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He L, Chen T, Zhao C, Zhao L, Zhao Q, Yao S, Zhu Z, Lu K, Wang C, Zhang Y. RST31 controls salt tolerance in rice (Oryza sativa) by regulating the cytokinin pathway. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 216:109075. [PMID: 39241632 DOI: 10.1016/j.plaphy.2024.109075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 08/07/2024] [Accepted: 08/25/2024] [Indexed: 09/09/2024]
Abstract
Salt stress affects the growth of rice, which reduces grain yield. However, the mechanism of the rice response to salt stress is not fully understood. The rice salt tolerance 31 (rst31) mutant exhibits longer shoots and greater dry weight than wild type (WT) plants under salt stress conditions. Through map-based cloning and genetic complementation methods, we determined that RST31 encodes a half-size ABCG transporter protein, ABCG18. We showed that mutation of RST31 reduces DNA damage under salt stress, with less accumulation of reactive oxygen species (ROS). The deficiency of RST31 suppressed the root-to-shoot transport of cytokinin, which resulted in a decrease in cytokinin content in the shoot and an increase in cytokinin content in the root. ROS accumulated abundantly in WT and rst31 mutant plants after exogenous treatment with trans-zeatin, reducing rst31 tolerance of salt stress. Collectively, our results suggest that high cytokinin level in shoots leads to an increase in ROS content and severe DNA damage under salt stress, which lead to sensitivity to salt stress. These findings enhance our understanding of plant responses to salt stress through cytokinin pathways.
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Affiliation(s)
- Lei He
- Institute of Food Crops, Jiangsu Academy of Agricultural Science, Key laboratory of Jiangsu Province for Agrobiology, East China Branch of National Center of Technology Innovation for Saline-Alkali Tolerant Rice, Nanjing, 210014, China; Zhongshan Biological Breeding Laboratory, Nanjing, 210014, China
| | - Tao Chen
- Institute of Food Crops, Jiangsu Academy of Agricultural Science, Key laboratory of Jiangsu Province for Agrobiology, East China Branch of National Center of Technology Innovation for Saline-Alkali Tolerant Rice, Nanjing, 210014, China; Zhongshan Biological Breeding Laboratory, Nanjing, 210014, China
| | - Chunfang Zhao
- Institute of Food Crops, Jiangsu Academy of Agricultural Science, Key laboratory of Jiangsu Province for Agrobiology, East China Branch of National Center of Technology Innovation for Saline-Alkali Tolerant Rice, Nanjing, 210014, China; Zhongshan Biological Breeding Laboratory, Nanjing, 210014, China
| | - Ling Zhao
- Institute of Food Crops, Jiangsu Academy of Agricultural Science, Key laboratory of Jiangsu Province for Agrobiology, East China Branch of National Center of Technology Innovation for Saline-Alkali Tolerant Rice, Nanjing, 210014, China; Zhongshan Biological Breeding Laboratory, Nanjing, 210014, China
| | - Qingyong Zhao
- Institute of Food Crops, Jiangsu Academy of Agricultural Science, Key laboratory of Jiangsu Province for Agrobiology, East China Branch of National Center of Technology Innovation for Saline-Alkali Tolerant Rice, Nanjing, 210014, China; Zhongshan Biological Breeding Laboratory, Nanjing, 210014, China
| | - Shu Yao
- Institute of Food Crops, Jiangsu Academy of Agricultural Science, Key laboratory of Jiangsu Province for Agrobiology, East China Branch of National Center of Technology Innovation for Saline-Alkali Tolerant Rice, Nanjing, 210014, China; Zhongshan Biological Breeding Laboratory, Nanjing, 210014, China
| | - Zhen Zhu
- Institute of Food Crops, Jiangsu Academy of Agricultural Science, Key laboratory of Jiangsu Province for Agrobiology, East China Branch of National Center of Technology Innovation for Saline-Alkali Tolerant Rice, Nanjing, 210014, China; Zhongshan Biological Breeding Laboratory, Nanjing, 210014, China
| | - Kai Lu
- Institute of Food Crops, Jiangsu Academy of Agricultural Science, Key laboratory of Jiangsu Province for Agrobiology, East China Branch of National Center of Technology Innovation for Saline-Alkali Tolerant Rice, Nanjing, 210014, China; Zhongshan Biological Breeding Laboratory, Nanjing, 210014, China
| | - Cailin Wang
- Institute of Food Crops, Jiangsu Academy of Agricultural Science, Key laboratory of Jiangsu Province for Agrobiology, East China Branch of National Center of Technology Innovation for Saline-Alkali Tolerant Rice, Nanjing, 210014, China; Zhongshan Biological Breeding Laboratory, Nanjing, 210014, China.
| | - Yadong Zhang
- Institute of Food Crops, Jiangsu Academy of Agricultural Science, Key laboratory of Jiangsu Province for Agrobiology, East China Branch of National Center of Technology Innovation for Saline-Alkali Tolerant Rice, Nanjing, 210014, China; Zhongshan Biological Breeding Laboratory, Nanjing, 210014, China.
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Ali MA, Sardar MF, Dar AA, Niaz M, Ali J, Wang Q, Zheng Y, Luo Y, Albasher G, Li F. Integrative approach to mitigate chromium toxicity in soil and enhance antioxidant activities in rice (Oryza sativa L.) using magnesium-iron nanocomposite and Staphylococcus aureus strains. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2024; 46:398. [PMID: 39190219 DOI: 10.1007/s10653-024-02145-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Accepted: 07/24/2024] [Indexed: 08/28/2024]
Abstract
Pollutants in soil, particularly chromium (Cr), pose high environmental and health risks due to their persistence, bioavailability, and potential for causing toxicity. Cr impairment in plants act as a deleterious environmental pollutant that enters the food chain and eventually disturbs human health. Current study demonstrated the potential of integrative foliar application of magnesium-iron (Mg + Fe) nanocomposite with Staphylococcus aureus strains to alleviate Cr toxicity in rice (Oryza sativa) crops by improving yield and defense system. Growth and yield traits such as shoot length (15%), root length (17%), shoot fresh weight (14%), shoot dry weight (9%), root fresh weight (23%), root dry weight (7%), number of tillers (33%), number of grains (10%) and spike length (13%) improved by combined application of Mg + Fe (20 mg L-1) nanocomposite and S. aureus strains with Cr (110 mg kg-1), compared to when applied alone. Mutual Mg + Fe and S. aureus strains application augmented the SPAD value (9%), total chlorophyll (11%), a (12%), b (17%), and carotenoids (32%), with Cr (110 mg kg-1), compared to alone. Malondialdehyde (13%), hydrogen peroxide (H2O2) (11%), and electrolyte leakage (7%) were significantly regulated in shoots with combined Mg + Fe and S. aureus strains application with Cr (110 mg kg-1) contrasted to alone. Peroxidase (20%), superoxide dismutase (17%), ascorbate peroxidase (18%), and catalase (20%) were increased in shoots with combined Mg + Fe and S. aureus strains application with Cr (110 mg kg-1) in comparison to alone. The combined application of Mg + Fe (20 mgL-1) nanocomposite and S. aureus strains with Cr (110 mg kg-1) enhanced the macro-micronutrients in shoots compared to alone. Cr accumulation in roots (21%), shoots (25%), and grains (47%) were significantly reduced under Cr (110 mg kg-1) with combined Mg + Fe and S. aureus strains application, compared to alone. Subsequently, applying combined Mg + Fe and S. aureus strains is a sustainable solution to boost crop production under Cr toxicity.
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Affiliation(s)
- Muhammad Azhar Ali
- Institute of Coastal Environmental Pollution Control, Ministry of Education Key Laboratory of Marine Environment and Ecology, College of Environmental Science and Engineering, Sanya Oceanographic Institution, Ocean University of China, Qingdao, 266100, China
| | - Muhammad Fahad Sardar
- Key Laboratory of Ecological Prewarning, Protection and Restoration of Bohai Sea, Ministry of Natural Resources, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Afzal Ahmed Dar
- Department of Building, Civil and Environmental Engineering, Concordia University, Montreal, Canada
| | - Mohsin Niaz
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, Shandong, China
| | - Jawad Ali
- Environment Research Institute, Shandong University, Qingdao, 266237, China
| | - Qian Wang
- Institute of Coastal Environmental Pollution Control, Ministry of Education Key Laboratory of Marine Environment and Ecology, College of Environmental Science and Engineering, Sanya Oceanographic Institution, Ocean University of China, Qingdao, 266100, China
| | - Yu Zheng
- Institute of Coastal Environmental Pollution Control, Ministry of Education Key Laboratory of Marine Environment and Ecology, College of Environmental Science and Engineering, Sanya Oceanographic Institution, Ocean University of China, Qingdao, 266100, China
| | - Yadan Luo
- Institute of Coastal Environmental Pollution Control, Ministry of Education Key Laboratory of Marine Environment and Ecology, College of Environmental Science and Engineering, Sanya Oceanographic Institution, Ocean University of China, Qingdao, 266100, China
| | - Gadah Albasher
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Fengmin Li
- Institute of Coastal Environmental Pollution Control, Ministry of Education Key Laboratory of Marine Environment and Ecology, College of Environmental Science and Engineering, Sanya Oceanographic Institution, Ocean University of China, Qingdao, 266100, China.
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, 266237, China.
