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Yu Y, He RR, Yang L, Feng YZ, Xue J, Liu Q, Zhou YF, Lei MQ, Zhang YC, Lian JP, Chen YQ. A transthyretin-like protein acts downstream of miR397 and LACCASE to regulate grain yield in rice. THE PLANT CELL 2024; 36:2893-2907. [PMID: 38735686 PMCID: PMC11289628 DOI: 10.1093/plcell/koae147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 04/03/2024] [Accepted: 05/07/2024] [Indexed: 05/14/2024]
Abstract
Increasing grain yield is a major goal of breeders due to the rising global demand for food. We previously reported that the miR397-LACCASE (OsLAC) module regulates brassinosteroid (BR) signaling and grain yield in rice (Oryza sativa). However, the precise roles of laccase enzymes in the BR pathway remain unclear. Here, we report that OsLAC controls grain yield by preventing the turnover of TRANSTHYRETIN-LIKE (OsTTL), a negative regulator of BR signaling. Overexpressing OsTTL decreased BR sensitivity in rice, while loss-of-function of OsTTL led to enhanced BR signaling and increased grain yield. OsLAC directly binds to OsTTL and regulates its phosphorylation-mediated turnover. The phosphorylation site Ser226 of OsTTL is essential for its ubiquitination and degradation. Overexpressing the dephosphorylation-mimic form of OsTTL (OsTTLS226A) resulted in more severe defects than did overexpressing OsTTL. These findings provide insight into the role of an ancient laccase in BR signaling and suggest that the OsLAC-OsTTL module could serve as a target for improving grain yield.
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Affiliation(s)
- Yang Yu
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, Guangzhou 510275, P. R. China
- Guangdong Key Laboratory of Crop Germplasm Resources Preservation and Utilization, Key Laboratory of South China Modern Biological Seed Industry, Ministry of Agriculture and Rural Affairs, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, P. R. China
| | - Rui-Rui He
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, Guangzhou 510275, P. R. China
| | - Lu Yang
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, Guangzhou 510275, P. R. China
| | - Yan-Zhao Feng
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, Guangzhou 510275, P. R. China
- Guangdong Key Laboratory of Crop Germplasm Resources Preservation and Utilization, Key Laboratory of South China Modern Biological Seed Industry, Ministry of Agriculture and Rural Affairs, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, P. R. China
| | - Jiao Xue
- Guangdong Key Laboratory of Crop Germplasm Resources Preservation and Utilization, Key Laboratory of South China Modern Biological Seed Industry, Ministry of Agriculture and Rural Affairs, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, P. R. China
| | - Qing Liu
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, P. R. China
| | - Yan-Fei Zhou
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, Guangzhou 510275, P. R. China
| | - Meng-Qi Lei
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, Guangzhou 510275, P. R. China
| | - Yu-Chan Zhang
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, Guangzhou 510275, P. R. China
| | - Jian-Ping Lian
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, Guangzhou 510275, P. R. China
| | - Yue-Qin Chen
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, Guangzhou 510275, P. R. 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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Guo C, Wuza R, Tao Z, Yuan X, Luo Y, Li F, Yang G, Chen Z, Yang Z, Sun Y, Ma J. Effects of elevated nitrogen fertilizer on the multi-level structure and thermal properties of rice starch granules and their relationship with chalkiness traits. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2023; 103:7302-7313. [PMID: 37499162 DOI: 10.1002/jsfa.12886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 06/02/2023] [Accepted: 07/28/2023] [Indexed: 07/29/2023]
Abstract
BACKGROUND Chalkiness in rice reduces its market value and affects consumer acceptance. Research on the mechanism of chalkiness formation has focused primarily on the activity of key enzymes of carbon metabolism and starch accumulation. The relationship between the formation of chalkiness induced by N fertilizer and rice starch's multi-level structure and thermal properties still needs to be fully elucidated. RESULTS In this study, the rates of chalky grains and degree of chalkiness decreased with the increase in N fertilizer dosage. This was attributed to an increased proportion of short chains, ordered structure carbon chains, small starch granules, and branched starches, and a higher degree of crystallinity and ΔHg in protein, and a decreased proportion of amylose, large starch granules, and weighted average diameter of starch granule surface area and volume. Application of N fertilizer promoted an increased proportion of short-branched chain amylopectin to develop a more ordered carbohydrate structure and crystalline lamella. These effects enhanced the normal development and compactness of starch granules in grains, and improved their arrangement morphology, thereby reducing the chalkiness in rice. CONCLUSION These changes in starch multi-level structure and protein improve the physicochemical characteristics of starch and enhance the fullness, crystallinity and compactness of starch granules, while synergistically increasing the regularity and homogeneity of starch granules and thus optimizing the stacking pattern of starch granules, leading to a reduction in rice chalkiness under nitrogen fertilization and thus improving the appearance of rice. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Changchun Guo
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Rice Research Institute, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Southwest Rice Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Rice and Sorghum Research Institute, Sichuan Academy of Agricultural Sciences, Deyang, China
| | - Riqu Wuza
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Ziling Tao
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xiaojuan Yuan
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yinghan Luo
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Feijie Li
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Guotao Yang
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, China
| | - Zongkui Chen
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Zhiyuan Yang
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yongjian Sun
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jun Ma
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Rice Research Institute, Sichuan Agricultural University, Chengdu, China
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Wang Q, Li MJ, Zhang JE, Liu ZQ, Yang K, Li HR, Luo MZ. Suitable stocking density of fish in paddy field contributes positively to 2-acetyl-1-pyrroline synthesis in grain and improves rice quality. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2023; 103:5126-5137. [PMID: 37005496 DOI: 10.1002/jsfa.12597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 02/28/2023] [Accepted: 04/02/2023] [Indexed: 06/08/2023]
Abstract
BACKGROUND Fragrant rice is increasingly popular with the public owing to its fresh aroma, and 2-acetyl-1-pyrroline (2-AP) is the main characteristic component of the aroma in fragrant rice. Rice-fish co-culture is an environmentally friendly practice in sustainable agriculture. However, the effect of rice-fish co-culture on 2-AP in grains has received little study. A conventional fragrant rice (Meixiangzhan 2) was used, and a related field experiment during three rice growing seasons was conducted to investigate the effects of rice-fish co-culture on 2-AP, as well as the rice quality, yield, plant nutrients, and precursors and enzyme activities of 2-AP biosynthesis in leaves. This study involved three fish stocking density treatments (i.e. 9000 (D1), 15 000 (D2), and 21 000 (D3) fish fries per hectare) and rice monocropping. RESULTS Rice-fish co-culture increased the 2-AP content in grains by 2.5-49.4% over that of the monocropping, with significant increases in the early and late rice seasons of 2020. Rice-fish co-culture treatments significantly promoted seed-setting rates by 3.39-7.65%, and improved leaf nutrients and rice quality. Notably, the D2 treatment significantly increased leaf total nitrogen (TN), total phosphorus (TP), and total potassium (TK) contents and the head rice rate at maturity stage, while significantly decreased chalkiness degree. There was no significant difference in rice yield. CONCLUSION Rice-fish co-culture had positive effects on 2-AP synthesis, rice quality, seed-setting rates, and plant nutrient contents. The better stocking density of field fish for rice-fish co-culture in this study was 15 000 fish ha-1 . © 2023 Society of Chemical Industry.
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Affiliation(s)
- Qi Wang
- Guangdong Provincial Key Laboratory of Eco-circular Agriculture, South China Agricultural University, Guangzhou, China
- College of Agriculture, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Technology Research Centre of Modern Eco-agriculture and Circular Agriculture, South China Agricultural University, Guangzhou, China
| | - Mei-Juan Li
- Guangdong Provincial Key Laboratory of Eco-circular Agriculture, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Technology Research Centre of Modern Eco-agriculture and Circular Agriculture, South China Agricultural University, Guangzhou, China
- Department of Ecology, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Jia-En Zhang
- Guangdong Provincial Key Laboratory of Eco-circular Agriculture, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Technology Research Centre of Modern Eco-agriculture and Circular Agriculture, South China Agricultural University, Guangzhou, China
- Department of Ecology, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
- Key Laboratory of Agro-Environment in the Tropics, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, China
| | - Zi-Qiang Liu
- Guangdong Provincial Key Laboratory of Eco-circular Agriculture, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Technology Research Centre of Modern Eco-agriculture and Circular Agriculture, South China Agricultural University, Guangzhou, China
- Department of Ecology, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
| | - Kai Yang
- Guangdong Provincial Key Laboratory of Eco-circular Agriculture, South China Agricultural University, Guangzhou, China
- College of Agriculture, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Technology Research Centre of Modern Eco-agriculture and Circular Agriculture, South China Agricultural University, Guangzhou, China
| | - Hong-Ru Li
- Guangdong Provincial Key Laboratory of Eco-circular Agriculture, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Technology Research Centre of Modern Eco-agriculture and Circular Agriculture, South China Agricultural University, Guangzhou, China
- Department of Ecology, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
| | - Ming-Zhu Luo
- Guangdong Provincial Key Laboratory of Eco-circular Agriculture, South China Agricultural University, Guangzhou, China
- College of Agriculture, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Technology Research Centre of Modern Eco-agriculture and Circular Agriculture, South China Agricultural University, Guangzhou, China
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Chen J, Xuan Y, Yi J, Xiao G, Yuan DP, Li D. Progress in rice sheath blight resistance research. FRONTIERS IN PLANT SCIENCE 2023; 14:1141697. [PMID: 37035075 PMCID: PMC10080073 DOI: 10.3389/fpls.2023.1141697] [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: 01/10/2023] [Accepted: 03/09/2023] [Indexed: 06/19/2023]
Abstract
Rice sheath blight (ShB) disease poses a major threat to rice yield throughout the world. However, the defense mechanisms against ShB in rice remain largely unknown. ShB resistance is a typical quantitative trait controlled by multiple genes. With the rapid development of molecular methods, many quantitative trait loci (QTLs) related to agronomic traits, biotic and abiotic stresses, and yield have been identified by genome-wide association studies. The interactions between plants and pathogens are controlled by various plant hormone signaling pathways, and the pathways synergistically or antagonistically interact with each other, regulating plant growth and development as well as the defense response. This review summarizes the regulatory effects of hormones including auxin, ethylene, salicylic acid, jasmonic acid, brassinosteroids, gibberellin, abscisic acid, strigolactone, and cytokinin on ShB and the crosstalk between the various hormones. Furthermore, the effects of sugar and nitrogen on rice ShB resistance, as well as information on genes related to ShB resistance in rice and their effects on ShB are also discussed. In summary, this review is a comprehensive description of the QTLs, hormones, nutrition, and other defense-related genes related to ShB in rice. The prospects of targeting the resistance mechanism as a strategy for controlling ShB in rice are also discussed.
