- HudsonAlpha Institute of Biotechnology, Huntsville, Alabama, USA
| | - Sherin Perera
- Plant Biology Graduate Program and Department of Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Yulin Jia
- United States Department of Agriculture-Agricultural Research Service, Dale Bumpers National Rice Research Center, Stuttgart, Arkansas, USA
| | - Ana L Caicedo
- Plant Biology Graduate Program and Department of Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
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9
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Gao G, Chen M, Mo R, Li N, Xu Y, Lu Y. Linking New Alleles at the Oscillator Loci to Flowering and Expansion of Asian Rice. Genes (Basel) 2023; 14:2027. [PMID: 38002970 PMCID: PMC10671530 DOI: 10.3390/genes14112027] [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: 09/10/2023] [Revised: 10/25/2023] [Accepted: 10/26/2023] [Indexed: 11/26/2023] Open
Abstract
The central oscillator is believed to be the key mechanism by which plants adapt to new environments. However, impacts from hybridization, the natural environment, and human selection have rarely been assessed on the oscillator of a crop. Here, from clearly identified alleles at oscillator loci (OsCCA1/LHY, OsPRR95, OsPRR37, OsPRR59, and OsPRR1) in ten diverse genomes of Oryza sativa, additional accessions, and functional analysis, we show that rice's oscillator was rebuilt primarily by new alleles from recombining parental sequences and subsequent 5' or/and coding mutations. New alleles may exhibit altered transcript levels from that of a parental allele and are transcribed variably among genetic backgrounds and natural environments in RIL lines. Plants carrying more expressed OsCCA1_a and less transcribed OsPRR1_e flower early in the paddy field. 5' mutations are instrumental in varied transcription, as shown by EMSA tests on one deletion at the 5' region of highly transcribed OsPRR1_a. Compared to relatively balanced mutations at oscillator loci of Arabidopsis thaliana, 5' mutations of OsPRR37 (and OsCCA1 to a less degree) were under negative selection while those of OsPRR1 alleles were under strong positive selection. Together, range expansion of Asian rice can be elucidated by human selection on OsPRR1 alleles via local flowering time-yield relationships.
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Affiliation(s)
- Guangtong Gao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing 100093, China; (G.G.); (M.C.); (N.L.); (Y.X.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Maoxian Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing 100093, China; (G.G.); (M.C.); (N.L.); (Y.X.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rong Mo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing 100093, China; (G.G.); (M.C.); (N.L.); (Y.X.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Nan Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing 100093, China; (G.G.); (M.C.); (N.L.); (Y.X.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yunzhang Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing 100093, China; (G.G.); (M.C.); (N.L.); (Y.X.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
| | - Yingqing Lu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing 100093, China; (G.G.); (M.C.); (N.L.); (Y.X.)
- University of Chinese Academy of Sciences, Beijing 100049, China
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10
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Gu S, Zhang Z, Li J, Sun J, Cui Z, Li F, Zhuang J, Chen W, Su C, Wu L, Wang X, Guo Z, Xu H, Zhao M, Ma D, Chen W. Natural variation in OsSEC13 HOMOLOG 1 modulates redox homeostasis to confer cold tolerance in rice. PLANT PHYSIOLOGY 2023; 193:2180-2196. [PMID: 37471276 DOI: 10.1093/plphys/kiad420] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/17/2023] [Accepted: 06/05/2023] [Indexed: 07/22/2023]
Abstract
Rice (Oryza sativa L.) is a cold-sensitive species that often faces cold stress, which adversely affects yield productivity and quality. However, the genetic basis for low-temperature adaptation in rice remains unclear. Here, we demonstrate that 2 functional polymorphisms in O. sativa SEC13 Homolog 1 (OsSEH1), encoding a WD40-repeat nucleoporin, between the 2 subspecies O. sativa japonica and O. sativa indica rice, may have facilitated cold adaptation in japonica rice. We show that OsSEH1 of the japonica variety expressed in OsSEH1MSD plants (transgenic line overexpressing the OsSEH1 allele from Mangshuidao [MSD], cold-tolerant landrace) has a higher affinity for O. sativa metallothionein 2b (OsMT2b) than that of OsSEH1 of indica. This high affinity of OsSEH1MSD for OsMT2b results in inhibition of OsMT2b degradation, with decreased accumulation of reactive oxygen species and increased cold tolerance. Transcriptome analysis indicates that OsSEH1 positively regulates the expression of the genes encoding dehydration-responsive element-binding transcription factors, i.e. OsDREB1 genes, and induces the expression of multiple cold-regulated genes to enhance cold tolerance. Our findings highlight a breeding resource for improving cold tolerance in rice.
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Affiliation(s)
- Shuang Gu
- Rice Research Institute/Collaborative Innovation Center for Genetic Improvement and High Quality and Efficiency Production of Northeast Japonica Rice in China, Shenyang Agricultural University, Shenyang 110866, China
| | - Zhe Zhang
- Rice Research Institute/Collaborative Innovation Center for Genetic Improvement and High Quality and Efficiency Production of Northeast Japonica Rice in China, Shenyang Agricultural University, Shenyang 110866, China
| | - Jinquan Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
- Strube Research GmbH & Co. KG, Söllingen 38387, Germany
| | - Jian Sun
- Rice Research Institute/Collaborative Innovation Center for Genetic Improvement and High Quality and Efficiency Production of Northeast Japonica Rice in China, Shenyang Agricultural University, Shenyang 110866, China
| | - Zhibo Cui
- Rice Research Institute/Collaborative Innovation Center for Genetic Improvement and High Quality and Efficiency Production of Northeast Japonica Rice in China, Shenyang Agricultural University, Shenyang 110866, China
| | - Fengcheng Li
- Rice Research Institute/Collaborative Innovation Center for Genetic Improvement and High Quality and Efficiency Production of Northeast Japonica Rice in China, Shenyang Agricultural University, Shenyang 110866, China
| | - Jia Zhuang
- Rice Research Institute/Collaborative Innovation Center for Genetic Improvement and High Quality and Efficiency Production of Northeast Japonica Rice in China, Shenyang Agricultural University, Shenyang 110866, China
| | - Wanchun Chen
- Rice Research Institute/Collaborative Innovation Center for Genetic Improvement and High Quality and Efficiency Production of Northeast Japonica Rice in China, Shenyang Agricultural University, Shenyang 110866, China
| | - Chang Su
- Rice Research Institute/Collaborative Innovation Center for Genetic Improvement and High Quality and Efficiency Production of Northeast Japonica Rice in China, Shenyang Agricultural University, Shenyang 110866, China
| | - Lian Wu
- Rice Research Institute/Collaborative Innovation Center for Genetic Improvement and High Quality and Efficiency Production of Northeast Japonica Rice in China, Shenyang Agricultural University, Shenyang 110866, China
| | - Xiaoliang Wang
- Rice Research Institute/Collaborative Innovation Center for Genetic Improvement and High Quality and Efficiency Production of Northeast Japonica Rice in China, Shenyang Agricultural University, Shenyang 110866, China
| | - Zhifu Guo
- Rice Research Institute/Collaborative Innovation Center for Genetic Improvement and High Quality and Efficiency Production of Northeast Japonica Rice in China, Shenyang Agricultural University, Shenyang 110866, China
| | - Hai Xu
- Rice Research Institute/Collaborative Innovation Center for Genetic Improvement and High Quality and Efficiency Production of Northeast Japonica Rice in China, Shenyang Agricultural University, Shenyang 110866, China
| | - Minghui Zhao
- Rice Research Institute/Collaborative Innovation Center for Genetic Improvement and High Quality and Efficiency Production of Northeast Japonica Rice in China, Shenyang Agricultural University, Shenyang 110866, China
| | | | - Wenfu Chen
- Rice Research Institute/Collaborative Innovation Center for Genetic Improvement and High Quality and Efficiency Production of Northeast Japonica Rice in China, Shenyang Agricultural University, Shenyang 110866, China
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11
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Zhao H, Huang X, Yang Z, Li F, Ge X. Synergistic optimization of crops by combining early maturation with other agronomic traits. TRENDS IN PLANT SCIENCE 2023; 28:1178-1191. [PMID: 37208203 DOI: 10.1016/j.tplants.2023.04.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 04/16/2023] [Accepted: 04/24/2023] [Indexed: 05/21/2023]
Abstract
Many newly created early maturing varieties exhibit poor stress resistance and low yield, whereas stress-resistant varieties are typically late maturing. For this reason, the polymerization of early maturity and other desired agronomic qualities requires overcoming the negative connection between early maturity, multi-resistance, and yield, which presents a formidable challenge in current breeding techniques. We review the most salient constraints of early maturity breeding in current crop planting practices and the molecular mechanisms of different maturation timeframes in diverse crops from their origin center to production areas. We explore current breeding tactics and the future direction of crop breeding and the issues that must be resolved to accomplish the polymerization of desirable traits in light of the current obstacles and limitations.
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Affiliation(s)
- Hang Zhao
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China; National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; College of Life Sciences, Qufu Normal University, Qufu, 273165, China
| | - Xianzhong Huang
- Center for Crop Biotechnology, College of Agriculture, Anhui Science and Technology University, Chuzhou, China
| | - Zhaoen Yang
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China; National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Fuguang Li
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China; National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100 Xinjiang, China; Hainan Yazhou Bay Seed Lab, Sanya 572000, Hainan, China.
| | - Xiaoyang Ge
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China; National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100 Xinjiang, China; Hainan Yazhou Bay Seed Lab, Sanya 572000, Hainan, China.
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12
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Kang M, Wang X, Chen J, Fang Q, Liu J, Tang L, Liu L, Cao W, Zhu Y, Liu B. Extreme low-temperature events can alleviate micronutrient deficiencies while increasing potential health risks from heavy metals in rice. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 334:122165. [PMID: 37429493 DOI: 10.1016/j.envpol.2023.122165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 07/05/2023] [Accepted: 07/07/2023] [Indexed: 07/12/2023]
Abstract
Despite global warming, extreme low-temperature stress (LTS) events pose a significant threat to rice production (especially in East Asia) that can significantly impact micronutrient and heavy metal elements in rice. With two billion people worldwide facing micronutrient deficiencies (MNDs) and widespread heavy metal pollution in rice, understanding these impacts is crucial. We conducted detailed extreme LTS experiments with two rice (Oryza sativa L.) cultivars (Huaidao 5 and Nanjing 46) grown under four temperature levels (from 21/27 °C to 6/12 °C) and three LTS durations (three, six, and nine days). We observed significant interaction effects for LTS at different growth stages, durations and temperature levels on the contents and accumulation of mineral elements. The contents of most mineral elements (such Fe, Zn, As, Cu, and Cd) increased significantly under severe LTS at flowering, but decreased under LTS at the grain-filling stage. The accumulations of all mineral elements decreased at the three growth stages under LTS due to decreased grain weight. The contents and accumulation of mineral elements were more sensitive to LTS at the peak flowering stage than at the other two stages. Furthermore, the contents of most mineral elements in Nanjing 46 show larger variation under LTS compared to Huaidao 5. Accumulated cold degree days (ACDD, °C·d) were found to be suitable for quantifying the effects of LTS on the relative contents and accumulations of mineral elements. LTS at the flowering stage will help alleviate MNDs, but may also increase potential health risks from heavy metals. These results provide valuable insights for evaluating future climate change impacts on rice grain quality and potential health risks from heavy metals.
