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Hu Y, Tian C, Feng Y, Ma W, Zhang Y, Yang Q, Zhang X. Transgenic early japonica rice: Integration and expression characterization of stem borer resistance Bt gene. Gene 2024; 927:148753. [PMID: 38972556 DOI: 10.1016/j.gene.2024.148753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 06/22/2024] [Accepted: 07/04/2024] [Indexed: 07/09/2024]
Abstract
BACKGROUND Transgenic insect-resistant rice offers an environmentally friendly approach to mitigate yield losses caused by lepidopteran pests, such as stem borers. Bt (Bacillus thuringiensis) genes encode insecticidal proteins and are widely used to confer insect resistance to genetically modified crops. This study investigated the integration, inheritance, and expression characteristics of codon-optimised synthetic Bt genes, cry1C* and cry2A*, in transgenic early japonica rice lines. METHODS The early japonica rice cultivar, Songgeng 9 (Oryza sativa), was transformed with cry1C* or cry2A*, which are driven by the ubi promoter via Agrobacterium tumefaciens-mediated transformation. Molecular analyses, including quantitative PCR (qPCR), enzyme-linked immunosorbent assay (ELISA), and Southern blot analysis were performed to confirm transgene integration, inheritance, transcriptional levels, and protein expression patterns across different tissues and developmental stages. RESULTS Stable transgenic early japonica lines exhibiting single-copy transgene integration were established. Transcriptional analysis revealed variations in Bt gene expression among lines, tissues, and growth stages, with higher expression levels observed in leaves than in other organs. Notably, cry2A* exhibited consistently higher mRNA and protein levels than cry1C* across all examined tissues and developmental time points. Bt protein accumulation followed the trend of leaves > stem sheaths > young panicles > brown rice, with peak expression during the filling stage in the vegetative tissues. CONCLUSIONS Synthetic cry2A* displayed markedly elevated transcription and translation compared to cry1C* in the transgenic early japonica rice lines examined. Distinct spatiotemporal patterns of Bt gene expression were elucidated, providing insights into the potential insect resistance conferred by these genes in rice. These findings will contribute to the development of insect-resistant japonica rice varieties and facilitate the rational deployment of Bt crops.
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Affiliation(s)
- Yueting Hu
- Rice Research Institute, Heilongjiang Academy of Agricultural Sciences, Jiamusi 154026, China.
| | - Chongbing Tian
- Rice Research Institute, Heilongjiang Academy of Agricultural Sciences, Jiamusi 154026, China
| | - Yanjiang Feng
- Rice Research Institute, Heilongjiang Academy of Agricultural Sciences, Jiamusi 154026, China
| | - Wendong Ma
- Rice Research Institute, Heilongjiang Academy of Agricultural Sciences, Jiamusi 154026, China
| | - Yunjiang Zhang
- Rice Research Institute, Heilongjiang Academy of Agricultural Sciences, Jiamusi 154026, China
| | - Qing Yang
- Rice Research Institute, Heilongjiang Academy of Agricultural Sciences, Jiamusi 154026, China
| | - Xirui Zhang
- Rice Research Institute, Heilongjiang Academy of Agricultural Sciences, Jiamusi 154026, China
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Li C, Zhou Z, Xiong X, Li C, Li C, Shen E, Wang J, Zha W, Wu B, Chen H, Zhou L, Lin Y, You A. Development of a multi-resistance and high-yield rice variety using multigene transformation and gene editing. PLANT BIOTECHNOLOGY JOURNAL 2024. [PMID: 39003591 DOI: 10.1111/pbi.14434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 05/10/2024] [Accepted: 07/01/2024] [Indexed: 07/15/2024]
Affiliation(s)
- Changyan Li
- Food Crops Institute, Hubei Academy of Agricultural Sciences, Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs, Wuhan, China
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Zaihui Zhou
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xinzhu Xiong
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Chuanxu Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Chuanhong Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Enlong Shen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jianyu Wang
- Food Crops Institute, Hubei Academy of Agricultural Sciences, Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Wenjun Zha
- Food Crops Institute, Hubei Academy of Agricultural Sciences, Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Bian Wu
- Food Crops Institute, Hubei Academy of Agricultural Sciences, Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Hao Chen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Lei Zhou
- Food Crops Institute, Hubei Academy of Agricultural Sciences, Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Yongjun Lin
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Aiqing You
- Food Crops Institute, Hubei Academy of Agricultural Sciences, Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
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Yu W, He J, Wu J, Xu Z, Lai F, Zhong X, Zhang M, Ji H, Fu Q, Zhou X, Peng Y. Resistance to Planthoppers and Southern Rice Black-Streaked Dwarf Virus in Rice Germplasms. PLANT DISEASE 2024:PDIS10232025RE. [PMID: 38127636 DOI: 10.1094/pdis-10-23-2025-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
The damage caused by the white-back planthopper (WBPH, Sogatella furcifera) and brown planthopper (BPH, Nilaparvata lugens), as well as southern rice black-streaked dwarf virus (SRBSDV), considerably decreases the grain yield of rice. Identification of rice germplasms with sufficient resistance to planthoppers and SRBSDV is essential to the breeding and deployment of resistant varieties and, hence, the control of the pests and disease. In this study, 318 rice accessions were evaluated for their reactions to the infestation of both BPH and WBPH at the seedling stage using the standard seed-box screening test method; insect quantification was further conducted at the end of the tillering and grain-filling stages in field trials. Accessions HN12-239 and HN12-328 were resistant to both BPH and WBPH at all tested stages. Field trials were conducted to identify resistance in the collection to SRBSDV based on the virus infection rate under artificial inoculation. Rathu Heenati (RHT) and HN12-239 were moderately resistant to SRBSDV. In addition, we found that WBPH did not penetrate stems with stylets but did do more probing bouts and xylem sap ingestion when feeding on HN12-239 than the susceptible control rice Taichung Native 1. The resistance of rice accessions HN12-239, HN12-328, and RHT to BPH, WBPH, and/or SRBSDV should be valuable to the development of resistant rice varieties.
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Affiliation(s)
- Wenjuan Yu
- Ministry of Agriculture Key Laboratory of Integrated Management of Pests on Crops in Southwest China, Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan 610066, China
| | - Jiachun He
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang 310006, China
| | - Jianxiang Wu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Zhi Xu
- Ministry of Agriculture Key Laboratory of Integrated Management of Pests on Crops in Southwest China, Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan 610066, China
| | - Fengxiang Lai
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang 310006, China
| | - Xuelian Zhong
- Ministry of Agriculture Key Laboratory of Integrated Management of Pests on Crops in Southwest China, Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan 610066, China
| | - Mei Zhang
- Plant Protection Station, Sichuan Provincial Department of Agriculture and Rural Affairs, Chengdu, Sichuan 610041, China
| | - Hongli Ji
- Ministry of Agriculture Key Laboratory of Integrated Management of Pests on Crops in Southwest China, Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan 610066, China
| | - Qiang Fu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang 310006, China
| | - Xueping Zhou
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yunliang Peng
- Ministry of Agriculture Key Laboratory of Integrated Management of Pests on Crops in Southwest China, Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan 610066, China
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang 310006, China
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Li X, Wu ME, Zhang J, Xu J, Diao Y, Li Y. The OsCLV2s-OsCRN1 co-receptor regulates grain shape in rice. J Genet Genomics 2024; 51:691-702. [PMID: 38575110 DOI: 10.1016/j.jgg.2024.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 03/29/2024] [Accepted: 03/29/2024] [Indexed: 04/06/2024]
Abstract
The highly conserved CLV-WUS negative feedback pathway plays a decisive role in regulating stem cell maintenance in shoot and floral meristems in higher plants, including Arabidopsis, rice, maize, and tomato. Here, we find significant natural variations in the OsCLV2c, OsCLV2d, and OsCRN1 loci in a genome-wide association study of grain shape in rice. OsCLV2a, OsCLV2c, OsCLV2d, and OsCRN1 negatively regulate grain length-width ratio and show distinctive geographical distribution, indica-japonica differentiation, and artificial selection signatures. Notably, OsCLV2a and OsCRN1 interact biochemically and genetically, suggesting that the two components function in a complex to regulate grain shape of rice. Furthermore, the genetic contributions of the haplotypes combining OsCLV2a, OsCLV2c, and OsCRN1 are significantly higher than those of each single gene alone in controlling key yield traits. These findings identify two groups of receptor-like kinases that may function as distinct co-receptors to control grain size in rice, thereby revealing a previously unrecognized role of the CLV class genes in regulating seed development and proposing a framework to understand the molecular mechanisms of the CLV-WUS pathway in rice and other crops.
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Affiliation(s)
- Xingxing Li
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, Hubei 430070, China; Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China
| | - Meng-En Wu
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, Hubei 430070, China; Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China
| | - Juncheng Zhang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, Hubei 430070, China; Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China
| | - Jingyue Xu
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, Hubei 430070, China; Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China
| | - Yuanfei Diao
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, Hubei 430070, China; Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China
| | - Yibo Li
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, Hubei 430070, China; Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China.
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Ye Y, Wang Y, Zou L, Wu X, Zhang F, Chen C, Xiong S, Liang B, Zhu Z, Wu W, Zhang S, Wu J, Hu J. Identification and candidate analysis of a new brown planthopper resistance locus in an Indian landrace of rice, paedai kalibungga. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2024; 44:45. [PMID: 38911334 PMCID: PMC11190133 DOI: 10.1007/s11032-024-01485-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 06/06/2024] [Indexed: 06/25/2024]
Abstract
The brown planthopper (Nilaparvata lugens Stål, BPH) is the most destructive pest of rice (Oryza sativa L.). Utilizing resistant rice cultivars that harbor resistance gene/s is an effective strategy for integrated pest management. Due to the co-evolution of BPH and rice, a single resistance gene may fail because of changes in the virulent BPH population. Thus, it is urgent to explore and map novel BPH resistance genes in rice germplasm. Previously, an indica landrace from India, Paedai kalibungga (PK), demonstrated high resistance to BPH in both in Wuhan and Fuzhou, China. To map BPH resistance genes from PK, a BC1F2:3 population derived from crosses of PK and a susceptible parent, Zhenshan 97 (ZS97), was developed and evaluated for BPH resistance. A novel BPH resistance locus, BPH39, was mapped on the short arm of rice chromosome 6 using next-generation sequencing-based bulked segregant analysis (BSA-seq). BPH39 was validated using flanking markers within the locus. Furthermore, near-isogenic lines carrying BPH39 (NIL-BPH39) were developed in the ZS97 background. NIL-BPH39 exhibited the physiological mechanisms of antibiosis and preference toward BPH. BPH39 was finally delimited to an interval of 84 Kb ranging from 1.07 to 1.15 Mb. Six candidate genes were identified in this region. Two of them (LOC_Os06g02930 and LOC_Os06g03030) encode proteins with a similar short consensus repeat (SCR) domain, which displayed many variations leading to amino acid substitutions and showed higher expression levels in NIL-BPH39. Thus, these two genes are considered reliable candidate genes for BPH39. Additionally, transcriptome sequencing, DEGs analysis, and gene RT-qPCR verification preliminary revealed that BPH39 may be involved in the jasmonic acid (JA) signaling pathway, thus mediating the molecular mechanism of BPH resistance. This work will facilitate map-based cloning and marker-assisted selection for the locus in breeding programs targeting BPH resistance. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-024-01485-6.
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Affiliation(s)
- Yangdong Ye
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Vector-Borne Virus Research Center, Fujian Agriculture and Forestry University, Fuzhou, Fujian China
| | - Yanan Wang
- Fujian Key Laboratory of Crop Breeding By Design and Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian China
| | - Ling Zou
- Fujian Key Laboratory of Crop Breeding By Design and Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian China
| | - Xiaoqing Wu
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Vector-Borne Virus Research Center, Fujian Agriculture and Forestry University, Fuzhou, Fujian China
| | - Fangming Zhang
- Fujian Key Laboratory of Crop Breeding By Design and Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian China
| | - Cheng Chen
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Vector-Borne Virus Research Center, Fujian Agriculture and Forestry University, Fuzhou, Fujian China
| | - Shangye Xiong
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Vector-Borne Virus Research Center, Fujian Agriculture and Forestry University, Fuzhou, Fujian China
| | - Baohui Liang
- Fujian Key Laboratory of Crop Breeding By Design and Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian China
| | - Zhihong Zhu
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Vector-Borne Virus Research Center, Fujian Agriculture and Forestry University, Fuzhou, Fujian China
| | - Weiren Wu
- Fujian Key Laboratory of Crop Breeding By Design and Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian China
| | - Shuai Zhang
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Vector-Borne Virus Research Center, Fujian Agriculture and Forestry University, Fuzhou, Fujian China
| | - Jianguo Wu
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Vector-Borne Virus Research Center, Fujian Agriculture and Forestry University, Fuzhou, Fujian China
| | - Jie Hu
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Vector-Borne Virus Research Center, Fujian Agriculture and Forestry University, Fuzhou, Fujian China
- Fujian Key Laboratory of Crop Breeding By Design and Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian China
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Xu S, Wei X, Yang Q, Hu D, Zhang Y, Yuan X, Kang F, Wu Z, Yan Z, Luo X, Sun Y, Wang S, Feng Y, Xu Q, Zhang M, Yang Y. A KNOX Ⅱ transcription factor suppresses the NLR immune receptor BRG8-mediated immunity in rice. PLANT COMMUNICATIONS 2024:101001. [PMID: 38863209 DOI: 10.1016/j.xplc.2024.101001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 04/21/2024] [Accepted: 06/10/2024] [Indexed: 06/13/2024]
Abstract
Nucleotide-binding site and leucine-rich repeat (NLR) proteins are activated by detecting pathogen effectors, which in turn trigger host defenses and cell death. Although many NLRs have been identified, the mechanisms responsible for NLR-triggered defense responses are still poorly understood. In this study, through a genome-wide association study approach, we identified a novel NLR gene, Blast Resistance Gene 8 (BRG8), which confers resistance to rice blast and bacterial blight diseases. BRG8 overexpression and complementation lines exhibit enhanced resistance to both pathogens. Subcellular localization assays showed that BRG8 is localized in both the cytoplasm and the nucleus. Additional evidence revealed that nuclear-localized BRG8 can enhance rice immunity without a hypersensitive response (HR)-like phenotype. We also demonstrated that the coiled-coil domain of BRG8 not only physically interacts with itself but also interacts with the KNOX Ⅱ protein HOMEOBOX ORYZA SATIVA59 (HOS59). Knockout mutants of HOS59 in the BRG8 background show enhanced resistance to Magnaporthe oryzae strain CH171 and Xoo strain CR4, similar to that of the BRG8 background. By contrast, overexpression of HOS59 in the BRG8 background will compromise the HR-like phenotype and resistance response. Further analysis revealed that HOS59 promotes the degradation of BRG8 via the 26S proteasome pathway. Collectively, our study highlights HOS59 as an NLR immune regulator that fine-tunes BRG8-mediated immune responses against pathogens, providing new insights into NLR associations and functions in plant immunity.
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Affiliation(s)
- Siliang Xu
- China National Center for Rice Improvement/State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Xinghua Wei
- China National Center for Rice Improvement/State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China; National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China
| | - Qinqin Yang
- China National Center for Rice Improvement/State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Dongxiu Hu
- China National Center for Rice Improvement/State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Yuanyuan Zhang
- China National Center for Rice Improvement/State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Xiaoping Yuan
- China National Center for Rice Improvement/State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Fengyu Kang
- China National Center for Rice Improvement/State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Zhaozhong Wu
- China National Center for Rice Improvement/State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Zhiqin Yan
- China National Center for Rice Improvement/State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China; National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China
| | - Xueqin Luo
- China National Center for Rice Improvement/State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China; National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China
| | - Yanfei Sun
- China National Center for Rice Improvement/State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Shan Wang
- China National Center for Rice Improvement/State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Yue Feng
- China National Center for Rice Improvement/State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Qun Xu
- China National Center for Rice Improvement/State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Mengchen Zhang
- China National Center for Rice Improvement/State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China; National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China.
| | - Yaolong Yang
- China National Center for Rice Improvement/State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China; National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China.