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Affiliation(s)
- Jingsheng Chen
- College of Biology and Food Engineering, Chongqing Three Gorges University, Wanzhou, China
| | - Yuanhu Xuan
- College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Jianghui Yi
- College of Biology and Food Engineering, Chongqing Three Gorges University, Wanzhou, China
| | - Guosheng Xiao
- College of Biology and Food Engineering, Chongqing Three Gorges University, Wanzhou, China
| | - De Peng Yuan
- College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Dandan Li
- College of Plant Protection, Shenyang Agricultural University, Shenyang, China
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Zhu D, Shao Y, Fang C, Li M, Yu Y, Qin Y. Effect of storage time on chemical compositions, physiological and cooking quality characteristics of different rice types. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2023; 103:2077-2087. [PMID: 36239993 DOI: 10.1002/jsfa.12275] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 09/18/2022] [Accepted: 10/14/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Storage affects rice quality significantly. The aim of this study was to investigate the changes in the chemical composition and in the physiological and cooking quality characteristics of three rice types after 1 year storage at 25 °C. RESULTS Two japonica, two indica, and two indica-japonica hybrid rice varieties were selected. After storage, the total starch content decreased. The amylose content of japonica, indica, and indica-japonica hybrid rice increased by 9.63%-11.65%, 2.99%-4.67%, and 8.07%-8.97%, respectively, and the fat content decreased by 60.00%-65.00%, 37.21%-46.51%, and 41.67%-42.42%, respectively. The abscisic acid (ABA) and raffinose content decreased after 1 year's storage; the former decreased gradually during the storage and the latter increased by 19.35%-45.45%, 7.02%-10.77%, and 16.13%-28.13%, respectively, after 4 months' storage and then decreased to the lowest level after 1 year's storage. The activity of antioxidant enzymes deceased, which resulted in the increases in fatty acid value and malondialdehyde (MDA). The changes in chemical composition after 1 year storage led to the deterioration of rice cooking quality, which was reflected in the decrease in viscosity and increases in gelatinization temperature and cooked rice hardness. CONCLUSION After 1 year's storage, the rice chemical composition changed and physiological and cooking quality characteristics decreased. Compared with japonica and indica-japonica hybrid rice, indica rice was more stable during 1 year storage. This may be due to the higher content of ABA and raffinose in fresh rice. Our findings will provide information for the identification and breeding of storable rice cultivars. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Dawei Zhu
- Rice Product Quality Supervision and Inspection Center, Ministry of Agriculture and Rural Affairs, China National Rice Research Institute, Hangzhou, China
| | - Yafang Shao
- Rice Product Quality Supervision and Inspection Center, Ministry of Agriculture and Rural Affairs, China National Rice Research Institute, Hangzhou, China
| | - Changyun Fang
- Rice Product Quality Supervision and Inspection Center, Ministry of Agriculture and Rural Affairs, China National Rice Research Institute, Hangzhou, China
| | - Min Li
- Rice Research Institute of Guizhou Province, Guiyang, China
| | - Yonghong Yu
- Rice Product Quality Supervision and Inspection Center, Ministry of Agriculture and Rural Affairs, China National Rice Research Institute, Hangzhou, China
| | - Yebo Qin
- Argo-Technical Extension Service Center of Zhejiang Province, Hangzhou, China
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7
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The involvement of an HMG-box gene in germ cell genesis in Pyropia haitanensis. ALGAL RES 2023. [DOI: 10.1016/j.algal.2023.102978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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8
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Lv B, Wu P, Chen XD. The surface mechanics of cooked rice as influenced by gastric fluids measured using a micro texture analyzer. J Texture Stud 2022; 53:465-477. [PMID: 35191036 DOI: 10.1111/jtxs.12667] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 02/09/2022] [Accepted: 02/13/2022] [Indexed: 12/31/2022]
Abstract
In this study, a micro texture analyzer (MTA) was employed to explore the texture characteristics of the surface of an individual steamed rice (SR) and fried rice (FR) grain exhibited in four simulated digestion environments in vitro. The elastic modulus, hardness and elastic index of the single cooked rice particle were measured using the MTA. The hardness of SR particles decreased by 66, 81, 89.1, and 95% after simulated digestion in distilled water, HCl, simulated gastric fluid (SGF), and simulated salivary and gastric fluid (SSF + SGF), respectively. This is in line with the most significant volume expansion and structure ruptures when digested in SSF + SGF. Similar mechanical and structural behaviors were shown for FR, but the hardness and elastic modulus decreased less than those of SR under the same digestion conditions. The different surface mechanics are consistent with the reduced expansion and more compact structure with smaller voids in FR during in vitro digestion. This could be attributed to the encapsulation by frying oil on the surface that would retard the diffusion of digestive fluids into the rice kernels. A weak negative correlation was found between the elastic modulus and the moisture content of the cooked rice. The present study has quantitatively assessed the surface mechanics of cooked rice as influenced by gastric fluids using the MTA. This is practically meaningful for gaining an in-depth understanding of the influence of textural modifications on disintegration of solid foods and release of nutrients during digestion.
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Affiliation(s)
- Boya Lv
- Life Quality Engineering Interest Group, School of Chemical and Environmental Engineering, College of Chemistry, Chemical Engineering and Material Science Soochow University, Suzhou, Jiangsu Province, China
| | - Peng Wu
- Life Quality Engineering Interest Group, School of Chemical and Environmental Engineering, College of Chemistry, Chemical Engineering and Material Science Soochow University, Suzhou, Jiangsu Province, China.,Xiao Dong Pro-health (Suzhou) Instrumentation Co Ltd, Suzhou, 215152, Jiangsu Province, China
| | - Xiao Dong Chen
- Life Quality Engineering Interest Group, School of Chemical and Environmental Engineering, College of Chemistry, Chemical Engineering and Material Science Soochow University, Suzhou, Jiangsu Province, China
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9
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Guo C, Yuan X, Yan F, Xiang K, Wu Y, Zhang Q, Wang Z, He L, Fan P, Yang Z, Chen Z, Sun Y, Ma J. Nitrogen Application Rate Affects the Accumulation of Carbohydrates in Functional Leaves and Grains to Improve Grain Filling and Reduce the Occurrence of Chalkiness. FRONTIERS IN PLANT SCIENCE 2022; 13:921130. [PMID: 35812970 PMCID: PMC9270005 DOI: 10.3389/fpls.2022.921130] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
Chalkiness, which is highly affected by nitrogen (N) management during grain filling, is critical in determining rice appearance quality and consumer acceptability. We investigated the effects of N application rates 75 (N1), 150 (N2), and 225 (N3) kg ha-1 on the source-sink carbohydrate accumulation and grain filling characteristics of two indica hybrid rice cultivars with different chalkiness levels in 2019 and 2020. We further explored the relationship between grain filling and formation of chalkiness in superior and inferior grains. In this study, carbohydrates in the functional leaves and grains of the two varieties, and grain filling parameters, could explain 66.2%, 68.0%, 88.7%, and 91.6% of the total variation of total chalky grain rate and whole chalkiness degree, respectively. They were primarily concentrated in the inferior grains. As the N fertilizer application rate increased, the chalky grain rate and chalkiness degree of both the superior and inferior grains decreased significantly. This interfered with the increase in total chalky grain rate and chalkiness. Moreover, the carbohydrate content in the functional leaves increased significantly in N2 and N3 compared with that in N1. The transfer of soluble sugar from the leaves to the grains decreased the soluble sugar and increased total starch contents, accelerated the development of grain length and width, increased grain water content, and effectively alleviated the contradiction between source and sink. These changes promoted the carbohydrate partition in superior and inferior grains, improved their average filling rate in the middle and later stages, optimized the uniformity of inferior grain fillings, and finally led to the overall reduction in rice chalkiness.
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Affiliation(s)
- Changchun Guo
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu, China
| | - Xiaojuan Yuan
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu, China
| | - Fengjun Yan
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu, China
| | - Kaihong Xiang
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu, China
| | - Yunxia Wu
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu, China
| | - Qiao Zhang
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu, China
| | - Zhonglin Wang
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu, China
| | - Limei He
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu, China
| | - Ping Fan
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu, China
| | - Zhiyuan Yang
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu, China
| | - Zongkui Chen
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu, China
| | - Yongjian Sun
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu, China
| | - Jun Ma
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu, China
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Zhang B, Ma L, Wu B, Xing Y, Qiu X. Introgression Lines: Valuable Resources for Functional Genomics Research and Breeding in Rice ( Oryza sativa L.). FRONTIERS IN PLANT SCIENCE 2022; 13:863789. [PMID: 35557720 PMCID: PMC9087921 DOI: 10.3389/fpls.2022.863789] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 04/01/2022] [Indexed: 05/14/2023]
Abstract
The narrow base of genetic diversity of modern rice varieties is mainly attributed to the overuse of the common backbone parents that leads to the lack of varied favorable alleles in the process of breeding new varieties. Introgression lines (ILs) developed by a backcross strategy combined with marker-assisted selection (MAS) are powerful prebreeding tools for broadening the genetic base of existing cultivars. They have high power for mapping quantitative trait loci (QTLs) either with major or minor effects, and are used for precisely evaluating the genetic effects of QTLs and detecting the gene-by-gene or gene-by-environment interactions due to their low genetic background noise. ILs developed from multiple donors in a fixed background can be used as an IL platform to identify the best alleles or allele combinations for breeding by design. In the present paper, we reviewed the recent achievements from ILs in rice functional genomics research and breeding, including the genetic dissection of complex traits, identification of elite alleles and background-independent and epistatic QTLs, analysis of genetic interaction, and genetic improvement of single and multiple target traits. We also discussed how to develop ILs for further identification of new elite alleles, and how to utilize IL platforms for rice genetic improvement.