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Affiliation(s)
- Min Kang
- National Engineering and Technology Center for Information Agriculture, Engineering Research Center of Smart Agriculture, Ministry of Education, Key Laboratory for Crop System Analysis and Decision Making, Ministry of Agriculture, Jiangsu Key Laboratory for Information Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, PR China.
| | - Xue Wang
- National Engineering and Technology Center for Information Agriculture, Engineering Research Center of Smart Agriculture, Ministry of Education, Key Laboratory for Crop System Analysis and Decision Making, Ministry of Agriculture, Jiangsu Key Laboratory for Information Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, PR China.
| | - Jiankun Chen
- National Engineering and Technology Center for Information Agriculture, Engineering Research Center of Smart Agriculture, Ministry of Education, Key Laboratory for Crop System Analysis and Decision Making, Ministry of Agriculture, Jiangsu Key Laboratory for Information Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, PR China.
| | - Qizhao Fang
- National Engineering and Technology Center for Information Agriculture, Engineering Research Center of Smart Agriculture, Ministry of Education, Key Laboratory for Crop System Analysis and Decision Making, Ministry of Agriculture, Jiangsu Key Laboratory for Information Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, PR China.
| | - Jiaming Liu
- National Engineering and Technology Center for Information Agriculture, Engineering Research Center of Smart Agriculture, Ministry of Education, Key Laboratory for Crop System Analysis and Decision Making, Ministry of Agriculture, Jiangsu Key Laboratory for Information Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, PR China.
| | - Liang Tang
- National Engineering and Technology Center for Information Agriculture, Engineering Research Center of Smart Agriculture, Ministry of Education, Key Laboratory for Crop System Analysis and Decision Making, Ministry of Agriculture, Jiangsu Key Laboratory for Information Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, PR China.
| | - Leilei Liu
- National Engineering and Technology Center for Information Agriculture, Engineering Research Center of Smart Agriculture, Ministry of Education, Key Laboratory for Crop System Analysis and Decision Making, Ministry of Agriculture, Jiangsu Key Laboratory for Information Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, PR China.
| | - Weixing Cao
- National Engineering and Technology Center for Information Agriculture, Engineering Research Center of Smart Agriculture, Ministry of Education, Key Laboratory for Crop System Analysis and Decision Making, Ministry of Agriculture, Jiangsu Key Laboratory for Information Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, PR China.
| | - Yan Zhu
- National Engineering and Technology Center for Information Agriculture, Engineering Research Center of Smart Agriculture, Ministry of Education, Key Laboratory for Crop System Analysis and Decision Making, Ministry of Agriculture, Jiangsu Key Laboratory for Information Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, PR China.
| | - Bing Liu
- National Engineering and Technology Center for Information Agriculture, Engineering Research Center of Smart Agriculture, Ministry of Education, Key Laboratory for Crop System Analysis and Decision Making, Ministry of Agriculture, Jiangsu Key Laboratory for Information Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, PR China.
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13
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Mandal SN, Sanchez J, Bhowmick R, Bello OR, Van-Beek CR, de Los Reyes BG. Novel genes and alleles of the BTB/POZ protein family in Oryza rufipogon. Sci Rep 2023; 13:15466. [PMID: 37726366 PMCID: PMC10509276 DOI: 10.1038/s41598-023-41269-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 08/24/2023] [Indexed: 09/21/2023] Open
Abstract
The BTB/POZ family of proteins is widespread in plants and animals, playing important roles in development, growth, metabolism, and environmental responses. Although members of the expanded BTB/POZ gene family (OsBTB) have been identified in cultivated rice (Oryza sativa), their conservation, novelty, and potential applications for allele mining in O. rufipogon, the direct progenitor of O. sativa ssp. japonica and potential wide-introgression donor, are yet to be explored. This study describes an analysis of 110 BTB/POZ encoding gene loci (OrBTB) across the genome of O. rufipogon as outcomes of tandem duplication events. Phylogenetic grouping of duplicated OrBTB genes was supported by the analysis of gene sequences and protein domain architecture, shedding some light on their evolution and functional divergence. The O. rufipogon genome encodes nine novel BTB/POZ genes with orthologs in its distant cousins in the family Poaceae (Sorghum bicolor, Brachypodium distachyon), but such orthologs appeared to have been lost in its domesticated descendant, O. sativa ssp. japonica. Comparative sequence analysis and structure comparisons of novel OrBTB genes revealed that diverged upstream regulatory sequences and regulon restructuring are the key features of the evolution of this large gene family. Novel genes from the wild progenitor serve as a reservoir of potential new alleles that can bring novel functions to cultivars when introgressed by wide hybridization. This study establishes a foundation for hypothesis-driven functional genomic studies and their applications for widening the genetic base of rice cultivars through the introgression of novel genes or alleles from the exotic gene pool.
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Affiliation(s)
- Swarupa Nanda Mandal
- Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA
| | - Jacobo Sanchez
- Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA
| | - Rakesh Bhowmick
- ICAR-Vivekananda Parvatiya Krishi Anusandhan Sansthan, Almora, Uttarakhand, 263601, India
| | - Oluwatobi R Bello
- Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA
| | - Coenraad R Van-Beek
- Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA
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14
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Mao X, Zheng X, Chen W, Li C. Characterization and Gene Mapping of an Open-Glume Oryza sativa L. Mutant. Int J Mol Sci 2023; 24:12702. [PMID: 37628883 PMCID: PMC10454609 DOI: 10.3390/ijms241612702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/04/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023] Open
Abstract
Floral organ development determines agricultural productivity by affecting seed development, seed quality, and final yield. In this study, we described the novel ogl mutant in rice (Oryza sativa L.), which is characterized by an open-glume phenotype, increased pistil number, reduced stamen number, decreased seed setting rate, and smaller rice grains. Genetic analysis showed that the open-glume phenotype might be controlled by a recessive qualitative trait locus. Employing bulked segregant analysis (BSA), one candidate region was identified on rice chromosome 1. The glume opening phenotype cosegregated with SNP (Chr1:1522703), which was located at the start codon of one transcript of OsJAG, resulting in partial loss of OsJAG function. cDNA analysis revealed that OsJAG encodes two transcript variants. Compared to normal plants, the expression of OsJAG.1 was upregulated in open-glume plants. When investigating the glume phenotype, we found that the expression of genes related to floral development changed greatly in open-glume plants. Taken together, this work increases our understanding of the developmental role of OsJAG in rice floral development.
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Affiliation(s)
- Xingxue Mao
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
| | - Xiaoyu Zheng
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
| | - Wenfeng Chen
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
| | - Chen Li
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
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15
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Long Q, Qiu S, Man J, Ren D, Xu N, Luo R. OsAAI1 Increases Rice Yield and Drought Tolerance Dependent on ABA-Mediated Regulatory and ROS Scavenging Pathway. RICE (NEW YORK, N.Y.) 2023; 16:35. [PMID: 37535208 PMCID: PMC10400514 DOI: 10.1186/s12284-023-00650-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 07/22/2023] [Indexed: 08/04/2023]
Abstract
In this study, we investigated the function of OsAAI1 in yield and drought tolerance by constructing overexpression line OE-OsAAI1 and mutant line osaai1. Bioinformatics analysis showed that the AAI gene-OsAAI1- belongs to the HPS_like subfamily of the AAI_LTSS superfamily, and OsAAI1 was localized in the nucleus. The expression of OsAAI1 was significantly induced by ABA and drought stress. OsAAI1 overexpression (OE19) significantly increased, and gene mutant (osaai1-1) repressed plant height, primary root length, lateral root number, grain size and yield in rice. Moreover, physiological and biochemical analyses showed that osaai1 was sensitive to drought stress, while OE19 enhanced the drought tolerance in rice. DAB and NBT staining revealed that under drought treatment, osaai1 accumulated a large amount of ROS compared with the wild type, while OE19 accumulated the least, and CAT, APX, GPX, GR activities were higher in OE19 and lower in osaai1, suggesting that OE19 improves rice tolerance to drought stress by enhancing ROS scavenging ability. OE19 also induce the expression of ABA-mediated regulatory pathway genes and enhance accumulation of ABA content in rice seedling. Predictably, OE19 displayed enhanced sensitivity to ABA, and ROS accumulation was significantly higher than in wild type and osaai1 under 3 µM ABA treatment. Thus, these results suggest that OsAAI1 is a positive regulator of rice yield and drought tolerance dependent on the ABA-mediated regulatory and ROS scavenging pathway.
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Affiliation(s)
- Qing Long
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Institute of Agro-bioengineering, Guizhou University, Guiyang, 550025, Guizhou Province, China
| | - Shichun Qiu
- Chongqing Three Gorges Academy of Agricultural Sciences, Wanzhou, Chongqing City, 404155, China
| | - Jianmin Man
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Institute of Agro-bioengineering, Guizhou University, Guiyang, 550025, Guizhou Province, China
| | - Denghong Ren
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Institute of Agro-bioengineering, Guizhou University, Guiyang, 550025, Guizhou Province, China
| | - Ning Xu
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Institute of Agro-bioengineering, Guizhou University, Guiyang, 550025, Guizhou Province, China.
| | - Rui Luo
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Institute of Agro-bioengineering, Guizhou University, Guiyang, 550025, Guizhou Province, China.
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16
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Wu D, Xie L, Sun Y, Huang Y, Jia L, Dong C, Shen E, Ye CY, Qian Q, Fan L. A syntelog-based pan-genome provides insights into rice domestication and de-domestication. Genome Biol 2023; 24:179. [PMID: 37537691 PMCID: PMC10401782 DOI: 10.1186/s13059-023-03017-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 07/19/2023] [Indexed: 08/05/2023] Open
Abstract
BACKGROUND Asian rice is one of the world's most widely cultivated crops. Large-scale resequencing analyses have been undertaken to explore the domestication and de-domestication genomic history of Asian rice, but the evolution of rice is still under debate. RESULTS Here, we construct a syntelog-based rice pan-genome by integrating and merging 74 high-accuracy genomes based on long-read sequencing, encompassing all ecotypes and taxa of Oryza sativa and Oryza rufipogon. Analyses of syntelog groups illustrate subspecies divergence in gene presence-and-absence and haplotype composition and identify massive genomic regions putatively introgressed from ancient Geng/japonica to ancient Xian/indica or its wild ancestor, including almost all well-known domestication genes and a 4.5-Mbp centromere-spanning block, supporting a single domestication event in main rice subspecies. Genomic comparisons between weedy and cultivated rice highlight the contribution from wild introgression to the emergence of de-domestication syndromes in weedy rice. CONCLUSIONS This work highlights the significance of inter-taxa introgression in shaping diversification and divergence in rice evolution and provides an exploratory attempt by utilizing the advantages of pan-genomes in evolutionary studies.
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Affiliation(s)
- Dongya Wu
- Hainan Institute of Zhejiang University, Sanya, 572025, China
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
- Center for Evolutionary & Organismal Biology, Zhejiang University, Hangzhou, 310058, China
| | - Lingjuan Xie
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
| | - Yanqing Sun
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
| | - Yujie Huang
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Lei Jia
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
| | - Chenfeng Dong
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
| | - Enhui Shen
- Hainan Institute of Zhejiang University, Sanya, 572025, China
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
| | - Chu-Yu Ye
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
| | - Qian Qian
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.
| | - Longjiang Fan
- Hainan Institute of Zhejiang University, Sanya, 572025, China.
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China.
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17
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Jing CY, Zhang FM, Wang XH, Wang MX, Zhou L, Cai Z, Han JD, Geng MF, Yu WH, Jiao ZH, Huang L, Liu R, Zheng XM, Meng QL, Ren NN, Zhang HX, Du YS, Wang X, Qiang CG, Zou XH, Gaut BS, Ge S. Multiple domestications of Asian rice. NATURE PLANTS 2023; 9:1221-1235. [PMID: 37550371 DOI: 10.1038/s41477-023-01476-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 07/04/2023] [Indexed: 08/09/2023]
Abstract
The origin of domesticated Asian rice (Oryza sativa L.) has been controversial for more than half a century. The debates have focused on two leading hypotheses: a single domestication event in China or multiple domestication events in geographically separate areas. These two hypotheses differ in their predicted history of genes/alleles selected during domestication. Here we amassed a dataset of 1,578 resequenced genomes, including an expanded sample of wild rice from throughout its geographic range. We identified 993 selected genes that generated phylogenetic trees on which japonica and indica formed a monophyletic group, suggesting that the domestication alleles of these genes originated only once in either japonica or indica. Importantly, the domestication alleles of most selected genes (~80%) stemmed from wild rice in China, but the domestication alleles of a substantial minority of selected genes (~20%) originated from wild rice in South and Southeast Asia, demonstrating separate domestication events of Asian rice.