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Pang R, Li S, Chen W, Yuan L, Xiao H, Xing K, Li Y, Zhang Z, He X, Zhang W. Insecticide resistance reduces the profitability of insect-resistant rice cultivars. J Adv Res 2024; 60:1-12. [PMID: 37499938 PMCID: PMC11156607 DOI: 10.1016/j.jare.2023.07.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 07/02/2023] [Accepted: 07/24/2023] [Indexed: 07/29/2023] Open
Abstract
INTRODUCTION Preventing crop yield loss caused by pests is critical for global agricultural production. Agricultural pest control has largely relied on chemical pesticides. The interaction between insecticide resistance and the adaptation of herbivorous pests to host plants may represent an emerging threat to future food security. OBJECTIVES This study aims to unveil genetic evidence for the reduction in the profitability of resistant cultivars derived from insecticide resistance in target pest insects. METHODS An experimental evolution system encompassing resistant rice and its major monophagous pest, the brown planthopper Nilaparvata lugens, was constructed. Whole genome resequencing and selective sweep analysis were utilized to identify the candidate gene loci related to the adaptation. RNA interference and induced expression assay were conducted to validate the function of the candidate loci. RESULTS We found that the imidacloprid-resistant population of N. lugens rapidly adapted to resistant rice IR36. Gene loci related to imidacloprid resistance may contribute to this phenomenon. Multiple alleles in the nicotinic acetylcholine receptor (nAChR)-7-like and P450 CYP4C61 were significantly correlated with changes in virulence to IR36 rice and insecticide resistance of N. lugens. One avirulent/susceptible genotype and two virulent/resistant genotypes could be inferred from the corresponding alleles. Importantly, we found that the virulent/resistant genotypes already exist in the wild in China, exhibiting increasing frequencies along with insecticide usage. We validated the relevance of these genotypes and the virulence to three more resistant rice cultivars. Knockdown of the above two genes in N. lugens significantly decreased both the resistance to imidacloprid and the virulence towards resistant rice. CONCLUSION Our findings provide direct genetic evidence to the eco-evolutionary consequence of insecticide resistance, and suggest an urgent need for the implementation of predictably sustainable pest management.
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Affiliation(s)
- Rui Pang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China; National Key Laboratory of Green Pesticide, College of Plant Protection, South China Agricultural University, Guangzhou, Guangdong, China
| | - Shihui Li
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Weiwen Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Longyu Yuan
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China; Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Hanxiang Xiao
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Ke Xing
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yanfang Li
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Zhenfei Zhang
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Xionglei He
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Wenqing Zhang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China.
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8
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Hui S, Zhang P, Yuan M. Optimizing nutrient transporters to enhance disease resistance in rice. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:2799-2808. [PMID: 38437153 DOI: 10.1093/jxb/erae087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 03/01/2024] [Indexed: 03/06/2024]
Abstract
Fertilizers and plant diseases contribute positively and negatively to crop production, respectively. Macro- and micronutrients provided by the soil and fertilizers are transported by various plant nutrient transporters from the soil to the roots and shoots, facilitating growth and development. However, the homeostasis of different nutrients has different effects on plant disease. This review is aimed at providing insights into the interconnected regulation between nutrient homeostasis and immune responses, and it highlights strategies to enhance disease resistance by optimal manipulation of nutrient transporters in rice. First, we highlight the essential roles of six macronutrients (nitrogen, phosphorus, potassium, sulfur, calcium, magnesium) and eight micronutrients (iron, manganese, zinc, copper, boron, molybdenum, silicon, nickel), and summarize the diverse effects of each on rice diseases. We then systematically review the molecular mechanisms of immune responses modulated by nutrient transporters and the genetic regulatory pathways that control the specific nutrient-mediated immune signaling that is regulated by the pathogens and the host plant. Finally, we discuss putative strategies for breeding disease-resistant rice by genetic engineering of nutrient transporters.
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Affiliation(s)
- Shugang Hui
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Peng Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Meng Yuan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- Yazhouwan National Laboratory, Sanya 572024, China
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9
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Wang M, Peng X, Wang C, Tang X. Identification of two plastid transit peptides for construction of pollen-inactivation system in rice. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2024; 44:33. [PMID: 38694254 PMCID: PMC11058180 DOI: 10.1007/s11032-024-01471-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 04/22/2024] [Indexed: 05/04/2024]
Abstract
Hybrid seed production technology (SPT) is achieved through the utilization of a recessive nuclear male-sterile mutant transformed with a transgenic cassette comprising three essential components: the wild-type gene to restore the fertility of the male-sterile mutant, an α-amylase gene to disrupt transgenic pollen grains, and red fluorescence protein gene DsRed to distinguish the transgenic seeds from the nontransgenic male sterile seeds. In rice, we establish the pollen disruption system by introducing an amyloplast targeting signal peptide (ASP) at the N-terminus of maize α-amylase protein ZM-AA1ΔSP (ZM-AA1 with the N-terminal signal peptide removed). The ASP facilitates the transport of ZM-AA1ΔSP protein into amyloplast where it degrades starch, resulting in disruption of the pollen fertility. To obtain such signal peptides for rice, we searched the rice proteins homologous to the defined wheat amyloplast proteins followed by protein-protein interaction network predictions and targeting signal peptides prediction. These analyses enabled the identification of four candidate ASPs in rice, which were designated as ASP1, ASP2, ASP3, and ASP4, respectively. ASP1 and ASP2, when linked with ZM-AA1ΔSP, exhibited the capability to disrupt transgenic pollen grains, whereas ASP3 and ASP4 did not produce this effect. Interestingly, the localization experiments showed that ASP3 and ASP4 were able to target the proteins into chloroplast. The ASP1 and ASP2 sequences provide valuable tools for genetic engineering of the rice male-sterile system, which will contribute to the hybrid rice breeding and production. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-024-01471-y.
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Affiliation(s)
- Menglong Wang
- School of Life Sciences, Huizhou University, Huizhou, 516007 China
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631 China
| | - Xiaoqun Peng
- School of Life Sciences, Huizhou University, Huizhou, 516007 China
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631 China
| | - Changjian Wang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631 China
| | - Xiaoyan Tang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120 China
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631 China
- Shenzhen Institute of Molecular Crop Design, Shenzhen, 518107 China
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10
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Wang H, Ye T, Guo Z, Yao Y, Tu H, Wang P, Zhang Y, Wang Y, Li X, Li B, Xiong H, Lai X, Xiong L. A double-stranded RNA binding protein enhances drought resistance via protein phase separation in rice. Nat Commun 2024; 15:2514. [PMID: 38514621 PMCID: PMC10957929 DOI: 10.1038/s41467-024-46754-2] [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: 09/19/2023] [Accepted: 03/08/2024] [Indexed: 03/23/2024] Open
Abstract
Drought stress significantly impacts global rice production, highlighting the critical need to understand the genetic basis of drought resistance in rice. Here, through a genome-wide association study, we reveal that natural variations in DROUGHT RESISTANCE GENE 9 (DRG9), encoding a double-stranded RNA (dsRNA) binding protein, contribute to drought resistance. Under drought stress, DRG9 condenses into stress granules (SGs) through liquid-liquid phase separation via a crucial α-helix. DRG9 recruits the mRNAs of OsNCED4, a key gene for the biosynthesis of abscisic acid, into SGs and protects them from degradation. In drought-resistant DRG9 allele, natural variations in the coding region, causing an amino acid substitution (G267F) within the zinc finger domain, increase DRG9's binding ability to OsNCED4 mRNA and enhance drought resistance. Introgression of the drought-resistant DRG9 allele into the elite rice Huanghuazhan significantly improves its drought resistance. Thus, our study underscores the role of a dsRNA-binding protein in drought resistance and its promising value in breeding drought-resistant rice.
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Affiliation(s)
- Huaijun Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Tiantian Ye
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Zilong Guo
- Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yilong Yao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Haifu Tu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Pengfei Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Yu Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Yao Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Xiaokai Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Bingchen Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Haiyan Xiong
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Xuelei Lai
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China.
| | - Lizhong Xiong
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China.
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11
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Han R, Yang Z, Wang C, Zhu S, Tang G, Shen X, Duanmu D, Cao Y, Huang R. Wild species rice OsCERK1DY-mediated arbuscular mycorrhiza symbiosis boosts yield and nutrient use efficiency in rice breeding. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2024; 44:22. [PMID: 38435473 PMCID: PMC10907559 DOI: 10.1007/s11032-024-01459-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 02/20/2024] [Indexed: 03/05/2024]
Abstract
Meeting the ever-increasing food demands of a growing global population while ensuring resource and environmental sustainability presents significant challenges for agriculture worldwide. Arbuscular mycorrhizal symbiosis (AMS) has emerged as a potential solution by increasing the surface area of a plant's root system and enhancing the absorption of phosphorus, nitrogen nutrients, and water. Consequently, there is a longstanding hypothesis that rice varieties exhibiting more efficient AMS could yield higher outputs at reduced input costs, paving the way for the development of Green Super Rice (GSR). Our prior research study identified a variant, OsCERK1DY, derived from Dongxiang wild-type rice, which notably enhanced AMS efficiency in the rice cultivar "ZZ35." This variant represents a promising gene for enhancing yield and nutrient use efficiency in rice breeding. In this study, we conducted a comparative analysis of biomass, crop growth characteristics, yield attributes, and nutrient absorption at varying soil nitrogen levels in the rice cultivar "ZZ35" and its chromosome single-segment substitution line, "GJDN1." In the field, GJDN1 exhibited a higher AM colonization level in its roots compared with ZZ35. Notably, GJDN1 displayed significantly higher effective panicle numbers and seed-setting rates than ZZ35. Moreover, the yield of GJDN1 with 75% nitrogen was 14.27% greater than the maximum yield achieved using ZZ35. At equivalent nitrogen levels, GJDN1 consistently outperformed ZZ35 in chlorophyll (Chl) content, dry matter accumulation, major nutrient element accumulation, N agronomic efficiency (NAE), N recovery efficiency (NRE), and N partial factor productivity (NPFP). The performance of OsCERK1DY overexpression lines corroborated these findings. These results support a model wherein the heightened level of AMS mediated by OsCERK1DY contributes to increased nitrogen, phosphorus, and potassium accumulation. This enhancement in nutrient utilization promotes higher fertilizer efficiency, dry matter accumulation, and ultimately, rice yield. Consequently, the OsCERK1DY gene emerges as a robust candidate for improving yield, reducing fertilizer usage, and facilitating a transition towards greener, lower-carbon agriculture. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-024-01459-8.
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Affiliation(s)
- Ruicai Han
- Nanchang Subcenter of National Research Center for Rice Engineering, Key Laboratory of Rice Physiology and Genetics of Jiangxi Province, Rice Research Institute, Jiangxi Academy of Agriculture Science, Nanchang, 330200 People’s Republic of China
| | - Zhou Yang
- Nanchang Subcenter of National Research Center for Rice Engineering, Key Laboratory of Rice Physiology and Genetics of Jiangxi Province, Rice Research Institute, Jiangxi Academy of Agriculture Science, Nanchang, 330200 People’s Republic of China
| | - Chunquan Wang
- Jiangxi Biotech Vocational College, Nanchang, 330200 People’s Republic of China
| | - Shan Zhu
- Nanchang Subcenter of National Research Center for Rice Engineering, Key Laboratory of Rice Physiology and Genetics of Jiangxi Province, Rice Research Institute, Jiangxi Academy of Agriculture Science, Nanchang, 330200 People’s Republic of China
| | - Guoping Tang
- Nanchang Subcenter of National Research Center for Rice Engineering, Key Laboratory of Rice Physiology and Genetics of Jiangxi Province, Rice Research Institute, Jiangxi Academy of Agriculture Science, Nanchang, 330200 People’s Republic of China
| | - Xianhua Shen
- Nanchang Subcenter of National Research Center for Rice Engineering, Key Laboratory of Rice Physiology and Genetics of Jiangxi Province, Rice Research Institute, Jiangxi Academy of Agriculture Science, Nanchang, 330200 People’s Republic of China
| | - Deqiang Duanmu
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Yangrong Cao
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Renliang Huang
- Nanchang Subcenter of National Research Center for Rice Engineering, Key Laboratory of Rice Physiology and Genetics of Jiangxi Province, Rice Research Institute, Jiangxi Academy of Agriculture Science, Nanchang, 330200 People’s Republic of China
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12
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Huang Y, Ji Z, Zhang S, Li S. Function of hormone signaling in regulating nitrogen-use efficiency in plants. JOURNAL OF PLANT PHYSIOLOGY 2024; 294:154191. [PMID: 38335845 DOI: 10.1016/j.jplph.2024.154191] [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: 12/24/2023] [Revised: 02/01/2024] [Accepted: 02/04/2024] [Indexed: 02/12/2024]
Abstract
Nitrogen (N) is one of the most important nutrients for crop plant performance, however, the excessive application of nitrogenous fertilizers in agriculture significantly increases production costs and causes severe environmental problems. Therefore, comprehensively understanding the molecular mechanisms of N-use efficiency (NUE) with the aim of developing new crop varieties that combine high yields with improved NUE is an urgent goal for achieving more sustainable agriculture. Plant NUE is a complex trait that is affected by multiple factors, of which hormones are known to play pivotal roles. In this review, we focus on the interaction between the biosynthesis and signaling pathways of plant hormones with N metabolism, and summarize recent studies on the interplay between hormones and N, including how N regulates multiple hormone biosynthesis, transport and signaling and how hormones modulate root system architecture (RSA) in response to external N sources. Finally, we explore potential strategies for promoting crop NUE by modulating hormone synthesis, transport and signaling. This provides insights for future breeding of N-efficient crop varieties and the advancement of sustainable agriculture.
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Affiliation(s)
- Yunzhi Huang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, China
| | - Zhe Ji
- Department of Biology, University of Oxford, Oxford, UK
| | - Siyu Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, China
| | - Shan Li
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, China; Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China.