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Affiliation(s)
- Bo Zhang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Ling Ma
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Bi Wu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Yongzhong Xing
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Xianjin Qiu
- College of Agriculture, Yangtze University, Jingzhou, China
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11
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Omics: a tool for resilient rice genetic improvement strategies. Mol Biol Rep 2022; 49:5075-5088. [PMID: 35298758 DOI: 10.1007/s11033-022-07189-4] [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: 07/24/2021] [Accepted: 01/24/2022] [Indexed: 10/18/2022]
Abstract
Rice is pivotal pyramid of about half of the world population. Bearing small genome size and worldwide utmost food crop rice has been known as ideal cereal crop for genome research. Currently, decreasing water table and soil fatigue are big challenges and intense consequences in changing climate. Whole sequenced genome of rice sized 389 Mb of which 95% is covered with excellent mapping order. Sequenced rice genome helps in molecular biology and transcriptomics of cereals as it provides whole genome sequence of indica and japonica sub species. Through rice genome sequencing and functional genomics, QTLs or genes, genetic variability and halophyte blocks for agronomic characters were identified which have proved much more useful in molecular breeding and direct selection. There are different numbers of genes or QTLs identified for yield related traits i.e., 6 QTLs/genes for plant architecture, 6 for panicle characteristics, 4 for grain number, 1 gene/QTL for tiller, HGW, grain filling and shattering. QTLS/genes for grain quality, biotic stresses and for abiotic stresses are 7, 23 and 13 respectively. Low yield, inferior quality and susceptibility to biotic and abiotic stresses of a crop is due to narrow genetic background of new evolving rice verities. Wild rice provides genetic resources for improvement of these characters, molecular and genomics tool at different stages can overcome these stresses and improve yield and quality of rice crop.
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12
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Li F, Han Z, Qiao W, Wang J, Song Y, Cui Y, Li J, Ge J, Lou D, Fan W, Li D, Nong B, Zhang Z, Cheng Y, Zhang L, Zheng X, Yang Q. High-Quality Genomes and High-Density Genetic Map Facilitate the Identification of Genes From a Weedy Rice. FRONTIERS IN PLANT SCIENCE 2021; 12:775051. [PMID: 34868173 PMCID: PMC8639688 DOI: 10.3389/fpls.2021.775051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 10/27/2021] [Indexed: 06/13/2023]
Abstract
Genes have been lost or weakened from cultivated rice during rice domestication and breeding. Weedy rice (Oryza sativa f. spontanea) is usually recognized as the progeny between cultivated rice and wild rice and is also known to harbor an gene pool for rice breeding. Therefore, identifying genes from weedy rice germplasms is an important way to break the bottleneck of rice breeding. To discover genes from weedy rice germplasms, we constructed a genetic map based on w-hole-genome sequencing of a F2 population derived from the cross between LM8 and a cultivated rice variety. We further identified 31 QTLs associated with 12 important agronomic traits and revealed that ORUFILM03g000095 gene may play an important role in grain length regulation and participate in grain formation. To clarify the genomic characteristics from weedy rice germplasms of LM8, we generated a high-quality genome assembly using single-molecule sequencing, Bionano optical mapping, and Hi-C technologies. The genome harbored a total size of 375.8 Mb, a scaffold N50 of 24.1 Mb, and originated approximately 0.32 million years ago (Mya) and was more closely related to Oryza sativa ssp. japonica. and contained 672 unique genes. It is related to the formation of grain shape, heading date and tillering. This study generated a high-quality reference genome of weedy rice and high-density genetic map that would benefit the analysis of genome evolution for related species and suggested an effective way to identify genes related to important agronomic traits for further rice breeding.
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Affiliation(s)
- Fei Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhenyun Han
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Weihua Qiao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Junrui Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Guangxi Key Laboratory for Polysaccharide Materials and Modifications, School of Marine Sciences and Biotechnology, Guangxi University for Nationalities, Nanning, China
| | - Yue Song
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yongxia Cui
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- School of Clinical Medicine, Southwest Medical University, Luzhou, China
| | - Jiaqi Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Little Berry Research Room, Liaoning Institute of Fruit Science, Yingkou, China
| | - Jinyue Ge
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Danjing Lou
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Weiya Fan
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Danting Li
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Baoxuan Nong
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Zongqiong Zhang
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Yunlian Cheng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lifang Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoming Zheng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qingwen Yang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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13
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Complex coacervation behavior and the mechanism between rice glutelin and gum arabic at pH 3.0 studied by turbidity, light scattering, fluorescence spectra and molecular docking. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2021.112084] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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14
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Wang C, Liu R, Liu Y, Hou W, Wang X, Miao Y, He Y, Ma Y, Li G, Wang D, Ji Y, Zhang H, Li M, Yan X, Zong X, Yang T. Development and application of the Faba_bean_130K targeted next-generation sequencing SNP genotyping platform based on transcriptome sequencing. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:3195-3207. [PMID: 34117907 DOI: 10.1007/s00122-021-03885-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 06/04/2021] [Indexed: 06/12/2023]
Abstract
KEY MESSAGE Large-scale faba bean transcriptome data are available, and the first genotyping platform based on liquid-phase probe targeted capture technology was developed for genetic and molecular breeding studies. Faba bean (Vicia faba L., 2n = 12) is an important food legume crop that is widely grown for multiple uses worldwide. However, no reference genome is currently available due to its very large genome size (approximately 13 Gb) and limited single nucleotide polymorphism (SNP) markers as well as highly efficient genotyping tools have been reported for faba bean. In this study, 16.7 billion clean reads were obtained from transcriptome libraries of flowers and leaves of 102 global faba bean accessions. A total of 243,120 unigenes were de novo assembled and functionally annotated. Moreover, a total of 1,579,411 SNPs were identified and further filtered according to a selection pipeline to develop a high-throughput, flexible, low-cost Faba_bean_130K targeted next-generation sequencing (TNGS) genotyping platform. A set of 69 Chinese faba bean accessions were genotyped with the TNGS genotyping platform, and the average mapping rate of captured reads to reference transcripts was 93.14%, of which 53.23% were located in the targeted regions. The TNGS genotyping results were validated by Sanger sequencing and the average consistency rate reached 93.6%. Comprehensive population genetic analysis was performed on the 69 Chinese faba bean accessions and identified four genetic subgroups correlated with the geographic distribution. This study provides valuable genomic resources and a reliable genotyping tool that could be implemented in genetic and molecular breeding studies to accelerate new cultivar development and improvement in faba bean.
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Affiliation(s)
- Chenyu Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Rong Liu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yujiao Liu
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Ningda Road No. 251, Xining, 810016, Qinghai, China
| | - Wanwei Hou
- Qinghai Academy of Agricultural and Forestry Sciences, Ningda Road No. 253, Xining, 810016, Qinghai, China
| | - Xuejun Wang
- Agricultural Institute of Riparian Region, Jiangsu, 226541, China
| | - Yamei Miao
- Agricultural Institute of Riparian Region, Jiangsu, 226541, China
| | - Yuhua He
- Institute of Grain Crops, Yunnan Academy of Agricultural Sciences, Kunming, 650205, China
| | - Yu Ma
- Department of Horticulture, Washington State University, Pullman, WA, 99164, USA
| | - Guan Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Dong Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yishan Ji
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hongyan Zhang
- Qinghai Academy of Agricultural and Forestry Sciences, Ningda Road No. 253, Xining, 810016, Qinghai, China
| | - Mengwei Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xin Yan
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xuxiao Zong
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Tao Yang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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15
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Zheng S, Ye C, Lu J, Liufu J, Lin L, Dong Z, Li J, Zhuang C. Improving the Rice Photosynthetic Efficiency and Yield by Editing OsHXK1 via CRISPR/Cas9 System. Int J Mol Sci 2021; 22:ijms22179554. [PMID: 34502462 PMCID: PMC8430575 DOI: 10.3390/ijms22179554] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/29/2021] [Accepted: 08/30/2021] [Indexed: 01/19/2023] Open
Abstract
Rice (Oryza sativa L.) is an important food crop species in China. Cultivating high-yielding rice varieties that have a high photosynthetic efficiency is an important goal of rice breeding in China. In recent years, due to the continual innovation of molecular breeding methods, many excellent genes have been applied in rice breeding, which is highly important for increasing rice yields. In this paper, the hexokinase gene OsHXK1 was knocked out via the CRISPR/Cas9 gene-editing method in the indica rice varieties Huanghuazhan, Meixiangzhan, and Wushansimiao, and OsHXK1-CRISPR/Cas9 lines were obtained. According to the results of a phenotypic analysis and agronomic trait statistics, the OsHXK1-CRISPR/Cas9 plants presented increased light saturation points, stomatal conductance, light tolerance, photosynthetic products, and rice yields. Moreover, transcriptome analysis showed that the expression of photosynthesis-related genes significantly increased. Taken together, our results revealed that knocking out OsHXK1 via the CRISPR/Cas9 gene-editing method could effectively lead to the cultivation of high-photosynthetic efficiency and high-yielding rice varieties. They also revealed the important roles of OsHXK1 in the regulation of rice yield and photosynthesis.
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Affiliation(s)
- Shaoyan Zheng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; (S.Z.); (C.Y.); (J.L.); (J.L.); (L.L.); (Z.D.); (J.L.)
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Chanjuan Ye
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; (S.Z.); (C.Y.); (J.L.); (J.L.); (L.L.); (Z.D.); (J.L.)
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Jingqin Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; (S.Z.); (C.Y.); (J.L.); (J.L.); (L.L.); (Z.D.); (J.L.)
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Jiamin Liufu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; (S.Z.); (C.Y.); (J.L.); (J.L.); (L.L.); (Z.D.); (J.L.)
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Lin Lin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; (S.Z.); (C.Y.); (J.L.); (J.L.); (L.L.); (Z.D.); (J.L.)
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Zequn Dong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; (S.Z.); (C.Y.); (J.L.); (J.L.); (L.L.); (Z.D.); (J.L.)
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Jing Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; (S.Z.); (C.Y.); (J.L.); (J.L.); (L.L.); (Z.D.); (J.L.)
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Chuxiong Zhuang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; (S.Z.); (C.Y.); (J.L.); (J.L.); (L.L.); (Z.D.); (J.L.)