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3
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Wang M, Zhu X, Huang Z, Chen M, Xu P, Liao S, Zhao Y, Gao Y, He J, Luo Y, Chen H, Wei X, Nie S, Dong J, Zhu L, Zhuang C, Zhao J, Liu Z, Zhou H. Controlling diurnal flower-opening time by manipulating the jasmonate pathway accelerates development of indica-japonica hybrid rice breeding. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:2267-2281. [PMID: 38526838 PMCID: PMC11258973 DOI: 10.1111/pbi.14343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 02/21/2024] [Accepted: 03/08/2024] [Indexed: 03/27/2024]
Abstract
Inter-subspecific indica-japonica hybrid rice (Oryza sativa) has the potential for increased yields over traditional indica intra-subspecies hybrid rice, but limited yield of F1 hybrid seed production (FHSP) hinders the development of indica-japonica hybrid rice breeding. Diurnal flower-opening time (DFOT) divergence between indica and japonica rice has been a major contributing factor to this issue, but few DFOT genes have been cloned. Here, we found that manipulating the expression of jasmonate (JA) pathway genes can effectively modulate DFOT to improve the yield of FHSP in rice. Treating japonica cultivar Zhonghua 11 (ZH11) with methyl jasmonate (MeJA) substantially advanced DFOT. Furthermore, overexpressing the JA biosynthesis gene OPDA REDUCTASE 7 (OsOPR7) and knocking out the JA inactivation gene CHILLING TOLERANCE 1 (OsHAN1) in ZH11 advanced DFOT by 1- and 2-h respectively; and knockout of the JA signal suppressor genes JASMONATE ZIM-DOMAIN PROTEIN 7 (OsJAZ7) and OsJAZ9 resulted in 50-min and 1.5-h earlier DFOT respectively. The yields of FHSP using japonica male-sterile lines GAZS with manipulated JA pathway genes were significantly higher than that of GAZS wildtype. Transcriptome analysis, cytological observations, measurements of elastic modulus and determination of cell wall components indicated that the JA pathway could affect the loosening of the lodicule cell walls by regulating their composition through controlling sugar metabolism, which in turn influences DFOT. This research has vital implications for breeding japonica rice cultivars with early DFOT to facilitate indica-japonica hybrid rice breeding.
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Affiliation(s)
- Mumei Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresourcesGuangdong Laboratory for Lingnan Modern AgricultureKey Laboratory for Enhancing Resource Use Efficiency of Crops in South ChinaMinistry of Agriculture and Rural AffairsCollege of Life SciencesSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern RegionShaoguan UniversityShaoguanChina
| | - Xiaopei Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresourcesGuangdong Laboratory for Lingnan Modern AgricultureKey Laboratory for Enhancing Resource Use Efficiency of Crops in South ChinaMinistry of Agriculture and Rural AffairsCollege of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Zhen Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresourcesGuangdong Laboratory for Lingnan Modern AgricultureKey Laboratory for Enhancing Resource Use Efficiency of Crops in South ChinaMinistry of Agriculture and Rural AffairsCollege of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Minghao Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresourcesGuangdong Laboratory for Lingnan Modern AgricultureKey Laboratory for Enhancing Resource Use Efficiency of Crops in South ChinaMinistry of Agriculture and Rural AffairsCollege of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Peng Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresourcesGuangdong Laboratory for Lingnan Modern AgricultureKey Laboratory for Enhancing Resource Use Efficiency of Crops in South ChinaMinistry of Agriculture and Rural AffairsCollege of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Shitang Liao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresourcesGuangdong Laboratory for Lingnan Modern AgricultureKey Laboratory for Enhancing Resource Use Efficiency of Crops in South ChinaMinistry of Agriculture and Rural AffairsCollege of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Yongzhen Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresourcesGuangdong Laboratory for Lingnan Modern AgricultureKey Laboratory for Enhancing Resource Use Efficiency of Crops in South ChinaMinistry of Agriculture and Rural AffairsCollege of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Yannan Gao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresourcesGuangdong Laboratory for Lingnan Modern AgricultureKey Laboratory for Enhancing Resource Use Efficiency of Crops in South ChinaMinistry of Agriculture and Rural AffairsCollege of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Jiahui He
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresourcesGuangdong Laboratory for Lingnan Modern AgricultureKey Laboratory for Enhancing Resource Use Efficiency of Crops in South ChinaMinistry of Agriculture and Rural AffairsCollege of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Yutong Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresourcesGuangdong Laboratory for Lingnan Modern AgricultureKey Laboratory for Enhancing Resource Use Efficiency of Crops in South ChinaMinistry of Agriculture and Rural AffairsCollege of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Huixuan Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresourcesGuangdong Laboratory for Lingnan Modern AgricultureKey Laboratory for Enhancing Resource Use Efficiency of Crops in South ChinaMinistry of Agriculture and Rural AffairsCollege of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Xiaoying Wei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresourcesGuangdong Laboratory for Lingnan Modern AgricultureKey Laboratory for Enhancing Resource Use Efficiency of Crops in South ChinaMinistry of Agriculture and Rural AffairsCollege of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Shuai Nie
- Rice Research InstituteGuangdong Academy of Agricultural Sciences & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering LaboratoryGuangzhouChina
| | - Jingfang Dong
- Rice Research InstituteGuangdong Academy of Agricultural Sciences & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering LaboratoryGuangzhouChina
| | - Liya Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresourcesGuangdong Laboratory for Lingnan Modern AgricultureKey Laboratory for Enhancing Resource Use Efficiency of Crops in South ChinaMinistry of Agriculture and Rural AffairsCollege of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Chuxiong Zhuang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresourcesGuangdong Laboratory for Lingnan Modern AgricultureKey Laboratory for Enhancing Resource Use Efficiency of Crops in South ChinaMinistry of Agriculture and Rural AffairsCollege of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Junliang Zhao
- Rice Research InstituteGuangdong Academy of Agricultural Sciences & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering LaboratoryGuangzhouChina
| | - Zhenlan Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresourcesGuangdong Laboratory for Lingnan Modern AgricultureKey Laboratory for Enhancing Resource Use Efficiency of Crops in South ChinaMinistry of Agriculture and Rural AffairsCollege of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Hai Zhou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresourcesGuangdong Laboratory for Lingnan Modern AgricultureKey Laboratory for Enhancing Resource Use Efficiency of Crops in South ChinaMinistry of Agriculture and Rural AffairsCollege of Life SciencesSouth China Agricultural UniversityGuangzhouChina
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4
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Zhu X, Wang M, Huang Z, Chen M, Xu P, Liao S, Gao Y, Zhao Y, Chen H, He J, Luo Y, Wei X, Zhu L, Liu C, Huang J, Zhao X, Zhao J, Zhang Z, Zhuang C, Liu Z, Zhou H. The OsMYC2-JA feedback loop regulates diurnal flower-opening time via cell wall loosening in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 38972041 DOI: 10.1111/tpj.16910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 05/21/2024] [Accepted: 06/19/2024] [Indexed: 07/09/2024]
Abstract
Diurnal flower-opening time (DFOT), the time of spikelet opening during the day, is an important trait for hybrid rice (Oryza sativa L.) seed production. Hybrids between indica and japonica rice varieties have strong heterosis, but the parental lines usually have different, nonoverlapping DFOTs. This reduces the success of hybrid seed production in crosses between indica and japonica subspecies, thus hindering the utilization of indica and japonica inter-subspecies heterosis. However, little is known about the molecular mechanisms regulating DFOT in rice. Here, we obtained japonica rice lines with a DFOT 1.5 h earlier than the wild type by overexpressing OsMYC2, a gene encoding a key transcription factor in the jasmonate (JA) signaling pathway. OsMYC2 is activated by JA signaling and directly regulates the transcription of genes related to JA biosynthesis and cell wall metabolism. Overexpressing OsMYC2 led to significantly increased JA contents and decreased cellulose and hemicellulose contents in lodicule cells, as well as the softening of lodicule cell walls. This may facilitate the swelling of lodicules, resulting in early diurnal flower-opening. These results suggest that the OsMYC2-JA feedback loop regulates DFOT in rice via cell wall remodeling. These findings shed light on the understanding of regulatory mechanism of the DFOT of plants, which should promote the development of indica and japonica varieties suitable for hybrid rice breeding.
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Affiliation(s)
- Xiaopei Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Mumei Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, Shaoguan University, Shaoguan, 512005, China
| | - Zhen Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Minghao Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Peng Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Shitang Liao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Yannan Gao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Yongzhen Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Huixuan Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Jiahui He
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Yutong Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Xiaoying Wei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Liya Zhu
- Instrumental Analysis and Research Center of South China Agricultural University, Guangzhou, 510642, China
| | - Chuanhe Liu
- Instrumental Analysis and Research Center of South China Agricultural University, Guangzhou, 510642, China
| | - Jilei Huang
- Instrumental Analysis and Research Center of South China Agricultural University, Guangzhou, 510642, China
| | - Xinhui Zhao
- Yahua Seeds Science Academy of Hunan, Changsha, 410119, China
| | - Junliang Zhao
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Zemin Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Chuxiong Zhuang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Zhenlan Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Hai Zhou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
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Malik AS, Sharma NK, Chandra AK, Kumar P, Tyagi S, Raghunandan K, Murukan N, Mallick N, Jha SK, Vinod. Conversion of superior bread wheat genotype HD3209 carrying Lr19/Sr25 into CMS line for development of rust-resistant wheat hybrids. Sci Rep 2024; 14:14112. [PMID: 38898132 PMCID: PMC11187221 DOI: 10.1038/s41598-024-65109-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 06/17/2024] [Indexed: 06/21/2024] Open
Abstract
Hybrid development is one of the most promising strategies for boosting crop yields. Parental lines used to create hybrids must have good per se performance and disease resistance for developing superior hybrids. Indian wheat line HD3209 was developed by introducing the rust resistance genes Lr19/Sr25 into the background of popular wheat variety HD2932. The wheat line HD3209 carrying Lr19/Sr25 has been successfully and rapidly converted to the CMS line A-HD3209, with 96.01% background genome recovery, based on selection for agro-morphological traits, rust resistance, pollen sterility, and foreground and background analyses utilizing SSR markers. The converted CMS line A-HD3209 was completely sterile and nearly identical to the recurrent parent HD3209. Based on high per se performance and rust resistance, the study concludes that the derived CMS line A-HD3209 is promising and can be employed successfully in hybrid development.