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13
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Wang Q, Gao H, Liu K, Wang H, Zhang F, Wei L, Lu K, Li M, Shi Y, Zhao J, Zhou W, Peng B, Yuan H. CRISPR/Cas9-mediated enhancement of semi-dwarf glutinous traits in elite Xiangdaowan rice ( Oryza sativa L.): targeting SD1 and Wx genes for yield and quality improvement. FRONTIERS IN PLANT SCIENCE 2024; 15:1333191. [PMID: 38434426 PMCID: PMC10904601 DOI: 10.3389/fpls.2024.1333191] [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: 11/04/2023] [Accepted: 02/02/2024] [Indexed: 03/05/2024]
Abstract
In rice cultivation, the traits of semi-dwarfism and glutinous texture are pivotal for optimizing yield potential and grain quality, respectively. Xiangdaowan (XDW) rice, renowned for its exceptional aromatic properties, has faced challenges due to its tall stature and high amylose content, resulting in poor lodging resistance and suboptimal culinary attributes. To address these issues, we employed CRISPR/Cas9 technology to precisely edit the SD1 and Wx genes in XDW rice, leading to the development of stable genetically homozygous lines with desired semi-dwarf and glutinous characteristics. The sd1-wx mutant lines exhibited reduced gibberellin content, plant height, and amylose content, while maintaining hardly changed germination rate and other key agronomic traits. Importantly, our study demonstrated that exogenous GA3 application effectively promoted growth by compensating for the deficiency of endogenous gibberellin. Based on this, a semi-dwarf glutinous elite rice (Oryza sativa L.) Lines was developed without too much effect on most agronomic traits. Furthermore, a comparative transcriptome analysis unveiled that differentially expressed genes (DEGs) were primarily associated with the anchored component of the membrane, hydrogen peroxide catabolic process, peroxidase activity, terpene synthase activity, and apoplast. Additionally, terpene synthase genes involved in catalyzing the biosynthesis of diterpenoids to gibberellins were enriched and significantly down-regulated. This comprehensive study provides an efficient method for simultaneously enhancing rice plant height and quality, paving the way for the development of lodging-resistant and high-quality rice varieties.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Hongyu Yuan
- College of Life Sciences, Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, China
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14
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Singh G, Kaur N, Khanna R, Kaur R, Gudi S, Kaur R, Sidhu N, Vikal Y, Mangat GS. 2Gs and plant architecture: breaking grain yield ceiling through breeding approaches for next wave of revolution in rice ( Oryza sativa L.). Crit Rev Biotechnol 2024; 44:139-162. [PMID: 36176065 DOI: 10.1080/07388551.2022.2112648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 07/10/2022] [Accepted: 07/27/2022] [Indexed: 11/03/2022]
Abstract
Rice is a principal food crop for more than half of the global population. Grain number and grain weight (2Gs) are the two complex traits controlled by several quantitative trait loci (QTLs) and are considered the most critical components for yield enhancement in rice. Novel molecular biology and QTL mapping strategies can be utilized in dissecting the complex genetic architecture of these traits. Discovering the valuable genes/QTLs associated with 2Gs traits hidden in the rice genome and utilizing them in breeding programs may bring a revolution in rice production. Furthermore, the positional cloning and functional characterization of identified genes and QTLs may aid in understanding the molecular mechanisms underlying the 2Gs traits. In addition, knowledge of modern genomic tools aids the understanding of the nature of plant and panicle architecture, which enhances their photosynthetic activity. Rice researchers continue to combine important yield component traits (including 2Gs for the yield ceiling) by utilizing modern breeding tools, such as marker-assisted selection (MAS), haplotype-based breeding, and allele mining. Physical co-localization of GW7 (for grain weight) and DEP2 (for grain number) genes present on chromosome 7 revealed the possibility of simultaneous introgression of these two genes, if desirable allelic variants were found in the single donor parent. This review article will reveal the genetic nature of 2Gs traits and use this knowledge to break the yield ceiling by using different breeding and biotechnological tools, which will sustain the world's food requirements.
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Affiliation(s)
- Gurjeet Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Navdeep Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Renu Khanna
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Rupinder Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Santosh Gudi
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Rajvir Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Navjot Sidhu
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Yogesh Vikal
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - G S Mangat
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
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15
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Jiang J, Wang L, Fan G, Long Y, Lu X, Wang R, Liu H, Qiu X, Zeng D, Li Z. Genetic Dissection of Panicle Morphology Traits in Super High-Yield Hybrid Rice Chaoyou 1000. PLANTS (BASEL, SWITZERLAND) 2024; 13:179. [PMID: 38256733 PMCID: PMC10818613 DOI: 10.3390/plants13020179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 12/26/2023] [Accepted: 01/05/2024] [Indexed: 01/24/2024]
Abstract
The morphological characteristics of the rice panicle play a pivotal role in influencing yield. In our research, we employed F2 and F2:3 populations derived from the high-yielding hybrid rice variety Chaoyou 1000. We screened 123 pairs of molecular markers, which were available, to construct the genetic linkage map. Subsequently, we assessed the panicle morphology traits of F2 populations in Lingshui County, Hainan Province, in 2017, and F2:3 populations in Hangzhou City, Zhejiang Province, in 2018. These two locations represent two types of ecology. Hangzhou's climate is characterized by high temperatures and humidity, while Lingshui's climate is characterized by a tropical monsoon climate. In total, 33 QTLs were identified, with eight of these being newly discovered, and two of them were consistently detected in two distinct environments. We identified fourteen QTL-by-environment interactions (QEs), which collectively explained 4.93% to 59.95% of the phenotypic variation. While most of the detected QTLs are consistent with the results of previous tests, the novel-detected QTLs will lay the foundation for rice yield increase and molecular breeding.
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Affiliation(s)
- Jing Jiang
- Institute of Crop Genetics and Breeding, Yangtze University, Jingzhou 434025, China; (J.J.); (H.L.)
| | - Li Wang
- Institute of Crop Genetics and Breeding, Yangtze University, Jingzhou 434025, China; (J.J.); (H.L.)
| | - Gucheng Fan
- Institute of Crop Genetics and Breeding, Yangtze University, Jingzhou 434025, China; (J.J.); (H.L.)
| | - Yu Long
- Institute of Crop Genetics and Breeding, Yangtze University, Jingzhou 434025, China; (J.J.); (H.L.)
| | - Xueli Lu
- China National Rice Research Institute, Hangzhou 310006, China (D.Z.)
| | - Run Wang
- Institute of Crop Genetics and Breeding, Yangtze University, Jingzhou 434025, China; (J.J.); (H.L.)
| | - Haiyang Liu
- Institute of Crop Genetics and Breeding, Yangtze University, Jingzhou 434025, China; (J.J.); (H.L.)
| | - Xianjin Qiu
- Institute of Crop Genetics and Breeding, Yangtze University, Jingzhou 434025, China; (J.J.); (H.L.)
| | - Dali Zeng
- China National Rice Research Institute, Hangzhou 310006, China (D.Z.)
| | - Zhixin Li
- Institute of Crop Genetics and Breeding, Yangtze University, Jingzhou 434025, China; (J.J.); (H.L.)
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16
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Tian Y, Chen X, Xu P, Wang Y, Wu X, Wu K, Fu X, Chin Y, Liao Y. Rapid Visual Detection of Elite Erect Panicle Dense and Erect Panicle 1 Allele for Marker-Assisted Improvement in Rice ( Oryza sativa L.) Using the Loop-Mediated Isothermal Amplification Method. Curr Issues Mol Biol 2024; 46:498-512. [PMID: 38248334 PMCID: PMC10814556 DOI: 10.3390/cimb46010032] [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: 11/30/2023] [Revised: 12/28/2023] [Accepted: 01/02/2024] [Indexed: 01/23/2024] Open
Abstract
Molecular-assisted breeding is an effective way to improve targeted agronomic traits. dep1 (dense and erect panicle 1) is a pleiotropic gene that regulates yield, quality, disease resistance, and stress tolerance, traits that are of great value in rice (Oryza sativa L.) breeding. In this study, a colorimetric LAMP (loop-mediated isothermal amplification) assay was developed for the detection of the dep1 allele and tested for the screening and selection of the heavy-panicle hybrid rice elite restorer line SHUHUI498, modified with the allele. InDel (Insertion and Deletion) primers (DEP1_F and DEP1_R) and LAMP primers (F3, B3, FIP, and BIP) for genotyping were designed using the Primer3 Plus (version 3.3.0) and PrimerExplore (version 5) software. Our results showed that both InDel and LAMP markers could be used for accurate genotyping. After incubation at a constant temperature of 65 °C for 60 min with hydroxynaphthol blue (HNB) as a color indicator, the color of the LAMP assay containing the dep1 allele changed to sky blue. The SHUHUI498 rice line that was detected in our LAMP assay displayed phenotypes consistent with the dep1 allele such as having a more compact plant architecture, straight stems and leaves, and a significant increase in the number of effective panicles and spikelets, demonstrating the effectiveness of our method in screening for the dep1 allele in rice breeding.
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Affiliation(s)
- Yonghang Tian
- College of Food Science and Engineering, Hainan Tropical Ocean University, No. 1 Yucai Road, Sanya 572022, China; (Y.T.); (X.C.)
- Marine Food Engineering Technology Research Center of Hainan Province, No. 1 Yucai Road, Sanya 572022, China
| | - Xiyi Chen
- College of Food Science and Engineering, Hainan Tropical Ocean University, No. 1 Yucai Road, Sanya 572022, China; (Y.T.); (X.C.)
- Marine Food Engineering Technology Research Center of Hainan Province, No. 1 Yucai Road, Sanya 572022, China
| | - Peizhou Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, No. 211 Huiming Road, Chengdu 611130, China; (P.X.); (Y.W.); (X.W.)
| | - Yuping Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, No. 211 Huiming Road, Chengdu 611130, China; (P.X.); (Y.W.); (X.W.)
| | - Xianjun Wu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, No. 211 Huiming Road, Chengdu 611130, China; (P.X.); (Y.W.); (X.W.)
| | - Kun Wu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Beijing 100101, China; (K.W.); (X.F.)
| | - Xiangdong Fu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Beijing 100101, China; (K.W.); (X.F.)
| | - Yaoxian Chin
- College of Food Science and Engineering, Hainan Tropical Ocean University, No. 1 Yucai Road, Sanya 572022, China; (Y.T.); (X.C.)
- Marine Food Engineering Technology Research Center of Hainan Province, No. 1 Yucai Road, Sanya 572022, China
| | - Yongxiang Liao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, No. 211 Huiming Road, Chengdu 611130, China; (P.X.); (Y.W.); (X.W.)
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17
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Zahra N, Uzair M, Zaid IU, Attia KA, Inam S, Fiaz S, Abdallah RM, Naeem MK, Farooq U, Rehman N, Ali GM, Xu J, Li Z, Khan MR. The comparative transcriptome analysis of two green super rice genotypes with varying tolerance to salt stress. Mol Biol Rep 2023; 51:22. [PMID: 38110786 DOI: 10.1007/s11033-023-08998-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 11/07/2023] [Indexed: 12/20/2023]
Abstract
BACKGROUND Salinity is one of the main abiotic factors that restrict plant growth, physiology, and crop productivity is salt stress. About 33% of the total irrigated land suffers from severe salinity because of intensive underground water extraction and irrigation with brackish water. Thus, it is important to understand the genetic mechanism and identify the novel genes involved in salt tolerance for the development of climate-resilient rice cultivars. METHODS AND RESULTS In this study, two rice genotypes with varying tolerance to salt stress were used to investigate the differential expressed genes and molecular pathways to adapt under saline soil by comparative RNA sequencing at 42 days of the seedling stage. Salt-susceptible (S3) and -tolerant (S13) genotypes revealed 3982 and 3463 differentially expressed genes in S3 and S13 genotypes. The up-regulated genes in both genotypes were substantially enriched in different metabolic processes and binding activities. Biosynthesis of secondary metabolites, phenylpropanoid biosynthesis, and plant signal transduction mechanisms were highly enriched. Salt-susceptible and -tolerant genotypes shared the same salt adaptability mechanism with no significant quantitative differences at the transcriptome level. Moreover, bHLH, ERF, NAC, WRKY, and MYB transcription factors were substantially up-regulated under salt stress. 391 out of 1806 identified novel genes involved in signal transduction mechanisms. Expression profiling of six novel genes further validated the findings from RNA-seq data. CONCLUSION These findings suggest that the differentially expressed genes and molecular mechanisms involved in salt stress adaptation are conserved in both salt-susceptible and salt-tolerant rice genotypes. Further molecular characterization of novel genes will help to understand the genetic mechanism underlying salt tolerance in rice.
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Affiliation(s)
- Nageen Zahra
- National Institute for Genomics and Advanced Biotechnology (NIGAB), NARC, Park Road, Islamabad, 45500, Pakistan
| | - Muhammad Uzair
- National Institute for Genomics and Advanced Biotechnology (NIGAB), NARC, Park Road, Islamabad, 45500, Pakistan
| | - Imdad Ullah Zaid
- National Institute for Genomics and Advanced Biotechnology (NIGAB), NARC, Park Road, Islamabad, 45500, Pakistan
| | - Kotb A Attia
- Department of Biochemistry, College of Science, King Saud University, P.O. Box 2455, 11451, Riyadh, Saudi Arabia
| | - Safeena Inam
- National Institute for Genomics and Advanced Biotechnology (NIGAB), NARC, Park Road, Islamabad, 45500, Pakistan
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur, 22620, Pakistan.
| | - Rizk M Abdallah
- Department of Rice, Field Crops Research Institute, ARC, Sakha, Kafrelshiekh, 33717, Egypt
| | - Muhammad Kashif Naeem
- National Institute for Genomics and Advanced Biotechnology (NIGAB), NARC, Park Road, Islamabad, 45500, Pakistan
| | - Umer Farooq
- National Institute for Genomics and Advanced Biotechnology (NIGAB), NARC, Park Road, Islamabad, 45500, Pakistan
| | - Nazia Rehman
- National Institute for Genomics and Advanced Biotechnology (NIGAB), NARC, Park Road, Islamabad, 45500, Pakistan
| | | | - Jianlong Xu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhikang Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Muhammad Ramzan Khan
- National Institute for Genomics and Advanced Biotechnology (NIGAB), NARC, Park Road, Islamabad, 45500, Pakistan.
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Yoo Y, Yoo YH, Lee DY, Jung KH, Lee SW, Park JC. Caffeine Produced in Rice Plants Provides Tolerance to Water-Deficit Stress. Antioxidants (Basel) 2023; 12:1984. [PMID: 38001837 PMCID: PMC10669911 DOI: 10.3390/antiox12111984] [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: 09/08/2023] [Revised: 11/03/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023] Open
Abstract
Exogenous or endogenous caffeine application confers resistance to diverse biotic stresses in plants. In this study, we demonstrate that endogenous caffeine in caffeine-producing rice (CPR) increases tolerance even to abiotic stresses such as water deficit. Caffeine produced by CPR plants influences the cytosolic Ca2+ ion concentration gradient. We focused on examining the expression of Ca2+-dependent protein kinase genes, a subset of the numerous proteins engaged in abiotic stress signaling. Under normal conditions, CPR plants exhibited increased expressions of seven OsCPKs (OsCPK10, OsCPK12, OsCPK21, OsCPK25, OsCPK26, OsCPK30, and OsCPK31) and biochemical modifications, including antioxidant enzyme (superoxide dismutase, catalase, peroxidase, and ascorbate peroxidase) activity and non-enzymatic antioxidant (ascorbic acid) content. CPR plants exhibited more pronounced gene expression changes and biochemical alterations in response to water-deficit stress. CPR plants revealed increased expressions of 16 OsCPKs (OsCPK1, OsCPK2, OsCPK3, OsCPK4, OsCPK5, OsCPK6, OsCPK9, OsCPK10, OsCPK11, OsCPK12, OsCPK14, OsCPK16, OsCPK18, OsCPK22, OsCPK24, and OsCPK25) and 8 genes (OsbZIP72, OsLEA25, OsNHX1, OsRab16d, OsDREB2B, OsNAC45, OsP5CS, and OsRSUS1) encoding factors related to abiotic stress tolerance. The activity of antioxidant enzymes increased, and non-enzymatic antioxidants accumulated. In addition, a decrease in reactive oxygen species, an accumulation of malondialdehyde, and physiological alterations such as the inhibition of chlorophyll degradation and the protection of photosynthetic machinery were observed. Our results suggest that caffeine is a natural chemical that increases the potential ability of rice to cope with water-deficit stress and provides robust resistance by activating a rapid and comprehensive resistance mechanism in the case of water-deficit stress. The discovery, furthermore, presents a new approach for enhancing crop tolerance to abiotic stress, including water deficit, via the utilization of a specific natural agent.