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China
- Correspondence:
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16
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Improved Anther Culture Media for Enhanced Callus Formation and Plant Regeneration in Rice ( Oryza sativa L.). PLANTS 2021; 10:plants10050839. [PMID: 33921954 PMCID: PMC8143452 DOI: 10.3390/plants10050839] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 04/09/2021] [Accepted: 04/16/2021] [Indexed: 11/17/2022]
Abstract
Anther culture technique is the most viable and efficient method of producing homozygous doubled haploid plants within a short period. However, the practical application of this technology in rice improvement is still limited by various factors that influence culture efficiency. The present study was conducted to determine the effects of two improved anther culture media, Ali-1 (A1) and Ali-2 (A2), a modified N6 medium, to enhance the callus formation and plant regeneration of japonica, indica, and hybrids of indica and japonica cross. The current study demonstrated that genotype and media had a significant impact (p < 0.001) on both callus induction frequency and green plantlet regeneration efficiency. The use of the A1 and A2 medium significantly enhanced callus induction frequency of japonica rice type, Nipponbare, and the hybrids of indica × japonica cross (CXY6, CXY24, and Y2) but not the indica rice type, NSIC Rc480. However, the A1 medium is found superior to the N6 medium as it significantly improved the green plantlet regeneration efficiency of CXY6, CXY24, and Y2 by almost 36%, 118%, and 277%, respectively. Furthermore, it substantially reduced the albino plantlet regeneration of the induced callus in two hybrids (CXY6 and Y2). Therefore, the improved anther culture medium A1 can produce doubled haploid rice plants for indica × japonica, which can be useful in different breeding programs that will enable the speedy development of rice varieties for resource-poor farmers.
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17
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Usman B, Zhao N, Nawaz G, Qin B, Liu F, Liu Y, Li R. CRISPR/Cas9 Guided Mutagenesis of Grain Size 3 Confers Increased Rice ( Oryza sativa L.) Grain Length by Regulating Cysteine Proteinase Inhibitor and Ubiquitin-Related Proteins. Int J Mol Sci 2021; 22:ijms22063225. [PMID: 33810044 PMCID: PMC8004693 DOI: 10.3390/ijms22063225] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/19/2021] [Accepted: 03/20/2021] [Indexed: 12/21/2022] Open
Abstract
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated protein (Cas9)-mediated genome editing has become an important way for molecular breeding in crop plants. To promote rice breeding, we edited the Grain Size 3 (GS3) gene for obtaining valuable and stable long-grain rice mutants. Furthermore, isobaric tags for the relative and absolute quantitation (iTRAQ)-based proteomic method were applied to determine the proteome-wide changes in the GS3 mutants compared with wild type (WT). Two target sites were designed to construct the vector, and the Agrobacterium-mediated method was used for rice transformation. Specific mutations were successfully introduced, and the grain length (GL) and 1000-grain weight (GWT) of the mutants were increased by 31.39% and 27.15%, respectively, compared with WT. The iTRAQ-based proteomic analysis revealed that a total of 31 proteins were differentially expressed in the GS3 mutants, including 20 up-regulated and 11 down-regulated proteins. Results showed that differentially expressed proteins (DEPs) were mainly related to cysteine synthase, cysteine proteinase inhibitor, vacuolar protein sorting-associated, ubiquitin, and DNA ligase. Furthermore, functional analysis revealed that DEPs were mostly enriched in cellular process, metabolic process, binding, transmembrane, structural, and catalytic activities. Pathway enrichment analysis revealed that DEPs were mainly involved in lipid metabolism and oxylipin biosynthesis. The protein-to-protein interaction (PPI) network found that proteins related to DNA damage-binding, ubiquitin-40S ribosomal, and cysteine proteinase inhibitor showed a higher degree of interaction. The homozygous mutant lines featured by stable inheritance and long-grain phenotype were obtained using the CRISPR/Cas9 system. This study provides a convenient and effective way of improving grain yield, which could significantly accelerate the breeding process of long-grain japonica parents and promote the development of high-yielding rice.
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Affiliation(s)
- Babar Usman
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (B.U.); (N.Z.); (G.N.); (B.Q.); (F.L.)
| | - Neng Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (B.U.); (N.Z.); (G.N.); (B.Q.); (F.L.)
| | - Gul Nawaz
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (B.U.); (N.Z.); (G.N.); (B.Q.); (F.L.)
| | - Baoxiang Qin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (B.U.); (N.Z.); (G.N.); (B.Q.); (F.L.)
| | - Fang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (B.U.); (N.Z.); (G.N.); (B.Q.); (F.L.)
| | - Yaoguang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agricultural Bioresources, South China Agricultural University, Guangzhou 510642, China
- Correspondence: (Y.L.); (R.L.); Tel.: +86-20-8528-1908 (Y.L.); +86-136-0009-4135 (R.L.)
| | - Rongbai Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (B.U.); (N.Z.); (G.N.); (B.Q.); (F.L.)
- Correspondence: (Y.L.); (R.L.); Tel.: +86-20-8528-1908 (Y.L.); +86-136-0009-4135 (R.L.)
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18
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Zhang J, Xiao Q, Guo T, Wang P. Effect of sodium chloride on the expression of genes involved in the salt tolerance of Bacillus sp. strain “SX4” isolated from salinized greenhouse soil. OPEN CHEM 2021. [DOI: 10.1515/chem-2020-0181] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
Salt stress is one of the important adverse conditions affecting bacterium growth. How bacteria isolated from greenhouse soil cope with salt stress and regulate the genes responsible for salt tolerance are still unclear. We conducted RNA transcriptome profiling of genes contributing to the salt tolerance of a Bacillus sp. strain (“SX4”) obtained from salinized soil. Results showed that NaCl effectively regulated the growth of “SX4” in terms of cell length and colony-forming unit number decrease. A total of 121 upregulated and 346 downregulated genes were detected under salt stress with reference to the control. The largest numbers of differential expression genes were 17 in carbon metabolism, 13 in the biosynthesis of amino acids, 10 in a two-component system, and 10 in ABC transporter pathways for adapting to salt stress. Our data revealed that cation, electron and transmembrane transport, and catalytic activity play important roles in the resistance of bacterial cells to salt ions. Single-nucleotide polymorphism and the mutation of base pair T:A to C:G play potential roles in the adaptation of “SX4” to high NaCl concentrations. The findings from this study provide new insights into the molecular mechanisms of strain “SX4” and will be helpful in promoting the application of salt-tolerant bacteria.
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Affiliation(s)
- Jian Zhang
- Institute of Horticulture, Anhui Academy of Agricultural Sciences , Nongke South Road 40# , Hefei , 230031, Anhui , China
- Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural Crops , Hefei , 230031, Anhui , China
| | - Qingqing Xiao
- School of Biology, Food and Environment, Hefei University , Hefei , 230601, Anhui , China
| | - Tingting Guo
- Institute of Horticulture, Anhui Academy of Agricultural Sciences , Nongke South Road 40# , Hefei , 230031, Anhui , China
- School of Life Sciences, Anhui Agricultural University , Hefei , 230036, Anhui , China
| | - Pengcheng Wang
- Institute of Horticulture, Anhui Academy of Agricultural Sciences , Nongke South Road 40# , Hefei , 230031, Anhui , China
- Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural Crops , Hefei , 230031, Anhui , China
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19
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Chen Z, Shen Z, Xu L, Zhao D, Zou Q. Regulator Network Analysis of Rice and Maize Yield-Related Genes. Front Cell Dev Biol 2021; 8:621464. [PMID: 33425929 PMCID: PMC7793993 DOI: 10.3389/fcell.2020.621464] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 11/12/2020] [Indexed: 11/13/2022] Open
Abstract
Rice and maize are the principal food crop species worldwide. The mechanism of gene regulation for the yield of rice and maize is still the research focus at present. Seed size, weight and shape are important traits of crop yield in rice and maize. Most members of three gene families, APETALA2/ethylene response factor, auxin response factors and MADS, were identified to be involved in yield traits in rice and maize. Analysis of molecular regulation mechanisms related to yield traits provides theoretical support for the improvement of crop yield. Genetic regulatory network analysis can provide new insights into gene families with the improvement of sequencing technology. Here, we analyzed the evolutionary relationships and the genetic regulatory network for the gene family members to predicted genes that may be involved in yield-related traits in rice and maize. The results may provide some theoretical and application guidelines for future investigations of molecular biology, which may be helpful for developing new rice and maize varieties with high yield traits.
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Affiliation(s)
- Zheng Chen
- School of Applied Chemistry and Biological Technology, Shenzhen Polytechnic, Shenzhen, China.,Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China
| | - Zijie Shen
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China
| | - Lei Xu
- School of Electronic and Communication Engineering, Shenzhen Polytechnic, Shenzhen, China
| | - Da Zhao
- School of Applied Chemistry and Biological Technology, Shenzhen Polytechnic, Shenzhen, China.,Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China
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20
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Zhu D, Fang C, Qian Z, Guo B, Huo Z. Differences in starch structure, physicochemical properties and texture characteristics in superior and inferior grains of rice varieties with different amylose contents. Food Hydrocoll 2021. [DOI: 10.1016/j.foodhyd.2020.106170] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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21
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Ding Y, Zhu J, Zhao D, Liu Q, Yang Q, Zhang T. Targeting Cis-Regulatory Elements for Rice Grain Quality Improvement. FRONTIERS IN PLANT SCIENCE 2021; 12:705834. [PMID: 34456947 PMCID: PMC8385297 DOI: 10.3389/fpls.2021.705834] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 07/08/2021] [Indexed: 05/05/2023]
Abstract
Rice is the most important source of food worldwide, providing energy, and nutrition for more than half of the population worldwide. Rice grain quality is a complex trait that is affected by several factors, such as the genotype and environment, and is a major target for rice breeders. Cis-regulatory elements (CREs) are the regions of non-coding DNA, which play a critical role in gene expression regulation. Compared with gene knockout, CRE modifications can fine-tune the expression levels of target genes. Genome editing has provided opportunities to modify the genomes of organisms in a precise and predictable way. Recently, the promoter modifications of coding genes using genome editing technologies in plant improvement have become popular. In this study, we reviewed the results of recent studies on the identification, characterization, and application of CREs involved in rice grain quality. We proposed CREs as preferred potential targets to create allelic diversity and to improve quality traits via genome editing strategies in rice. We also discussed potential challenges and experimental considerations for the improvement in grain quality in crop plants.