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Affiliation(s)
- Abhimanyu Singh Malik
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Nand Kishore Sharma
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Ajay Kumar Chandra
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Parvesh Kumar
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Sandhya Tyagi
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - K Raghunandan
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Niranjana Murukan
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Niharika Mallick
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Shailendra Kumar Jha
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
| | - Vinod
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
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Gao M, Hao Z, Ning Y, He Z. Revisiting growth-defence trade-offs and breeding strategies in crops. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1198-1205. [PMID: 38410834 PMCID: PMC11022801 DOI: 10.1111/pbi.14258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/02/2023] [Accepted: 11/20/2023] [Indexed: 02/28/2024]
Abstract
Plants have evolved a multi-layered immune system to fight off pathogens. However, immune activation is costly and is often associated with growth and development penalty. In crops, yield is the main breeding target and is usually affected by high disease resistance. Therefore, proper balance between growth and defence is critical for achieving efficient crop improvement. This review highlights recent advances in attempts designed to alleviate the trade-offs between growth and disease resistance in crops mediated by resistance (R) genes, susceptibility (S) genes and pleiotropic genes. We also provide an update on strategies for optimizing the growth-defence trade-offs to breed future crops with desirable disease resistance and high yield.
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Affiliation(s)
- Mingjun Gao
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science and Institute of Eco‐Chongming, School of Life SciencesFudan UniversityShanghaiChina
| | - Zeyun Hao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
| | - Yuese Ning
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
| | - Zuhua He
- CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghaiChina
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7
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Guha PK, Magar ND, Kommana M, Barbadikar KM, Suneel B, Gokulan C, Lakshmi DV, Patel HK, Sonti RV, Sundaram RM, Madhav MS. Strong culm: a crucial trait for developing next-generation climate-resilient rice lines. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:665-686. [PMID: 38737321 PMCID: PMC11087419 DOI: 10.1007/s12298-024-01445-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 03/24/2024] [Accepted: 03/27/2024] [Indexed: 05/14/2024]
Abstract
Lodging, a phenomenon characterized by the bending or breaking of rice plants, poses substantial constraints on productivity, particularly during the harvesting phase in regions susceptible to strong winds. The rice strong culm trait is influenced by the intricate interplay of genetic, physiological, epigenetic, and environmental factors. Stem architecture, encompassing morphological and anatomical attributes, alongside the composition of both structural and non-structural carbohydrates, emerges as a critical determinant of lodging resistance. The adaptive response of the rice culm to various biotic and abiotic environmental factors further modulates the propensity for lodging. Advancements in next-generation sequencing technologies have expedited the genetic dissection of lodging resistance, enabling the identification of pertinent genes, quantitative trait loci, and novel alleles. Concurrently, contemporary breeding strategies, ranging from biparental approaches to more sophisticated methods such as multi-parent-based breeding, gene pyramiding, genomic selection, genome-wide association studies, and haplotype-based breeding, offer perspectives on the genetic underpinnings of culm strength. This review comprehensively delves into physiological attributes, culm histology, epigenetic determinants, and gene expression profiles associated with lodging resistance, with a specialized focus on leveraging next-generation sequencing for candidate gene discovery.
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Affiliation(s)
- Pritam Kanti Guha
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Hyderabad, India
- Department of Microbiology, Yogi Vemana University., Y.S.R Kadapa, India
| | - Nakul D. Magar
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - Madhavilatha Kommana
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - Kalyani M. Barbadikar
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - B. Suneel
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - C. Gokulan
- Department of Biotechnology, CSIR-Center for Cellular and Molecular Biology, Hyderabad, India
| | - D. Vijay Lakshmi
- Department of Microbiology, Yogi Vemana University., Y.S.R Kadapa, India
| | - Hitendra Kumar Patel
- Department of Biotechnology, CSIR-Center for Cellular and Molecular Biology, Hyderabad, India
| | - Ramesh V. Sonti
- Department of Biotechnology, CSIR-Center for Cellular and Molecular Biology, Hyderabad, India
- International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - R. M. Sundaram
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - Maganti Sheshu Madhav
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Hyderabad, India
- ICAR-Central Tobacco Research Institute, Rajahmundry, India
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8
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Yu L, Zhou J, Lin J, Chen M, Liu F, Zheng X, Zhou L, Wang R, Xiao L, Liu Y. Perception of strigolactones and the coordinated phytohormonal regulation on rice ( Oryza sativa) tillering is affected by endogenous ascorbic acid. FUNCTIONAL PLANT BIOLOGY : FPB 2024; 51:FP23148. [PMID: 38326230 DOI: 10.1071/fp23148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 01/16/2024] [Indexed: 02/09/2024]
Abstract
Phytohormones play a key role in regulating tiller number. Ascorbic acid (Asc)-phytohormone interaction plays a pivotal role in the regulation of senescence. We analysed the relationship between Asc and the enzyme concentrations and gene transcript abundances related to the signal perception of strigolactones (SLs), the contents of four phytohormones (abscisic acid, ABA; jasmonic acid, JA; indole acetic acid, IAA; cytokinin, CTK), the enzyme concentrations and gene transcript abundances related to the synthesis or transportation of these four phytohormones. Our results showed that Asc deficiency leads to the upregulation of enzyme concentrations, gene transcript abundances related to the SL signal perception, ABA synthesis and IAA transport. The altered level of Asc also leads to a change in the contents of ABA, JA, IAA and CTK. These findings support the conclusion that Asc or Asc/DHA play an important role in the signal perception and transduction of SLs, and Asc may affect the coordinated regulation of SL, IAA and CTK on rice (Oryza sativa ) tillering.
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Affiliation(s)
- Le Yu
- College of Life Science, Zhaoqing University, Zhaoqing, Guangdong 526061, China
| | - Jiankai Zhou
- College of Life Science, Zhaoqing University, Zhaoqing, Guangdong 526061, China
| | - Junlong Lin
- College of Life Science, Zhaoqing University, Zhaoqing, Guangdong 526061, China
| | - Mengwei Chen
- College of Life Science, Zhaoqing University, Zhaoqing, Guangdong 526061, China
| | - Fang Liu
- College of Life Science, Zhaoqing University, Zhaoqing, Guangdong 526061, China
| | - Xinlin Zheng
- College of Life Science, Zhaoqing University, Zhaoqing, Guangdong 526061, China
| | - Liping Zhou
- College of Life Science, Zhaoqing University, Zhaoqing, Guangdong 526061, China
| | - Ruozhong Wang
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Langtao Xiao
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Yonghai Liu
- College of Life Science, Zhaoqing University, Zhaoqing, Guangdong 526061, China; and Zhaoqing Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Zhaoqing, Guangdong 526238, China
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9
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Tian Y, Chen X, Xu P, Wang Y, Wu X, Wu K, Fu X, Chin Y, Liao Y. Rapid Visual Detection of Elite Erect Panicle Dense and Erect Panicle 1 Allele for Marker-Assisted Improvement in Rice ( Oryza sativa L.) Using the Loop-Mediated Isothermal Amplification Method. Curr Issues Mol Biol 2024; 46:498-512. [PMID: 38248334 PMCID: PMC10814556 DOI: 10.3390/cimb46010032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 12/28/2023] [Accepted: 01/02/2024] [Indexed: 01/23/2024] Open
Abstract
Molecular-assisted breeding is an effective way to improve targeted agronomic traits. dep1 (dense and erect panicle 1) is a pleiotropic gene that regulates yield, quality, disease resistance, and stress tolerance, traits that are of great value in rice (Oryza sativa L.) breeding. In this study, a colorimetric LAMP (loop-mediated isothermal amplification) assay was developed for the detection of the dep1 allele and tested for the screening and selection of the heavy-panicle hybrid rice elite restorer line SHUHUI498, modified with the allele. InDel (Insertion and Deletion) primers (DEP1_F and DEP1_R) and LAMP primers (F3, B3, FIP, and BIP) for genotyping were designed using the Primer3 Plus (version 3.3.0) and PrimerExplore (version 5) software. Our results showed that both InDel and LAMP markers could be used for accurate genotyping. After incubation at a constant temperature of 65 °C for 60 min with hydroxynaphthol blue (HNB) as a color indicator, the color of the LAMP assay containing the dep1 allele changed to sky blue. The SHUHUI498 rice line that was detected in our LAMP assay displayed phenotypes consistent with the dep1 allele such as having a more compact plant architecture, straight stems and leaves, and a significant increase in the number of effective panicles and spikelets, demonstrating the effectiveness of our method in screening for the dep1 allele in rice breeding.
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Affiliation(s)
- Yonghang Tian
- College of Food Science and Engineering, Hainan Tropical Ocean University, No. 1 Yucai Road, Sanya 572022, China; (Y.T.); (X.C.)
- Marine Food Engineering Technology Research Center of Hainan Province, No. 1 Yucai Road, Sanya 572022, China
| | - Xiyi Chen
- College of Food Science and Engineering, Hainan Tropical Ocean University, No. 1 Yucai Road, Sanya 572022, China; (Y.T.); (X.C.)
- Marine Food Engineering Technology Research Center of Hainan Province, No. 1 Yucai Road, Sanya 572022, China
| | - Peizhou Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, No. 211 Huiming Road, Chengdu 611130, China; (P.X.); (Y.W.); (X.W.)
| | - Yuping Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, No. 211 Huiming Road, Chengdu 611130, China; (P.X.); (Y.W.); (X.W.)
| | - Xianjun Wu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, No. 211 Huiming Road, Chengdu 611130, China; (P.X.); (Y.W.); (X.W.)
| | - Kun Wu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Beijing 100101, China; (K.W.); (X.F.)
| | - Xiangdong Fu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Beijing 100101, China; (K.W.); (X.F.)
| | - Yaoxian Chin
- College of Food Science and Engineering, Hainan Tropical Ocean University, No. 1 Yucai Road, Sanya 572022, China; (Y.T.); (X.C.)
- Marine Food Engineering Technology Research Center of Hainan Province, No. 1 Yucai Road, Sanya 572022, China
| | - Yongxiang Liao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, No. 211 Huiming Road, Chengdu 611130, China; (P.X.); (Y.W.); (X.W.)