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Affiliation(s)
- Youngchul Yoo
- Advanced Radiation Technology Institute (ARTI), Korea Atomic Energy Research Institute (KAERI), Jeongeup 56212, Republic of Korea;
| | - Yo-Han Yoo
- Central Area Crop Breeding Division, Department of Central Area Crop Science, National Institute of Crop Science, RDA, Suwon 16429, Republic of Korea;
| | - Dong Yoon Lee
- Graduate School of Green-Bio Science, Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea; (D.Y.L.); (K.-H.J.)
| | - Ki-Hong Jung
- Graduate School of Green-Bio Science, Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea; (D.Y.L.); (K.-H.J.)
| | - Sang-Won Lee
- Graduate School of Green-Bio Science, Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea; (D.Y.L.); (K.-H.J.)
| | - Jong-Chan Park
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
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19
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Li X, Zhang J, Shangguan X, Yin J, Zhu L, Hu J, Du B, Lv W. Knockout of OsWRKY71 impairs Bph15-mediated resistance against brown planthopper in rice. FRONTIERS IN PLANT SCIENCE 2023; 14:1260526. [PMID: 38023936 PMCID: PMC10652391 DOI: 10.3389/fpls.2023.1260526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 10/09/2023] [Indexed: 12/01/2023]
Abstract
The Bph15 gene, known for its ability to confer resistance to the brown planthopper (BPH; Nilaparvata lugens Stål), has been extensively employed in rice breeding. However, the molecular mechanism by which Bph15 provides resistance against BPH in rice remains poorly understood. In this study, we reported that the transcription factor OsWRKY71 was highly responsive to BPH infestation and exhibited early-induced expression in Bph15-NIL (near-isogenic line) plants, and OsWRKY71 was localized in the nucleus of rice protoplasts. The knockout of OsWRKY71 in the Bph15-NIL background by CRISPR-Cas9 technology resulted in an impaired Bph15-mediated resistance against BPH. Transcriptome analysis revealed that the transcript profiles responsive to BPH differed between the wrky71 mutant and Bph15-NIL, and the knockout of OsWRKY71 altered the expression of defense genes. Subsequent quantitative RT-PCR analysis identified three genes, namely sesquiterpene synthase OsSTPS2, EXO70 family gene OsEXO70J1, and disease resistance gene RGA2, which might participate in BPH resistance conferred by OsWRKY71 in Bph15-NIL plants. Our investigation demonstrated the pivotal involvement of OsWRKY71 in Bph15-mediated resistance and provided new insights into the rice defense mechanisms against BPH.
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Affiliation(s)
- Xiaozun Li
- Shandong Academy of Agricultural Sciences, Jinan, China
| | - Jian Zhang
- Shandong Academy of Agricultural Sciences, Jinan, China
| | - Xinxin Shangguan
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Zhoukou, China
| | - Jingjing Yin
- Shandong Academy of Agricultural Sciences, Jinan, China
| | - Lili Zhu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jie Hu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Bo Du
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Wentang Lv
- Shandong Academy of Agricultural Sciences, Jinan, China
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20
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Wang W, Ji D, Peng S, Loladze I, Harrison MT, Davies WJ, Smith P, Xia L, Wang B, Liu K, Zhu K, Zhang W, Ouyang L, Liu L, Gu J, Zhang H, Yang J, Wang F. Eco-physiology and environmental impacts of newly developed rice genotypes for improved yield and nitrogen use efficiency coordinately. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 896:165294. [PMID: 37414171 DOI: 10.1016/j.scitotenv.2023.165294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/30/2023] [Accepted: 07/01/2023] [Indexed: 07/08/2023]
Abstract
Significant advancements have been made in understanding the genetic regulation of nitrogen use efficiency (NUE) and identifying crucial NUE genes in rice. However, the development of rice genotypes that simultaneously exhibit high yield and NUE has lagged behind these theoretical advancements. The grain yield, NUE, and greenhouse gas (GHG) emissions of newly-bred rice genotypes under reduced nitrogen application remain largely unknown. To address this knowledge gap, field experiments were conducted, involving 80 indica (14 to 19 rice genotypes each year in Wuxue, Hubei) and 12 japonica (8 to 12 rice genotypes each year in Yangzhou, Jiangsu). Yield, NUE, agronomy, and soil parameters were assessed, and climate data were recorded. The experiments aimed to assess genotypic variations in yield and NUE among these genotypes and to investigate the eco-physiological basis and environmental impacts of coordinating high yield and high NUE. The results showed significant variations in yield and NUE among the genotypes, with 47 genotypes classified as moderate-high yield with high NUE (MHY_HNUE). These genotypes demonstrated the higher yields and NUE levels, with 9.6 t ha-1, 54.4 kg kg-1, 108.1 kg kg-1, and 64 % for yield, NUE for grain and biomass production, and N harvest index, respectively. Nitrogen uptake and tissue concentration were key drivers of the relationship between yield and NUE, particularly N uptake at heading and N concentrations in both straw and grain at maturity. Increase in pre-anthesis temperature consistently lowered yield and NUE. Genotypes within the MHY_HNUE group exhibited higher methane emissions but lower nitrous oxide emissions compared to those in the low to middle yield and NUE group, resulting in a 12.8 % reduction in the yield-scaled greenhouse gas balance. In conclusion, prioritizing crop breeding efforts on yield and resource use efficiency, as well as developing genotypes resilient to high temperatures with lower GHGs, can mitigate planetary warming.
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Affiliation(s)
- Weilu Wang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou 225009, China; Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Dongling Ji
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Shaobing Peng
- MARA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Irakli Loladze
- Bryan College of Health Sciences, Bryan Medical Center, Lincoln, NE 68506, USA
| | - Matthew Tom Harrison
- Tasmanian Institute of Agriculture, University of Tasmania, Newnham Drive, Launceston, Tasmania 7248, Australia
| | | | - Pete Smith
- School of Biological Sciences, University of Aberdeen, Aberdeen AB24 3UU, UK
| | - Longlong Xia
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Bin Wang
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ke Liu
- Tasmanian Institute of Agriculture, University of Tasmania, Newnham Drive, Launceston, Tasmania 7248, Australia
| | - Kuanyu Zhu
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Wen Zhang
- State Key Laboratory of Atmospheric Boundary Layer Physics and Atmospheric Chemistry, Institute of Atmospheric Physics, Chinese Academy of Sciences, Beijing 100071, China
| | - Linhan Ouyang
- College of Economics and Management, Department of Management Science and Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China
| | - Lijun Liu
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Junfei Gu
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Hao Zhang
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Jianchang Yang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou 225009, China; Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China.
| | - Fei Wang
- MARA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
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Teng Z, Chen J, Wang J, Wu S, Chen R, Lin Y, Shen L, Jackson R, Zhou J, Yang C. Panicle-Cloud: An Open and AI-Powered Cloud Computing Platform for Quantifying Rice Panicles from Drone-Collected Imagery to Enable the Classification of Yield Production in Rice. PLANT PHENOMICS (WASHINGTON, D.C.) 2023; 5:0105. [PMID: 37850120 PMCID: PMC10578299 DOI: 10.34133/plantphenomics.0105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 09/19/2023] [Indexed: 10/19/2023]
Abstract
Rice (Oryza sativa) is an essential stable food for many rice consumption nations in the world and, thus, the importance to improve its yield production under global climate changes. To evaluate different rice varieties' yield performance, key yield-related traits such as panicle number per unit area (PNpM2) are key indicators, which have attracted much attention by many plant research groups. Nevertheless, it is still challenging to conduct large-scale screening of rice panicles to quantify the PNpM2 trait due to complex field conditions, a large variation of rice cultivars, and their panicle morphological features. Here, we present Panicle-Cloud, an open and artificial intelligence (AI)-powered cloud computing platform that is capable of quantifying rice panicles from drone-collected imagery. To facilitate the development of AI-powered detection models, we first established an open diverse rice panicle detection dataset that was annotated by a group of rice specialists; then, we integrated several state-of-the-art deep learning models (including a preferred model called Panicle-AI) into the Panicle-Cloud platform, so that nonexpert users could select a pretrained model to detect rice panicles from their own aerial images. We trialed the AI models with images collected at different attitudes and growth stages, through which the right timing and preferred image resolutions for phenotyping rice panicles in the field were identified. Then, we applied the platform in a 2-season rice breeding trial to valid its biological relevance and classified yield production using the platform-derived PNpM2 trait from hundreds of rice varieties. Through correlation analysis between computational analysis and manual scoring, we found that the platform could quantify the PNpM2 trait reliably, based on which yield production was classified with high accuracy. Hence, we trust that our work demonstrates a valuable advance in phenotyping the PNpM2 trait in rice, which provides a useful toolkit to enable rice breeders to screen and select desired rice varieties under field conditions.
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Affiliation(s)
- Zixuan Teng
- Digital Fujian Research Institute of Big Data for Agriculture and Forestry, College of Computer and Information Sciences,
Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Smart Agriculture and Forestry (Fujian Agriculture and Forestry University),
Fujian Province University, Fuzhou 350002, China
| | - Jiawei Chen
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, academy for Advanced Interdisciplinary Studies,
Nanjing Agricultural University, Nanjing 210095, China
| | - Jian Wang
- Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan 750002, China
| | - Shuixiu Wu
- Digital Fujian Research Institute of Big Data for Agriculture and Forestry, College of Computer and Information Sciences,
Fujian Agriculture and Forestry University, Fuzhou 350002, China
- College of Mechanical and Electrical Engineering,
Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Riqing Chen
- Digital Fujian Research Institute of Big Data for Agriculture and Forestry, College of Computer and Information Sciences,
Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yaohai Lin
- Digital Fujian Research Institute of Big Data for Agriculture and Forestry, College of Computer and Information Sciences,
Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Liyan Shen
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, academy for Advanced Interdisciplinary Studies,
Nanjing Agricultural University, Nanjing 210095, China
| | - Robert Jackson
- Cambridge Crop Research,
National Institute of Agricultural Botany (NIAB), Cambridge CB3 0LE, UK
| | - Ji Zhou
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, academy for Advanced Interdisciplinary Studies,
Nanjing Agricultural University, Nanjing 210095, China
- Cambridge Crop Research,
National Institute of Agricultural Botany (NIAB), Cambridge CB3 0LE, UK
| | - Changcai Yang
- Digital Fujian Research Institute of Big Data for Agriculture and Forestry, College of Computer and Information Sciences,
Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Center for Agroforestry Mega Data Science, School of Future Technology,
Fujian Agriculture and Forestry University, Fuzhou 350002, China
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22
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Feng X, Wang Z, Zeng Z, Zhou Y, Lan Y, Zou W, Gong H, Qi L. Size measurement and filled/unfilled detection of rice grains using backlight image processing. FRONTIERS IN PLANT SCIENCE 2023; 14:1213486. [PMID: 37900751 PMCID: PMC10613065 DOI: 10.3389/fpls.2023.1213486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 09/20/2023] [Indexed: 10/31/2023]
Abstract
Measurements of rice physical traits, such as length, width, and percentage of filled/unfilled grains, are essential steps of rice breeding. A new approach for measuring the physical traits of rice grains for breeding purposes was presented in this study, utilizing image processing techniques. Backlight photography was used to capture a grayscale image of a group of rice grains, which was then analyzed using a clustering algorithm to differentiate between filled and unfilled grains based on their grayscale values. The impact of backlight intensity on the accuracy of the method was also investigated. The results show that the proposed method has excellent accuracy and high efficiency. The mean absolute percentage error of the method was 0.24% and 1.36% in calculating the total number of grain particles and distinguishing the number of filled grains, respectively. The grain size was also measured with a little margin of error. The mean absolute percentage error of grain length measurement was 1.11%, while the measurement error of grain width was 4.03%. The method was found to be highly accurate, non-destructive, and cost-effective when compared to conventional methods, making it a promising approach for characterizing physical traits for crop breeding.
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Affiliation(s)
- Xiao Feng
- College of Engineering, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, Guangdong, China
| | - Zhiqi Wang
- College of Engineering, South China Agricultural University, Guangzhou, Guangdong, China
| | - Zhiwei Zeng
- Department of Agricultural Engineering Technology, University of Wisconsin-River Falls, River Falls, WI, United States
| | - Yuhao Zhou
- College of Engineering, South China Agricultural University, Guangzhou, Guangdong, China
| | - Yunting Lan
- College of Engineering, South China Agricultural University, Guangzhou, Guangdong, China
| | - Wei Zou
- R&D Center, Top-Leading Intelligent Technology Co. ltd., Guangzhou, Guangdong, China
| | - Hao Gong
- College of Engineering, South China Agricultural University, Guangzhou, Guangdong, China
| | - Long Qi
- College of Engineering, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, Guangdong, China
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23
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Dong W, Tu J, Deng W, Zhang J, Xu Y, Gu A, An H, Fan K, Wang R, Zhang J, Kui L, Li X. Genome-wide identification of DUF506 gene family in Oryzasativa and expression profiling under abiotic stresses. PeerJ 2023; 11:e16168. [PMID: 37790624 PMCID: PMC10544316 DOI: 10.7717/peerj.16168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 09/03/2023] [Indexed: 10/05/2023] Open
Abstract
The domain of unknown function 560 (DUF560), also known as the PDDEXK_6 family, is a ubiquitous plant protein that has been confirmed to play critical roles in Arabidopsis root development as well as ABA and abiotic responses. However, genome-wide identification and expression pattern analysis in rice (Oryza sativa) still need to be improved. Based on the phylogenetic relationship, 10 OsDUF506 genes were identified and classified into four subfamilies. Segmental duplication was essential to the expansion of OsDUF506s, which were subjected to purifying selective pressure. Except for OsDUF50609 and OsDUF50610, the OsDUF506s shared colinear gene pairs with five monocot species, showing that they were conserved in evolution. Furthermore, the conserved domains, gene structures, SNPs distribution, and targeting miRNAs were systematically investigated. Massive cis-regulatory elements were discovered in promoter regions, implying that OsDUF506s may be important in hormone regulation and abiotic stress response. Therefore, we analyzed plant hormone-induced transcriptome data and performed qRT-PCR on eight OsDUF506s under drought, cold, and phosphorus-deficient stresses. The results revealed that most OsDUF506s respond to ABA and JA treatment, as well as drought and cold conditions. In conclusion, our findings provided insights into the evolution and function of OsDUF506s, which could benefit crop breeding in the future.
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Affiliation(s)
- Wei Dong
- Yunnan Academy of Agricultural Sciences, Food Crops Research Institute, Kunming, China
| | - Jian Tu
- Yunnan Academy of Agricultural Sciences, Food Crops Research Institute, Kunming, China
| | - Wei Deng
- Yunnan Academy of Agricultural Sciences, Food Crops Research Institute, Kunming, China
| | - Jianhua Zhang
- Yunnan Academy of Agricultural Sciences, Food Crops Research Institute, Kunming, China
| | - Yuran Xu
- Yunnan Academy of Agricultural Sciences, Food Crops Research Institute, Kunming, China
| | - Anyu Gu
- Yunnan Academy of Agricultural Sciences, Food Crops Research Institute, Kunming, China
| | - Hua An
- Yunnan Academy of Agricultural Sciences, Food Crops Research Institute, Kunming, China
| | - Kui Fan
- Yunnan Grain Industry Group Co., Ltd, Kunming, China
| | - Rui Wang
- Yunnan Grain Industry Group Co., Ltd, Kunming, China
| | | | - Limei Kui
- Yunnan Academy of Agricultural Sciences, Food Crops Research Institute, Kunming, China
| | - Xiaolin Li
- Yunnan Academy of Agricultural Sciences, Food Crops Research Institute, Kunming, China
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24
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Lu Y, Wang J, Fu L, Yu L, Liu Q. High-throughput and separating-free phenotyping method for on-panicle rice grains based on deep learning. FRONTIERS IN PLANT SCIENCE 2023; 14:1219584. [PMID: 37790779 PMCID: PMC10544938 DOI: 10.3389/fpls.2023.1219584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 08/28/2023] [Indexed: 10/05/2023]
Abstract
Rice is a vital food crop that feeds most of the global population. Cultivating high-yielding and superior-quality rice varieties has always been a critical research direction. Rice grain-related traits can be used as crucial phenotypic evidence to assess yield potential and quality. However, the analysis of rice grain traits is still mainly based on manual counting or various seed evaluation devices, which incur high costs in time and money. This study proposed a high-precision phenotyping method for rice panicles based on visible light scanning imaging and deep learning technology, which can achieve high-throughput extraction of critical traits of rice panicles without separating and threshing rice panicles. The imaging of rice panicles was realized through visible light scanning. The grains were detected and segmented using the Faster R-CNN-based model, and an improved Pix2Pix model cascaded with it was used to compensate for the information loss caused by the natural occlusion between the rice grains. An image processing pipeline was designed to calculate fifteen phenotypic traits of the on-panicle rice grains. Eight varieties of rice were used to verify the reliability of this method. The R2 values between the extraction by the method and manual measurements of the grain number, grain length, grain width, grain length/width ratio and grain perimeter were 0.99, 0.96, 0.83, 0.90 and 0.84, respectively. Their mean absolute percentage error (MAPE) values were 1.65%, 7.15%, 5.76%, 9.13% and 6.51%. The average imaging time of each rice panicle was about 60 seconds, and the total time of data processing and phenotyping traits extraction was less than 10 seconds. By randomly selecting one thousand grains from each of the eight varieties and analyzing traits, it was found that there were certain differences between varieties in the number distribution of thousand-grain length, thousand-grain width, and thousand-grain length/width ratio. The results show that this method is suitable for high-throughput, non-destructive, and high-precision extraction of on-panicle grains traits without separating. Low cost and robust performance make it easy to popularize. The research results will provide new ideas and methods for extracting panicle traits of rice and other crops.