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Affiliation(s)
- Yu Ding
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Jiannan Zhu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Dongsheng Zhao
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Qiaoquan Liu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Qingqing Yang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, China
- Department of Biotechnology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
- *Correspondence: Qingqing Yang
| | - Tao Zhang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, China
- Tao Zhang
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Xian P, Cai Z, Cheng Y, Lin R, Lian T, Ma Q, Nian H. Wild Soybean Oxalyl-CoA Synthetase Degrades Oxalate and Affects the Tolerance to Cadmium and Aluminum Stresses. Int J Mol Sci 2020; 21:E8869. [PMID: 33238600 PMCID: PMC7700444 DOI: 10.3390/ijms21228869] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/18/2020] [Accepted: 11/19/2020] [Indexed: 11/16/2022] Open
Abstract
Acyl activating enzyme 3 (AAE3) was identified as being involved in the acetylation pathway of oxalate degradation, which regulates the responses to biotic and abiotic stresses in various higher plants. Here, we investigated the role of Glycine sojaAAE3 (GsAAE3) in Cadmium (Cd) and Aluminum (Al) tolerances. The recombinant GsAAE3 protein showed high activity toward oxalate, with a Km of 105.10 ± 12.30 μM and Vmax of 12.64 ± 0.34 μmol min-1 mg-1 protein, suggesting that it functions as an oxalyl-CoA synthetase. The expression of a GsAAE3-green fluorescent protein (GFP) fusion protein in tobacco leaves did not reveal a specific subcellular localization pattern of GsAAE3. An analysis of the GsAAE3 expression pattern revealed an increase in GsAAE3 expression in response to Cd and Al stresses, and it is mainly expressed in root tips. Furthermore, oxalate accumulation induced by Cd and Al contributes to the inhibition of root growth in wild soybean. Importantly, GsAAE3 overexpression increases Cd and Al tolerances in A. thaliana and soybean hairy roots, which is associated with a decrease in oxalate accumulation. Taken together, our data provide evidence that the GsAAE3-encoded protein plays an important role in coping with Cd and Al stresses.
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Affiliation(s)
- Peiqi Xian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; (P.X.); (Z.C.); (Y.C.); (R.L.); (T.L.); (Q.M.)
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
- The Guangdong Subcenter of the National Center for Soybean Improvement, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, South China Agricultural University, Guangzhou 510642, China
| | - Zhandong Cai
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; (P.X.); (Z.C.); (Y.C.); (R.L.); (T.L.); (Q.M.)
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
- The Guangdong Subcenter of the National Center for Soybean Improvement, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, South China Agricultural University, Guangzhou 510642, China
| | - Yanbo Cheng
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; (P.X.); (Z.C.); (Y.C.); (R.L.); (T.L.); (Q.M.)
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
- The Guangdong Subcenter of the National Center for Soybean Improvement, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, South China Agricultural University, Guangzhou 510642, China
| | - Rongbin Lin
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; (P.X.); (Z.C.); (Y.C.); (R.L.); (T.L.); (Q.M.)
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
- The Guangdong Subcenter of the National Center for Soybean Improvement, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Tengxiang Lian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; (P.X.); (Z.C.); (Y.C.); (R.L.); (T.L.); (Q.M.)
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
- The Guangdong Subcenter of the National Center for Soybean Improvement, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, South China Agricultural University, Guangzhou 510642, China
| | - Qibin Ma
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; (P.X.); (Z.C.); (Y.C.); (R.L.); (T.L.); (Q.M.)
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
- The Guangdong Subcenter of the National Center for Soybean Improvement, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, South China Agricultural University, Guangzhou 510642, China
| | - Hai Nian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; (P.X.); (Z.C.); (Y.C.); (R.L.); (T.L.); (Q.M.)
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
- The Guangdong Subcenter of the National Center for Soybean Improvement, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, South China Agricultural University, Guangzhou 510642, China
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23
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Zhao N, Sheng M, Zhao J, Ma X, Wei Q, Song Q, Zhang K, Xu W, Sun C, Liu F, Su Z. Over-Expression of HDA710 Delays Leaf Senescence in Rice ( Oryza sativa L.). Front Bioeng Biotechnol 2020; 8:471. [PMID: 32509751 PMCID: PMC7248171 DOI: 10.3389/fbioe.2020.00471] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 04/22/2020] [Indexed: 11/13/2022] Open
Abstract
Histone deacetylases (HDACs) influence chromatin state and gene expression. Eighteen HDAC genes with important biological functions have been identified in rice. In this study, we surveyed the gene presence frequency of all 18 rice HDAC genes in 3,010 rice accessions. HDA710/OsHDAC2 showed insertion/deletion (InDel) polymorphisms in almost 98.8% japonica accessions but only 1% indica accessions. InDel polymorphism association analysis showed that accessions with partial deletions in HDA710 tended to display early leaf senescence. Further transgenic results confirmed that HDA710 delayed leaf senescence in rice. The over-expression of HDA710 delayed leaf senescence, and the knock-down of HDA710 accelerated leaf senescence. Transcriptome analysis showed that photosynthesis and chlorophyll biosynthesis related genes were up-regulated in HDA710 over-expression lines, while some programmed cell death and disease resistance related genes were down-regulated. Co-expression network analysis with gene expression view revealed that HDA710 was co-expressed with multiple genes, particularly OsGSTU12, which was significantly up-regulated in 35S::HDA710-sense lines. InDels in the promoter region of OsGSTU12 and in the gene region of HDA710 occurred coincidentally among more than 90% accessions, and we identified multiple W-box motifs at the InDel position of OsGSTU12. Over-expression of OsGSTU12 also delayed leaf senescence in rice. Taken together, our results suggest that both HDA710 and OsGSTU12 are involved in regulating the process of leaf senescence in rice.
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Affiliation(s)
- Nannan Zhao
- College of Biological Sciences, China Agricultural University, Beijing, China
| | - Minghao Sheng
- College of Biological Sciences, China Agricultural University, Beijing, China
| | - Jie Zhao
- Beijing Key Laboratory of Crop, Ministry of Education (MOE) Laboratory of Crop Heterosis and Utilization, National Center for Evaluation of Agricultural Wild Plants (Rice), Beijing, China.,Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China
| | - Xuelian Ma
- College of Biological Sciences, China Agricultural University, Beijing, China
| | - Qiang Wei
- College of Biological Sciences, China Agricultural University, Beijing, China
| | - Qian Song
- College of Biological Sciences, China Agricultural University, Beijing, China
| | - Kang Zhang
- College of Biological Sciences, China Agricultural University, Beijing, China
| | - Wenying Xu
- College of Biological Sciences, China Agricultural University, Beijing, China
| | - Chuanqing Sun
- Beijing Key Laboratory of Crop, Ministry of Education (MOE) Laboratory of Crop Heterosis and Utilization, National Center for Evaluation of Agricultural Wild Plants (Rice), Beijing, China.,Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China
| | - Fengxia Liu
- Beijing Key Laboratory of Crop, Ministry of Education (MOE) Laboratory of Crop Heterosis and Utilization, National Center for Evaluation of Agricultural Wild Plants (Rice), Beijing, China.,Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China
| | - Zhen Su
- College of Biological Sciences, China Agricultural University, Beijing, China
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24
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Mbanjo EGN, Kretzschmar T, Jones H, Ereful N, Blanchard C, Boyd LA, Sreenivasulu N. The Genetic Basis and Nutritional Benefits of Pigmented Rice Grain. Front Genet 2020; 11:229. [PMID: 32231689 PMCID: PMC7083195 DOI: 10.3389/fgene.2020.00229] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 02/26/2020] [Indexed: 12/31/2022] Open
Abstract
Improving the nutritional quality of rice grains through modulation of bioactive compounds and micronutrients represents an efficient means of addressing nutritional security in societies which depend heavily on rice as a staple food. White rice makes a major contribution to the calorific intake of Asian and African populations, but its nutritional quality is poor compared to that of pigmented (black, purple, red orange, or brown) variants. The compounds responsible for these color variations are the flavonoids anthocyanin and proanthocyanidin, which are known to have nutritional value. The rapid progress made in the technologies underlying genome sequencing, the analysis of gene expression and the acquisition of global 'omics data, genetics of grain pigmentation has created novel opportunities for applying molecular breeding to improve the nutritional value and productivity of pigmented rice. This review provides an update on the nutritional value and health benefits of pigmented rice grain, taking advantage of both indigenous and modern knowledge, while also describing the current approaches taken to deciphering the genetic basis of pigmentation.
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Affiliation(s)
- Edwige Gaby Nkouaya Mbanjo
- International Rice Research Institute, Los Baños, Philippines
- International Institute for Tropical Agriculture, Ibadan, Oyo, Nigeria
| | - Tobias Kretzschmar
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW, Australia
| | - Huw Jones
- National Institute of Agricultural Botany, Cambridge, United Kingdom
| | - Nelzo Ereful
- National Institute of Agricultural Botany, Cambridge, United Kingdom
| | - Christopher Blanchard
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW, Australia
| | - Lesley Ann Boyd
- National Institute of Agricultural Botany, Cambridge, United Kingdom
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25
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Wang W, Ge J, Xu K, Gao H, Liu G, Wei H, Zhang H. Differences in starch structure, thermal properties, and texture characteristics of rice from main stem and tiller panicles. Food Hydrocoll 2020. [DOI: 10.1016/j.foodhyd.2019.105341] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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26
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Shen X, Zhao R, Liu L, Zhu C, Li M, Du H, Zhang Z. Identification of a candidate gene underlying qKRN5b for kernel row number in Zea mays L. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:3439-3448. [PMID: 31612262 DOI: 10.1007/s00122-019-03436-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 09/17/2019] [Indexed: 06/10/2023]
Abstract
A quantitative trait locus for kernel row number, qKRN5, was dissected into two tightly linked loci, qKRN5a and qKRN5b. Fine mapping, comparative analysis of nucleotide sequences and gene expression established the endonuclease/exonuclease/phosphatase family protein-encoding gene Zm00001d013603 as a causal gene of qKRN5b. Maize grain yield is determined by agronomically important traits that are controlled by interactions among and between genes and environmental factors. Considerable efforts have been made to identify major quantitative trait loci (QTLs) for yield-related traits; however, few were previously isolated and characterized in maize. In this study, we divided a QTL for kernel row number (KRN), qKRN5, into two tightly linked loci, qKRN5a and qKRN5b, using advanced backcross populations derived from near-isogenic lines. KRN was greater in individuals that were homozygous for the NX531 allele, which showed coupling-phase linkage. The major QTL qKRN5b had an additive effect of approximately one kernel row. Furthermore, fine mapping narrowed qKRN5b within a 147.2-kb region. The upstream sequence Zm00001d013603 and its expression in the ear inflorescence showed obvious differences between qKRN5b near-isogenic lines. In situ hybridization located Zm00001d013603 on the primordia of the spikelet pair meristems and spikelet meristems, but not in the inflorescence meristem, which indicates a role in regulating the initiation of reproductive axillary meristems of ear inflorescences. Expression analysis and nucleotide sequence alignment revealed that Zm00001d013603, which encodes an endonuclease/exonuclease/phosphatase family protein that hydrolyzes phosphatidyl inositol diphosphates, is the causal gene of qKRN5b. These results provide insight into the genetic basis of KRN and have potential value for enhancing maize grain yield.