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10
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Yu H, Kou L, Li J. 10k-level integrated rice database shows power for exploiting rare variants. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:2539-2540. [PMID: 37877412 DOI: 10.1111/jipb.13576] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 10/20/2023] [Indexed: 10/26/2023]
Abstract
This Highlight features a recent study by Shang Lianguang and Qian Qian's groups, who re-analyzed published resequencing data covering 10,548 accessions of Asian cultivated rice Oryza sativa and wild rice Oryza rufipogon from 98 countries worldwide to generate a super-large rice genomic variation dataset.
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Affiliation(s)
- Hong Yu
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Liquan Kou
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jiayang Li
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Yazhouwan National Laboratory, Sanya, 572024, China
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11
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Wang H, Lin YN, Yan S, Hong JP, Tan JR, Chen YQ, Cao YS, Fang W. NRTPredictor: identifying rice root cell state in single-cell RNA-seq via ensemble learning. PLANT METHODS 2023; 19:119. [PMID: 37925413 PMCID: PMC10625708 DOI: 10.1186/s13007-023-01092-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 10/15/2023] [Indexed: 11/06/2023]
Abstract
BACKGROUND Single-cell RNA sequencing (scRNA-seq) measurements of gene expression show great promise for studying the cellular heterogeneity of rice roots. How precisely annotating cell identity is a major unresolved problem in plant scRNA-seq analysis due to the inherent high dimensionality and sparsity. RESULTS To address this challenge, we present NRTPredictor, an ensemble-learning system, to predict rice root cell stage and mine biomarkers through complete model interpretability. The performance of NRTPredictor was evaluated using a test dataset, with 98.01% accuracy and 95.45% recall. With the power of interpretability provided by NRTPredictor, our model recognizes 110 marker genes partially involved in phenylpropanoid biosynthesis. Expression patterns of rice root could be mapped by the above-mentioned candidate genes, showing the superiority of NRTPredictor. Integrated analysis of scRNA and bulk RNA-seq data revealed aberrant expression of Epidermis cell subpopulations in flooding, Pi, and salt stresses. CONCLUSION Taken together, our results demonstrate that NRTPredictor is a useful tool for automated prediction of rice root cell stage and provides a valuable resource for deciphering the rice root cellular heterogeneity and the molecular mechanisms of flooding, Pi, and salt stresses. Based on the proposed model, a free webserver has been established, which is available at https://www.cgris.net/nrtp .
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Affiliation(s)
- Hao Wang
- The Innovation Team of Crop Germplasm Resources Preservation and Information, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yu-Nan Lin
- The Innovation Team of Crop Germplasm Resources Preservation and Information, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Shen Yan
- The Innovation Team of Crop Germplasm Resources Preservation and Information, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jing-Peng Hong
- The Innovation Team of Crop Germplasm Resources Preservation and Information, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jia-Rui Tan
- The Innovation Team of Crop Germplasm Resources Preservation and Information, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yan-Qing Chen
- The Innovation Team of Crop Germplasm Resources Preservation and Information, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Yong-Sheng Cao
- The Innovation Team of Crop Germplasm Resources Preservation and Information, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Wei Fang
- The Innovation Team of Crop Germplasm Resources Preservation and Information, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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12
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Yang J, Miao J, Li N, Zhou Z, Dai K, Ji F, Yang M, Tan C, Liu J, Wang H, Tang W. Genetic dissection of cold tolerance at the budding stage of rice in an indica-japonica recombination inbred line population. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 204:108086. [PMID: 37890228 DOI: 10.1016/j.plaphy.2023.108086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 09/07/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023]
Abstract
Rice is highly cold-sensitive, and thus, the promotion of cold resistance in buds is essential. In this study, we conducted a mapping analysis to identify quantitative trait loci (QTLs) associated with cold tolerance in buds. The analysis was performed using a recombinant inbred line (RIL) population consisting of 192 lines derived from the cold-tolerant strain 02428 and the cold-sensitive strain YZX. Seven additive loci on chromosomes 1, 4, 5, and 6 were identified, of which loci 3 and 7 were found in two crop seasons, indicating stability. Three epistatic interactions, one present over two seasons, were found. Loci 3 and 7 pyramided with two main-effect QTLs observed to control the rate of low-temperature germination in our previous study. Two materials with good cold resistance at the germination and bud stages were obtained, namely, G93 and G146. Transcriptome sequencing analysis of the two parent buds after cold treatment found that genes expressed differentially between the two parents were related to photosynthesis, energy metabolism, and reactive oxygen scavenging. Five candidate genes, namely, Os01g0385400, Os01g0388000, Os06g0287700, Os06g0289200, and Os06g0291100, were selected in the two stable intervals based on gene expression profiles and annotations. These genetic loci exhibit strong potential as targets for breeding cold tolerance in buds and require additional investigation. In conclusion, this work provides valuable genetic resources that can be utilized to improve the cold tolerance of rice.
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Affiliation(s)
- Jing Yang
- Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming 650500, China
| | - Jiahao Miao
- Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming 650500, China
| | - Nan Li
- Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming 650500, China
| | - Zixian Zhou
- Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming 650500, China
| | - Kunyan Dai
- Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming 650500, China
| | - Faru Ji
- Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming 650500, China
| | - Min Yang
- Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming 650500, China
| | - Chen Tan
- Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming 650500, China
| | - Jing Liu
- Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming 650500, China.
| | - Hongyang Wang
- Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming 650500, China.
| | - Wei Tang
- Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming 650500, China.
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13
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Gu Z, Gong J, Zhu Z, Li Z, Feng Q, Wang C, Zhao Y, Zhan Q, Zhou C, Wang A, Huang T, Zhang L, Tian Q, Fan D, Lu Y, Zhao Q, Huang X, Yang S, Han B. Structure and function of rice hybrid genomes reveal genetic basis and optimal performance of heterosis. Nat Genet 2023; 55:1745-1756. [PMID: 37679493 PMCID: PMC10562254 DOI: 10.1038/s41588-023-01495-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 08/02/2023] [Indexed: 09/09/2023]
Abstract
Exploitation of crop heterosis is crucial for increasing global agriculture production. However, the quantitative genomic analysis of heterosis was lacking, and there is currently no effective prediction tool to optimize cross-combinations. Here 2,839 rice hybrid cultivars and 9,839 segregation individuals were resequenced and phenotyped. Our findings demonstrated that indica-indica hybrid-improving breeding was a process that broadened genetic resources, pyramided breeding-favorable alleles through combinatorial selection and collaboratively improved both parents by eliminating the inferior alleles at negative dominant loci. Furthermore, we revealed that widespread genetic complementarity contributed to indica-japonica intersubspecific heterosis in yield traits, with dominance effect loci making a greater contribution to phenotypic variance than overdominance effect loci. On the basis of the comprehensive dataset, a genomic model applicable to diverse rice varieties was developed and optimized to predict the performance of hybrid combinations. Our data offer a valuable resource for advancing the understanding and facilitating the utilization of heterosis in rice.
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Affiliation(s)
- Zhoulin Gu
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Junyi Gong
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Zhou Zhu
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhen Li
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Qi Feng
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Changsheng Wang
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Yan Zhao
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Qilin Zhan
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Congcong Zhou
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Ahong Wang
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Tao Huang
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Lei Zhang
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Qilin Tian
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Danlin Fan
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Yiqi Lu
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Qiang Zhao
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Xuehui Huang
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Shihua Yang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China.
| | - Bin Han
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.
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14
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Rice heterosis: quantitatively characterized and optimized hybrid breeding. Nat Genet 2023; 55:1619-1620. [PMID: 37723264 DOI: 10.1038/s41588-023-01496-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/20/2023]
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15
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Wang S, Wu H, Lu Z, Liu W, Wang X, Fang Z, He X. Combining Ability Analysis of Yield-Related Traits of Two Elite Rice Restorer Lines in Chinese Hybrid Rice. Int J Mol Sci 2023; 24:12395. [PMID: 37569770 PMCID: PMC10418745 DOI: 10.3390/ijms241512395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 07/30/2023] [Accepted: 07/31/2023] [Indexed: 08/13/2023] Open
Abstract
Hybrid rice breeding is an important strategy for enhancing grain yield. Breeding high-performance parental lines and identifying combining abilities is a top priority for hybrid breeding. Yuenongsimiao (YNSM) and its derivative variety Yuehesimiao (YHSM) are elite restorer lines with a high ability of fertility restoration, from which 67 derived hybrid combinations have been authorized to different degrees in more than 110 instances in China. In this study, we found that YNSM and YHSM contained three candidate restorer-of-fertility (Rf) genes, Rf3, Rf4, and Rf5/Rf1a, that might confer their restoration ability. Subsequently, we investigated heterosis and combining ability of YNSM and YHSM using 50 F1 hybrids from a 5 × 10 incomplete diallelic mating design. Our results indicated that hybrid combinations exhibited significant genetic differences, and the additive effects of the parental genes played a preponderant role in the inheritance of observed traits. The metrics of plant height (PH), 1000-grain weight (TGW), panicle length (PL), and the number of spikelets per panicle (NSP) were mainly affected by genetic inheritance with higher heritability. Notably, the general combining ability (GCA) of YHSM exhibited the largest positive effect on the number of grains per panicle (NGP), NSP, PL, and TGW. Thus, YHSM had the largest GCA effect on yield per plant (YPP). In addition, the GCA of YNSM exhibited a positive impact on YPP, mainly due to the critical contribution of seed setting percentage (SSP). Moreover, YNSM and YHSM exhibited negative GCA effects on PH, implying that YNSM and YHSM could effectively enhance plant lodging resistance by reducing the plant height of the derived hybrids. Remarkably, among the hybrids, Yuanxiang A/YNSM (YXA/YNSM), Shen 08S/Yuemeizhan (S08S/YMZ), and Quan 9311A/YHSM (Q9311A/YHSM) represent promising new combinations with a higher specific combining ability (SCA) effect value on YPP with a value more than 3.50. Our research thus highlights the promising application for the rational utilization of YNSM and YHSM in hybrid rice breeding.
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Affiliation(s)
- Shiguang Wang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (S.W.); (H.W.); (Z.L.); (W.L.); (X.W.); (Z.F.)