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Affiliation(s)
- Yuwei Lu
- Key Laboratory of Biomedical Engineering of Hainan Province, School of Biomedical Engineering, Hainan University, Haikou, China
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei, China
- MoE Key Laboratory for Biomedical Photonics, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jinhu Wang
- Key Laboratory of Biomedical Engineering of Hainan Province, School of Biomedical Engineering, Hainan University, Haikou, China
| | - Ling Fu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei, China
- MoE Key Laboratory for Biomedical Photonics, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Department of Physics, School of Science, Hainan University, Haikou, China
| | - Lejun Yu
- Key Laboratory of Biomedical Engineering of Hainan Province, School of Biomedical Engineering, Hainan University, Haikou, China
| | - Qian Liu
- Key Laboratory of Biomedical Engineering of Hainan Province, School of Biomedical Engineering, Hainan University, Haikou, China
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25
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Ma Z, Lv J, Wu W, Fu D, Lü S, Ke Y, Yang P. Regulatory network of rice in response to heat stress and its potential application in breeding strategy. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:68. [PMID: 37608925 PMCID: PMC10440324 DOI: 10.1007/s11032-023-01415-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 08/14/2023] [Indexed: 08/24/2023]
Abstract
The rapid development of global industrialization has led to serious environmental problems, among which global warming has become one of the major concerns. The gradual rise in global temperature resulted in the loss of food production, and hence a serious threat to world food security. Rice is the main crop for approximately half of the world's population, and its geographic distribution, yield, and quality are frequently reduced due to elevated temperature stress, and breeding rice varieties with tolerance to heat stress is of immense significance. Therefore, it is critical to study the molecular mechanism of rice in response to heat stress. In the last decades, large amounts of studies have been conducted focusing on rice heat stress response. Valuable information has been obtained, which not only sheds light on the regulatory network underlying this physiological process but also provides some candidate genes for improved heat tolerance breeding in rice. In this review, we summarized the studies in this field. Hopefully, it will provide some new insights into the mechanisms of rice under high temperature stress and clues for future engineering breeding of improved heat tolerance rice.
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Affiliation(s)
- Zemin Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062 China
| | - Jun Lv
- Institute of Infection and Immunity, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000 China
| | - Wenhua Wu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062 China
| | - Dong Fu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062 China
| | - Shiyou Lü
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062 China
| | - Yinggen Ke
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062 China
- Hubei Hongshan Laboratory, Wuhan, 430070 China
| | - Pingfang Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062 China
- Hubei Hongshan Laboratory, Wuhan, 430070 China
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Liu L, Cui K, Qi X, Wu Y, Huang J, Peng S. Varietal responses of root characteristics to low nitrogen application explain the differing nitrogen uptake and grain yield in two rice varieties. FRONTIERS IN PLANT SCIENCE 2023; 14:1244281. [PMID: 37600168 PMCID: PMC10435752 DOI: 10.3389/fpls.2023.1244281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 07/18/2023] [Indexed: 08/22/2023]
Abstract
Rice root characteristics are tightly associated with high-efficient nitrogen uptake. To understand the relationship of root plastic responses with nitrogen uptake when reducing nitrogen application for green rice production, a hydroponic experiment and a soil pot experiment were conducted under high (HN) and low (LN) nitrogen applications, using two rice (Oryza sativa L.) varieties, NK57 and YD6, three nitrogen absorption traits (total nitrogen accumulation, net NH4 + influx on root surface, nitrogen uptake via apoplasmic pathway) and root characteristics were investigated. In comparison with HN, LN significantly reduced nitrogen absorption and grain yield in both varieties. Concomitantly, there was a decrease in total root length, root surface area, root number, root volume, and root cortical area under LN, while single root length, root aerenchyma area, and root lignin content increased. The expression of OsAMT1;1 and OsAMT1;2 down-regulated in both varieties. The findings revealed that YD6 had smaller reduction degree for the three nitrogen absorption traits and grain yield, accompanied by smaller reduction degree in total root length, root surface area, root cortical area, and expression of the two genes under LN. These root characteristics were significantly and positively correlated with the three nitrogen absorption traits and grain yield, especially under LN. These results indicate that a large root system, lower reduction degree in several root characters, and high expression of OsAMT genes in YD6 explains its high nitrogen accumulation and grain yield under reduced nitrogen application. The study may provide rationale for developing varieties with low nitrogen fertilizer requirements for enabling green rice production.
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Affiliation(s)
- Lei Liu
- National Key Laboratory of Crop Genetic Improvement, Wuhan, Hubei, China
- Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, Wuhan, Hubei, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Kehui Cui
- National Key Laboratory of Crop Genetic Improvement, Wuhan, Hubei, China
- Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, Wuhan, Hubei, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Xiaoli Qi
- National Key Laboratory of Crop Genetic Improvement, Wuhan, Hubei, China
- Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, Wuhan, Hubei, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yu Wu
- National Key Laboratory of Crop Genetic Improvement, Wuhan, Hubei, China
- Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, Wuhan, Hubei, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Jianliang Huang
- National Key Laboratory of Crop Genetic Improvement, Wuhan, Hubei, China
- Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, Wuhan, Hubei, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Shaobing Peng
- National Key Laboratory of Crop Genetic Improvement, Wuhan, Hubei, China
- Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, Wuhan, Hubei, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
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Yan L, Luo T, Huang D, Wei M, Ma Z, Liu C, Qin Y, Zhou X, Lu Y, Li R, Qin G, Zhang Y. Recent Advances in Molecular Mechanism and Breeding Utilization of Brown Planthopper Resistance Genes in Rice: An Integrated Review. Int J Mol Sci 2023; 24:12061. [PMID: 37569437 PMCID: PMC10419156 DOI: 10.3390/ijms241512061] [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: 06/29/2023] [Revised: 07/24/2023] [Accepted: 07/26/2023] [Indexed: 08/13/2023] Open
Abstract
Over half of the world's population relies on rice as their staple food. The brown planthopper (Nilaparvata lugens Stål, BPH) is a significant insect pest that leads to global reductions in rice yields. Breeding rice varieties that are resistant to BPH has been acknowledged as the most cost-effective and efficient strategy to mitigate BPH infestation. Consequently, the exploration of BPH-resistant genes in rice and the development of resistant rice varieties have become focal points of interest and research for breeders. In this review, we summarized the latest advancements in the localization, cloning, molecular mechanisms, and breeding of BPH-resistant rice. Currently, a total of 70 BPH-resistant gene loci have been identified in rice, 64 out of 70 genes/QTLs were mapped on chromosomes 1, 2, 3, 4, 6, 8, 10, 11, and 12, respectively, with 17 of them successfully cloned. These genes primarily encode five types of proteins: lectin receptor kinase (LecRK), coiled-coil-nucleotide-binding-leucine-rich repeat (CC-NB-LRR), B3-DNA binding domain, leucine-rich repeat domain (LRD), and short consensus repeat (SCR). Through mediating plant hormone signaling, calcium ion signaling, protein kinase cascade activation of cell proliferation, transcription factors, and miRNA signaling pathways, these genes induce the deposition of callose and cell wall thickening in rice tissues, ultimately leading to the inhibition of BPH feeding and the formation of resistance mechanisms against BPH damage. Furthermore, we discussed the applications of these resistance genes in the genetic improvement and breeding of rice. Functional studies of these insect-resistant genes and the elucidation of their network mechanisms establish a strong theoretical foundation for investigating the interaction between rice and BPH. Furthermore, they provide ample genetic resources and technical support for achieving sustainable BPH control and developing innovative insect resistance strategies.
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Affiliation(s)
- Liuhui Yan
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China; (L.Y.); (T.L.); (D.H.); (M.W.); (Z.M.); (C.L.); (X.Z.)
- Liuzhou Branch, Guangxi Academy of Agricultural Sciences, Liuzhou Research Center of Agricultural Sciences, Liuzhou 545000, China;
| | - Tongping Luo
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China; (L.Y.); (T.L.); (D.H.); (M.W.); (Z.M.); (C.L.); (X.Z.)
| | - Dahui Huang
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China; (L.Y.); (T.L.); (D.H.); (M.W.); (Z.M.); (C.L.); (X.Z.)
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China;
| | - Minyi Wei
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China; (L.Y.); (T.L.); (D.H.); (M.W.); (Z.M.); (C.L.); (X.Z.)
| | - Zengfeng Ma
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China; (L.Y.); (T.L.); (D.H.); (M.W.); (Z.M.); (C.L.); (X.Z.)
| | - Chi Liu
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China; (L.Y.); (T.L.); (D.H.); (M.W.); (Z.M.); (C.L.); (X.Z.)
| | - Yuanyuan Qin
- Agricultural Science and Technology Information Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China;
| | - Xiaolong Zhou
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China; (L.Y.); (T.L.); (D.H.); (M.W.); (Z.M.); (C.L.); (X.Z.)
| | - Yingping Lu
- Liuzhou Branch, Guangxi Academy of Agricultural Sciences, Liuzhou Research Center of Agricultural Sciences, Liuzhou 545000, China;
| | - Rongbai Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China;
| | - Gang Qin
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China; (L.Y.); (T.L.); (D.H.); (M.W.); (Z.M.); (C.L.); (X.Z.)
| | - Yuexiong Zhang
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China; (L.Y.); (T.L.); (D.H.); (M.W.); (Z.M.); (C.L.); (X.Z.)
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China;
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Qin X, Li X, Xiao J, Wu Q, Li Y, Li C, Jiang D, Tang T, Nan W, Liang Y, Zhang H. Transcriptomic and Physiological Analyses of Two Rice Restorer Lines under Different Nitrogen Supplies Provide Novel Insights into Hybrid Rice Breeding. PLANTS (BASEL, SWITZERLAND) 2023; 12:2276. [PMID: 37375901 DOI: 10.3390/plants12122276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/02/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023]
Abstract
Improving plant nitrogen-use efficiency (NUE) has great significance for various crops, particularly in hybrid breeding. Reducing nitrogen inputs is key to achieving sustainable rice production and mitigating environmental problems. In this study, we analyzed the transcriptomic and physiological changes in two indica restorer lines (Nanhui511 [NH511] and Minghui23 [MH23]) under high nitrogen (HN) and low nitrogen (LN) conditions. Compared to MH23, NH511 was more sensitive to different nitrogen supplies and exhibited higher nitrogen uptake and NUE under HN conditions by increasing lateral root and tiller numbers in the seedling and maturation stages, respectively. NH511 also exhibited a lower survival rate than MH23 when planted in a chlorate-containing hydroponic solution, indicating its HN uptake ability under different nitrogen-supply conditions. Transcriptomic analysis showed that NH511 has 2456 differentially expressed genes, whereas MH23 had only 266. Furthermore, these genes related to nitrogen utilization showed differential expression in NH511 under HN conditions, while the opposite was observed in MH23. Our findings revealed that NH511 could be regarded as elite rice and used for breeding high-NUE restorer lines by regulating and integrating nitrogen-utilization genes, which provides novel insights for the cultivation of high-NUE hybrid rice.
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Affiliation(s)
- Xiaojian Qin
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
- Key Laboratory of Molecular Biology of Plants Environmental Adaptations, Chongqing Normal University, Chongqing 401331, China
| | - Xiaowei Li
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
| | - Juan Xiao
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
| | - Qian Wu
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
| | - Yuntong Li
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
| | - Cuiping Li
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
| | - Dan Jiang
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
| | - Tingting Tang
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
| | - Wenbin Nan
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
- Key Laboratory of Molecular Biology of Plants Environmental Adaptations, Chongqing Normal University, Chongqing 401331, China
| | - Yongshu Liang
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
- Key Laboratory of Molecular Biology of Plants Environmental Adaptations, Chongqing Normal University, Chongqing 401331, China
| | - Hanma Zhang
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
- Key Laboratory of Molecular Biology of Plants Environmental Adaptations, Chongqing Normal University, Chongqing 401331, China
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Li Y, Wang W, Hu C, Yang S, Ma C, Wu J, Wang Y, Xu Z, Li L, Huang Z, Zhu J, Jia X, Ye X, Yang Z, Sun Y, Liu H, Chen R. Ectopic Expression of a Maize Gene ZmDUF1645 in Rice Increases Grain Length and Yield, but Reduces Drought Stress Tolerance. Int J Mol Sci 2023; 24:9794. [PMID: 37372942 DOI: 10.3390/ijms24129794] [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: 05/09/2023] [Revised: 05/27/2023] [Accepted: 06/02/2023] [Indexed: 06/29/2023] Open
Abstract
As the human population grows rapidly, food shortages will become an even greater problem; therefore, increasing crop yield has become a focus of rice breeding programs. The maize gene, ZmDUF1645, encoding a putative member of the DUF1645 protein family with an unknown function, was transformed into rice. Phenotypic analysis showed that enhanced ZmDUF1645 expression significantly altered various traits in transgenic rice plants, including increased grain length, width, weight, and number per panicle, resulting in a significant increase in yield, but a decrease in rice tolerance to drought stress. qRT-PCR results showed that the expression of the related genes regulating meristem activity, such as MPKA, CDKA, a novel crop grain filling gene (GIF1), and GS3, was significantly changed in the ZmDUF1645-overexpression lines. Subcellular colocalization showed that ZmDUF1645 was primarily localized on cell membrane systems. Based on these findings, we speculate that ZmDUF1645, like the OsSGL gene in the same protein family, may regulate grain size and affect yield through the cytokinin signaling pathway. This research provides further knowledge and understanding of the unknown functions of the DUF1645 protein family and may serve as a reference for biological breeding engineering to increase maize crop yield.