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Affiliation(s)
- Xiaomeng Shen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan, 430030, China
| | - Ran Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan, 430030, China
| | - Lei Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan, 430030, China
| | - Can Zhu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan, 430030, China
| | - Manfei Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan, 430030, China
| | - Hewei Du
- Hubei Collaborative Innovation Center for Grain Crops, Yangtze University, Jingzhou, 434025, China
| | - Zuxin Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan, 430030, China.
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27
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Chang TG, Chang S, Song QF, Perveen S, Zhu XG. Systems models, phenomics and genomics: three pillars for developing high-yielding photosynthetically efficient crops. IN SILICO PLANTS 2019; 1:ISP-01-01-diy003. [PMID: 33381682 PMCID: PMC7731669 DOI: 10.1093/insilicoplants/diy003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 12/17/2018] [Accepted: 02/13/2019] [Indexed: 05/18/2023]
Abstract
Recent years witnessed a stagnation in yield enhancement in major staple crops, which leads plant biologists and breeders to focus on an urgent challenge to dramatically increase crop yield to meet the growing food demand. Systems models have started to show their capacity in guiding crops improvement for greater biomass and grain yield production. Here we argue that systems models, phenomics and genomics combined are three pillars for the future breeding for high-yielding photosynthetically efficient crops (HYPEC). Briefly, systems models can be used to guide identification of breeding targets for a particular cultivar and define optimal physiological and architectural parameters for a particular crop to achieve high yield under defined environments. Phenomics can support collection of architectural, physiological, biochemical and molecular parameters in a high-throughput manner, which can be used to support both model validation and model parameterization. Genomic techniques can be used to accelerate crop breeding by enabling more efficient mapping between genotypic and phenotypic variation, and guide genome engineering or editing for model-designed traits. In this paper, we elaborate on these roles and how they can work synergistically to support future HYPEC breeding.
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Affiliation(s)
- Tian-Gen Chang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Shuoqi Chang
- State Key Laboratory of Hybrid Rice, HHRRC, Changsha 410125, China
| | - Qing-Feng Song
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Shahnaz Perveen
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xin-Guang Zhu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200031, China
- Corresponding author’s e-mail address:
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28
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Gene diagnosis and targeted breeding for blast-resistant Kongyu 131 without changing regional adaptability. J Genet Genomics 2018; 45:539-547. [PMID: 30391410 DOI: 10.1016/j.jgg.2018.08.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 07/17/2018] [Accepted: 08/28/2018] [Indexed: 12/11/2022]
Abstract
The fungus Magnaporthe oryzae threatens the rice production of Kongyu 131 (KY131), a leading japonica variety in Northeast China. In this study, two rice lines, KP1 and KP2-Hd1, were obtained by introgressing the blast resistance genes Pi1 and Pi2 into KY131, respectively. However, both lines headed later than KY131. RICE60K SNP array analysis showed that Hd1 closely linked to Pi2 was introgressed into KP2-Hd1, and the linkage drag of Hd1 was broken by recombination. On the other hand, no known flowering genes were introgressed into KP1. Gene diagnosis by resequencing six flowering genes showed that KP1 carried functional Hd16 and Ghd8 alleles. Due to its suppression role in heading under long-day conditions, Ghd8 was chosen as the target for gene editing to disrupt its function. Four sgRNAs targeting different sites within Ghd8 were utilized to induce large-deletion mutations, which were easy to detect via agarose gel electrophoresis. All the ghd8-mutated KP1 lines were resistant to rice blast disease and headed earlier than the control KP1, even than KY131, under natural long-day conditions, which ensures its growth in Northeast China. This study confirmed that a combination of gene diagnosis and targeted gene editing is a highly efficient way to quickly eliminate undesired traits in a breeding line.
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29
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Qian Q. Genomics-assisted germplasm improvement. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2018; 60:82-84. [PMID: 29314723 DOI: 10.1111/jipb.12629] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Affiliation(s)
- Qian Qian
- State Key Lab. of Rice Biology, China National Rice Research Institute, Hangzhou, China
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30
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Zhang H, Yu C, Hou D, Liu H, Zhang H, Tao R, Cai H, Gu J, Liu L, Zhang Z, Wang Z, Yang J. Changes in mineral elements and starch quality of grains during the improvement of japonica rice cultivars. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2018; 98:122-133. [PMID: 28543034 DOI: 10.1002/jsfa.8446] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 05/18/2017] [Accepted: 05/20/2017] [Indexed: 05/12/2023]
Abstract
BACKGROUND The improvement of rice cultivars plays an important role in yield increase. However, little is known about the changes in starch quality and mineral elements during the improvement of rice cultivars. This study was conducted to investigate the changes in starch quality and mineral elements in japonica rice cultivars. RESULTS Twelve typical rice cultivars, applied in the production in Jiangsu province during the last 60 years, were grown in the paddy fields. These cultivars were classified into six types according to their application times, plant types and genotypes. The nitrogen (N), phosphorus (P) and, and potassium (K) were mainly distributed in endosperm, bran and bran, respectively. Secondary and micromineral nutrients were distributed throughout grains. With the improvement of cultivars, total N contents gradually decreased, while total P, K and magnesium contents increased in grains. Total copper and zinc contents in type 80'S in grains were highest. The improvement of cultivars enhanced palatability (better gelatinisation enthalpy and amylose content), taste (better protein content) and protein quality (better protein components and essential amino acids). Correlation analysis indicated the close relationship between mineral elements and starch quality. CONCLUSION The mineral elements and starch quality of grains during the improvement of japonica rice cultivars are improved. © 2017 Society of Chemical Industry.
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Affiliation(s)
- Hao Zhang
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Chao Yu
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Danping Hou
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Hailang Liu
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Huiting Zhang
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Rongrong Tao
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Han Cai
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Junfei Gu
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Lijun Liu
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Zujian Zhang
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Zhiqin Wang
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Jianchang Yang
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
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31
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Garrett KA, Andersen KF, Asche F, Bowden RL, Forbes GA, Kulakow PA, Zhou B. Resistance Genes in Global Crop Breeding Networks. PHYTOPATHOLOGY 2017; 107:1268-1278. [PMID: 28742460 DOI: 10.1094/phyto-03-17-0082-fi] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Resistance genes are a major tool for managing crop diseases. The networks of crop breeders who exchange resistance genes and deploy them in varieties help to determine the global landscape of resistance and epidemics, an important system for maintaining food security. These networks function as a complex adaptive system, with associated strengths and vulnerabilities, and implications for policies to support resistance gene deployment strategies. Extensions of epidemic network analysis can be used to evaluate the multilayer agricultural networks that support and influence crop breeding networks. Here, we evaluate the general structure of crop breeding networks for cassava, potato, rice, and wheat. All four are clustered due to phytosanitary and intellectual property regulations, and linked through CGIAR hubs. Cassava networks primarily include public breeding groups, whereas others are more mixed. These systems must adapt to global change in climate and land use, the emergence of new diseases, and disruptive breeding technologies. Research priorities to support policy include how best to maintain both diversity and redundancy in the roles played by individual crop breeding groups (public versus private and global versus local), and how best to manage connectivity to optimize resistance gene deployment while avoiding risks to the useful life of resistance genes. [Formula: see text] Copyright © 2017 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .