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
| | - Haoxiang Wu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (S.W.); (H.W.); (Z.L.); (W.L.); (X.W.); (Z.F.)
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
| | - Zhanhua Lu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (S.W.); (H.W.); (Z.L.); (W.L.); (X.W.); (Z.F.)
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
| | - Wei Liu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (S.W.); (H.W.); (Z.L.); (W.L.); (X.W.); (Z.F.)
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
| | - Xiaofei Wang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (S.W.); (H.W.); (Z.L.); (W.L.); (X.W.); (Z.F.)
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
| | - Zhiqiang Fang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (S.W.); (H.W.); (Z.L.); (W.L.); (X.W.); (Z.F.)
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
| | - Xiuying He
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (S.W.); (H.W.); (Z.L.); (W.L.); (X.W.); (Z.F.)
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
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Zhao X, Yi L, Zuo Y, Gao F, Cheng Y, Zhang H, Zhou Y, Jia X, Su S, Zhang D, Zhang X, Ren Y, Mu Y, Jin X, Li Q, Bateer S, Lu Z. High-Quality Genome Assembly and Genome-Wide Association Study of Male Sterility Provide Resources for Flax Improvement. PLANTS (BASEL, SWITZERLAND) 2023; 12:2773. [PMID: 37570928 PMCID: PMC10421198 DOI: 10.3390/plants12152773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/21/2023] [Accepted: 07/23/2023] [Indexed: 08/13/2023]
Abstract
Flax is an economic crop with a long history. It is grown worldwide and is mainly used for edible oil, industry, and textiles. Here, we reported a high-quality genome assembly for "Neiya No. 9", a popular variety widely grown in China. Combining PacBio long reads, Hi-C sequencing, and a genetic map reported previously, a genome assembly of 473.55 Mb was constructed, which covers ~94.7% of the flax genome. These sequences were anchored onto 15 chromosomes. The N50 lengths of the contig and scaffold were 0.91 Mb and 31.72 Mb, respectively. A total of 32,786 protein-coding genes were annotated, and 95.9% of complete BUSCOs were found. Through morphological and cytological observation, the male sterility of flax was considered dominant nuclear sterility. Through GWAS analysis, the gene LUSG00017705 (cysteine synthase gene) was found to be closest to the most significant SNP, and the expression level of this gene was significantly lower in male sterile plants than in fertile plants. Among the significant SNPs identified in the GWAS analysis, only two were located in the coding region, and these two SNPs caused changes in the protein encoded by LUSG00017565 (cysteine protease gene). It was speculated that these two genes may be related to male sterility in flax. This is the first time the molecular mechanism of male sterility in flax has been reported. The high-quality genome assembly and the male sterility genes revealed, provided a solid foundation for flax breeding.
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Affiliation(s)
- Xiaoqing Zhao
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China
| | - Liuxi Yi
- Agricultural College, Inner Mongolia Agricultural University, Hohhot 010019, China
| | - Yongchun Zuo
- College of Life Sciences, Inner Mongolia University, Hohhot 010070, China
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Hohhot 010019, China
| | - Fengyun Gao
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China
| | - Yuchen Cheng
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China
- College of Life Sciences, Inner Mongolia University, Hohhot 010070, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot 010031, China
- Inner Mongolia Conservation Tillage Engineering Technology Research Center, Hohhot 010031, China
| | - Hui Zhang
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China
| | - Yu Zhou
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China
| | - Xiaoyun Jia
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China
| | - Shaofeng Su
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China
| | - Dejian Zhang
- College of Life Sciences, Inner Mongolia University, Hohhot 010070, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot 010031, China
- Inner Mongolia Conservation Tillage Engineering Technology Research Center, Hohhot 010031, China
| | - Xiangqian Zhang
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China
- College of Life Sciences, Inner Mongolia University, Hohhot 010070, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot 010031, China
- Inner Mongolia Conservation Tillage Engineering Technology Research Center, Hohhot 010031, China
| | - Yongfeng Ren
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China
- College of Life Sciences, Inner Mongolia University, Hohhot 010070, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot 010031, China
- Inner Mongolia Conservation Tillage Engineering Technology Research Center, Hohhot 010031, China
| | - Yanxin Mu
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China
- College of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Xiaolei Jin
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China
| | - Qiang Li
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China
| | - Siqin Bateer
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China
- College of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Zhanyuan Lu
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China
- College of Life Sciences, Inner Mongolia University, Hohhot 010070, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot 010031, China
- Inner Mongolia Conservation Tillage Engineering Technology Research Center, Hohhot 010031, China
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Li W, Yan J, Zhang Y, Zhang F, Guan Z, Yao Y, Chang Y, Tu H, Li X, Wang H, Xiong H, Lai X, Yin P, Xiong L. Serine protease NAL1 exerts pleiotropic functions through degradation of TOPLESS-related corepressor in rice. NATURE PLANTS 2023; 9:1130-1142. [PMID: 37349549 DOI: 10.1038/s41477-023-01449-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 05/24/2023] [Indexed: 06/24/2023]
Abstract
NARROW LEAF 1 (NAL1) is a breeding-valuable pleiotropic gene that affects multiple agronomic traits in rice, although the molecular mechanism is largely unclear. Here, we report that NAL1 is a serine protease and displays a novel hexameric structure consisting of two ATP-mediated doughnut-shaped trimeric complexes. Moreover, we identified TOPLESS-related corepressor OsTPR2 involved in multiple growth and development processes as the substrate of NAL1. We found that NAL1 degraded OsTPR2, thus modulating the expression of downstream genes related to hormone signalling pathways, eventually achieving its pleiotropic physiological function. An elite allele, NAL1A, which may have originated from wild rice, could increase grain yield. Furthermore, the NAL1 homologues in different crops have a similar pleiotropic function to NAL1. Our study uncovers a NAL1-OsTPR2 regulatory module and provides gene resources for the design of high-yield crops.
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Affiliation(s)
- Wenjing Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Junjie Yan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Yu Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Fei Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Zeyuan Guan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Yilong Yao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Yu Chang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Haifu Tu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Xiaokai Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Huaijun Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Haiyan Xiong
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Xuelei Lai
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Ping Yin
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Lizhong Xiong
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China.
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18
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Wang M, Chen M, Huang Z, Zhou H, Liu Z. Advances on the Study of Diurnal Flower-Opening Times of Rice. Int J Mol Sci 2023; 24:10654. [PMID: 37445832 DOI: 10.3390/ijms241310654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 06/13/2023] [Accepted: 06/23/2023] [Indexed: 07/15/2023] Open
Abstract
The principal goal of rice (Oryza sativa L.) breeding is to increase the yield. In the past, hybrid rice was mainly indica intra-subspecies hybrids, but its yield has been difficult to improve. The hybridization between the indica and japonica subspecies has stronger heterosis; the utilization of inter-subspecies heterosis is important for long-term improvement of rice yields. However, the different diurnal flower-opening times (DFOTs) between the indica and japonica subspecies seriously reduce the efficiency of cross-pollination and yield and increase the cost of indica-japonica hybrid rice seeds, which has become one of the main constraints for the development of indica-japonica hybrid rice breeding. The DFOT of plants is adapted to their growing environment and is also closely related to species stability and evolution. Herein, we review the structure and physiological basis of rice flower opening, the factors that affect DFOT, and the progress of cloning and characterization of DFOT genes in rice. We also analyze the problems in the study of DFOT and provide corresponding suggestions.
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Affiliation(s)
- Mumei Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Minghao Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Zhen Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Hai Zhou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Zhenlan Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
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Wang A, Jing Y, Cheng Q, Zhou H, Wang L, Gong W, Kou L, Liu G, Meng X, Chen M, Ma H, Shu X, Yu H, Wu D, Li J. Loss of function of SSIIIa and SSIIIb coordinately confers high RS content in cooked rice. Proc Natl Acad Sci U S A 2023; 120:e2220622120. [PMID: 37126676 PMCID: PMC10175802 DOI: 10.1073/pnas.2220622120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 03/28/2023] [Indexed: 05/03/2023] Open
Abstract
The sedentary lifestyle and refined food consumption significantly lead to obesity, type 2 diabetes, and related complications, which have become one of the major threats to global health. This incidence could be potentially reduced by daily foods rich in resistant starch (RS). However, it remains a challenge to breed high-RS rice varieties. Here, we reported a high-RS mutant rs4 with an RS content of ~10.8% in cooked rice. The genetic study revealed that the loss-of-function SSIIIb and SSIIIa together with a strong Wx allele in the background collaboratively contributed to the high-RS phenotype of the rs4 mutant. The increased RS contents in ssIIIa and ssIIIa ssIIIb mutants were associated with the increased amylose and lipid contents. SSIIIb and SSIIIa proteins were functionally redundant, whereas SSIIIb mainly functioned in leaves and SSIIIa largely in endosperm owing to their divergent tissue-specific expression patterns. Furthermore, we found that SSIII experienced duplication in different cereals, of which one SSIII paralog was mainly expressed in leaves and another in the endosperm. SSII but not SSIV showed a similar evolutionary pattern to SSIII. The copies of endosperm-expressed SSIII and SSII were associated with high total starch contents and low RS levels in the seeds of tested cereals, compared with low starch contents and high RS levels in tested dicots. These results provided critical genetic resources for breeding high-RS rice cultivars, and the evolutionary features of these genes may facilitate to generate high-RS varieties in different cereals.