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Affiliation(s)
- Yaqi Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China
| | - Wei Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China
| | - Changqiong Hu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China
| | - Songjin Yang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China
| | - Chuan Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China
| | - Jiacheng Wu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China
| | - Yuwei Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China
| | - Zhengjun Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China
| | - Lihua Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China
| | - Zhengjian Huang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China
| | - Jianqing Zhu
- Demonstration Base for International Science & Technology Cooperation of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaomei Jia
- Demonstration Base for International Science & Technology Cooperation of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaoying Ye
- Demonstration Base for International Science & Technology Cooperation of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Zhiyuang Yang
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China
| | - Yongjian Sun
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China
| | - Huainian Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China
| | - Rongjun Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China
- Demonstration Base for International Science & Technology Cooperation of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China
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30
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Lu L, Wang Q, Shi Z, Li C, Guo Z, Li J. Emergence of Rice Blast AVR-Pi9 Resistance Breaking Haplotypes in Yunnan Province, China. Life (Basel) 2023; 13:1320. [PMID: 37374103 DOI: 10.3390/life13061320] [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: 04/07/2023] [Revised: 05/24/2023] [Accepted: 05/31/2023] [Indexed: 06/29/2023] Open
Abstract
The rice blast disease (caused by Magnaporthe oryzae) is a devastating disease in China. Understanding the molecular mechanisms of interaction for the cognate avirulence (AVR) gene with host resistance (R) genes, as well as their genetic evolution is essential for sustainable rice production. In the present study, we conducted a high-throughput nucleotide sequence polymorphism analysis of the AVR-Pi9 gene that was amplified from the rice-growing regions of the Yunnan Province in China. We detected the presence of seven novel haplotypes from 326 rice samples. In addition, the sequences of AVR-Pi9 were also obtained from two non-rice hosts, Eleusine coracana and Eleusine indica. The sequence analysis revealed the insertions and deletions in the coding and non-coding regions of the gene. The pathogenicity experiments of these haplotypes on previously characterized monogenic lines showed that the newly identified haplotypes are virulent in nature. The breakdown of resistance was attributed to the development of new haplotypes. Our results suggest that the mutation in the AVR-Pi9 gene is an alarming situation in the Yunnan province and thus needs attention.
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Affiliation(s)
- Lin Lu
- Flower Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, China
| | - Qun Wang
- Yunnan Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests, Agricultural Environment and Resource Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, China
| | - Zhufeng Shi
- Yunnan Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests, Agricultural Environment and Resource Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, China
| | - Chengyun Li
- The Ministry of Education Key Laboratory for Agricultural Biodiversity and Pest Management, Yunnan Agricultural University, Kunming 650200, China
| | - Zhixiang Guo
- Yunnan Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests, Agricultural Environment and Resource Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, China
| | - Jinbin Li
- Yunnan Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests, Agricultural Environment and Resource Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, China
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Qin X, Li X, Li C, Li Y, Wu Q, Wen H, Jiang D, Tang T, Nan W, Liang Y, Zhang H. Genome-wide identification of nitrate-responsive microRNAs by small RNA sequencing in the rice restorer cultivar Nanhui 511. FRONTIERS IN PLANT SCIENCE 2023; 14:1198809. [PMID: 37332718 PMCID: PMC10272429 DOI: 10.3389/fpls.2023.1198809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 05/18/2023] [Indexed: 06/20/2023]
Abstract
Rice productivity relies heavily on nitrogen fertilization, and improving nitrogen use efficiency (NUE) is important for hybrid rice breeding. Reducing nitrogen inputs is the key to achieving sustainable rice production and reducing environmental problems. Here, we analyzed the genome-wide transcriptomic changes in microRNAs (miRNAs) in the indica rice restorer cultivar Nanhui 511 (NH511) under high (HN) and low nitrogen (LN) conditions. The results showed that NH511 is sensitive to nitrogen supplies and HN conditions promoted the growth its lateral roots at the seedling stage. Furthermore, we identified 483 known miRNAs and 128 novel miRNAs by small RNA sequencing in response to nitrogen in NH511. We also detected 100 differentially expressed genes (DEGs), including 75 upregulated and 25 downregulated DEGs, under HN conditions. Among these DEGs, 43 miRNAs that exhibited a 2-fold change in their expression were identified in response to HN conditions, including 28 upregulated and 15 downregulated genes. Additionally, some differentially expressed miRNAs were further validated by qPCR analysis, which showed that miR443, miR1861b, and miR166k-3p were upregulated, whereas miR395v and miR444b.1 were downregulated under HN conditions. Moreover, the degradomes of possible target genes for miR166k-3p and miR444b.1 and expression variations were analyzed by qPCR at different time points under HN conditions. Our findings revealed comprehensive expression profiles of miRNAs responsive to HN treatments in an indica rice restorer cultivar, which advances our understanding of the regulation of nitrogen signaling mediated by miRNAs and provides novel data for high-NUE hybrid rice cultivation.
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Affiliation(s)
- Xiaojian Qin
- College of Life Sciences, Chongqing Normal University, Chongqing, China
- Key Laboratory of Molecular Biology of Plants Environmental Adaptations, Chongqing Normal University, Chongqing, China
| | - Xiaowei Li
- College of Life Sciences, Chongqing Normal University, Chongqing, China
| | - Cuiping Li
- College of Life Sciences, Chongqing Normal University, Chongqing, China
| | - Yuntong Li
- College of Life Sciences, Chongqing Normal University, Chongqing, China
| | - Qian Wu
- College of Life Sciences, Chongqing Normal University, Chongqing, China
| | - Huan Wen
- College of Life Sciences, Chongqing Normal University, Chongqing, China
| | - Dan Jiang
- College of Life Sciences, Chongqing Normal University, Chongqing, China
| | - Tingting Tang
- College of Life Sciences, Chongqing Normal University, Chongqing, China
| | - Wenbin Nan
- College of Life Sciences, Chongqing Normal University, Chongqing, China
- Key Laboratory of Molecular Biology of Plants Environmental Adaptations, Chongqing Normal University, Chongqing, China
| | - Yongshu Liang
- College of Life Sciences, Chongqing Normal University, Chongqing, China
- Key Laboratory of Molecular Biology of Plants Environmental Adaptations, Chongqing Normal University, Chongqing, China
| | - Hanma Zhang
- College of Life Sciences, Chongqing Normal University, Chongqing, China
- Key Laboratory of Molecular Biology of Plants Environmental Adaptations, Chongqing Normal University, Chongqing, China
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Yang Y, Wu Z, He X, Xu H, Lu Z. Processing Properties and Potency of Bacillus thuringiensis Cry Toxins in the Rice Leaffolder Cnaphalocrocis medinalis (Guenée). Toxins (Basel) 2023; 15:toxins15040275. [PMID: 37104213 PMCID: PMC10143973 DOI: 10.3390/toxins15040275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/30/2023] [Accepted: 04/04/2023] [Indexed: 04/08/2023] Open
Abstract
Different Cry toxins derived from Bacillus thuringiensis (Bt) possess different insecticidal spectra, whereas insects show variations in their susceptibilities to different Cry toxins. Degradation of Cry toxins by insect midgut extracts was involved in the action of toxins. In this study, we explored the processing patterns of different Cry toxins in Cnaphalocrocis medinalis (Lepidoptera: Crambidae) midgut extracts and evaluated the impact of Cry toxins degradation on their potency against C. medinalis to better understand the function of midgut extracts in the action of different Cry toxins. The results indicated that Cry1Ac, Cry1Aa, and Cry1C toxins could be degraded by C. medinalis midgut extracts, and degradation of Cry toxins by midgut extracts differed among time or concentration effects. Bioassays demonstrated that the toxicity of Cry1Ac, Cry1Aa, and Cry1C toxins decreased after digestion by midgut extracts of C. medinalis. Our findings in this study suggested that midgut extracts play an important role in the action of Cry toxins against C. medinalis, and the degradation of Cry toxins by C. medinalis midgut extracts could reduce their toxicities to C. medinalis. They will provide insights into the action of Cry toxins and the application of Cry toxins in C. medinalis management in paddy fields.
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Affiliation(s)
- Yajun Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Zhihong Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Xiaochan He
- Jinhua Academy of Agricultural Sciences, Jinhua 321000, China
| | - Hongxing Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Zhongxian Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
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Zhang C, Yun P, Xia J, Zhou K, Wang L, Zhang J, Zhao B, Yin D, Fu Z, Wang Y, Ma T, Li Z, Wu D. CRISPR/Cas9-mediated editing of Wx and BADH2 genes created glutinous and aromatic two-line hybrid rice. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:24. [PMID: 37313522 PMCID: PMC10248662 DOI: 10.1007/s11032-023-01368-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 03/02/2023] [Indexed: 06/15/2023]
Abstract
Amylose content (AC) is one of the physicochemical indexes of rice quality, which is largely determined by the Waxy (Wx) gene. Fragrance in rice is favored because it adds good flavor and a faint scent. Loss of function of the BADH2 (FGR) gene promotes the biosynthesis of 2-acetyl-1-pyrroline (2AP), which is the main compound responsible for aroma in rice. Here, we used a CRISPR/Cas9 system to simultaneously knock out Wx and FGR genes in 1892S and M858, which are the parents of an indica two-line hybrid rice, Huiliangyou 858 (HLY858). Four T-DNA-free homozygous mutants (1892Swxfgr-1, 1892Swxfgr-2, M858wxfgr-1, and M858wxfgr-2) were obtained. The 1892Swxfgr and M858wxfgr were crossed to generate double mutant hybrid lines HLY858wxfgr-1 and HLY858wxfgr-2. Size-exclusion chromatography (SEC) data indicated that true AC of the wx mutant starches ranged from 0.22 to 1.63%, much lower than those of the wild types (12.93 to 13.76%). However, the gelatinization temperature (GT) of the wx mutants in backgrounds of 1892S, M858, and HLY858 were still high, and showed no significant differences with the wild type controls. The aroma compounds 2AP content in grains of HLY858wxfgr-1 and HLY858wxfgr-2 were 153.0 μg/kg and 151.0 μg/kg, respectively. In contrast, 2AP was not detected in grains of HLY858. There were no significant differences in major agronomic traits between the mutants and HLY858. This study provides guidelines for cultivation of ideal glutinous and aromatic hybrid rice by gene editing.
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Affiliation(s)
- Caijuan Zhang
- College of Agronomy, Anhui Agricultural University, Hefei, 230036 China
- Rice Research Institute/Key Laboratory of Rice Genetics and Breeding of Anhui Province, Anhui Academy of Agricultural Sciences, Hefei, 230031 China
| | - Peng Yun
- Rice Research Institute/Key Laboratory of Rice Genetics and Breeding of Anhui Province, Anhui Academy of Agricultural Sciences, Hefei, 230031 China
| | - Jiafa Xia
- Rice Research Institute/Key Laboratory of Rice Genetics and Breeding of Anhui Province, Anhui Academy of Agricultural Sciences, Hefei, 230031 China
| | - Kunneng Zhou
- Rice Research Institute/Key Laboratory of Rice Genetics and Breeding of Anhui Province, Anhui Academy of Agricultural Sciences, Hefei, 230031 China
| | - Lili Wang
- College of Agronomy, Anhui Agricultural University, Hefei, 230036 China
| | - Jingwen Zhang
- College of Agronomy, Anhui Agricultural University, Hefei, 230036 China
| | - Bo Zhao
- College of Agronomy, Anhui Agricultural University, Hefei, 230036 China
| | - Daokun Yin
- College of Agronomy, Anhui Agricultural University, Hefei, 230036 China
| | - Zhe Fu
- College of Agronomy, Anhui Agricultural University, Hefei, 230036 China
| | - Yuanlei Wang
- Rice Research Institute/Key Laboratory of Rice Genetics and Breeding of Anhui Province, Anhui Academy of Agricultural Sciences, Hefei, 230031 China
| | - Tingchen Ma
- Rice Research Institute/Key Laboratory of Rice Genetics and Breeding of Anhui Province, Anhui Academy of Agricultural Sciences, Hefei, 230031 China
| | - Zefu Li
- Rice Research Institute/Key Laboratory of Rice Genetics and Breeding of Anhui Province, Anhui Academy of Agricultural Sciences, Hefei, 230031 China
| | - Dexiang Wu
- College of Agronomy, Anhui Agricultural University, Hefei, 230036 China
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Kumar A, Thomas J, Gill N, Dwiningsih Y, Ruiz C, Famoso A, Pereira A. Molecular mapping and characterization of QTLs for grain quality traits in a RIL population of US rice under high nighttime temperature stress. Sci Rep 2023; 13:4880. [PMID: 36966148 PMCID: PMC10039871 DOI: 10.1038/s41598-023-31399-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 03/10/2023] [Indexed: 03/27/2023] Open
Abstract
Elevated nighttime temperatures resulting from climate change significantly impact the rice crop worldwide. The rice (Oryza sativa L.) plant is highly sensitive to high nighttime temperature (HNT) during grain-filling (reproductive stage). HNT stress negatively affects grain quality traits and has a major impact on the value of the harvested rice crop. In addition, along with grain dimensions determining rice grain market classes, the grain appearance and quality traits determine the rice grain market value. During the last few years, there has been a major concern for rice growers and the rice industry over the prevalence of rice grains opacity and the reduction of grain dimensions affected by HNT stress. Hence, the improvement of heat-stress tolerance to maintain grain quality of the rice crop under HNT stress will bolster future rice value in the market. In this study, 185 F12-recombinant inbred lines (RILs) derived from two US rice cultivars, Cypress (HNT-tolerant) and LaGrue (HNT-sensitive) were screened for the grain quality traits grain length (GL), grain width (GW), and percent chalkiness (%chalk) under control and HNT stress conditions and evaluated to identify the genomic regions associated with the grain quality traits. In total, there were 15 QTLs identified; 6 QTLs represented under control condition explaining 3.33% to 8.27% of the phenotypic variation, with additive effects ranging from - 0.99 to 0.0267 on six chromosomes and 9 QTLs represented under HNT stress elucidating 6.39 to 51.53% of the phenotypic variation, with additive effects ranging from - 8.8 to 0.028 on nine chromosomes for GL, GW, and % chalk. These 15 QTLs were further characterized and scanned for natural genetic variation in a japonica diversity panel (JDP) to identify candidate genes for GL, GW, and %chalk. We found 6160 high impact single nucleotide polymorphisms (SNPs) characterized as such depending on their type, region, functional class, position, and proximity to the gene and/or gene features, and 149 differentially expressed genes (DEGs) in the 51 Mbp genomic region comprising of the 15 QTLs. Out of which, 11 potential candidate genes showed high impact SNP associations. Therefore, the analysis of the mapped QTLs and their genetic dissection in the US grown Japonica rice genotypes at genomic and transcriptomic levels provide deep insights into genetic variation beneficial to rice breeders and geneticists for understanding the mechanisms related to grain quality under heat stress in rice.
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Affiliation(s)
- Anuj Kumar
- Departemnt of Crop, Soil, & Environmental Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Julie Thomas
- Departemnt of Crop, Soil, & Environmental Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Navdeep Gill
- Department of Biological Sciences, Nova Southeastern University, Fort Lauderdale, FL, 33314, USA
| | - Yheni Dwiningsih
- Departemnt of Crop, Soil, & Environmental Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Charles Ruiz
- Departemnt of Crop, Soil, & Environmental Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Adam Famoso
- H. Rouse Caffey Rice Research Station, Louisiana State University Agricultural Center, Rayne, LA, 70578, USA
| | - Andy Pereira
- Departemnt of Crop, Soil, & Environmental Sciences, University of Arkansas, Fayetteville, AR, 72701, USA.
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Approaches to Reduce Rice Blast Disease Using Knowledge from Host Resistance and Pathogen Pathogenicity. Int J Mol Sci 2023; 24:ijms24054985. [PMID: 36902415 PMCID: PMC10003181 DOI: 10.3390/ijms24054985] [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: 01/21/2023] [Revised: 02/23/2023] [Accepted: 03/03/2023] [Indexed: 03/08/2023] Open
Abstract
Rice is one of the staple foods for the majority of the global population that depends directly or indirectly on it. The yield of this important crop is constantly challenged by various biotic stresses. Rice blast, caused by Magnaporthe oryzae (M. oryzae), is a devastating rice disease causing severe yield losses annually and threatening rice production globally. The development of a resistant variety is one of the most effective and economical approaches to control rice blast. Researchers in the past few decades have witnessed the characterization of several qualitative resistance (R) and quantitative resistance (qR) genes to blast disease as well as several avirulence (Avr) genes from the pathogen. These provide great help for either breeders to develop a resistant variety or pathologists to monitor the dynamics of pathogenic isolates, and ultimately to control the disease. Here, we summarize the current status of the isolation of R, qR and Avr genes in the rice-M. oryzae interaction system, and review the progresses and problems of these genes utilized in practice for reducing rice blast disease. Research perspectives towards better managing blast disease by developing a broad-spectrum and durable blast resistance variety and new fungicides are also discussed.