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Affiliation(s)
- K A Garrett
- First and second authors: Plant Pathology Department, Emerging Pathogens Institute, and Institute for Sustainable Food Systems, University of Florida, Gainesville 32611; third author: School of Forest Resources and Conservation and Institute for Sustainable Food Systems, University of Florida, Gainesville; fourth author: United States Department of Agriculture-Agricultural Research Service Hard Winter Wheat Genetics Research Unit, 4008 Throckmorton Hall, Kansas State University, Manhattan 66506; fifth author: International Potato Center, Lima, Peru; sixth author: International Institute of Tropical Agriculture, Ibadan, Nigeria; and seventh author: International Rice Research Institute, Manila, Philippines
| | - K F Andersen
- First and second authors: Plant Pathology Department, Emerging Pathogens Institute, and Institute for Sustainable Food Systems, University of Florida, Gainesville 32611; third author: School of Forest Resources and Conservation and Institute for Sustainable Food Systems, University of Florida, Gainesville; fourth author: United States Department of Agriculture-Agricultural Research Service Hard Winter Wheat Genetics Research Unit, 4008 Throckmorton Hall, Kansas State University, Manhattan 66506; fifth author: International Potato Center, Lima, Peru; sixth author: International Institute of Tropical Agriculture, Ibadan, Nigeria; and seventh author: International Rice Research Institute, Manila, Philippines
| | - F Asche
- First and second authors: Plant Pathology Department, Emerging Pathogens Institute, and Institute for Sustainable Food Systems, University of Florida, Gainesville 32611; third author: School of Forest Resources and Conservation and Institute for Sustainable Food Systems, University of Florida, Gainesville; fourth author: United States Department of Agriculture-Agricultural Research Service Hard Winter Wheat Genetics Research Unit, 4008 Throckmorton Hall, Kansas State University, Manhattan 66506; fifth author: International Potato Center, Lima, Peru; sixth author: International Institute of Tropical Agriculture, Ibadan, Nigeria; and seventh author: International Rice Research Institute, Manila, Philippines
| | - R L Bowden
- First and second authors: Plant Pathology Department, Emerging Pathogens Institute, and Institute for Sustainable Food Systems, University of Florida, Gainesville 32611; third author: School of Forest Resources and Conservation and Institute for Sustainable Food Systems, University of Florida, Gainesville; fourth author: United States Department of Agriculture-Agricultural Research Service Hard Winter Wheat Genetics Research Unit, 4008 Throckmorton Hall, Kansas State University, Manhattan 66506; fifth author: International Potato Center, Lima, Peru; sixth author: International Institute of Tropical Agriculture, Ibadan, Nigeria; and seventh author: International Rice Research Institute, Manila, Philippines
| | - G A Forbes
- First and second authors: Plant Pathology Department, Emerging Pathogens Institute, and Institute for Sustainable Food Systems, University of Florida, Gainesville 32611; third author: School of Forest Resources and Conservation and Institute for Sustainable Food Systems, University of Florida, Gainesville; fourth author: United States Department of Agriculture-Agricultural Research Service Hard Winter Wheat Genetics Research Unit, 4008 Throckmorton Hall, Kansas State University, Manhattan 66506; fifth author: International Potato Center, Lima, Peru; sixth author: International Institute of Tropical Agriculture, Ibadan, Nigeria; and seventh author: International Rice Research Institute, Manila, Philippines
| | - P A Kulakow
- First and second authors: Plant Pathology Department, Emerging Pathogens Institute, and Institute for Sustainable Food Systems, University of Florida, Gainesville 32611; third author: School of Forest Resources and Conservation and Institute for Sustainable Food Systems, University of Florida, Gainesville; fourth author: United States Department of Agriculture-Agricultural Research Service Hard Winter Wheat Genetics Research Unit, 4008 Throckmorton Hall, Kansas State University, Manhattan 66506; fifth author: International Potato Center, Lima, Peru; sixth author: International Institute of Tropical Agriculture, Ibadan, Nigeria; and seventh author: International Rice Research Institute, Manila, Philippines
| | - B Zhou
- First and second authors: Plant Pathology Department, Emerging Pathogens Institute, and Institute for Sustainable Food Systems, University of Florida, Gainesville 32611; third author: School of Forest Resources and Conservation and Institute for Sustainable Food Systems, University of Florida, Gainesville; fourth author: United States Department of Agriculture-Agricultural Research Service Hard Winter Wheat Genetics Research Unit, 4008 Throckmorton Hall, Kansas State University, Manhattan 66506; fifth author: International Potato Center, Lima, Peru; sixth author: International Institute of Tropical Agriculture, Ibadan, Nigeria; and seventh author: International Rice Research Institute, Manila, Philippines
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Rasheed A, Hao Y, Xia X, Khan A, Xu Y, Varshney RK, He Z. Crop Breeding Chips and Genotyping Platforms: Progress, Challenges, and Perspectives. MOLECULAR PLANT 2017; 10:1047-1064. [PMID: 28669791 DOI: 10.1016/j.molp.2017.06.008] [Citation(s) in RCA: 219] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 05/29/2017] [Accepted: 06/19/2017] [Indexed: 05/18/2023]
Abstract
There is a rapidly rising trend in the development and application of molecular marker assays for gene mapping and discovery in field crops and trees. Thus far, more than 50 SNP arrays and 15 different types of genotyping-by-sequencing (GBS) platforms have been developed in over 25 crop species and perennial trees. However, much less effort has been made on developing ultra-high-throughput and cost-effective genotyping platforms for applied breeding programs. In this review, we discuss the scientific bottlenecks in existing SNP arrays and GBS technologies and the strategies to develop targeted platforms for crop molecular breeding. We propose that future practical breeding platforms should adopt automated genotyping technologies, either array or sequencing based, target functional polymorphisms underpinning economic traits, and provide desirable prediction accuracy for quantitative traits, with universal applications under wide genetic backgrounds in crops. The development of such platforms faces serious challenges at both the technological level due to cost ineffectiveness, and the knowledge level due to large genotype-phenotype gaps in crop plants. It is expected that such genotyping platforms will be achieved in the next ten years in major crops in consideration of (a) rapid development in gene discovery of important traits, (b) deepened understanding of quantitative traits through new analytical models and population designs, (c) integration of multi-layer -omics data leading to identification of genes and pathways responsible for important breeding traits, and (d) improvement in cost effectiveness of large-scale genotyping. Crop breeding chips and genotyping platforms will provide unprecedented opportunities to accelerate the development of cultivars with desired yield potential, quality, and enhanced adaptation to mitigate the effects of climate change.
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Affiliation(s)
- Awais Rasheed
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China; International Maize and Wheat Improvement Center (CIMMYT), c/o CAAS, Beijing 100081, China
| | - Yuanfeng Hao
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Xianchun Xia
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Awais Khan
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Geneva, NY, USA
| | - Yunbi Xu
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China; International Maize and Wheat Improvement Center (CIMMYT), c/o CAAS, Beijing 100081, China
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, India
| | - Zhonghu He
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China; International Maize and Wheat Improvement Center (CIMMYT), c/o CAAS, Beijing 100081, China.
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33
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Jiang S, Sun S, Bai L, Ding G, Wang T, Xia T, Jiang H, Zhang X, Zhang F. Resequencing and variation identification of whole genome of the japonica rice variety "Longdao24" with high yield. PLoS One 2017; 12:e0181037. [PMID: 28715430 PMCID: PMC5513431 DOI: 10.1371/journal.pone.0181037] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 06/26/2017] [Indexed: 01/04/2023] Open
Abstract
Japonica rice mainly distributes in north of China, which accounts for more than half of the total japonica rice cultivated area of China. High yield, good grain quality and early heading date were the main breeding traits and commercial property in this region. We performed re-sequencing and genome wide variation analysis of one typical northern japonica rice variety Longdao24 and its parents (Longdao5 and Jigeng83) using the Illumina sequencing technology. 53.17 G clean bases were generated and more than 96.8% of the reads were mapped to the genomic reference sequence. An overall average effective depth of 43.67 × coverage was achieved. We identified 420,475 SNPs, 95,624 InDels, and 14,112 SVs in Longdao24 genome with the genomic sequence of the japonica cultivar Nipponbare as reference. We identified 361,117 SNPs and 81,488 InDels between Longdao24 genome and Longdao5 genome. We also detected 428,908 SNPs and 97,209 InDels between Longdao24 genome and Jigeng83 genome. Twenty-two yield related genes, twenty-two grain quality related genes and thirty-nine heading date genes were analyzed in Longdao24. The alleles of Gn1a, EP3, SCM2, Wx, ALK, OsLF and Hd17 came from the female parent Longdao5. The other alleles of qGW8, SSIVa, SBE3, SSIIIb, SSIIc, DTH2, Ehd3 and OsMADS56 came from the male parent Jigeng83. These results will help us to research the genetics basis of yield, grain quality and early heading date in northern rice of China.
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Affiliation(s)
- Shukun Jiang
- Cultivation and Farming Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, P.R.China
- * E-mail:
| | - Shichen Sun
- Cultivation and Farming Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, P.R.China
| | - Liangming Bai
- Cultivation and Farming Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, P.R.China
| | - Guohua Ding
- Cultivation and Farming Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, P.R.China
| | - Tongtong Wang
- Cultivation and Farming Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, P.R.China
| | - Tianshu Xia
- Cultivation and Farming Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, P.R.China
| | - Hui Jiang
- Cultivation and Farming Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, P.R.China
| | - Xijuan Zhang
- Cultivation and Farming Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, P.R.China
| | - Fengming Zhang
- Cultivation and Farming Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, P.R.China
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Das G, Patra JK, Baek KH. Insight into MAS: A Molecular Tool for Development of Stress Resistant and Quality of Rice through Gene Stacking. FRONTIERS IN PLANT SCIENCE 2017; 8:985. [PMID: 28659941 PMCID: PMC5469070 DOI: 10.3389/fpls.2017.00985] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 05/24/2017] [Indexed: 05/21/2023]
Abstract
Rice yield is subjected to severe losses due to adverse effect of a number of stress factors. The most effective method of controlling reduced crop production is utilization of host resistance. Recent technological advances have led to the improvement of DNA based molecular markers closely linked to genes or QTLs in rice chromosome that bestow tolerance to various types of abiotic stresses and resistance to biotic stress factors. Transfer of several genes with potential characteristics into a single genotype is possible through the process of marker assisted selection (MAS), which can quicken the advancement of tolerant/resistant cultivars in the lowest number of generations with the utmost precision through the process of gene pyramiding. Overall, this review presented various types of molecular tools including MAS that can be reasonable and environmental friendly approach for the improvement of abiotic and biotic stress resistant rice with enhanced quality.
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Affiliation(s)
- Gitishree Das
- Research Institute of Biotechnology and Medical Converged Science, Dongguk University SeoulGoyang-si, South Korea
| | - Jayanta Kumar Patra
- Research Institute of Biotechnology and Medical Converged Science, Dongguk University SeoulGoyang-si, South Korea
| | - Kwang-Hyun Baek
- Department of Biotechnology, Yeungnam UniversityGyeongsan, South Korea
- *Correspondence: Kwang-Hyun Baek
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Hu J, Xiao C, He Y. Recent progress on the genetics and molecular breeding of brown planthopper resistance in rice. RICE (NEW YORK, N.Y.) 2016; 9:30. [PMID: 27300326 PMCID: PMC4908088 DOI: 10.1186/s12284-016-0099-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2016] [Accepted: 05/23/2016] [Indexed: 05/20/2023]
Abstract
Brown planthopper (BPH) is the most devastating pest of rice. Host-plant resistance is the most desirable and economic strategy in the management of BPH. To date, 29 major BPH resistance genes have been identified from indica cultivars and wild rice species, and more than ten genes have been fine mapped to chromosome regions of less than 200 kb. Four genes (Bph14, Bph26, Bph17 and bph29) have been cloned. The increasing number of fine-mapped and cloned genes provide a solid foundation for development of functional markers for use in breeding. Several BPH resistant introgression lines (ILs), near-isogenic lines (NILs) and pyramided lines (PLs) carrying single or multiple resistance genes were developed by marker assisted backcross breeding (MABC). Here we review recent progress on the genetics and molecular breeding of BPH resistance in rice. Prospect for developing cultivars with durable, broad-spectrum BPH resistance are discussed.
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Affiliation(s)
- Jie Hu
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- National Key Laboratory of Crop Genetic Improvement and National Center of Crop Molecular Breeding, Huazhong Agricultural University, Wuhan, 430070, China
| | - Cong Xiao
- National Key Laboratory of Crop Genetic Improvement and National Center of Crop Molecular Breeding, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuqing He
- National Key Laboratory of Crop Genetic Improvement and National Center of Crop Molecular Breeding, Huazhong Agricultural University, Wuhan, 430070, China.