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Affiliation(s)
- Anqi Wang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing100101, China
| | - Yanhui Jing
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing100101, China
| | - Qiao Cheng
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing100101, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Hongju Zhou
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing100101, China
| | - Lijun Wang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing100101, China
| | - Wanxin Gong
- State Key Laboratory of Rice Biology and Key Lab of the Ministry of Agriculture for Nuclear Agricultural Sciences, Institute of Nuclear Agriculture Sciences, Zhejiang University, Hangzhou310029, China
| | - Liquan Kou
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing100101, China
| | - Guifu Liu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing100101, China
| | - Xiangbing Meng
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing100101, China
| | - Mingjiang Chen
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing100101, China
| | - Haiyan Ma
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing100101, China
| | - Xiaoli Shu
- State Key Laboratory of Rice Biology and Key Lab of the Ministry of Agriculture for Nuclear Agricultural Sciences, Institute of Nuclear Agriculture Sciences, Zhejiang University, Hangzhou310029, China
| | - Hong Yu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing100101, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Dianxing Wu
- State Key Laboratory of Rice Biology and Key Lab of the Ministry of Agriculture for Nuclear Agricultural Sciences, Institute of Nuclear Agriculture Sciences, Zhejiang University, Hangzhou310029, China
| | - Jiayang Li
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing100101, China
- University of Chinese Academy of Sciences, Beijing100049, China
- Yazhou Bay Laboratory, Sanya572025, China
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20
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Li M, Li R, Zhang J, Liu S, Hei Z, Wang Q. Mixed cropping with duck co-culture: an agroecological system to improve grain quality and farm profitability. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2023; 103:3028-3040. [PMID: 36515187 DOI: 10.1002/jsfa.12386] [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: 04/11/2022] [Revised: 12/10/2022] [Accepted: 12/14/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Previous studies found that mixed cropping combined with duck co-culture (MCDC) system could improve the efficiency of grain production and positively affect soil nutrient contents. However, the effects on grain quality, and profitable income have not been evaluated yet. In this study, a field experiment with four combinations of different rice varieties and ducks was conducted during both the early and late rice growing seasons. RESULTS The field survey demonstrated that MCDC system significantly decreased the grain appearance of chalky rice rate and the chalkiness degree with an average of 56.82%, and 54.28%, respectively. Leaf SPAD value, photosynthetic rate, and aboveground dry weight were all improved in the MCDC and mixed-cropping systems, relative to the mono-cropping system. The net income obtained from the mono-cropping, mixed cropping (no ducks), and MCDC (with ducks) systems (from grain and ducks' meat) was 581.2 USD ha-1 yr-1 , 1001.8 USD ha-1 yr-1 , and 5242.1 USD ha-1 yr-1 in both growing seasons, respectively. CONCLUSION Planting genetically diverse rice varieties and co-culture with ducks increased rice growth rates, productivity and grain quality. The MCDC system would provide more ecological and economic benefits compared with the conventional mono-cropping system. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Meijuan Li
- Department of Ecology, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, P. R. China
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, P. R. China
| | - Ronghua Li
- Department of Ecology, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, P. R. China
- Guangdong Provincial Key Laboratory of Eco-circular Agriculture, South China Agricultural University, Guangzhou, P. R. China
- Guangdong Engineering Technology Research Centre of Modern Eco-agriculture and Circular Agriculture, Guangzhou, P. R. China
- Key Laboratory of Agro-Environment in the Tropics, Ministry of Agriculture, Guangzhou, P. R. China
| | - Jiaen Zhang
- Department of Ecology, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, P. R. China
- Guangdong Provincial Key Laboratory of Eco-circular Agriculture, South China Agricultural University, Guangzhou, P. R. China
- Guangdong Engineering Technology Research Centre of Modern Eco-agriculture and Circular Agriculture, Guangzhou, P. R. China
- Key Laboratory of Agro-Environment in the Tropics, Ministry of Agriculture, Guangzhou, P. R. China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, P. R. China
| | - Shiwei Liu
- Department of Ecology, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, P. R. China
| | - Zewen Hei
- Department of Ecology, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, P. R. China
| | - Qi Wang
- Department of Ecology, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, P. R. China
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Gao JG, Zhu XG. The legacies of the "Father of Hybrid Rice" and the seven representative achievements of Chinese rice research: A pioneering perspective towards sustainable development. FRONTIERS IN PLANT SCIENCE 2023; 14:1087768. [PMID: 37025150 PMCID: PMC10070957 DOI: 10.3389/fpls.2023.1087768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 03/13/2023] [Indexed: 06/19/2023]
Abstract
The "Father of Hybrid Rice", Yuan Longping, created high-yield hybrid rice that can feed tens of millions of people annually. The research achievements of Yuan and his team on low cadmium-accumulating rice and sea rice, in addition to hybrid rice, as well as those of a large number of Chinese scientists engaged in rice research in other six areas, including the rice genome, purple endosperm rice, de novo domestication of tetraploid rice, perennial rice, rice blast disease, and key genes for high nitrogen use efficiency, play an important role in promoting the realization of the United Nations Sustainable Development Goals 2 and 12. The purpose of this review is not to elaborate on the details of each research, but to innovatively summarize the significance and inspiration of these achievements to ensure global food security and achieve sustainable agriculture. In the future, cultivating new rice varieties through modern biotechnology, such as genome editing, will not only reduce hunger, but potentially reduce human-land conflicts, improve the environment, and mitigate climate change.
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Affiliation(s)
- Jian-Guo Gao
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, China
- Department of Ecology, Peking University, Beijing, China
| | - Xin-Guang Zhu
- National Key Laboratory for Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
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22
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Ma B, Zhang L, He Z. Understanding the regulation of cereal grain filling: The way forward. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:526-547. [PMID: 36648157 DOI: 10.1111/jipb.13456] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 01/17/2023] [Indexed: 06/17/2023]
Abstract
During grain filling, starch and other nutrients accumulate in the endosperm; this directly determines grain yield and grain quality in crops such as rice (Oryza sativa), maize (Zea mays), and wheat (Triticum aestivum). Grain filling is a complex trait affected by both intrinsic and environmental factors, making it difficult to explore the underlying genetics, molecular regulation, and the application of these genes for breeding. With the development of powerful genetic and molecular techniques, much has been learned about the genes and molecular networks related to grain filling over the past decades. In this review, we highlight the key factors affecting grain filling, including both biological and abiotic factors. We then summarize the key genes controlling grain filling and their roles in this event, including regulators of sugar translocation and starch biosynthesis, phytohormone-related regulators, and other factors. Finally, we discuss how the current knowledge of valuable grain filling genes could be integrated with strategies for breeding cereal varieties with improved grain yield and quality.
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Affiliation(s)
- Bin Ma
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Lin Zhang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Zuhua He
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
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23
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Tan Q, Chen S, Gan Z, Lu Q, Yan Z, Chen G, Lin S, Yang W, Zhao J, Ba Y, Zhu H, Bu S, Liu G, Liu Z, Wang S, Zhang G. Grain shape is a factor affecting the stigma exsertion rate in rice. FRONTIERS IN PLANT SCIENCE 2023; 14:1087285. [PMID: 36798706 PMCID: PMC9927237 DOI: 10.3389/fpls.2023.1087285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
Stigma exsertion rate (SER) is an index of outcrossing ability in rice and is a key trait of male sterile lines (MSLs) in hybrid rice. In this study, it was found that the maintainer lines carrying gs3 and gs3/gw8 showed higher SER. Single-segment substitution lines (SSSLs) carrying gs3, gw5, GW7 or gw8 genes for grain shape and gene pyramiding lines were used to reveal the relationship between grain shape and SER. The results showed that the grain shape regulatory genes had pleiotropic effects on SER. The SERs were affected by grain shapes including grain length, grain width and the ratio of length to width (RLW) not only in low SER background, but also in high SER background. The coefficients of determination (R2) between grain length and SER, grain width and SER, and grain RLW and SER were 0.78, 0.72, and 0.91 respectively. The grain RLW was the most important parameter affecting SER, and a larger grain RLW was beneficial to stigma exsertion. The pyramiding line PL-gs3/GW7/gw8 showed the largest grain RLW and the highest SER, which will be a fine breeding resource. Further research showed that the grain shape regulatory genes had pleiotropic effects on stigma shape, although the R2 values between grain shape and stigma shape, and stigma shape and SER were lower. Our results demonstrate that grain shape is a factor affecting SER in rice, in part by affecting stigma shape. This finding will be helpful for breeding MSLs with high SER in hybrid rice.
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Affiliation(s)
- Quanya Tan
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Songliang Chen
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Zhenpeng Gan
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Qimiao Lu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Zhenguang Yan
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Guodong Chen
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Shaojun Lin
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Weifeng Yang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Jiao Zhao
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Yuanyuan Ba
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Haitao Zhu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Suhong Bu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Guifu Liu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Zupei Liu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Shaokui Wang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Guiquan Zhang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
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Hamad HS, Bleih EM, Gewaily EE, Abou Elataa AE, El Sherbiny HA, Abdelhameid NM, Rehan M. Cyanobacteria Application Ameliorates Floral Traits and Outcrossing Rate in Diverse Rice Cytoplasmic Male Sterile Lines. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11243411. [PMID: 36559523 PMCID: PMC9781212 DOI: 10.3390/plants11243411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 11/04/2022] [Accepted: 12/05/2022] [Indexed: 05/14/2023]
Abstract
In rice, cytoplasmic male sterility (CMS) represents an irreplaceable strategy for producing high-yielding hybrid rice based on the commercial exploitation of heterosis. Thereupon, enhancing floral traits and outcrossing rates in CMS lines increase hybrid seed production and ensure global food security. The exogenous application of cyanobacteria could enhance outcrossing rates in CMS lines and, accordingly, hybrid rice seed production. In the present study, we aimed at exploring the impact of cyanobacteria implementation such as Anabaena oryzae, Nostoc muscorum, and their mixture to promote the floral traits, outcrossing rates, and seed production in hybrid rice. The impact of cyanobacteria (Anabaena Oryza (T2), Nostoc muscorum (T3), and their combination (T4) versus the untreated control (T1) was investigated for two years on the growth, floral, and yield traits of five diverse CMS lines, namely IR69625A (L1), IR58025A (L2), IR70368A (L3), G46A (L4), and K17A(L5). The evaluated CMS lines exhibited significant differences in all measured floral traits (days to heading (DTH), total stigma length (TSL), stigma width (SW), duration of spikelet opening (DSO), spikelet opening angle (SOA)). Additionally, L4 displayed the uppermost total stigma length and stigma width, whereas L1 and L5 recorded the best duration of spikelet opening and spikelet opening angle. Notably, these mentioned CMS lines exhibited the highest plant growth and yield traits, particularly under T4 treatment. Strong positive relationships were distinguished between the duration of the spikelet opening, panicle exertion, panicle weight, seed set, grain yield, total stigma length, spikelet opening angle, stigma width, and number of fertile panicles per hill. Cyanobacteria is a potential promising tool to increase floral traits and seed production in hybrid rice.