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Transcriptome and Metabolome Reveal the Molecular Mechanism of Barley Genotypes Underlying the Response to Low Nitrogen and Resupply. Int J Mol Sci 2023; 24:ijms24054706. [PMID: 36902137 PMCID: PMC10003240 DOI: 10.3390/ijms24054706] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 02/16/2023] [Accepted: 02/27/2023] [Indexed: 03/05/2023] Open
Abstract
Nitrogen is one of the most important mineral elements for plant growth and development. Excessive nitrogen application not only pollutes the environment, but also reduces the quality of crops. However, are few studies on the mechanism of barley tolerance to low nitrogen at both the transcriptome and metabolomics levels. In this study, the nitrogen-efficient genotype (W26) and the nitrogen-sensitive genotype (W20) of barley were treated with low nitrogen (LN) for 3 days and 18 days, then treated with resupplied nitrogen (RN) from 18 to 21 days. Later, the biomass and the nitrogen content were measured, and RNA-seq and metabolites were analyzed. The nitrogen use efficiency (NUE) of W26 and W20 treated with LN for 21 days was estimated by nitrogen content and dry weight, and the values were 87.54% and 61.74%, respectively. It turned out to have a significant difference in the two genotypes under the LN condition. According to the transcriptome analysis, 7926 differentially expressed genes (DEGs) and 7537 DEGs were identified in the leaves of W26 and W20, respectively, and 6579 DEGs and 7128 DEGs were found in the roots of W26 and W20, respectively. After analysis of the metabolites, 458 differentially expressed metabolites (DAMs) and 425 DAMs were found in the leaves of W26 and W20, respectively, and 486 DAMs and 368 DAMs were found in the roots of W26 and W20, respectively. According to the KEGG joint analysis of DEGs and DAMs, it was discovered that glutathione (GSH) metabolism was the pathway of significant enrichment in the leaves of both W26 and W20. In this study, the metabolic pathways of nitrogen metabolism and GSH metabolism of barley under nitrogen were constructed based on the related DAMs and DEGs. In leaves, GSH, amino acids, and amides were the main identified DAMs, while in roots, GSH, amino acids, and phenylpropanes were mainly found DAMs. Finally, some nitrogen-efficient candidate genes and metabolites were selected based on the results of this study. The responses of W26 and W20 to low nitrogen stress were significantly different at the transcriptional and metabolic levels. The candidate genes that have been screened will be verified in future. These data not only provide new insights into how barley responds to LN, but also provide new directions for studying the molecular mechanisms of barley under abiotic stress.
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Molecular bases of rice grain size and quality for optimized productivity. Sci Bull (Beijing) 2023; 68:314-350. [PMID: 36710151 DOI: 10.1016/j.scib.2023.01.026] [Citation(s) in RCA: 39] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/30/2022] [Accepted: 01/16/2023] [Indexed: 01/19/2023]
Abstract
The accomplishment of further optimization of crop productivity in grain yield and quality is a great challenge. Grain size is one of the crucial determinants of rice yield and quality; all of these traits are typical quantitative traits controlled by multiple genes. Research advances have revealed several molecular and developmental pathways that govern these traits of agronomical importance. This review provides a comprehensive summary of these pathways, including those mediated by G-protein, the ubiquitin-proteasome system, mitogen-activated protein kinase, phytohormone, transcriptional regulators, and storage product biosynthesis and accumulation. We also generalize the excellent precedents for rice variety improvement of grain size and quality, which utilize newly developed gene editing and conventional gene pyramiding capabilities. In addition, we discuss the rational and accurate breeding strategies, with the aim of better applying molecular design to breed high-yield and superior-quality varieties.
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Peng Y, Ma T, Wang X, Zhang M, Xu Y, Wei J, Sha W, Li J. Proteomic and Transcriptomic Responses of the Desiccation-Tolerant Moss Racomitrium canescens in the Rapid Rehydration Processes. Genes (Basel) 2023; 14:390. [PMID: 36833319 PMCID: PMC9956249 DOI: 10.3390/genes14020390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 01/29/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
The moss Racomitrium canescens (R. canescens) has strong desiccation tolerance. It can remain desiccated for years and yet recover within minutes of rehydration. Understanding the responses and mechanisms underlying this rapid rehydration capacity in bryophytes could identify candidate genes that improve crop drought tolerance. We explored these responses using physiology, proteomics, and transcriptomics. Label-free quantitative proteomics comparing desiccated plants and samples rehydrated for 1 min or 6 h suggesting that damage to chromatin and the cytoskeleton had occurred during desiccation, and pointing to the large-scale degradation of proteins, the production of mannose and xylose, and the degradation of trehalose immediately after rehydration. The assembly and quantification of transcriptomes from R. canescens across different stages of rehydration established that desiccation was physiologically stressful for the plants; however, the plants recovered rapidly once rehydrated. According to the transcriptomics data, vacuoles appear to play a crucial role in the early stages of R. canescens recovery. Mitochondria and cell reproduction might recover before photosynthesis; most biological functions potentially restarted after ~6 h. Furthermore, we identified novel genes and proteins related to desiccation tolerance in bryophytes. Overall, this study provides new strategies for analyzing desiccation-tolerant bryophytes and identifying candidate genes for improving plant drought tolerance.
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Affiliation(s)
- Yifang Peng
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, China
- The Key Laboratory of Resistance Genetic Engineering and Coldland Biodiversity Conservation, College of Life Sciences, Agriculture and Forestry, Qiqihar University, Qiqihar 161006, China
| | - Tianyi Ma
- The Key Laboratory of Resistance Genetic Engineering and Coldland Biodiversity Conservation, College of Life Sciences, Agriculture and Forestry, Qiqihar University, Qiqihar 161006, China
| | - Xin Wang
- The Key Laboratory of Resistance Genetic Engineering and Coldland Biodiversity Conservation, College of Life Sciences, Agriculture and Forestry, Qiqihar University, Qiqihar 161006, China
| | - Meijuan Zhang
- The Key Laboratory of Resistance Genetic Engineering and Coldland Biodiversity Conservation, College of Life Sciences, Agriculture and Forestry, Qiqihar University, Qiqihar 161006, China
| | - Yingxu Xu
- The Key Laboratory of Resistance Genetic Engineering and Coldland Biodiversity Conservation, College of Life Sciences, Agriculture and Forestry, Qiqihar University, Qiqihar 161006, China
| | - Jie Wei
- The Key Laboratory of Resistance Genetic Engineering and Coldland Biodiversity Conservation, College of Life Sciences, Agriculture and Forestry, Qiqihar University, Qiqihar 161006, China
| | - Wei Sha
- The Key Laboratory of Resistance Genetic Engineering and Coldland Biodiversity Conservation, College of Life Sciences, Agriculture and Forestry, Qiqihar University, Qiqihar 161006, China
| | - Jing Li
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, China
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Jin SK, Xu LN, Yang QQ, Zhang MQ, Wang SL, Wang RA, Tao T, Hong LM, Guo QQ, Jia SW, Song T, Leng YJ, Cai XL, Gao JP. High-resolution quantitative trait locus mapping for rice grain quality traits using genotyping by sequencing. FRONTIERS IN PLANT SCIENCE 2023; 13:1050882. [PMID: 36714703 PMCID: PMC9878556 DOI: 10.3389/fpls.2022.1050882] [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: 09/22/2022] [Accepted: 12/23/2022] [Indexed: 06/18/2023]
Abstract
Rice is a major food crop that sustains approximately half of the world population. Recent worldwide improvements in the standard of living have increased the demand for high-quality rice. Accurate identification of quantitative trait loci (QTLs) for rice grain quality traits will facilitate rice quality breeding and improvement. In the present study, we performed high-resolution QTL mapping for rice grain quality traits using a genotyping-by-sequencing approach. An F2 population derived from a cross between an elite japonica variety, Koshihikari, and an indica variety, Nona Bokra, was used to construct a high-density genetic map. A total of 3,830 single nucleotide polymorphism markers were mapped to 12 linkage groups spanning a total length of 2,456.4 cM, with an average genetic distance of 0.82 cM. Seven grain quality traits-the percentage of whole grain, percentage of head rice, percentage of area of head rice, transparency, percentage of chalky rice, percentage of chalkiness area, and degree of chalkiness-of the F2 population were investigated. In total, 15 QTLs with logarithm of the odds (LOD) scores >4 were identified, which mapped to chromosomes 6, 7, and 9. These loci include four QTLs for transparency, four for percentage of chalky rice, four for percentage of chalkiness area, and three for degree of chalkiness, accounting for 0.01%-61.64% of the total phenotypic variation. Of these QTLs, only one overlapped with previously reported QTLs, and the others were novel. By comparing the major QTL regions in the rice genome, several key candidate genes reported to play crucial roles in grain quality traits were identified. These findings will expedite the fine mapping of these QTLs and QTL pyramiding, which will facilitate the genetic improvement of rice grain quality.
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Affiliation(s)
- Su-Kui Jin
- JiangsuKey Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou, China
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Li-Na Xu
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Qing-Qing Yang
- JiangsuKey Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Ming-Qiu Zhang
- JiangsuKey Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Shui-Lian Wang
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Ruo-An Wang
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Tao Tao
- JiangsuKey Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Lian-Min Hong
- JiangsuKey Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Qian-Qian Guo
- JiangsuKey Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Shu-Wen Jia
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Tao Song
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yu-Jia Leng
- JiangsuKey Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Xiu-Ling Cai
- JiangsuKey Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou, China
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Ji-Ping Gao
- JiangsuKey Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou, China
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
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40
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Jiang W, Ye Q, Wu Z, Zhang Q, Wang L, Liu J, Hu X, Guo D, Wang X, Zhang Z, He H, Hu L. Analysis of CAT Gene Family and Functional Identification of OsCAT3 in Rice. Genes (Basel) 2023; 14:138. [PMID: 36672879 PMCID: PMC9858675 DOI: 10.3390/genes14010138] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/27/2022] [Accepted: 12/31/2022] [Indexed: 01/05/2023] Open
Abstract
Catalase (CAT) is an important antioxidant enzyme in plants that plays a key role in plant growth and stress responses. CAT is usually encoded by a small gene family that has been cloned and functionally studied in some species, such as Arabidopsis, wheat and cucumber, but its specific roles in rice are not clear at present. In this study, we identified three CAT family genes (OsCAT1, OsCAT2 and OsCAT3) in the rice genome and performed a systematic bioinformatics analysis. RT-PCR analysis revealed that OsCAT1-OsCAT3 was primarily expressed in vegetative tissues such as roots, stems and leaves. Since OsCAT3 showed the highest expression level among the three OsCAT genes, we then focused on its related functions. OsCAT3 prokaryotic expression protein has an obvious ability to remove H2O2. The OsCAT3crispr plant was short and had a low survival rate, the leaves were small with brown lesions, and the activities of the CAT, POD and SOD enzymes were significantly reduced. A microarray analysis showed that differentially expressed genes were primarily enriched in toxin metabolism and photosynthesis. This study laid a foundation for further understanding the function of the rice OsCAT gene.
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Affiliation(s)
- Wenxiang Jiang
- College of Agriculture, Jiangxi Agricultural University, Nanchang 330045, China
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang 330045, China
| | - Qing Ye
- College of Agriculture, Jiangxi Agricultural University, Nanchang 330045, China
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang 330045, China
| | - Zheng Wu
- College of Agriculture, Jiangxi Agricultural University, Nanchang 330045, China
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang 330045, China
| | - Qiuyun Zhang
- College of Agriculture, Jiangxi Agricultural University, Nanchang 330045, China
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang 330045, China
| | - Lianhong Wang
- College of Agriculture, Jiangxi Agricultural University, Nanchang 330045, China
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang 330045, China
| | - Jialin Liu
- College of Agriculture, Jiangxi Agricultural University, Nanchang 330045, China
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang 330045, China
| | - Xiafei Hu
- College of Agriculture, Jiangxi Agricultural University, Nanchang 330045, China
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang 330045, China
| | - Dandan Guo
- College of Agriculture, Jiangxi Agricultural University, Nanchang 330045, China
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang 330045, China
| | - Xiaoqing Wang
- College of Agriculture, Jiangxi Agricultural University, Nanchang 330045, China
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang 330045, China
| | - Zelin Zhang
- College of Agriculture, Jiangxi Agricultural University, Nanchang 330045, China
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang 330045, China
| | - Haohua He
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang 330045, China
| | - Lifang Hu
- College of Agriculture, Jiangxi Agricultural University, Nanchang 330045, China
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41
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Hu B, Wang W, Chen J, Liu Y, Chu C. Genetic improvement toward nitrogen-use efficiency in rice: Lessons and perspectives. MOLECULAR PLANT 2023; 16:64-74. [PMID: 36380584 DOI: 10.1016/j.molp.2022.11.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 11/08/2022] [Accepted: 11/11/2022] [Indexed: 06/16/2023]
Abstract
The indispensable role of nitrogen fertilizer in ensuring world food security together with the severe threats it poses to the ecosystem makes the usage of nitrogen fertilizer a major challenge for sustainable agriculture. Genetic improvement of crops with high nitrogen-use efficiency (NUE) is one of the most feasible solutions for tackling this challenge. In the last two decades, extensive efforts toward dissecting the variation of NUE-related traits and the underlying genetic basis in different germplasms have been made, and a series of achievements have been obtained in crops, especially in rice. Here, we summarize the approaches used for genetic dissection of NUE and the functions of the causal genes in modulating NUE as well as their applications in NUE improvement in rice. Strategies for exploring the variants controlling NUE and breeding future crops with "less-input-more-output" for sustainable agriculture are also proposed.
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Affiliation(s)
- Bin Hu
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, 510642, Guangzhou, China.
| | - Wei Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, 510642, Guangzhou, China
| | - Jiajun Chen
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Yongqiang Liu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Chengcai Chu
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, 510642, Guangzhou, China.
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Feng X, Li D, Wang H, Yu X, Shentu X. Fitness costs of resistance to insecticide pymetrozine combined with antimicrobial zhongshengmycin in Nilaparvata lugens (Stål). Front Physiol 2023; 14:1160873. [PMID: 37123267 PMCID: PMC10133562 DOI: 10.3389/fphys.2023.1160873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 03/29/2023] [Indexed: 05/02/2023] Open
Abstract
The brown planthopper, Nilaparvata lugens (Stål), is a major pest of rice crops, and its control is critical for food security. Pymetrozine has been recommended as an alternative to imidacloprid for controlling N. lugens, but the pest has developed high resistance to it, making its prohibition and restriction urgent. To address this issue, we conducted a study using a mixture of pymetrozine and zhongshengmycin with the effective ratio of 1:40, to evaluate the fitness costs in N. lugens. Our results showed that N. lugens had a relative fitness of 0.03 under this ratio, with significantly reduced longevity, female and male adult periods, total pre-oviposition days, and fecundity. Moreover, the expression levels of the uricase gene (EC1.7.3.3) and farnesyl diphosphate farnesyl transferase gene (EC2.5.1.21) were reduced in N. lugens. These genes are involved in urea metabolism and steroid biosynthesis pathway, respectively, and their suppression can interfere with the normal nutritional function of N. lugens. Our study demonstrates that the combination of chemical insecticides and antimicrobials can delay the development of resistance and improve the efficiency of pest control. This information is valuable for researchers developing management strategies to delay the development of pymetrozine resistance in N. lugens.