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Affiliation(s)
- Chun-Yan Jing
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Fu-Min Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiu-Hua Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mei-Xia Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lian Zhou
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Zhe Cai
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Jing-Dan Han
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Mu-Fan Geng
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wen-Hao Yu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zi-Hui Jiao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lei Huang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Rong Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiao-Ming Zheng
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qing-Lin Meng
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ning-Ning Ren
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hong-Xiang Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yu-Su Du
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xin Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Cheng-Gen Qiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xin-Hui Zou
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | | | - Song Ge
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
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18
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Lu Y. Gene Genealogy-Based Mutation Analysis Reveals Emergence of Aus, Tropical japonica, and Aromatic of Oryza sativa during the Later Stage of Rice Domestication. Genes (Basel) 2023; 14:1412. [PMID: 37510316 PMCID: PMC10379336 DOI: 10.3390/genes14071412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/20/2023] [Accepted: 07/03/2023] [Indexed: 07/30/2023] Open
Abstract
Asian rice (Oryza sativa L.) has become a model for understanding gene functions and domestication in recent decades; however, its own diversification is still controversial. Although the division of indica and japonica and five subgroups (aus, indica (sensu stricto), japonica (sensu stricto), tropical japonica, and aromatic) are broadly accepted, how they are phylogenetically related is not transparent. To clarify their relationships, a sample of 121 diverse genes was chosen here from 12 Oryza genomes (two parental and ten O. sativa (Os)) in parallel to allow gene genealogy-based mutation (GGM) analysis. From the sample, 361 Os mutations were shared by two or more subgroups (referred to here as trans mutations) from 549 mutations identified at 51 Os loci. The GGM analysis and related tests indicates that aus diverged from indica at a time significantly earlier than when tropical japonica split from japonica. The results also indicate that aromatic was selected from hybrid progeny of aus and tropical japonica and that all five subgroups share a significant number of the early mutations identified previously. The results suggest that aus, tropical japonica, and aromatic emerged sequentially within the most recent 4-5 millennia of rice domestication after the split of indica and japonica.
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Affiliation(s)
- Yingqing Lu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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19
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Ren W, Wang H, Du Y, Li Y, Feng Z, Zhou X, Kang G, Shu Q, Guo T, Guo H, Yu L, Jin W, Yang F, Li J, Ma J, Li W, Xu C, Chen X, Liu X, Yang C, Liu L, Zhou L. Multi-generation study of heavy ion beam-induced mutations and agronomic trait variations to accelerate rice breeding. FRONTIERS IN PLANT SCIENCE 2023; 14:1213807. [PMID: 37416884 PMCID: PMC10322207 DOI: 10.3389/fpls.2023.1213807] [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: 04/28/2023] [Accepted: 06/05/2023] [Indexed: 07/08/2023]
Abstract
Heavy ion beam (HIB) is an effective physical mutagen that has been widely used in plant mutational breeding. Systemic knowledge of the effects caused by different HIB doses at developmental and genomic levels will facilitate efficient breeding for crops. Here we examined the effects of HIB systematically. Kitaake rice seeds were irradiated by ten doses of carbon ion beams (CIB, 25 - 300 Gy), which is the most widely used HIB. We initially examined the growth, development and photosynthetic parameters of the M1 population and found that doses exceeding 125 Gy caused significant physiological damages to rice. Subsequently, we analyzed the genomic variations in 179 M2 individuals from six treatments (25 - 150 Gy) via whole-genome sequencing (WGS). The mutation rate peaks at 100 Gy (2.66×10-7/bp). Importantly, we found that mutations shared among different panicles of the same M1 individual are at low ratios, validating the hypothesis that different panicles may be derived from different progenitor cells. Furthermore, we isolated 129 mutants with distinct phenotypic variations, including changes in agronomic traits, from 11,720 M2 plants, accounting for a 1.1% mutation rate. Among them, about 50% possess stable inheritance in M3. WGS data of 11 stable M4 mutants, including three lines with higher yields, reveal their genomic mutational profiles and candidate genes. Our results demonstrate that HIB is an effective tool that facilitates breeding, that the optimal dose range for rice is 67 - 90% median lethal dose (LD50), and that the mutants isolated here can be further used for functional genomic research, genetic analysis, and breeding.
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Affiliation(s)
- Weibin Ren
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - He Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Yan Du
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yan Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Zhuo Feng
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xinhui Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Guisen Kang
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qingyao Shu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Tao Guo
- National Engineering Research Center of Plant Space Breeding, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Huijun Guo
- National Key Facility for Crop Gene Resources and Genetic Improvement, National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lixia Yu
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wenjie Jin
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - Fu Yang
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Jingpeng Li
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Jianzhong Ma
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, China
| | - Wenjian Li
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chaoli Xu
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xia Chen
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiao Liu
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chenan Yang
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Luxiang Liu
- National Key Facility for Crop Gene Resources and Genetic Improvement, National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Libin Zhou
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Beijing, China
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20
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Subudhi PK. Molecular Research in Rice. Int J Mol Sci 2023; 24:10063. [PMID: 37373210 DOI: 10.3390/ijms241210063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 06/01/2023] [Indexed: 06/29/2023] Open
Abstract
Rice is the most important source of nutrition for approximately half of the human population [...].
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Affiliation(s)
- Prasanta K Subudhi
- School of Plant, Environmental, and Soil Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
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21
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Osnato M. Evolution of flowering time genes in rice: From the paleolithic to the anthropocene. PLANT, CELL & ENVIRONMENT 2023; 46:1046-1059. [PMID: 36411270 DOI: 10.1111/pce.14495] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 11/08/2022] [Accepted: 11/12/2022] [Indexed: 06/16/2023]
Abstract
The evolutionary paths of humans and plants have crossed more than once throughout millennia. While agriculture contributed to the evolution of societies in prehistory, human selection of desirable traits contributed to the evolution of crops during centuries of cultivation. Among cereal crops, rice is currently grown around the globe and represents staple food for almost half of the world population. Over time, rice cultivation has expanded from subtropical to temperate regions thanks to artificial selection of mutants with impaired response to photoperiod. Additional regulatory mechanisms control flowering in response to diverse environmental cues, anticipating or delaying the floral transition to produce seeds in more favourable conditions. Nevertheless, the changing climate is threatening grain production because modern cultivars are sensitive to external fluctuations that go beyond their physiological range. One possibility to guarantee food production could be the exploitation of novel varieties obtained by crossing highly productive Asian rice with stress tolerant African rice. This review explores the genetic basis of the key traits that marked the long journey of rice cultivation from the end of the paleolithic to the anthropocene, with a focus on heading date. By 2050, will rice plants of the future flower in the outer space?
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Affiliation(s)
- Michela Osnato
- Institut de Ciència i Tecnologia Ambientals, Universitat Autónoma de Barcelona (ICTA-UAB), Bellaterra, Spain
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22
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Huang L, Yu J, Liu Q, Yu K, Zhang Q, Fan M, Jiang F, Han J, Wei H, Jian W, Zhao Z. Study on tillering stage cold tolerant response in overwintering cultivated rice via comparative transcriptomic. Food Energy Secur 2023. [DOI: 10.1002/fes3.450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2023] Open
Affiliation(s)
- Lunxiao Huang
- College of Life Sciences, Chongqing Engineering Research Center of Specialty Crop Resources Chongqing Normal University Chongqing China
| | - Jie Yu
- College of Life Sciences, Chongqing Engineering Research Center of Specialty Crop Resources Chongqing Normal University Chongqing China
| | - Qian Liu
- College of Life Sciences, Chongqing Engineering Research Center of Specialty Crop Resources Chongqing Normal University Chongqing China
| | - Kunchi Yu
- College of Life Sciences, Chongqing Engineering Research Center of Specialty Crop Resources Chongqing Normal University Chongqing China
| | - Qiuyu Zhang
- College of Life Sciences, Chongqing Engineering Research Center of Specialty Crop Resources Chongqing Normal University Chongqing China
| | - Mao Fan
- College of Life Sciences, Chongqing Engineering Research Center of Specialty Crop Resources Chongqing Normal University Chongqing China
| | - Fei Jiang
- College of Life Sciences, Chongqing Engineering Research Center of Specialty Crop Resources Chongqing Normal University Chongqing China
| | - Jiajia Han
- College of Life Sciences, Chongqing Engineering Research Center of Specialty Crop Resources Chongqing Normal University Chongqing China
| | - Hongyu Wei
- College of Life Sciences, Chongqing Engineering Research Center of Specialty Crop Resources Chongqing Normal University Chongqing China
| | - Wei Jian
- College of Life Sciences, Chongqing Engineering Research Center of Specialty Crop Resources Chongqing Normal University Chongqing China
| | - Zhengwu Zhao
- College of Life Sciences, Chongqing Engineering Research Center of Specialty Crop Resources Chongqing Normal University Chongqing China
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23
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Yang J, Chen A, Wei J, Xu J, Chen S, Tang W, Liu J, Wang H. Identification of QTLs and candidate genes for rice seed germinability under low temperature using high‐density genetic mapping and RNA‐seq. Food Energy Secur 2023. [DOI: 10.1002/fes3.452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023] Open
Affiliation(s)
- Jing Yang
- Yunnan Key Laboratory of Potato Biology Yunnan Normal University Kunming China
| | - Aie Chen
- Teaching Affairs Department Yunnan Normal University Kunming China
| | - Ji Wei
- Yunnan Key Laboratory of Potato Biology Yunnan Normal University Kunming China
| | - Jifen Xu
- Yunnan Key Laboratory of Potato Biology Yunnan Normal University Kunming China
| | - Shengnan Chen
- Yunnan Key Laboratory of Potato Biology Yunnan Normal University Kunming China
| | - Wei Tang
- Yunnan Key Laboratory of Potato Biology Yunnan Normal University Kunming China
| | - Jing Liu
- Yunnan Key Laboratory of Potato Biology Yunnan Normal University Kunming China
| | - Hongyang Wang
- Yunnan Key Laboratory of Potato Biology Yunnan Normal University Kunming China
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24
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Jiang S, Zhang X, Yang X, Liu C, Wang L, Ma B, Miao Y, Hu J, Tan K, Wang Y, Jiang H, Wang J. A chromosome-level genome assembly of an early matured aromatic Japonica rice variety Qigeng10 to accelerate rice breeding for high grain quality in Northeast China. FRONTIERS IN PLANT SCIENCE 2023; 14:1134308. [PMID: 36909446 PMCID: PMC9995481 DOI: 10.3389/fpls.2023.1134308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
Early-matured aromatic japonica rice from the Northeast is the most popular rice commodity in the Chinese market. The Qigeng10 (QG10) was one of the varieties with the largest planting area in this region in recent years. It was an early-matured japonica rice variety with a lot of superior traits such as semi-dwarf, lodging resistance, long grain, aromatic and good quality. Therefore, a high-quality assembly of Qigeng10 genome is critical and useful for japonica research and breeding. In this study, we produced a high-precision QG10 chromosome-level genome by using a combination of Nanopore and Hi-C platforms. Finally, we assembled the QG10 genome into 77 contigs with an N50 length of 11.80 Mb in 27 scaffolds with an N50 length of 30.55 Mb. The assembled genome size was 378.31Mb with 65 contigs and constituted approximately 99.59% of the 12 chromosomes. We identified a total of 1,080,819 SNPs and 682,392 InDels between QG10 and Nipponbare. We also annotated 57,599 genes by the Ab initio method, homology-based technique, and RNA-seq. Based on the assembled genome sequence, we detected the sequence variation in a total of 63 cloned genes involved in grain yield, grain size, disease tolerance, lodging resistance, fragrance, and many other important traits. Finally, we identified five elite alleles (qTGW2Nipponbare , qTGW3Nanyangzhan , GW5IR24 , GW6Suyunuo , and qGW8Basmati385 ) controlling long grain size, four elite alleles (COLD1Nipponbare , bZIP73Nipponbare , CTB4aKunmingxiaobaigu , and CTB2Kunmingxiaobaigu ) controlling cold tolerance, three non-functional alleles (DTH7Kitaake , Ghd7Hejiang19 , and Hd1Longgeng31 ) for early heading, two resistant alleles (PiaAkihikari and Pid4Digu ) for rice blast, a resistant allele STV11Kasalath for rice stripe virus, an NRT1.1BIR24 allele for higher nitrate absorption activity, an elite allele SCM3Chugoku117 for stronger culms, and the typical aromatic gene badh2-E2 for fragrance in QG10. These results not only help us to better elucidate the genetic mechanisms underlying excellent agronomic traits in QG10 but also have wide-ranging implications for genomics-assisted breeding in early-matured fragrant japonica rice.