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Affiliation(s)
- Hassan Sh. Hamad
- Rice Research and Training Department, Field Crops Research Institute, Agricultural Research Center, Kafrelsheikh 33717, Egypt
| | - Eman M. Bleih
- Rice Research and Training Department, Field Crops Research Institute, Agricultural Research Center, Kafrelsheikh 33717, Egypt
| | - Elsayed E. Gewaily
- Rice Research and Training Department, Field Crops Research Institute, Agricultural Research Center, Kafrelsheikh 33717, Egypt
| | - Ahmed E. Abou Elataa
- Rice Research and Training Department, Field Crops Research Institute, Agricultural Research Center, Kafrelsheikh 33717, Egypt
| | - Heba A. El Sherbiny
- Rice Research and Training Department, Field Crops Research Institute, Agricultural Research Center, Kafrelsheikh 33717, Egypt
| | - Noha M. Abdelhameid
- Soil Fertility and Microbiology Department, Desert Research Center (DRC), Cairo 11753, Egypt
| | - Medhat Rehan
- Department of Plant Production and Protection, College of Agriculture and Veterinary Medicine, Qassim University, Buraydah 51452, Saudi Arabia
- Department of Genetics, Faculty of Agriculture, Kafrelsheikh University, Kafr El-Sheikh 33516, Egypt
- Correspondence: or
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25
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Profile of Dr. Qian Qian. SCIENCE CHINA. LIFE SCIENCES 2022; 65:2145-2147. [PMID: 35997918 DOI: 10.1007/s11427-022-2162-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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26
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Wang P, Liu J, Lyu Y, Huang Z, Zhang X, Sun B, Li P, Jing X, Li H, Zhang C. A Review of Vector-Borne Rice Viruses. Viruses 2022; 14:v14102258. [PMID: 36298813 PMCID: PMC9609659 DOI: 10.3390/v14102258] [Citation(s) in RCA: 10] [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: 09/15/2022] [Revised: 10/04/2022] [Accepted: 10/09/2022] [Indexed: 11/05/2022] Open
Abstract
Rice (Oryza sativa L.) is one of the major staple foods for global consumption. A major roadblock to global rice production is persistent loss of crops caused by plant diseases, including rice blast, sheath blight, bacterial blight, and particularly various vector-borne rice viral diseases. Since the late 19th century, 19 species of rice viruses have been recorded in rice-producing areas worldwide and cause varying degrees of damage on the rice production. Among them, southern rice black-streaked dwarf virus (SRBSDV) and rice black-streaked dwarf virus (RBSDV) in Asia, rice yellow mottle virus (RYMV) in Africa, and rice stripe necrosis virus (RSNV) in America currently pose serious threats to rice yields. This review systematizes the emergence and damage of rice viral diseases, the symptomatology and transmission biology of rice viruses, the arm races between viruses and rice plants as well as their insect vectors, and the strategies for the prevention and control of rice viral diseases.
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Affiliation(s)
- Pengyue Wang
- Department of Plant Pathology, College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China
| | - Jianjian Liu
- Department of Plant Pathology, College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China
- Hubei Engineering Research Center for Pest Forewarning and Management, College of Agronomy, Yangtze University, Jingzhou 434025, China
| | - Yajing Lyu
- Department of Plant Pathology, College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China
- Co-Construction State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
| | - Ziting Huang
- Department of Plant Pathology, College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China
| | - Xiaoli Zhang
- Department of Plant Pathology, College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China
| | - Bingjian Sun
- Department of Plant Pathology, College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China
| | - Pengbai Li
- Department of Plant Pathology, College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China
| | - Xinxin Jing
- Department of Plant Pathology, College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China
| | - Honglian Li
- Department of Plant Pathology, College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China
| | - Chao Zhang
- Department of Plant Pathology, College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China
- Correspondence:
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27
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Design and test of smashing and scattering device of double-channel feeding ratoon rice harvester. Sci Rep 2022; 12:15943. [PMID: 36153337 PMCID: PMC9509330 DOI: 10.1038/s41598-022-18938-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 08/22/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractSince it is requested that the smashed straw should not be scattered onto the stubble in the first season harvest, a smashing and scattering device matched with the first season harvester of ratoon rice was designed in this paper to smash and scatter the straw into the rolling area. The main structural parameters affecting the straw scattering performance were determined by theoretical analysis of the deflecting performance of the straw deflector. EDEM software was used to simulate and analyze the straw scattering situation under the action of the deflector. Taking the qualified rate of straw scattering as the performance index, the optimal parameter combination of the straw deflector was determined by L27 (313) orthogonal test, and the operating performance of the device was verified by bench test and field comparison test. The test results show that: The optimal parameter combination was 45° between the straw deflector and the vertical direction, 200 mm height difference between straw deflector and outlet, 0° inclination angle of inner deflector and 35° inclination angle of outer deflector. The qualified rate of straw scattering was 72.2% in the corresponding simulation test, 93.6% in the bench test and 95.2% in the field test, which could meet the demand of first season harvest of ratoon rice.
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28
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Ge L, Guo H, Li X, Tang M, Guo C, Bao H, Huang L, Yi Y, Cui Y, Chen L. OsSIDP301, a Member of the DUF1644 Family, Negatively Regulates Salt Stress and Grain Size in Rice. FRONTIERS IN PLANT SCIENCE 2022; 13:863233. [PMID: 35968081 PMCID: PMC9366248 DOI: 10.3389/fpls.2022.863233] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 06/13/2022] [Indexed: 06/15/2023]
Abstract
As a major environmental factor, salt stress substantially retards growth and reduces the productivity of rice (Oryza sativa). Members of the DUF1644 family, "the domains of unknown function 1644 motif" are predicted to play an essential regulatory role in response to abiotic stress. However, the specific molecular mechanisms of most members of this family remain elusive. Here, we report that the OsSIDP301 (stress-induced DUF1644 protein) was induced by salt stress and abscisic acid (ABA). We found that overexpression of OsSIDP301 (OE) in plants conferred salt hypersensitivity and reduced grain size, whereas plants with OsSIDP301 RNA interference (RNAi) exhibited salt tolerance and increased grain size in rice. OsSIDP301 determines salt stress tolerance by modulating genes involved in the salt-response and ABA signaling pathways. Further studies suggest that OsSIDP301 regulates grain size by influencing cell expansion in spikelet hulls. Moreover, OsSIDP301 interacts with OsBUL1 COMPLEX1 (OsBC1), which positively regulates grain size in rice. Our findings reveal that OsSIDP301 functions as a negative regulator of salt stress and grain size, and repressing its expression represents a promising strategy for improving salt stress tolerance and yield in rice.
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Affiliation(s)
- Li Ge
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, China
| | - Hongming Guo
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, China
| | - Xiu Li
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, China
| | - Ming Tang
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Chiming Guo
- Fujian Key Laboratory of Subtropical Plant Physiology and Biochemistry, Fujian Institute of Subtropical Botany, Xiamen, China
| | - Han Bao
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, China
| | - Linjuan Huang
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, China
| | - Yin Yi
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Yuchao Cui
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, China
| | - Liang Chen
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, China
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29
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Malik P, Huang M, Neelam K, Bhatia D, Kaur R, Yadav B, Singh J, Sneller C, Singh K. Genotyping-by-Sequencing Based Investigation of Population Structure and Genome Wide Association Studies for Seven Agronomically Important Traits in a Set of 346 Oryza rufipogon Accessions. RICE (NEW YORK, N.Y.) 2022; 15:37. [PMID: 35819660 PMCID: PMC9276952 DOI: 10.1186/s12284-022-00582-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
Being one of the most important staple dietary constituents globally, genetic enhancement of cultivated rice for yield, agronomically important traits is of substantial importance. Even though the climatic factors and crop management practices impact complex traits like yield immensely, the contribution of variation by underlying genetic factors surpasses them all. Previous studies have highlighted the importance of utilizing exotic germplasm, landraces in enhancing the diversity of gene pool, leading to better selections and thus superior cultivars. Thus, to fully exploit the potential of progenitor of Asian cultivated rice for productivity related traits, genome wide association study (GWAS) for seven agronomically important traits was conducted on a panel of 346 O. rufipogon accessions using a set of 15,083 high-quality single nucleotide polymorphic markers. The phenotypic data analysis indicated large continuous variation for all the traits under study, with a significant negative correlation observed between grain parameters and agronomic parameters like plant height, culm thickness. The presence of 74.28% admixtures in the panel as revealed by investigating population structure indicated the panel to be very poorly genetically differentiated, with rapid LD decay. The genome-wide association analyses revealed a total of 47 strong MTAs with 19 SNPs located in/close to previously reported QTL/genic regions providing a positive analytic proof for our studies. The allelic differences of significant MTAs were found to be statistically significant at 34 genomic regions. A total of 51 O. rufipogon accessions harboured combination of superior alleles and thus serve as potential candidates for accelerating rice breeding programs. The present study identified 27 novel SNPs to be significantly associated with different traits. Allelic differences between cultivated and wild rice at significant MTAs determined superior alleles to be absent at 12 positions implying substantial scope of improvement by their targeted introgression into cultivars. Introgression of novel significant genomic regions into breeder's pool would broaden the genetic base of cultivated rice, thus making the crop more resilient.