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Affiliation(s)
| | | | | | - Xiaoping Yu
- *Correspondence: Xiaoping Yu, ; Xuping Shentu,
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Ascorbate-Glutathione Cycle Genes Families in Euphorbiaceae: Characterization and Evolutionary Analysis. BIOLOGY 2022; 12:biology12010019. [PMID: 36671712 PMCID: PMC9855080 DOI: 10.3390/biology12010019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/12/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022]
Abstract
Ascorbate peroxidase (APX), Monodehydroascorbate Reductase (MDAR), Dehydroascorbate Reductase (DHAR) and Glutathione Reductase (GR) enzymes participate in the ascorbate-glutathione cycle, which exerts a central role in the antioxidant metabolism in plants. Despite the importance of this antioxidant system in different signal transduction networks related to development and response to environmental stresses, the pathway has not yet been comprehensively characterized in many crop plants. Among different eudicotyledons, the Euphorbiaceae family is particularly diverse with some species highly tolerant to drought. Here the APX, MDAR, DHAR, and GR genes in Ricinus communis, Jatropha curcas, Manihot esculenta, and Hevea brasiliensis were identified and characterized. The comprehensive phylogenetic and genomic analyses allowed the classification of the genes into different classes, equivalent to cytosolic, peroxisomal, chloroplastic, and mitochondrial enzymes, and revealed the duplication events that contribute to the expansion of these families within plant genomes. Due to the high drought stress tolerance of Ricinus communis, the expression patterns of ascorbate-glutathione cycle genes in response to drought were also analyzed in leaves and roots, indicating a differential expression during the stress. Altogether, these data contributed to the characterization of the expression pattern and evolutionary analysis of these genes, filling the gap in the proposed functions of core components of the antioxidant mechanism during stress response in an economically relevant group of plants.
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Patel A, Sahu KP, Mehta S, Balamurugan A, Kumar M, Sheoran N, Kumar S, Krishnappa C, Ashajyothi M, Kundu A, Goyal T, Narayanasamy P, Kumar A. Rice leaf endophytic Microbacterium testaceum: Antifungal actinobacterium confers immunocompetence against rice blast disease. Front Microbiol 2022; 13:1035602. [PMID: 36619990 PMCID: PMC9810758 DOI: 10.3389/fmicb.2022.1035602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 11/07/2022] [Indexed: 12/24/2022] Open
Abstract
Genetic and functional characteristics of rice leaf endophytic actinobacterial member, Microbacterium are described. Morphotyping, multilocus sequence analysis and transmission electron microscopy indicated the species identity of the endophytic bacterium, OsEnb-ALM-D18, as Microbacterium testaceum. The endophytic Microbacterium showed probiotic solubilization of plant nutrients/minerals, produced hydrolytic enzyme/phytohormones, and showed endophytism in rice seedlings. Further, the endophytic colonization by M. testaceum OsEnb-ALM-D18 was confirmed using reporter gene coding for green fluorescence protein. Microbacterium OsEnb-ALM-D18 showed volatilome-mediated antibiosis (95.5% mycelial inhibition) on Magnaporthe oryzae. Chemical profiling of M. testaceum OsEnb-ALM-D18 volatilome revealed the abundance of 9-Octadecenoic acid, Hexadecanoic acid, 4-Methyl-2-pentanol, and 2,5-Dihydro-thiophene. Upon endobacterization of rice seedlings, M. testaceum altered shoot and root phenotype suggestive of activated defense. Over 80.0% blast disease severity reduction was observed on the susceptible rice cultivar Pusa Basmati-1 upon foliar spray with M. testaceum. qPCR-based gene expression analysis showed induction of OsCERK1, OsPAD4, OsNPR1.3, and OsFMO1 suggestive of endophytic immunocompetence against blast disease. Moreover, M. testaceum OsEnb-ALM-D18 conferred immunocompetence, and antifungal antibiosis can be the future integrated blast management strategy.
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Affiliation(s)
- Asharani Patel
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | - Sahil Mehta
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | - Mukesh Kumar
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Neelam Sheoran
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Shanu Kumar
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | | | - Aditi Kundu
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Tushar Goyal
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | - Aundy Kumar
- ICAR-Indian Agricultural Research Institute, New Delhi, India,*Correspondence: Aundy Kumar, ; ; orcid.org/0000-0002-7401-9885
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Natural variation of DROT1 confers drought adaptation in upland rice. Nat Commun 2022; 13:4265. [PMID: 35871266 PMCID: PMC9308802 DOI: 10.1038/s41467-022-31844-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 07/05/2022] [Indexed: 01/03/2023] Open
Abstract
AbstractUpland rice is a distinct ecotype that grows in aerobic environments and tolerates drought stress. However, the genetic basis of its drought resistance is unclear. Here, using an integrative approach combining a genome-wide association study with analyses of introgression lines and transcriptomic profiles, we identify a gene, DROUGHT1 (DROT1), encoding a COBRA-like protein that confers drought resistance in rice. DROT1 is specifically expressed in vascular bundles and is directly repressed by ERF3 and activated by ERF71, both drought-responsive transcription factors. DROT1 improves drought resistance by adjusting cell wall structure by increasing cellulose content and maintaining cellulose crystallinity. A C-to-T single-nucleotide variation in the promoter increases DROT1 expression and drought resistance in upland rice. The potential elite haplotype of DROT1 in upland rice could originate in wild rice (O. rufipogon) and may be beneficial for breeding upland rice varieties.
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Ul Haq SI, Zheng D, Feng N, Jiang X, Qiao F, He JS, Qiu QS. Progresses of CRISPR/Cas9 genome editing in forage crops. JOURNAL OF PLANT PHYSIOLOGY 2022; 279:153860. [PMID: 36371870 DOI: 10.1016/j.jplph.2022.153860] [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: 10/18/2022] [Accepted: 11/02/2022] [Indexed: 06/16/2023]
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) mediated-genome editing has evolved into a powerful tool that is widely used in plant species to induce editing in the genome for analyzing gene function and crop improvement. CRISPR/Cas9 is an RNA-guided genome editing tool consisting of a Cas9 nuclease and a single-guide RNA (sgRNA). The CRISPR/Cas9 system enables more accurate and efficient genome editing in crops. In this review, we summarized the advances of the CRISPR/Cas9 technology in plant genome editing and its applications in forage crops. We described briefly about the development of CRISPR/Cas9 technology in plant genome editing. We assessed the progress of CRISPR/Cas9-mediated targeted-mutagenesis in various forage crops, including alfalfa, Medicago truncatula, Hordeum vulgare, Sorghum bicolor, Setaria italica and Panicum virgatum. The potentials and challenges of CRISPR/Cas9 in forage breeding were discussed.
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Affiliation(s)
- Syed Inzimam Ul Haq
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, 730000, China
| | - Dianfeng Zheng
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong, 524088, China
| | - Naijie Feng
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong, 524088, China
| | - Xingyu Jiang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong, 524088, China
| | - Feng Qiao
- Academy of Plateau Science and Sustainability, School of Life Sciences, Qinghai Normal University, Xining, Qinghai, 810016, China
| | - Jin-Sheng He
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Lanzhou University, Lanzhou, Gansu, 730000, China
| | - Quan-Sheng Qiu
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, 730000, China; State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Lanzhou University, Lanzhou, Gansu, 730000, China; Academy of Plateau Science and Sustainability, School of Life Sciences, Qinghai Normal University, Xining, Qinghai, 810016, China; College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong, 524088, China.
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Identification of QTLs for Heat Tolerance at the Flowering Stage Using Chromosome Segment Substitution Lines in Rice. Genes (Basel) 2022; 13:genes13122248. [PMID: 36553515 PMCID: PMC9777623 DOI: 10.3390/genes13122248] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/24/2022] [Accepted: 11/26/2022] [Indexed: 12/05/2022] Open
Abstract
High temperature is a major stress in rice production. Although considerable progress has been made in investigating heat tolerance (HT) in rice, the genetic basis of HT at the heading stage remains largely unknown. In this study, a novel set of chromosome segment substitution lines (CSSLs) consisting of 113 lines derived from a heat-resistant indica variety N22 and a heat-sensitive indica variety 9311 was developed and used for the analysis of the genetic basis of HT. The heat sensitivity index (HSI) calculated based on seed-setting rates under natural and high-temperature environments was used to evaluate the influence of HT at the rice heading stage. In total, five quantitative trait loci (QTLs) associated with HT were detected based on seed-setting rate (SSR) evaluation; these were named qSSR6-1, qSSR7-1, qSSR8-1, qSSR9-1 and qSSR11-1 located on chromosomes 6, 7, 8, 9 and 11, respectively. Heat-tolerant alleles of the QTLs were all derived from N22. Among them, qSSR9-1 overlapped with QTLs identified previously, while the remaining QTLs were found novel. In particular, qSSR7-1 explained a high phenotypic variation of 26.35% with a LOD score of 10.75, thus deserved to be further validated. These findings will increase our understanding of the genetic mechanism underlying HT and facilitate the breeding of heat-tolerant rice varieties.
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Lv L, Chen X, Li H, Huang J, Liu Y, Zhao A. Different adaptive patterns of wheat with different drought tolerance under drought stresses and rehydration revealed by integrated metabolomic and transcriptomic analysis. FRONTIERS IN PLANT SCIENCE 2022; 13:1008624. [PMID: 36311061 PMCID: PMC9608176 DOI: 10.3389/fpls.2022.1008624] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 08/26/2022] [Indexed: 05/27/2023]
Abstract
Wheat as a staple food crop is enduring ever-frequent intermittent and changing drought with the climate change. It is of great significance to highlight the adaptive approaches under such variable conditions at multiple levels to provide a comprehensive understanding of drought tolerance and facilitate the genetic breeding of wheat. Therefore, three wheat lines with different drought tolerance (drought-tolerant mutant Mu > common wheat CK > drought susceptible mutant mu) were analyzed under moderate and severe drought stresses as well as rehydration. Samples were subjected to transcriptomic and metabolomic profiling in combination with physiological and biochemical determination. The moderate drought stress rendered 198 and 115 differentially expressed metabolites (DEMs) in CK and Mu, respectively. The severe drought stress rendered 166, 151 and 137 DEMs in CK, Mu and mu, respectively. The rehydration rendered 150 and 127 DEMs in CK and Mu. 12,557 and 10,402 differentially expressed genes (DEGs) were identified for CK and Mu under moderate drought stress, respectively. 9,893, 7,924, and 9,387 DEGs were identified for CK, Mu, and mu under severe drought stress, respectively. 13,874 and 14,839 were identified in CK and Mu under rehydration, respectively. Metabolomics results showed that amino acid was the most differentially expressed metabolites, followed by phenolic acids. Flavonoids played an important role in drought tolerance. Most enriched pathways under drought included biosynthesis of secondary metabolites, metabolic pathways and photosynthesis. Metabolites and genes involved in osmotic regulation, antioxidase activities, and ABA signaling were more enriched in Mu than in CK and mu. Various drought-responsive genes and metabolites in Mu showed different trends with those in CK and mu. Increased amino acids biosynthetic capability and ROS scavenging ability resulted from higher antioxidase activities and increased flavonoids may be the mechanisms underlying the drought tolerance characteristic of Mu. Recovery from reversible ROS damage and rapid amino acid biosynthesis may contribute to the rapid recovery of Mu. The present study provides new insights for mechanisms of wheat under complex drought conditions.
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Melatonin Enhances Drought Tolerance in Rice Seedlings by Modulating Antioxidant Systems, Osmoregulation, and Corresponding Gene Expression. Int J Mol Sci 2022; 23:ijms232012075. [PMID: 36292930 PMCID: PMC9603070 DOI: 10.3390/ijms232012075] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 09/30/2022] [Accepted: 10/06/2022] [Indexed: 11/19/2022] Open
Abstract
Rice is the third largest food crop in the world, especially in Asia. Its production in various regions is affected to different degrees by drought stress. Melatonin (MT), a novel growth regulator, plays an essential role in enhancing stress resistance in crops. Nevertheless, the underlying mechanism by which melatonin helps mitigate drought damage in rice remains unclear. Therefore, in the present study, rice seedlings pretreated with melatonin (200 μM) were stressed with drought (water potential of −0.5 MPa). These rice seedlings were subsequently examined for their phenotypes and physiological and molecular properties, including metabolite contents, enzyme activities, and the corresponding gene expression levels. The findings demonstrated that drought stress induced an increase in malondialdehyde (MDA) levels, lipoxygenase (LOX) activity, and reactive oxygen species (ROS, e.g., O2− and H2O2) in rice seedlings. However, the melatonin application significantly reduced LOX activity and the MDA and ROS contents (O2− production rate and H2O2 content), with a decrease of 29.35%, 47.23%, and (45.54% and 49.33%), respectively. It activated the expression of ALM1, OsPOX1, OsCATC, and OsAPX2, which increased the activity of antioxidant enzymes such as superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), and ascorbate peroxidase (APX), respectively. Meanwhile, the melatonin pretreatment enhanced the proline, fructose, and sucrose content by inducing OsP5CS, OsSUS7, and OsSPS1 gene expression levels. Moreover, the melatonin pretreatment considerably up-regulated the expression levels of the melatonin synthesis genes TDC2 and ASMT1 under drought stress by 7-fold and 5-fold, approximately. These improvements were reflected by an increase in the relative water content (RWC) and the root-shoot ratio in the drought-stressed rice seedlings that received a melatonin application. Consequently, melatonin considerably reduced the adverse effects of drought stress on rice seedlings and improved rice’s ability to tolerate drought by primarily boosting endogenous antioxidant enzymes and osmoregulation abilities.
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50
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Zhang A, Liu Y, Wang F, Kong D, Bi J, Zhang F, Luo X, Wang J, Liu G, Luo L, Yu X. Molecular Breeding of Water-Saving and Drought-Resistant Rice for Blast and Bacterial Blight Resistance. PLANTS (BASEL, SWITZERLAND) 2022; 11:2641. [PMID: 36235507 PMCID: PMC9573181 DOI: 10.3390/plants11192641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/02/2022] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
Rice production is often affected by biotic and abiotic stressors. The breeding of resistant cultivars is a cost-cutting and environmentally friendly strategy to maintain a sustainable high production level. An elite water-saving and drought-resistant rice (WDR), Hanhui3, is susceptible to blast and bacterial blight (BB). This study was conducted to introgress three resistance genes (Pi2, xa5, and Xa23) for blast and BB into Hanhui3, using marker-assisted selection (MAS) for the foreground selection and a whole-genome single-nucleotide polymorphism (SNP) array for the background selection. As revealed by the whole-genome SNP array, the recurrent parent genome (RPG) recovery of the improved NIL was 94.2%. The resistance levels to blast and BB of the improved NIL and its derived hybrids were higher than that of the controls. In addition, the improved NIL and its derived hybrids retained the desired agronomic traits from Hanhui3, such as yield. The improved NIL could be useful to enhance resistance against biotic stressors and produce stable grain yields in Oryza sativa subspecies indica rice breeding programs.
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Affiliation(s)
- Anning Zhang
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai Agrobiological Gene Center, Shanghai 201106, China
| | - Yi Liu
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai Agrobiological Gene Center, Shanghai 201106, China
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of life Sciences, Hubei University, Wuhan 430062, China
| | - Feiming Wang
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai Agrobiological Gene Center, Shanghai 201106, China
| | - Deyan Kong
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai Agrobiological Gene Center, Shanghai 201106, China
| | - Junguo Bi
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai Agrobiological Gene Center, Shanghai 201106, China
| | - Fenyun Zhang
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai Agrobiological Gene Center, Shanghai 201106, China
| | - Xingxing Luo
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai Agrobiological Gene Center, Shanghai 201106, China
| | - Jiahong Wang
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai Agrobiological Gene Center, Shanghai 201106, China
| | - Guolan Liu
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai Agrobiological Gene Center, Shanghai 201106, China
| | - Lijun Luo
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai Agrobiological Gene Center, Shanghai 201106, China
| | - Xinqiao Yu
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai Agrobiological Gene Center, Shanghai 201106, China
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