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Affiliation(s)
- Shukun Jiang
- Qiqihar Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
- Heilongjiang Provincial Key Laboratory of Crop Physiology and Ecology in Cold Region, Heilongjiang Provincial Engineering Technology Research Center of Crop Cold Damage, Harbin, China
- Northeast Branch of National Salt-Alkali Tolerant Rice Technology Innovation Center, Harbin, China
| | - Xijuan Zhang
- Heilongjiang Provincial Key Laboratory of Crop Physiology and Ecology in Cold Region, Heilongjiang Provincial Engineering Technology Research Center of Crop Cold Damage, Harbin, China
- Northeast Branch of National Salt-Alkali Tolerant Rice Technology Innovation Center, Harbin, China
- Crop Cultivation and Tillage Institute of Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Xianli Yang
- Heilongjiang Provincial Key Laboratory of Crop Physiology and Ecology in Cold Region, Heilongjiang Provincial Engineering Technology Research Center of Crop Cold Damage, Harbin, China
- Northeast Branch of National Salt-Alkali Tolerant Rice Technology Innovation Center, Harbin, China
- Crop Cultivation and Tillage Institute of Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Chuanzeng Liu
- Qiqihar Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
- Northeast Branch of National Salt-Alkali Tolerant Rice Technology Innovation Center, Harbin, China
| | - Lizhi Wang
- Heilongjiang Provincial Key Laboratory of Crop Physiology and Ecology in Cold Region, Heilongjiang Provincial Engineering Technology Research Center of Crop Cold Damage, Harbin, China
- Northeast Branch of National Salt-Alkali Tolerant Rice Technology Innovation Center, Harbin, China
- Crop Cultivation and Tillage Institute of Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Bo Ma
- Qiqihar Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
- Northeast Branch of National Salt-Alkali Tolerant Rice Technology Innovation Center, Harbin, China
| | - Yi Miao
- Qiqihar Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
- Northeast Branch of National Salt-Alkali Tolerant Rice Technology Innovation Center, Harbin, China
| | - Jifang Hu
- Qiqihar Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
- Northeast Branch of National Salt-Alkali Tolerant Rice Technology Innovation Center, Harbin, China
| | - Kefei Tan
- Qiqihar Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
- Northeast Branch of National Salt-Alkali Tolerant Rice Technology Innovation Center, Harbin, China
| | - Yuxian Wang
- Qiqihar Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
- Northeast Branch of National Salt-Alkali Tolerant Rice Technology Innovation Center, Harbin, China
| | - Hui Jiang
- Keshan Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
| | - Junhe Wang
- Heilongjiang Provincial Key Laboratory of Crop Physiology and Ecology in Cold Region, Heilongjiang Provincial Engineering Technology Research Center of Crop Cold Damage, Harbin, China
- Crop Cultivation and Tillage Institute of Heilongjiang Academy of Agricultural Sciences, Harbin, China
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25
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Zhang B, Pan X, Yang Y, Dong F, Xu J, Wu X, Zheng Y. Dissipation dynamics and comparative dietary exposure assessment of mefentrifluconazole in rice. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 250:114482. [PMID: 36586164 DOI: 10.1016/j.ecoenv.2022.114482] [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: 07/13/2022] [Revised: 11/08/2022] [Accepted: 12/24/2022] [Indexed: 06/17/2023]
Abstract
A fast and sensitive analytical method based on UHPLC coupled with tandem mass spectrometry was established to investigate the dissipation and final residual amounts of mefentrifluconazole in rice, and dietary risk to consumers was evaluated. The method provided good linearity (R2 ≥ 0.9979), accuracy (recovery range, 79.0-101.5%), precision (relative standard deviation range, 1.3-13.9%), and sensitivity (limit of quantification, 0.005 mg/kg). The dissipation dynamics of mefentrifluconazole in rice followed first-order kinetics, with half-lives of 2.8-16.6 days. The final residues of mefentrifluconazole in various samples of harvested brown rice ranged from less than the limit of quantification to 0.092 mg/kg, the latter value being higher than the maximum residue limit recommended by the European Union. Comparative dietary exposure of mefentrifluconazole was assessed using field data and Chinese dietary patterns for different genders, regions, and age data. Although the results showed acceptable levels of risk for both acute exposure (the percentage of the acute reference dose ≤ 0.7483%) and chronic dietary intake (the percentage of acceptable daily intake ≤ 31.8516%), more studies of children are needed because they are at higher risk than other groups. This work provides the necessary data for registering and establishing the maximum residue limit for mefentrifluconazole in rice in China and reveals the potential risks to different groups of long-term application of mefentrifluconazole to rice and other crops.
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Affiliation(s)
- Binbin Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xinglu Pan
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Yun Yang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Fengshou Dong
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jun Xu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xiaohu Wu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yongquan Zheng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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26
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Toledo MC, Lee JS, Batista BL, Olympio KPK, Nardocci AC. Exposure to Inorganic Arsenic in Rice in Brazil: A Human Health Risk Assessment. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:16460. [PMID: 36554339 PMCID: PMC9778750 DOI: 10.3390/ijerph192416460] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 12/03/2022] [Accepted: 12/05/2022] [Indexed: 06/17/2023]
Abstract
In certain populations, rice is the main source of exposure to inorganic arsenic (iAs), which is associated with cancer and non-cancer effects. Although rice is a staple food in Brazil, there have been few studies about the health risks for the Brazilian population. The objective of this study was to assess the risks of exposure to iAs from white rice and brown rice in Brazil, in terms of the carcinogenic and non-carcinogenic effects, and to propose measures to mitigate those risks. The incremental lifetime cancer risk (ILCR) and hazard quotient (HQ) were calculated in a probabilistic framework. The mean ILCR was 1.5 × 10-4 for white rice and 6.0 × 10-6 for brown rice. The HQ for white and brown rice was under 1. The ILCR for white and brown rice was high, even though the iAs concentration in rice is below the maximum contaminant level. The risk for brown rice consumption was lower, which was not expected. Various mitigation measures discussed in this report are estimated to reduce the risk from rice consumption by 5-67%. With the support of public policies, measures to reduce these risks for the Brazilian population would have a positive impact on public health.
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Affiliation(s)
- Michele C. Toledo
- School of Public Health, University of São Paulo, São Paulo 01246-904, Brazil
| | - Janice S. Lee
- United States Environmental Protection Agency, Research Triangle Park, NC 27711, USA
| | - Bruno L. Batista
- Center for Natural and Human Sciences, Federal University of the ABC, Santo André 09210-580, Brazil
| | - Kelly P. K. Olympio
- School of Public Health, University of São Paulo, São Paulo 01246-904, Brazil
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Shahidi F, Danielski R, Rhein SO, Meisel LA, Fuentes J, Speisky H, Schwember AR, de Camargo AC. Wheat and Rice beyond Phenolic Acids: Genetics, Identification Database, Antioxidant Properties, and Potential Health Effects. PLANTS (BASEL, SWITZERLAND) 2022; 11:3283. [PMID: 36501323 PMCID: PMC9739071 DOI: 10.3390/plants11233283] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/23/2022] [Accepted: 11/24/2022] [Indexed: 06/17/2023]
Abstract
Wheat and rice play a vital role in human nutrition and food security. A better understanding of the potential health benefits associated with consuming these cereals, combined with studies by plant scientists and food chemists to view the entire food value chain from the field, pre and post-harvest processing, and subsequent "fork" consumption, may provide the necessary tools to optimize wheat and rice production towards the goal of better human health improvement and food security, providing tools to better adapt to the challenges associated with climate change. Since the available literature usually focuses on only one food chain segment, this narrative review was designed to address the identities and concentration of phenolics of these cereal crops from a farm-to-fork perspective. Wheat and rice genetics, phenolic databases, antioxidant properties, and potential health effects are summarized. These cereals contain much more than phenolic acids, having significant concentrations of flavonoids (including anthocyanins) and proanthocyanidins in a cultivar-dependent manner. Their potential health benefits in vitro have been extensively studied. According to a number of in vivo studies, consumption of whole wheat, wheat bran, whole rice, and rice bran may be strategies to improve health. Likewise, anthocyanin-rich cultivars have shown to be very promising as functional foods.
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Affiliation(s)
- Fereidoon Shahidi
- Department of Biochemistry, Memorial University of Newfoundland, St. John’s, NL A1C 5S7, Canada
| | - Renan Danielski
- Department of Biochemistry, Memorial University of Newfoundland, St. John’s, NL A1C 5S7, Canada
| | - Samantha Ottani Rhein
- Nutrition and Food Technology Institute, University of Chile, Santiago 7830490, Chile
| | - Lee A. Meisel
- Nutrition and Food Technology Institute, University of Chile, Santiago 7830490, Chile
| | - Jocelyn Fuentes
- Nutrition and Food Technology Institute, University of Chile, Santiago 7830490, Chile
| | - Hernan Speisky
- Nutrition and Food Technology Institute, University of Chile, Santiago 7830490, Chile
| | - Andrés R. Schwember
- Departament of Plant Sciences, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
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28
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Abdirad S, Wu Y, Ghorbanzadeh Z, Tazangi SE, Amirkhani A, Fitzhenry MJ, Kazemi M, Ghaffari MR, Koobaz P, Zeinalabedini M, Habibpourmehraban F, Masoomi-Aladizgeh F, Atwell BJ, Mirzaei M, Salekdeh GH, Haynes PA. Proteomic analysis of the meristematic root zone in contrasting genotypes reveals new insights in drought tolerance in rice. Proteomics 2022; 22:e2200100. [PMID: 35920597 DOI: 10.1002/pmic.202200100] [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: 03/11/2022] [Revised: 07/18/2022] [Accepted: 07/21/2022] [Indexed: 12/29/2022]
Abstract
Drought is responsible for major losses in rice production. Root tips contain meristematic and elongation zones that play major roles in determination of root traits and adaptive strategies to drought. In this study we analysed two contrasting genotypes of rice: IR64, a lowland, drought-susceptible, and shallow-rooting genotype; and Azucena, an upland, drought-tolerant, and deep-rooting genotype. Samples were collected of root tips of plants grown under control and water deficit stress conditions. Quantitative proteomics analysis resulted in the identification of 7294 proteins from the root tips of IR64 and 6307 proteins from Azucena. Data are available via ProteomeXchange with identifier PXD033343. Using a Partial Least Square Discriminant Analysis on 4170 differentially abundant proteins, 1138 statistically significant proteins across genotypes and conditions were detected. Twenty two enriched biological processes showing contrasting patterns between two genotypes in response to stress were detected through gene ontology enrichment analysis. This included identification of novel proteins involved in root elongation with specific expression patterns in Azucena, including four Expansins and seven Class III Peroxidases. We also detected an antioxidant network and a metallo-sulfur cluster assembly machinery in Azucena, with roles in reactive oxygen species and iron homeostasis, and positive effects on root cell cycle, growth and elongation.