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36
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Sun L, Xu X, Jiang Y, Zhu Q, Yang F, Zhou J, Yang Y, Huang Z, Li A, Chen L, Tang W, Zhang G, Wang J, Xiao G, Huang D, Chen C. Genetic Diversity, Rather than Cultivar Type, Determines Relative Grain Cd Accumulation in Hybrid Rice. FRONTIERS IN PLANT SCIENCE 2016; 7:1407. [PMID: 27708659 PMCID: PMC5030296 DOI: 10.3389/fpls.2016.01407] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 09/02/2016] [Indexed: 05/26/2023]
Abstract
Cadmium (Cd) is a toxic element, and rice is known to be a leading source of dietary Cd for people who consume rice as their main caloric resource. Hybrid rice has dominated rice production in southern China and has been adopted worldwide. The characteristics of high yield heterosis of rice hybrids makes the public think intuitively that the hybrid rice accumulates more Cd in grain than do inbred cultivars. A detailed understanding of the genetic basis of grain Cd accumulation in hybrids and developing Cd-safe rice are one of the top priorities for hybrid rice breeders at present. In this study, we investigated genetic diversity and grain Cd levels in 617 elite rice hybrids collected from the middle and lower Yangtze River Valley in China and 68 inbred cultivars from around the world. We found that there are large variations in grain Cd accumulation in both the hybrids and their inbred counterparts. However, we found grain Cd levels in the rice hybrids to be similar to the levels in indica rice inbreds, suggesting that the hybrids do not accumulate more Cd than do the inbred rice cultivars. Further analysis revealed that the high heritability of Cd accumulation in the grain and the single indica population structure increases the risk of Cd over-accumulation in hybrid rice. The genetic effects of Cd-related QTLs, which have been identified in related Cd-QTL mapping studies, were also determined in the hybrid rice population. Four QTLs were identified as being associated with the variation in grain Cd levels; three of these loci exhibited obvious indica-japonica differentiations. Our study will provide a better understanding of grain Cd accumulations in hybrid rice, and pave the way toward effective breeding for high-yielding, low grain-Cd hybrids in the future.
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Affiliation(s)
- Liang Sun
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of SciencesChangsha, China
| | - Xiaxu Xu
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of SciencesChangsha, China
| | - Youru Jiang
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of SciencesChangsha, China
- Institute of Rice Science, Hunan Agricultural UniversityChangsha, China
| | - Qihong Zhu
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of SciencesChangsha, China
| | - Fei Yang
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of SciencesChangsha, China
| | - Jieqiang Zhou
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of SciencesChangsha, China
- Institute of Rice Science, Hunan Agricultural UniversityChangsha, China
| | - Yuanzhu Yang
- Yuanlongping High-Tech Agriculture Co., LTDChangsha, China
| | - Zhiyuan Huang
- China National Hybrid Rice R&D CenterChangsha, China
| | - Aihong Li
- Lixiahe Agricultural Research Institute of Jiangsu ProvinceYangzhou, China
| | - Lianghui Chen
- Beishan Agricultural Service Center of Changsha CountyChangsha, China
| | - Wenbang Tang
- Institute of Rice Science, Hunan Agricultural UniversityChangsha, China
| | - Guoyu Zhang
- Beishan Agricultural Service Center of Changsha CountyChangsha, China
| | - Jiurong Wang
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of SciencesChangsha, China
| | - Guoying Xiao
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of SciencesChangsha, China
| | - Daoyou Huang
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of SciencesChangsha, China
| | - Caiyan Chen
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of SciencesChangsha, China
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37
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Zhang C, Zhou L, Zhu Z, Lu H, Zhou X, Qian Y, Li Q, Lu Y, Gu M, Liu Q. Characterization of Grain Quality and Starch Fine Structure of Two Japonica Rice (Oryza Sativa) Cultivars with Good Sensory Properties at Different Temperatures during the Filling Stage. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2016; 64:4048-57. [PMID: 27128366 DOI: 10.1021/acs.jafc.6b00083] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Temperature during the growing season is a critical factor affecting grain quality. High temperatures at grain filling affect kernel development, resulting in reduced yield, increased chalkiness, reduced amylose content, and poor milling quality. Here, we investigated the grain quality and starch structure of two japonica rice cultivars with good sensory properties grown at different temperatures during the filling stage under natural field conditions. Compared to those grown under normal conditions, rice grains grown under hot conditions showed significantly reduced eating and cooking qualities, including a higher percentage of grains with chalkiness, lower protein and amylose contents, and higher pasting properties. Under hot conditions, rice starch contained reduced long-chain amylose (MW 10(7.1) to 10(7.4)) and significantly fewer short-chain amylopectin (DP 5-12) but more intermediate- (DP 13-34) and long- (DP 45-60) chain amylopectin than under normal conditions, as well as higher crystallinity and gelatinization properties.
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Affiliation(s)
- Changquan Zhang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University , Yangzhou 225009, China
| | - Lihui Zhou
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University , Yangzhou 225009, China
- Jiangsu High Quality Rice Research and Development Center, Institute of Food Crops, Jiangsu Academy of Agricultural Sciences , Nanjing 210014, China
| | - Zhengbin Zhu
- Suzhou Seed Administration Station , Suzhou 215011, China
| | - Huwen Lu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University , Yangzhou 225009, China
| | - Xingzhong Zhou
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University , Yangzhou 225009, China
| | - Yiting Qian
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University , Yangzhou 225009, China
| | - Qianfeng Li
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University , Yangzhou 225009, China
| | - Yan Lu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University , Yangzhou 225009, China
| | - Minghong Gu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University , Yangzhou 225009, China
| | - Qiaoquan Liu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University , Yangzhou 225009, China
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38
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Abstract
Abstract
A large number of pathogenic microorganisms cause rice diseases that lead to enormous yield losses worldwide. Such losses are important because rice is a staple food for more than half of the world's population. Over the past two decades, the extensive study of the molecular interactions between rice and the fungal pathogen Magnaporthe oryzae and between rice and the bacterial pathogen Xanthomonas oryzae pv. oryzae has made rice a model for investigating plant–microbe interactions of monocotyledons. Impressive progress has been recently achieved in understanding the molecular basis of rice pathogen-associated molecular pattern-immunity and effector-triggered immunity. Here, we briefly summarize these recent advances, emphasizing the diverse functions of the structurally conserved fungal effectors, the regulatory mechanisms of the immune receptor complexes, and the novel strategies for breeding disease resistance. We also discuss future research challenges.
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Affiliation(s)
- Wende Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Guo-Liang Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Department of Plant Pathology, Ohio State University, Columbus, OH 43210, USA
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39
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Qian Q, Guo L, Smith SM, Li J. Breeding high-yield superior quality hybrid super rice by rational design. Natl Sci Rev 2016. [DOI: 10.1093/nsr/nww006] [Citation(s) in RCA: 124] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Abstract
The challenge of meeting the increasing demand for worldwide rice production has driven a sustained quest for advances in rice breeding for yield. Two breakthroughs that led to quantum leaps in productivity last century were the introduction of semidwarf varieties and of hybrid rice. Subsequent gains in yield have been incremental. The next major leap in rice breeding is now upon us through the application of rational design to create defined ideotypes. The exploitation of wide-cross compatibility and intersubspecific heterosis, combined with rapid genome sequencing and the molecular identification of genes for major yield and quality traits have now unlocked the potential for rational design.
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Affiliation(s)
- Qian Qian
- State Key Laboratory for Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Longbiao Guo
- State Key Laboratory for Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Steven M. Smith
- School of Biological Sciences, University of Tasmania, Hobart, 7001, Australia
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jiayang Li
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
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40
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Qiu J, Hou Y, Tong X, Wang Y, Lin H, Liu Q, Zhang W, Li Z, Nallamilli BR, Zhang J. Quantitative phosphoproteomic analysis of early seed development in rice (Oryza sativa L.). PLANT MOLECULAR BIOLOGY 2016; 90:249-265. [PMID: 26613898 DOI: 10.1007/s11103-015-0410-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 11/23/2015] [Indexed: 06/05/2023]
Abstract
Rice (Oryza sativa L.) seed serves as a major food source for over half of the global population. Though it has been long recognized that phosphorylation plays an essential role in rice seed development, the phosphorylation events and dynamics in this process remain largely unknown so far. Here, we report the first large scale identification of rice seed phosphoproteins and phosphosites by using a quantitative phosphoproteomic approach. Thorough proteomic studies in pistils and seeds at 3, 7 days after pollination resulted in the successful identification of 3885, 4313 and 4135 phosphopeptides respectively. A total of 2487 proteins were differentially phosphorylated among the three stages, including Kip related protein 1, Rice basic leucine zipper factor 1, Rice prolamin box binding factor and numerous other master regulators of rice seed development. Moreover, differentially phosphorylated proteins may be extensively involved in the biosynthesis and signaling pathways of phytohormones such as auxin, gibberellin, abscisic acid and brassinosteroid. Our results strongly indicated that protein phosphorylation is a key mechanism regulating cell proliferation and enlargement, phytohormone biosynthesis and signaling, grain filling and grain quality during rice seed development. Overall, the current study enhanced our understanding of the rice phosphoproteome and shed novel insight into the regulatory mechanism of rice seed development.
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Affiliation(s)
- Jiehua Qiu
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 311400, People's Republic of China
| | - Yuxuan Hou
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 311400, People's Republic of China
| | - Xiaohong Tong
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 311400, People's Republic of China
| | - Yifeng Wang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 311400, People's Republic of China
| | - Haiyan Lin
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 311400, People's Republic of China
| | - Qing Liu
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 311400, People's Republic of China
| | - Wen Zhang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 311400, People's Republic of China
| | - Zhiyong Li
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 311400, People's Republic of China
| | - Babi R Nallamilli
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Jian Zhang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 311400, People's Republic of China.
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41
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Anacleto R, Cuevas RP, Jimenez R, Llorente C, Nissila E, Henry R, Sreenivasulu N. Prospects of breeding high-quality rice using post-genomic tools. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:1449-66. [PMID: 25993897 DOI: 10.1007/s00122-015-2537-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 05/08/2015] [Indexed: 05/15/2023]
Abstract
The holistic understanding derived from integrating grain quality and sensory research outcomes in breeding high-quality rice in the light of post-genomics resources has been synthesized. Acceptance of new rice genotypes by producers and consumers hinges not only on their potential for higher yield but recent emphasis has also been on premium-value genotypes that have the ability to satisfy consumer preferences for grain quality. This review article provides insights into how to link grain quality attributes and sensory perception to support breeding superior rice varieties. Recent advances in quality profiling and omics technologies have provided efficient approaches to identify the key genes and biochemical markers involved in rice quality traits. Emphasis has been given to the upcoming area of holistic understanding of grain quality and attributes derived from sensory evaluation to leverage integrative gene discovery strategies that enable breeding programs to efficiently tap the huge genetic diversity in rice for novel genes that enhance rice food quality.
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Affiliation(s)
- Roslen Anacleto
- International Rice Research Institute, DAPO Box 7777, Metro Manila, 1301, Philippines,
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