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Affiliation(s)
- Somayeh Abdirad
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran
| | - Yunqi Wu
- Australian Proteome Analysis Facility, Macquarie University, North Ryde, New South Wales, Australia
| | - Zahra Ghorbanzadeh
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran
| | - Sara Esmaeili Tazangi
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran
| | - Ardeshir Amirkhani
- Australian Proteome Analysis Facility, Macquarie University, North Ryde, New South Wales, Australia
| | - Matthew J Fitzhenry
- Australian Proteome Analysis Facility, Macquarie University, North Ryde, New South Wales, Australia
| | - Mehrbano Kazemi
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran
| | - Mohammad Reza Ghaffari
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran
| | - Parisa Koobaz
- Department of Molecular Physiology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran
| | - Mehrshad Zeinalabedini
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran
| | | | | | - Brian J Atwell
- School of Natural Sciences, Macquarie University, North Ryde, New South Wales, Australia
| | - Mehdi Mirzaei
- Australian Proteome Analysis Facility, Macquarie University, North Ryde, New South Wales, Australia.,School of Natural Sciences, Macquarie University, North Ryde, New South Wales, Australia
| | - Ghasem Hosseini Salekdeh
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran.,School of Natural Sciences, Macquarie University, North Ryde, New South Wales, Australia
| | - Paul A Haynes
- School of Natural Sciences, Macquarie University, North Ryde, New South Wales, Australia
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29
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Zhang M, Zhao R, Huang K, Huang S, Wang H, Wei Z, Li Z, Bian M, Jiang W, Wu T, Du X. The OsWRKY63-OsWRKY76-OsDREB1B module regulates chilling tolerance in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:383-398. [PMID: 35996876 DOI: 10.1111/tpj.15950] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 08/05/2022] [Accepted: 08/18/2022] [Indexed: 06/15/2023]
Abstract
Rice (Oryza sativa) is sensitive to low temperatures, which affects the yield and quality of rice. Therefore, uncovering the molecular mechanisms behind chilling tolerance is a critical task for improving cold tolerance in rice cultivars. Here, we report that OsWRKY63, a WRKY transcription factor with an unknown function, negatively regulates chilling tolerance in rice. OsWRKY63-overexpressing rice lines are more sensitive to cold stress. Conversely, OsWRKY63-knockout mutants generated using a CRISPR/Cas9 genome editing approach exhibited increased chilling tolerance. OsWRKY63 was expressed in all rice tissues, and OsWRKY63 expression was induced under cold stress, dehydration stress, high salinity stress, and ABA treatment. OsWRKY63 localized in the nucleus plays a role as a transcription repressor and downregulates many cold stress-related genes and reactive oxygen species scavenging-related genes. Molecular, biochemical, and genetic assays showed that OsWRKY76 is a direct target gene of OsWRKY63 and that its expression is suppressed by OsWRKY63. OsWRKY76-knockout lines had dramatically decreased cold tolerance, and the cold-induced expression of five OsDREB1 genes was repressed. OsWRKY76 interacted with OsbHLH148, transactivating the expression of OsDREB1B to enhance chilling tolerance in rice. Thus, our study suggests that OsWRKY63 negatively regulates chilling tolerance through the OsWRKY63-OsWRKY76-OsDREB1B transcriptional regulatory cascade in rice.
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Affiliation(s)
- Mingxing Zhang
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Ranran Zhao
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Kai Huang
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Shuangzhan Huang
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Haitao Wang
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Zhiqi Wei
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Zhao Li
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Mingdi Bian
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Wenzhu Jiang
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Tao Wu
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Xinglin Du
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
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30
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Wang X, Wang W, Tai S, Li M, Gao Q, Hu Z, Hu W, Wu Z, Zhu X, Xie J, Li F, Zhang Z, Zhi L, Zhang F, Ma X, Yang M, Xu J, Li Y, Zhang W, Yang X, Chen Y, Zhao Y, Fu B, Zhao X, Li J, Wang M, Yue Z, Fang X, Zeng W, Yin Y, Zhang G, Xu J, Zhang H, Li Z, Li Z. Selective and comparative genome architecture of Asian cultivated rice (Oryza sativa L.) attributed to domestication and modern breeding. J Adv Res 2022; 42:1-16. [PMID: 35988902 PMCID: PMC9788959 DOI: 10.1016/j.jare.2022.08.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 07/28/2022] [Accepted: 08/07/2022] [Indexed: 12/27/2022] Open
Abstract
INTRODUCTION Rice, Oryza sativa L. (Os), is one of the oldest domesticated cereals that has also gone through extensive improvement in modern breeding. OBJECTIVES How rice was domesticated and impacted by modern breeding. METHODS We performed comprehensive analyses of genomic sequences of 504 accessions of Os and 456 accessions of O. rufipogon/O. nivara (Or). RESULTS The natural selection on Or before domestication and the natural and artificial selection during domestication together shaped the well-differentiated genomes of two subspecies, geng(j) (japonica) and xian(i) (indica), while breeding has made apparent genomic imprints between landrace and modern varieties of each subspecies, and also between primary modern and advanced modern varieties of xian(i). Selection during domestication and breeding left genome-wide selective signals covering ∼ 22.8 % and ∼ 8.6 % of the Os genome, significantly reduced within-population genomic diversity by ∼ 22 % in xian(i) and ∼ 53 % in geng(j) plus more pronounced subspecific differentiation. Only ∼ 10 % reduction in the total genomic diversity was observed between the Os and Or populations, indicating domestication did not suffer severe genetic bottleneck. CONCLUSION Our results revealed clear differentiation of the Or accessions into three large populations, two of which correspond to the well-differentiated Os subspecies, geng(j) and xian(i). Improved productivity and common changes in the same suit of adaptive traits in xian(i) and geng(j) during domestication and breeding resulted apparently from compensatory and convergent selections for different genes/alleles acting in the common KEGG terms and/or same gene families, and thus maintaining or even increasing the within population diversity and subspecific differentiation of Os, while more genes/alleles of novel function were selected during domestication than modern breeding. Our results supported the multiple independent domestication of Os in Asia and suggest the more efficient utilization of the rich diversity within Os by exploiting inter-subspecific and among population diversity in future rice improvement.
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Affiliation(s)
- Xueqiang Wang
- State Key Laboratory of Agrobiotechnology / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China,Institute of Crop Science, Plant Precision Breeding Academy, Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Wensheng Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China,The College of Agronomy, Anhui Agricultural University, Hefei, China
| | | | - Min Li
- The College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Qiang Gao
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Zhiqiang Hu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Wushu Hu
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Zhichao Wu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaoyang Zhu
- State Key Laboratory of Agrobiotechnology / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Jianyin Xie
- State Key Laboratory of Agrobiotechnology / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Fengmei Li
- State Key Laboratory of Agrobiotechnology / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zhifang Zhang
- State Key Laboratory of Agrobiotechnology / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Linran Zhi
- State Key Laboratory of Agrobiotechnology / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Fan Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China,The College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Xiaoqian Ma
- State Key Laboratory of Agrobiotechnology / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Ming Yang
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Jiabao Xu
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Yanhong Li
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Wenzhuo Zhang
- State Key Laboratory of Agrobiotechnology / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Xiyu Yang
- State Key Laboratory of Agrobiotechnology / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Ying Chen
- College of Information and Electrical Engineering, China Agricultural University, Beijing 100193, China
| | - Yan Zhao
- State Key Laboratory of Agrobiotechnology / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Binying Fu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiuqin Zhao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jinjie Li
- State Key Laboratory of Agrobiotechnology / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Miao Wang
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Zhen Yue
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | | | - Wei Zeng
- The College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Ye Yin
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Gengyun Zhang
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China,State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Jianlong Xu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China,Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Hongliang Zhang
- State Key Laboratory of Agrobiotechnology / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China,Corresponding authors at: Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China (Z. Li).
| | - Zichao Li
- State Key Laboratory of Agrobiotechnology / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China,Corresponding authors at: Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China (Z. Li).
| | - Zhikang Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China,The College of Agronomy, Anhui Agricultural University, Hefei, China,Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China,Corresponding authors at: Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China (Z. Li).
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31
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Bates J. The Fits and Starts of Indian Rice Domestication: How the Movement of Rice Across Northwest India Impacted Domestication Pathways and Agricultural Stories. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.924977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Rice is currently the staple food for over 3.5 billion people and is arguably the most important crop exploited by humans. Understanding how we came to the point where a single crop dominates the lives of almost half of the Earth’s population has major significance for our future, even more so given the climatic instability we face today, as rice is a cereal that is dependent on water to an extreme degree. In this study, the nature of early rice agriculture in South Asia is explored, looking at how this critical crop may have begun to be exploited, cultivated, and then brought under agricultural regimes during the long span between c.6500 and 1500 BC. There is now clear evidence for early Holocene cultivation of rice in the Middle Gangetic plains of northern India, but there is still considerable debate about the timing of when this cultivation began and whether it involved domestication of rice. By 3200 BC, however, rice agriculture was present outside the Ganges in the Indus Civilization. The data show accelerated domestication in the Indus environment and agricultural systems that played a part in later hybridization with the arrival of Chinese rice. Understanding how this move from its place of origin to a new environment may have become entangled in the domestication pathways of South Asia rice prior to the arrival of Chinese rice c.1500 BC are important to the overall rice story, as they play into modern concerns relating to biodiversity and different ways of growing and watering rice.
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32
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Zhou J, Yang Y, Lv Y, Pu Q, Li J, Zhang Y, Deng X, Wang M, Wang J, Tao D. Interspecific Hybridization Is an Important Driving Force for Origin and Diversification of Asian Cultivated Rice Oryza sativa L. FRONTIERS IN PLANT SCIENCE 2022; 13:932737. [PMID: 35845644 PMCID: PMC9280345 DOI: 10.3389/fpls.2022.932737] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 05/25/2022] [Indexed: 06/15/2023]
Abstract
As one of the most important crops, Asian cultivated rice has evolved into a complex group including several subgroups adapting various eco-climate-systems around the globe. Here, we pictured a comprehensive view of its original domestication, divergences, and the origin of different subgroups by integrating agriculture, archeology, genetics, nuclear, and cytoplasm genome results. Then, it was highlighted that interspecific hybridization-introgression has played important role in improving the genetic diversity and adaptation of Oryza sativa during its evolution process. Natural hybridization-introgression led to the origin of indica, aus, and basmatic subgroups, which adapted to changing cultivated environments, and produced feral weedy rice coexisting and competing with cultivars under production management. Artificial interspecific hybridization-introgression gained several breakthroughs in rice breeding, such as developing three-line hybrid rice, new rice for Africa (NERICA), and some important pest and disease resistance genes in rice genetic improvement, contributing to the stable increase of rice production to meet the expanding human population. We proposed a series to exploit the virtues of hybridization-introgression in the genetic improvement of Asian cultivated rice. But some key issues such as reproductive barriers especially hybrid sterility should be investigated further, which are conducive to gene exchange between cultivated rice and its relatives, and even is beneficial to exploiting interspecific hybrid vigor. New technologies help introduce favorable genes from distant wild species to Asian cultivated rice, such as transgenic and genome editing systems. Rising introgression lines in a wider range with multi-donor benefits allele mining, understanding genetic network of rice growth and development, yield formation, and environmental adaptation. Then, integration of new tools and interspecific hybridization can be a future direction to develop more usable breeding populations which can make Asian cultivated rice more resilient to the changing climate and world.
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Affiliation(s)
- Jiawu Zhou
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Ying Yang
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Yonggang Lv
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Qiuhong Pu
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Jing Li
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Yu Zhang
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Xianneng Deng
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Min Wang
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
- Institute of Plant Resources, Yunnan University, Kunming, China
| | - Jie Wang
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
- Institute of Plant Resources, Yunnan University, Kunming, China
| | - Dayun Tao
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
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33
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Zhang Y, Wang J, Pu Q, Yang Y, Lv Y, Zhou J, Li J, Deng X, Wang M, Tao D. Understanding the Nature of Hybrid Sterility and Divergence of Asian Cultivated Rice. FRONTIERS IN PLANT SCIENCE 2022; 13:908342. [PMID: 35832226 PMCID: PMC9272003 DOI: 10.3389/fpls.2022.908342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 05/30/2022] [Indexed: 06/15/2023]
Abstract
Intraspecific hybrid sterility is a common form of postzygotic reproductive isolation in Asian cultivated rice, which is also the major obstacle to utilize the strong heterosis in the rice breeding program. Here, we review recent progress in classification and hybrid sterility in Asian cultivated rice. A genome-wide analysis of numerous wild relatives of rice and Asian cultivated rice has provided insights into the origin and differentiation of Asian cultivated rice, and divided Asian cultivated rice into five subgroups. More than 40 conserved and specific loci were identified to be responsible for the hybrid sterility between subgroup crosses by genetic mapping, which also contributed to the divergence of Asian cultivated rice. Most of the studies are focused on the sterile barriers between indica and japonica crosses, ignoring hybrid sterility among other subgroups, leading to neither a systematical understanding of the nature of hybrid sterility and subgroup divergence, nor effectively utilizing strong heterosis between the subgroups in Asian cultivated rice. Future studies will aim at identifying and characterizing genes for hybrid sterility and segregation distortion, comparing and understanding the molecular mechanism of hybrid sterility, and drawing a blueprint for intraspecific hybrid sterility loci derived from cross combinations among the five subgroups. These studies would provide scientific and accurate guidelines to overcome the intraspecific hybrid sterility according to the parent subgroup type identification, allowing the utilization of heterosis among subgroups, also helping us unlock the mysterious relationship between hybrid sterility and Asian cultivated rice divergence.
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Affiliation(s)
- Yu Zhang
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences (YAAS), Kunming, China
| | - Jie Wang
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences (YAAS), Kunming, China
- Institute of Plant Resources, Yunnan University, Kunming, China
| | - Qiuhong Pu
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences (YAAS), Kunming, China
| | - Ying Yang
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences (YAAS), Kunming, China
| | - Yonggang Lv
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences (YAAS), Kunming, China
| | - Jiawu Zhou
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences (YAAS), Kunming, China
| | - Jing Li
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences (YAAS), Kunming, China
| | - Xianneng Deng
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences (YAAS), Kunming, China
| | - Min Wang
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences (YAAS), Kunming, China
- Institute of Plant Resources, Yunnan University, Kunming, China
| | - Dayun Tao
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences (YAAS), Kunming, China
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34
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Chamberlain-Irwin HN, Hufford MB. Convergent domestication: Finding the genes that make crops. Curr Biol 2022; 32:R585-R588. [PMID: 35728534 DOI: 10.1016/j.cub.2022.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A recent study shows that convergent selection of orthologs encoding a WD40 protein in maize and rice occurs during domestication. Knockout of these genes increases yield in both crops with no detectable effects on other agronomic traits. Identification of convergent selection can focus improvement efforts.
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Affiliation(s)
| | - Matthew B Hufford
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA.
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35
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Discovery of the Earliest Rice Paddy in the Mixed Rice–Millet Farming Area of China. LAND 2022. [DOI: 10.3390/land11060831] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Neolithic rice remains were recovered from a mixed rice–millet farming area in China outside the original centers of rice farming. Whether the rice remains were the result of local cultivation or obtained through trade remains unclear. Rice paddy fields are direct evidence of local cultivation. In this study, phytolith samples from the Zhangwangzhuang site were analyzed. The discriminant function distinguished 17 of 30 samples in the suspected paddy field area as rice paddy fields with an average probability of 74%; The proportion of rice bulliform phytoliths with ≥9 scales indicated that rice (Oryza sativa) was still being domesticated and, moreover, six η-type phytoliths from broomcorn millet (Panicum miliaceum) were identified. These results suggested that the suspected paddy field at Zhangwangzhuang might be the earliest rice paddy field (ca. 6000 cal. BP) in northern China and that mixed farming was practiced here since the early Yangshao period. This study adopted discriminant analysis methods to discover ancient rice paddy fields, observed rice paddy fields outside the core rice origin area, and provided the earliest evidence regarding the development of mixed rice–millet farming in the upper Huai River region.
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Zhang J, Sun Y, Zhou Z, Zhang Y, Yang Y, Zan X, Li X, Wan J, Gao X, Chen R, Huang Z, Li L, Xu Z. OsSCL30 overexpression reduces the tolerance of rice seedlings to low temperature, drought and salt. Sci Rep 2022; 12:8385. [PMID: 35589923 PMCID: PMC9120446 DOI: 10.1038/s41598-022-12438-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 05/11/2022] [Indexed: 01/19/2023] Open
Abstract
Rice is one of the main food crops for the world population. Various abiotic stresses, such as low temperature, drought, and high salinity, affect rice during the entire growth period, determining its yield and quality, and even leading to plant death. In this study, by constructing overexpression vectors D-163 + 1300:OsSCL30 and D-163 + 1300-AcGFP:OsSCL30-GFP, the mechanism of action of OsSCL30 in various abiotic stresses was explored. Bioinformatics analysis showed that OsSCL30 was located on the chromosome 12 of rice Nipponbare, belonging to the plant-specific SCL subfamily of the SR protein family. The 1500 bp section upstream of the open reading frame start site contains stress-related cis-acting elements such as ABRE, MYC, and MYB. Under normal conditions, the expression of OsSCL30 was higher in leaves and leaf sheaths. The results of reverse transcription polymerase chain reaction showed that the expression of OsSCL30 decreased after low temperature, drought and salt treatment. In root cells OsSCL30 was localized in the nuclei. The results of the rice seedling tolerance and recovery tests showed that overexpression of OsSCL30 diminished the resistance to low temperature, drought and salt stresses in transgenic rice and resulted in larger accumulation of reactive oxygen species. This study is of great significance for exploring the response mechanisms of SR proteins under abiotic stresses.
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Affiliation(s)
- Jia Zhang
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Rice Research Institute of Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yihao Sun
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Rice Research Institute of Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Zhanmei Zhou
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Rice Research Institute of Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yifan Zhang
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Rice Research Institute of Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yanmei Yang
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Rice Research Institute of Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xiaofei Zan
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Rice Research Institute of Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xiaohong Li
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Rice Research Institute of Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Jiale Wan
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Rice Research Institute of Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xiaoling Gao
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Rice Research Institute of Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Rongjun Chen
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Rice Research Institute of Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Zhengjian Huang
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Rice Research Institute of Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Lihua Li
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Rice Research Institute of Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
| | - Zhengjun Xu
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Rice Research Institute of Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
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Lu R, Chen Y, Zhang X, Feng Y, Comes HP, Li Z, Zheng Z, Yuan Y, Wang L, Huang Z, Guo Y, Sun G, Olsen KM, Chen J, Qiu Y. Genome sequencing and transcriptome analyses provide insights into the origin and domestication of water caltrop (Trapa spp., Lythraceae). PLANT BIOTECHNOLOGY JOURNAL 2022; 20:761-776. [PMID: 34861095 PMCID: PMC8989495 DOI: 10.1111/pbi.13758] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 11/25/2021] [Indexed: 06/13/2023]
Abstract
Humans have domesticated diverse species from across the plant kingdom; however, our current understanding of plant domestication is largely founded on major cereal crops. Here, we examine the evolutionary processes and genetic basis underlying the domestication of water caltrop (Trapa spp., Lythraceae), a traditional, yet presently underutilized non-cereal crop that sustained early Chinese agriculturalists. We generated a chromosome-level genome assembly of tetraploid T. natans, and then divided the allotetraploid genome into two subgenomes. Based on resequencing data from 57 accessions, representing cultivated diploid T. natans, wild T. natans (2x and 4x) and diploid T. incisa, we showed that water caltrop was likely first domesticated in the Yangtze River Valley as early as 6300 yr BP, and experienced a second improvement c. 800 years ago. We also provided strong support for an allotetraploid origin of T. natans within the past 230 000-310 000 years. By integrating selective sweep and transcriptome profiling analyses, we identified a number of genes potentially selected and/or differentially expressed during domestication, some of which likely contributed not only to larger fruit sizes but also to a more vigorous root system, facilitating nutrient uptake, environmental stress response and underwater photosynthesis. Our results shed light on the evolutionary and domestication history of water caltrop, one of the earliest domesticated crops in China. This study has implications for genomic-assisted breeding of this presently underutilized aquatic plant, and improves our general understanding of plant domestication.
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Affiliation(s)
- Rui‐Sen Lu
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life SciencesZhejiang UniversityHangzhouZhejiangChina
- Institute of BotanyJiangsu Province and Chinese Academy of SciencesNanjingChina
| | - Yang Chen
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life SciencesZhejiang UniversityHangzhouZhejiangChina
| | - Xin‐Yi Zhang
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life SciencesZhejiang UniversityHangzhouZhejiangChina
| | - Yu Feng
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life SciencesZhejiang UniversityHangzhouZhejiangChina
| | | | - Zheng Li
- Department of Ecology and Evolutionary BiologyUniversity of ArizonaTucsonAZUSA
| | - Zhai‐Sheng Zheng
- Jinhua Academy of Agricultural Sciences (Zhejiang Institute of Agricultural Machinery)JinhuaZhejiangChina
| | - Ye Yuan
- Jiaxing Academy of Agricultural SciencesJiaxingChina
| | - Ling‐Yun Wang
- Jinhua Academy of Agricultural Sciences (Zhejiang Institute of Agricultural Machinery)JinhuaZhejiangChina
| | - Zi‐Jian Huang
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life SciencesZhejiang UniversityHangzhouZhejiangChina
| | - Yi Guo
- Department of Archaeology, Cultural Heritage and MuseologyZhejiang UniversityHangzhouChina
| | - Guo‐Ping Sun
- Zhejiang Provincial Research Institute of Cultural Relics and ArchaeologyHangzhouChina
| | - Kenneth M. Olsen
- Department of BiologyWashington University in St LouisSt LouisMOUSA
| | - Jun Chen
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life SciencesZhejiang UniversityHangzhouZhejiangChina
| | - Ying‐Xiong Qiu
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life SciencesZhejiang UniversityHangzhouZhejiangChina
- Wuhan Botanical GardenChinese Academy of SciencesWuhanHubeiChina
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Zhou Z, Jin J, Wang L. Modeling the effects of elevation and precipitation on Rice (Oryza sativa L.) production considering multiple planting methods and cultivars in Central China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 813:152679. [PMID: 34971681 DOI: 10.1016/j.scitotenv.2021.152679] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 12/09/2021] [Accepted: 12/21/2021] [Indexed: 06/14/2023]
Abstract
In this study, we investigated the effects of elevation and precipitation on rice (Oryza sativa L.) production using the Crop Environment Resource Synthesis (CERES)-Rice model in Hubei province, China. We divided our study area into four zones based on elevation and precipitation. For each zone, our simulations were conducted using three planting methods: dry direct-seeded rice (DDSR), wet direct-seeded rice (WDSR), and transplanted-flooded rice (TFR), with three rice cultivars of different growth duration: Yangliangyou6 (long-duration), Huanghuazhan (mid-duration), and Lvhan1 (short-duration). Additionally, the optimal irrigation strategy for WDSR was determined with the CERES-Rice model. Our results indicated that the yields of WDSR with the optimal irrigation strategy were comparable with those of TFR in low-elevation regions but were less than the TFR yields in high-elevation areas. Furthermore, the rice yields increased at first and then decreased with increasing elevation, which was affected by growing period length and photosynthesis rate. Compared with the other two cultivars, the short-duration cultivar may be more suitable for growing in high-elevation regions. In addition, high precipitation could facilitate the cultivation of the long-duration cultivar in low-elevation regions, as it gives DDSR a yield potential comparable to that of WDSR for the short-duration cultivar in high-elevation regions. This study could help farmers choose optimal field management practices based on elevation and precipitation, ensuring sustainable and improved rice production.
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Affiliation(s)
- Zeyu Zhou
- College of Water Resources and Architectural Engineering, Northwest A&F University, Yangling 712100, Shaanxi Province, China; Key Laboratory of Agricultural Soil and Water Engineering in Arid and Semiarid Areas, Ministry of Education, Northwest A&F University, Yangling 712100, Shaanxi Province, China
| | - Jiming Jin
- College of Resources and Environment, Yangtze University, Wuhan 430100, Hubei Province, China.
| | - Lingmeng Wang
- College of Water Resources and Architectural Engineering, Northwest A&F University, Yangling 712100, Shaanxi Province, China; Key Laboratory of Agricultural Soil and Water Engineering in Arid and Semiarid Areas, Ministry of Education, Northwest A&F University, Yangling 712100, Shaanxi Province, China
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Population Structure of a Worldwide Collection of Tropical Japonica Rice Indicates Limited Geographic Differentiation and Shows Promising Genetic Variability Associated with New Plant Type. Genes (Basel) 2022; 13:genes13030484. [PMID: 35328038 PMCID: PMC8956019 DOI: 10.3390/genes13030484] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 03/07/2022] [Accepted: 03/08/2022] [Indexed: 12/15/2022] Open
Abstract
Abating the approaching yield plateau in rice requires taking advantage of potential technologies that requires knowledge on genetic diversity. Hybrid breeding, particularly in indica rice, requires the recruitment of large genetic variability from outside because the available genetic diversity of the cultivated pool has already been utilized to a great extent. In this study, we examined an assembly of 200 tropical japonica lines collected worldwide for population genetic structure and variability in yield-associated traits. Tested along with 30 indica and six wild rice lines belonging to India, the tropical japonica lines indicated great phenotypic variability, particularly related to new plant type (NPT) phenology, and formed six clusters. Furthermore, a marker-based characterization using a universal diversity marker panel classified the genotype assembly into four clusters, of which three encompassed tropical japonica lines, while the last cluster included mostly indica lines. The population structure of the panel also revealed a similar pattern, with tropical japonica lines forming three subpopulations. Remarkable variation in the allelic distribution was observed between the subpopulations. Superimposing the geographical sources of the genotypes over the population structure did not reveal any pattern. The genotypes sourced closer to the center of origin of rice showed relatively little diversity compared with the ones obtained from other parts of the world, suggesting migration from a common region of origin. The tropical japonica lines can be a great source of parental diversification for hybrid development after confirming the presence of widely compatible genes.
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Basit F, Akhter Bhat J, Han J, Guan Y, Latief Jan B, Shakoor A, Alansi S. Screening of rice cultivars for Cr-stress response by using the parameters of seed germination, morpho-physiological and antioxidant analysis. Saudi J Biol Sci 2022; 29:3918-3928. [PMID: 35844371 PMCID: PMC9280261 DOI: 10.1016/j.sjbs.2022.02.038] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 02/20/2022] [Accepted: 02/21/2022] [Indexed: 01/07/2023] Open
Abstract
Rice is the most important crop for the majority of population across the world with sensitive behavior toward heavy metals such as chromium (Cr) in polluted regions. Although, there is no information on the Cr resistance phenotyping in rice. Herein, two different groups of rice cultivars (normal, and hybrid) were used, each group with 14 different rice cultivars. Firstly, seed germination analysis was conducted by evaluating various seed germination indices to identify the rice cultivars with greatest seed germination vigor. Furthermore, exposure of chromium (Cr) toxicity to 28 different rice varieties (NV1-NV14, HV1-HV14) caused noticeable plant biomass reduction. Subsequently, NV2, NV6, NV10, NV12, NV13 (normal type), HV1, HV4, HV8, and HV9 (hybrid types) were pragmatic as moderately sensitive varieties, while NV3, NV4, NV9, and NV14 (normal type), HV3, HV6, HV7, and HV13 were observed as moderately tolerant. Although, NV7, and HV10 were ranked most sensitive cultivars, and NV11, and HV14 were considered as most tolerant varieties as compared to the other rice (both groups) genotypes. Afterward, Cr induced reduction in chlorophyll pigments were significantly lesser in HV14 relative to NV11, NV7, and especially HV10, and as a result HV14 modulated the total soluble sugar level as well as reduced ROS accumulation, and MDA contents production by stimulating the antioxidant defense mechanism conspicuously which further reduced the electrolyte leakage as well. Our outcomes provide support to explore the Cr tolerance mechanism in cereal crops as well as knowledge about rice breeding with increased tolerance against Cr stress.
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Genome-wide in silico analysis indicates the involvement of OsSWEET transporters in abiotic and heavy metal (loid) stress responses in rice. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01022-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Guo L, Zhao L, Ye J, Ji Z, Tang JJ, Bai K, Zheng S, Hu L, Chen X. Using aquatic animals as partners to increase yield and maintain soil nitrogen in the paddy ecosystems. eLife 2022; 11:73869. [PMID: 35190027 PMCID: PMC8863371 DOI: 10.7554/elife.73869] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 01/13/2022] [Indexed: 12/31/2022] Open
Abstract
Whether species coculture can overcome the shortcomings of crop monoculture requires additional study. Here, we show how aquatic animals (i.e. carp, crabs, and softshell turtles) benefit paddy ecosystems when cocultured with rice. Three separate field experiments and three separate mesocosm experiments were conducted. Each experiment included a rice monoculture (RM) treatment and a rice-aquatic animal (RA) coculture treatment; RA included feed addition for aquatic animals. In the field experiments, rice yield was higher with RA than with RM, and RA also produced aquatic animal yields that averaged 0.52–2.57 t ha-1. Compared to their corresponding RMs, the three RAs had significantly higher apparent nitrogen (N)-use efficiency and lower weed infestation, while soil N contents were stable over time. Dietary reconstruction analysis based on 13C and 15N showed that 16.0–50.2% of aquatic animal foods were from naturally occurring organisms in the rice fields. Stable-isotope-labeling (13C) in the field experiments indicated that the organic matter decomposition rate was greater with RA than with RM. Isotope 15N labeling in the mesocosm experiments indicated that rice used 13.0–35.1% of the aquatic animal feed-N. All these results suggest that rice-aquatic animal coculture increases food production, increases N-use efficiency, and maintains soil N content by reducing weeds and promoting decomposition and complementary N use. Our study supports the view that adding species to monocultures may enhance agroecosystem functions. Monoculture, where only one type of crop is grown to the exclusion of any other organism, is a pillar of modern agriculture. Yet this narrow focus disregards how complex inter-species interactions can increase crop yield and biodiversity while decreasing the need for fertilizers or pesticides. For example, many farmers across Asia introduce carps, crabs, turtles or other freshwater grazers into their rice paddies. This coculture approach yields promising results but remains poorly understood. In particular, it is unclear how these animals’ behaviours and biological processes benefit the ecosystem. To examine these questions, Guo, Zhao et al. conducted three separate four-year field experiments; they compared rice plots inhabited by either carp, mitten crabs or Chinese softshell turtles with fields where these organisms were not present. With animals, the rice paddies had less weeds, better crop yields and steady levels of nitrogen (a natural fertiliser) in their soil. These ecosystems could breakdown organic matter faster, use it better and had a reduced need for added fertilizer. While animal feed was provided in the areas that were studied, carp, crabs and turtles obtained up to half their food from the field itself, eating weeds, algae and pests and therefore reducing competition for the crops. This work helps to understand the importance of species interactions, showing that diversifying monocultures may boost yields and make agriculture more sustainable.
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Affiliation(s)
- Liang Guo
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Lufeng Zhao
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Junlong Ye
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Zijun Ji
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Jian-Jun Tang
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Keyu Bai
- Bioversity International, Maccarese, Italy
| | - Sijun Zheng
- Bioversity International, Maccarese, Italy.,Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Liangliang Hu
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Xin Chen
- College of Life Sciences, Zhejiang University, Hangzhou, China
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Wu Q, Liu Y, Huang J. CRISPR-Cas9 Mediated Mutation in OsPUB43 Improves Grain Length and Weight in Rice by Promoting Cell Proliferation in Spikelet Hull. Int J Mol Sci 2022; 23:ijms23042347. [PMID: 35216463 PMCID: PMC8877319 DOI: 10.3390/ijms23042347] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/14/2022] [Accepted: 02/15/2022] [Indexed: 12/27/2022] Open
Abstract
Grain weight, a crucial trait that determines the grain yield in rice, is influenced by grain size. Although a series of regulators that control grain size have been identified in rice, the mechanisms underlying grain development are not yet well understood. In this study, we identified OsPUB43, a U-box E3 ubiquitin ligase, as an important negative regulator determining the gain size and grain weight in rice. Phenotypes of large grain are observed in ospub43 mutants, whereas overexpression of OsPUB43 results in short grains. Scanning electron microscopy analysis reveals that OsPUB43 modulates the grain size mainly by inhibiting cell proliferation in the spikelet hull. The OsPUB43 protein is localized in the cytoplasm and nucleus. The ospub43 mutants display high sensitivity to exogenous BR, while OsPUB43-OE lines are hyposensitive to BR. Furthermore, the transient transcriptional activity assay shows that OsBZR1 can activate the expression of OsPUB43. Collectively, our results indicate that OsPUB43 negatively controls the gain size by modulating the expression of BR-responsive genes as well as MADS-box genes that are required for lemma/palea specification, suggesting that OsPUB43 has a potential valuable application in the enlargement of grain size in rice.
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Lu Y, Xu Y, Li N. Early Domestication History of Asian Rice Revealed by Mutations and Genome-Wide Analysis of Gene Genealogies. RICE (NEW YORK, N.Y.) 2022; 15:11. [PMID: 35166949 PMCID: PMC8847465 DOI: 10.1186/s12284-022-00556-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 01/22/2022] [Indexed: 05/05/2023]
Abstract
BACKGROUND Asian rice (Oryza sativa L.) has been a model plant but its cultivation history is inadequately understood, and its origin still under debate. Several enigmas remain, including how this annual crop shifted its growth habit from its perennial ancestor, O. rufipogon, why genetic divergence between indica and japonica appears older than the history of human domestication, and why some domestication genes do not show signals of introgression between subgroups. Addressing these issues may benefit both basic research and rice breeding. RESULTS Gene genealogy-based mutation (GGM) analysis shows that history of Asian rice is divided into two phases (Phase I and II) of about equal lengths. Mutations occurred earlier than the partition of indica and japonica to Os genome mark Phase-I period. We diagnosed 91 such mutations among 101 genes sampled across 12 chromosomes of Asian rice and its wild relatives. Positive selection, detected more at 5' regions than at coding regions of some of the genes, involved 22 loci (e.g., An-1, SH4, Rc, Hd3a, GL3.2, OsMYB3, OsDFR, and OsMYB15), which affected traits from easy harvesting, grain color, flowering time, productivity, to likely taste and tolerance. Phase-I mutations of OsMYB3, OsHd3a and OsDFR were experimentally tested and all caused enhanced functions of the genes in vivo. Phase-II period features separate cultivations, lineage-specific selection, and expanded domestication to more genes. Further genomic analysis, along with phenotypic comparisons, indicates that O. sativa is hybrid progeny of O. rufipogon and O. nivara, inherited slightly more genes of O. rufipogon. Congruently, modern alleles of the sampled genes are approximately 6% ancient, 38% uni-specific, 40% bi-specific (mixed), and 15% new after accumulating significant mutations. Results of sequencing surveys across modern cultivars/landraces indicate locus-specific usages of various alleles while confirming the associated mutations. CONCLUSIONS Asian rice was initially domesticated as one crop and later separate selection mediated by human resulted in its major subgroups. This history and the hybrid origin well explain previous puzzles. Positive selection, particularly in 5' regions, was the major force underlying trait domestication. Locus-specific domestication can be characterized and the result may facilitate breeders in developing better rice varieties in future.
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Affiliation(s)
- Yingqing Lu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing, 100093 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Yunzhang Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing, 100093 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
- Present Address: College of Agriculture and Animal Husbandry, Qinghai University, Xining, 810016 China
| | - Nan Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing, 100093 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
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Yin Z, Sheng H, Xiao H, Xue Y, Man Z, Huang D, Zhou Q. Inter-annual reduction in rice Cd and its eco-environmental controls in 6-year biannual mineral amendment in subtropical double-rice cropping ecosystems. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 293:118566. [PMID: 34822944 DOI: 10.1016/j.envpol.2021.118566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 10/31/2021] [Accepted: 11/20/2021] [Indexed: 06/13/2023]
Abstract
The alkaline mineral amendment is a practical means of alleviating Cd concentration in rice grain (CdR) in the short-term; however, the long-term remediation effect of mineral amendment on the CdR and the eco-environmental controls remains unknown. Here a mineral (Si-Ca-Mg) amendment, calcined primarily from molybdenum tailings and dolomite, was applied biannually over 6 years (12 seasons) to acidic and moderately Cd-contaminated double-rice cropping ecosystems. This study investigated the inter-annual variation of Cd in the rice-soil ecosystem and the eco-environmental controls in subtropical rice ecosystems. CdR was reduced by 50%-86% following mineral amendment. The within-year reduction in CdR was similar between early rice (50%-86%, mean of 68%) and late rice (68%-85%, mean of 74%), leading to CdR in all early rice and in 83% of late rice samples below the upper limit (0.2 mg kg-1) of the China National Food Safety Standards. In contrast, the inter-annual reduction in CdR was moderately variable, showing a greater CdR reduction in the later 3 years (73%-86%) than in the former 3 years (54%-79%). Three years continuous mineral amendment was required to guarantee the safety rice production. The concentrations of DTPA-extractable and exchangeable Cd fractions in soil were reduced, while the concentration of oxides-bound Cd was increased. In addition, the soil pH, concentrations of Olsen-P and exchangeable Ca and Mg were elevated. These imply a lower apparent phytoavailability of Cd in the soil following mineral amendment. An empirical model of the 3-variable using soil DTPA-Cd, soil Olsen-P, and a climatic factor (precipitation) effectively predicted temporal changes in CdR. Our study demonstrates that Cd phytoavailability in soil (indexed by DTPA-extractable Cd) and climatic factors (e.g., temperature and precipitation) may directly/indirectly control the inter-annual reduction in CdR following mineral amendment in slightly and moderately Cd-contaminated paddy ecosystems.
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Affiliation(s)
- Zerun Yin
- College of Resources & Environment, Hunan Agricultural University, Changsha 410128, China
| | - Hao Sheng
- College of Resources & Environment, Hunan Agricultural University, Changsha 410128, China.
| | - Huacui Xiao
- College of Resources & Environment, Hunan Agricultural University, Changsha 410128, China
| | - Yi Xue
- College of Resources & Environment, Hunan Agricultural University, Changsha 410128, China
| | - Zhiyong Man
- College of Resources & Environment, Hunan Agricultural University, Changsha 410128, China
| | - Dezhi Huang
- College of Resources & Environment, Hunan Agricultural University, Changsha 410128, China
| | - Qing Zhou
- College of Resources & Environment, Hunan Agricultural University, Changsha 410128, China
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Liu Y, Chen X, Xue S, Quan T, Cui D, Han L, Cong W, Li M, Yun D, Liu B, Xu Z. SET DOMAIN GROUP 721 protein functions in saline-alkaline stress tolerance in the model rice variety Kitaake. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:2576-2588. [PMID: 34416090 PMCID: PMC8633509 DOI: 10.1111/pbi.13683] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 08/07/2021] [Accepted: 08/10/2021] [Indexed: 06/12/2023]
Abstract
To isolate the genetic locus responsible for saline-alkaline stress tolerance, we developed a high-throughput activation tagging-based T-DNA insertion mutagenesis method using the model rice (Oryza sativa L.) variety Kitaake. One of the activation-tagged insertion lines, activation tagging 7 (AC7), showed increased tolerance to saline-alkaline stress. This phenotype resulted from the overexpression of a gene that encodes a SET DOMAIN GROUP 721 protein with H3K4 methyltransferase activity. Transgenic plants overexpressing OsSDG721 showed saline-alkaline stress-tolerant phenotypes, along with increased leaf angle, advanced heading and ripening dates. By contrast, ossdg721 loss-of-function mutants showed increased sensitivity to saline-alkaline stress characterized by decreased survival rates and reduction in plant height, grain size, grain weight and leaf angle. RNA sequencing (RNA-seq) analysis of wild-type Kitaake and ossdg721 mutants indicated that OsSDG721 positively regulates the expression level of HIGH-AFFINITY POTASSIUM (K+ ) TRANSPORTER1;5 (OsHKT1;5), which encodes a Na+ -selective transporter that maintains K+ /Na+ homeostasis under salt stress. Furthermore, we showed that OsSDG721 binds to and deposits the H3K4me3 mark in the promoter and coding region of OsHKT1;5, thereby upregulating OsHKT1;5 expression under saline-alkaline stress. Overall, by generating Kitaake activation-tagging pools, we established that the H3K4 methyltransferase OsSDG721 enhances saline-alkaline stress tolerance in rice.
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Affiliation(s)
- Yutong Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE)Northeast Normal UniversityChangchunP. R. China
| | - Xi Chen
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE)Northeast Normal UniversityChangchunP. R. China
| | - Shangyong Xue
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE)Northeast Normal UniversityChangchunP. R. China
| | - Taiyong Quan
- School of Life ScienceShandong UniversityQingdaoP. R. China
| | - Di Cui
- Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingP. R. China
| | - Longzhi Han
- Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingP. R. China
| | - Weixuan Cong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE)Northeast Normal UniversityChangchunP. R. China
| | - Mengting Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE)Northeast Normal UniversityChangchunP. R. China
| | - Dae‐Jin Yun
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE)Northeast Normal UniversityChangchunP. R. China
- Department of Biomedical Science and EngineeringKonkuk UniversitySeoulSouth Korea
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE)Northeast Normal UniversityChangchunP. R. China
| | - Zheng‐Yi Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE)Northeast Normal UniversityChangchunP. R. China
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Introduction: New Discoveries and Theoretical Implications for the Last Foraging and First Farming in East Asia. QUATERNARY 2021. [DOI: 10.3390/quat4040037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Worldwide, scientific understanding about domestication and the origins of food production is undergoing rapid change based on new data from discoveries in paleoclimates and environments, paleobiology, and archaeology [...]
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Liu J, Meng Q, Xiang H, Shi F, Ma L, Li Y, Liu C, Liu Y, Su B. Genome-wide analysis of Dof transcription factors and their response to cold stress in rice (Oryza sativa L.). BMC Genomics 2021; 22:800. [PMID: 34742240 PMCID: PMC8572462 DOI: 10.1186/s12864-021-08104-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 10/19/2021] [Indexed: 11/18/2022] Open
Abstract
Background Rice (Oryza sativa L.) is a food crop for humans worldwide. However, temperature has an effect during the vegetative and reproductive stages. In high-latitude regions where rice is cultivated, cold stress is a major cause of yield loss and plant death. Research has identified a group of plant-specific transcription factors, DNA binding with one zinc fingers (DOFs), with a diverse range of functions, including stress signaling and stress response during plant growth. The aim of this study was to identify Dof genes in two rice subspecies, indica and japonica, and screen for Dof genes that may be involved in cold tolerance during plant growth. Results A total of 30 rice Dofs (OsDofs) were identified using bioinformatics and genome-wide analyses and phylogenetically analyzed. The 30 OsDOFs were classified into six subfamilies, and 24 motifs were identified based on protein sequence alignment. The chromosome locations of OsDofs were determined and nine gene duplication events were identified. A joint phylogenetic analysis was performed on DOF protein sequences obtained from four monocotyledon species to examine the evolutionary relationship of DOF proteins. Expression profiling of OsDofs from two japonica cultivars (Longdao5, which is cold-tolerant, and Longjing11, which is cold-sensitive) revealed that OsDof1 and OsDof19 are cold-inducible genes. We examined the seed setting rates in OsDof1- and OsDof19-overexpression and RNAi lines and found that OsDof1 showed a response to cold stress. Conclusions Our investigation identified OsDof1 as a potential target for genetic breeding of rice with enhanced cold tolerance. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08104-0.
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Affiliation(s)
- Jia Liu
- Institute of Plant Protection, Heilongjiang Academy of Agricultural Sciences, No. 368 Xuefu Road, Nangang District, 150086, Harbin, China
| | - Qinglin Meng
- Institute of Plant Protection, Heilongjiang Academy of Agricultural Sciences, No. 368 Xuefu Road, Nangang District, 150086, Harbin, China.
| | - Hongtao Xiang
- Institute of Farming and Cultivation, Heilongjiang Academy of Agricultural Sciences, 150086, Harbin, China
| | - Fengmei Shi
- Institute of Plant Protection, Heilongjiang Academy of Agricultural Sciences, No. 368 Xuefu Road, Nangang District, 150086, Harbin, China
| | - Ligong Ma
- Institute of Plant Protection, Heilongjiang Academy of Agricultural Sciences, No. 368 Xuefu Road, Nangang District, 150086, Harbin, China
| | - Yichu Li
- Institute of Plant Protection, Heilongjiang Academy of Agricultural Sciences, No. 368 Xuefu Road, Nangang District, 150086, Harbin, China
| | - Chunlai Liu
- Institute of Plant Protection, Heilongjiang Academy of Agricultural Sciences, No. 368 Xuefu Road, Nangang District, 150086, Harbin, China
| | - Yu Liu
- Institute of Plant Protection, Heilongjiang Academy of Agricultural Sciences, No. 368 Xuefu Road, Nangang District, 150086, Harbin, China
| | - Baohua Su
- Institute of Plant Protection, Heilongjiang Academy of Agricultural Sciences, No. 368 Xuefu Road, Nangang District, 150086, Harbin, China
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Tiozon RJN, Sartagoda KJD, Fernie AR, Sreenivasulu N. The nutritional profile and human health benefit of pigmented rice and the impact of post-harvest processes and product development on the nutritional components: A review. Crit Rev Food Sci Nutr 2021:1-28. [PMID: 34709089 DOI: 10.1080/10408398.2021.1995697] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Pigmented rice has attracted considerable attention due to its nutritional value, which is in large conferred by its abundant content of phenolic compounds, considerable micronutrient concentrations, as well as its higher resistant starch and thereby slower digestibility properties. A wide range of phenolic compounds identified in pigmented rice exhibit biological activities such as antioxidant activity, anti-inflammatory, anticancer, and antidiabetic properties. Post-harvest processes significantly reduce the levels of these phytochemicals, but recent developments in processing methods have allowed greater retention of their contents. Pigmented rice has also been converted to different products for food preservation and to derive functional foods. Profiling a large set of pigmented rice cultivars will thus not only provide new insights into the phytochemical diversity of rice and the genes underlying the vast array of secondary metabolites present in this species but also provide information concerning their nutritional benefits, which will be instrumental in breeding healthier rice. The present review mainly focuses on the nutritional composition of pigmented rice and how it can impact human health alongside the effects of post-harvest processes and product development methods to retain the ambient level of phytochemicals in the final processed form in which it is consumed.
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Affiliation(s)
- Rhowell Jr N Tiozon
- Consumer-driven Grain Quality and Nutrition Center, Strategic Innovation Platform, International Rice Research Institute, Los Baños, Philippines.,Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Kristel June D Sartagoda
- Consumer-driven Grain Quality and Nutrition Center, Strategic Innovation Platform, International Rice Research Institute, Los Baños, Philippines
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Nese Sreenivasulu
- Consumer-driven Grain Quality and Nutrition Center, Strategic Innovation Platform, International Rice Research Institute, Los Baños, Philippines
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Lin F, Letuma P, Li Z, Lin S, Rensing C, Lin W. Rhizospheric pathogen proliferation and ROS production are associated with premature senescence of the osvha-a1 rice mutant. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:7247-7263. [PMID: 34297101 DOI: 10.1093/jxb/erab338] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 07/22/2021] [Indexed: 06/13/2023]
Abstract
Root-pathogen interactions influence premature senescence in rice, however, few studies have addressed the underlying mechanism. In this study, when premature senescence significantly occurred in the osvha-a1 mutant (loss of tonoplast H+-ATPase activity), the relative abundance of rhizospheric bacterial communities was similar between the mutant and its wild type, while the fungi in the rhizosphere of the osvha-a1 mutant significantly differed from the wild type. Furthermore, one key fungal strain in the rhizospheric soil of the osvha-a1 mutant, Gibberella intermedia, increased substantially during the late growing phase, resulting in severe accumulation of reactive oxygen species (ROS). By contrast, the wild type showed much lower levels of ROS when infected by G. intermedia. Using high performance liquid chromatography, sugars in root exudates were identified to be different between osvha-a1 mutant and the wild type. G. intermedia could use mannose and rhamnose in root exudates from the mutant more efficiently than any other sugar. Finally, antagonistic bacteria could be employed for limiting the proliferation of G. intermedia in the rhizosphere, thereby alleviating the early senescent phenotypes of the osvha-a1 mutant, and improving grain yield.
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Affiliation(s)
- Feifan Lin
- College of Life Sciences, Fujian Agricultural and Forestry University, Fuzhou, China
- Key Laboratory of Crop Physiology and Molecular Ecology, Fujian Agricultural and Forestry University, Fuzhou, China
| | - Puleng Letuma
- Crop Science Department, Faculty of Agriculture, National University of Lesotho, Maseru, Lesotho
| | - Zhaowei Li
- College of Life Sciences, Fujian Agricultural and Forestry University, Fuzhou, China
- Key Laboratory of Crop Physiology and Molecular Ecology, Fujian Agricultural and Forestry University, Fuzhou, China
| | - Sheng Lin
- College of Life Sciences, Fujian Agricultural and Forestry University, Fuzhou, China
- Key Laboratory of Crop Physiology and Molecular Ecology, Fujian Agricultural and Forestry University, Fuzhou, China
| | - Christopher Rensing
- College of Resources and Environment, Fujian Agricultural and Forestry University, Fuzhou, China
| | - Wenxiong Lin
- College of Life Sciences, Fujian Agricultural and Forestry University, Fuzhou, China
- Key Laboratory of Crop Physiology and Molecular Ecology, Fujian Agricultural and Forestry University, Fuzhou, China
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