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Affiliation(s)
- Palvi Malik
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
- Department of Horticulture and Crop Science, OARDC, The Ohio State University, Wooster, USA
| | - Mao Huang
- Department of Horticulture and Crop Science, OARDC, The Ohio State University, Wooster, USA
| | - Kumari Neelam
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India.
| | - Dharminder Bhatia
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Ramanjeet Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Bharat Yadav
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
- Crop Pathology and Genetics Lab, University of British Columbia, Vancouver, Canada
| | - Jasdeep Singh
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Clay Sneller
- Department of Horticulture and Crop Science, OARDC, The Ohio State University, Wooster, USA
| | - Kuldeep Singh
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana, India
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30
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Bin Rahman ANMR, Zhang J. Trends in rice research: 2030 and beyond. Food Energy Secur 2022. [DOI: 10.1002/fes3.390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Affiliation(s)
| | - Jianhua Zhang
- Department of Biology Hong Kong Baptist University Hong Kong China
- State Key Laboratory of Agrobiotechnology The Chinese University of Hong Kong Hong Kong China
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31
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Zhang G, Huang Q, Song K, Zhu X, Ma J, Zhang Y, Yan X, Xu H. Gaseous emissions and grain-heavy metal contents in rice paddies: A three-year partial organic substitution experiment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 826:154106. [PMID: 35219683 DOI: 10.1016/j.scitotenv.2022.154106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 02/19/2022] [Accepted: 02/19/2022] [Indexed: 06/14/2023]
Abstract
To reduce the utilization of chemical fertilisers, which cause substantial nitrogen loss and widespread nonpoint source pollution, the application of organic manure has become an increasingly popular alternative in rice agriculture. It plays key roles in improving soil quality and maintaining rice yields, but its integrated impacts on trace gas emissions and heavy metal contents in rice grains remain poorly documented. We conducted a three-year field experiment with two application ratios (25% and 50%) of sewage sludge compost (S) and pig manure compost (P) during the rice season in eastern China. The emissions of methane (CH4), nitrous oxide (N2O), ammonia (NH3), and the grain contents of nickel (Ni), copper (Cu), zinc (Zn), cadmium (Cd), and lead (Pb) were measured. Compared with urea, partial organic application, particularly 50%S and 50%P, led to a considerable increase in CH4 emission (52%-71%), global warming potential (GWP, 50%-69%), and greenhouse gas intensity (46%-68%). However, it substantially decreased N2O emission and NH3 volatilisation, thus lowering the cumulative nitrogen loss by 32%-62%. Moreover, the average concentrations of Ni, Cu, Zn, Cd, and Pb in rice grains were 100-151 μg kg-1, 2.31-2.78 mg kg-1, 20.3-24.3 mg kg-1, 44.3-123 μg kg-1, and 8.69-15.2 μg kg-1, respectively, which were significantly lower than food standard limits for rice in China. Both 25%S and 50%S achieved the highest grain yields while significantly decreasing grain Ni and Cd contents. Health risk assessment showed that the target hazard quotient of all the metals was <1 (0.006-0.73), and the hazard index that represents additive effects of pollutants was higher than the threshold, except for 25%S and 50%S. The results suggested 25%S as a potential fertilisation practice in rice fields that not only maintains low GWP and high yields but also seldom poses grain pollution or health risks.
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Affiliation(s)
- Guangbin Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Qiong Huang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kaifu Song
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoli Zhu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Ma
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Yao Zhang
- Natural Resource Ecology Laboratory, Colorado State University, Fort Collins, CO, USA
| | - Xiaoyuan Yan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Hua Xu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China.
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32
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Wang M, Zhu X, Peng G, Liu M, Zhang S, Chen M, Liao S, Wei X, Xu P, Tan X, Li F, Li Z, Deng L, Luo Z, Zhu L, Zhao S, Jiang D, Li J, Liu Z, Xie X, Wang S, Wu A, Zhuang C, Zhou H. Methylesterification of cell-wall pectin controls the diurnal flower-opening times in rice. MOLECULAR PLANT 2022; 15:956-972. [PMID: 35418344 DOI: 10.1016/j.molp.2022.04.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 03/28/2022] [Accepted: 04/11/2022] [Indexed: 06/14/2023]
Abstract
Flowers are the core reproductive organ of plants, and flowering is essential for cross-pollination. Diurnal flower-opening time is thus a key trait influencing reproductive isolation, hybrid breeding, and thermostability in plants. However, the molecular mechanisms controlling this trait remain unknown. Here, we report that rice Diurnal Flower Opening Time 1 (DFOT1) modulates pectin methylesterase (PME) activity to regulate pectin methylesterification levels of the lodicule cell walls, which affect lodicule swelling to control diurnal flower-opening time. DFOT1 is specifically expressed in the lodicules, and its expression gradually increases with the approach to flowering but decreases with flowering. Importantly, a knockout of DFOT1 showed earlier diurnal flower opening. We demonstrate that DFOT1 interacts directly with multiple PMEs to promote their activity. Knockout of PME40 also resulted in early diurnal flower opening, whereas overexpression of PME42 delayed diurnal flower opening. Lower PME activity was observed to be associated with higher levels of pectin methylesterification and the softening of cell walls in lodicules, which contribute to the absorption of water by lodicules and cause them to swell, thus promoting early diurnal flower opening. Higher PME activity had the opposite effect. Collectively, our work uncovers a molecular mechanism underlying the regulation of diurnal flower-opening time in rice, which would help reduce the costs of hybrid breeding and improve the heat tolerance of flowering plants by avoiding higher temperatures at anthesis.
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Affiliation(s)
- Mumei Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Xiaopei Zhu
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Guoqing Peng
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Minglong Liu
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Shuqing Zhang
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Minghao Chen
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Shitang Liao
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Xiaoying Wei
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Peng Xu
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Xiyu Tan
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Fangping Li
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Zhichuan Li
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Li Deng
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Ziliang Luo
- Agronomy Department, University of Florida, Gainesville, FL 32610, USA
| | - Liya Zhu
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Shuai Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Dagang Jiang
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Jing Li
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Zhenlan Liu
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Xianrong Xie
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Shaokui Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Aimin Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
| | - Chuxiong Zhuang
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Hai Zhou
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China.
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33
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Ouyang X, Zhong X, Chang S, Qian Q, Zhang Y, Zhu X. Partially functional NARROW LEAF1 balances leaf photosynthesis and plant architecture for greater rice yield. PLANT PHYSIOLOGY 2022; 189:772-789. [PMID: 35377451 PMCID: PMC9157069 DOI: 10.1093/plphys/kiac135] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 02/20/2022] [Indexed: 06/14/2023]
Abstract
NARROW LEAF1 (NAL1) is an elite gene in rice (Oryza sativa), given its close connection to leaf photosynthesis, hybrid vigor, and yield-related agronomic traits; however, the underlying mechanism by which this gene affects these traits remains elusive. In this study, we systematically measured leaf photosynthetic parameters, leaf anatomical parameters, architectural parameters, and agronomic traits in indica cultivar 9311, in 9311 with the native NAL1 replaced by the Nipponbare NAL1 (9311-NIL), and in 9311 with the NAL1 fully mutated (9311-nal1). Leaf length, width, and spikelet number gradually increased from lowest to highest in 9311-nal1, 9311, and 9311-NIL. In contrast, the leaf photosynthetic rate on a leaf area basis, leaf thickness, and panicle number gradually decreased from highest to lowest in 9311-nal1, 9311, and 9311-NIL. RNA-seq analysis showed that NAL1 negatively regulates the expression of photosynthesis-related genes; NAL1 also influenced expression of many genes related to phytohormone signaling, as also shown by different leaf contents of 3-Indoleacetic acid, jasmonic acid, Gibberellin A3, and isopentenyladenine among these genotypes. Furthermore, field experiments with different planting densities showed that 9311 had a larger biomass and yield advantage under low planting density compared to either 9311-NIL or 9311-nall. This study shows both direct and indirect effects of NAL1 on leaf photosynthesis; furthermore, we show that a partially functional NAL1 allele helps maintain a balanced leaf photosynthesis and plant architecture for increased biomass and grain yield in the field.
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Affiliation(s)
- Xiang Ouyang
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center (HHRRC), Changsha 410125, China
- National Key Laboratory of Plant Molecular Genetics, CAS Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Xiaoyu Zhong
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center (HHRRC), Changsha 410125, China
- College of Bioscience and Biotechnology, Hunan Agriculture University, Changsha 410128, China
| | - Shuoqi Chang
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center (HHRRC), Changsha 410125, China
| | - Qian Qian
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Yuzhu Zhang
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center (HHRRC), Changsha 410125, China
| | - Xinguang Zhu
- National Key Laboratory of Plant Molecular Genetics, CAS Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
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Wang D, Wang J, Sun W, Qiu X, Yuan Z, Yu S. Verifying the Breeding Value of A Rare Haplotype of Chalk7, GS3, and Chalk5 to Improve Grain Appearance Quality in Rice. PLANTS (BASEL, SWITZERLAND) 2022; 11:1470. [PMID: 35684243 PMCID: PMC9182975 DOI: 10.3390/plants11111470] [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: 04/29/2022] [Revised: 05/28/2022] [Accepted: 05/28/2022] [Indexed: 06/15/2023]
Abstract
Grain quality is a key determinant of commercial value in rice. Efficiently improving grain quality, without compromising grain yield, is a challenge in rice breeding programs. Here we report on the identification and application of a grain quality gene, Chalk7, which causes a slender shape and decreases grain chalkiness in rice. Three allele-specific markers for Chalk7, and two other grain genes (GS3 and Chalk5) were developed, and used to stack the desirable alleles at these loci. The effects of individual or combined alleles at the loci were evaluated using a set of near-isogenic lines, each containing one to three favorable alleles in a common background of an elite variety. We found that the favorable allele combination of the three loci, which rarely occurs in natural rice germplasm, greatly reduces chalky grains without negatively impacting on grain yield. The data for newly developed allele-specific markers and pre-breeding lines will facilitate the improvement of grain appearance quality in rice.
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Affiliation(s)
- Dianwen Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (D.W.); (W.S.); (Z.Y.)
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China;
| | - Jilin Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China;
- Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Wenqiang Sun
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (D.W.); (W.S.); (Z.Y.)
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xianjin Qiu
- College of Agriculture, Yangtze University, Jingzhou 434025, China;
| | - Zhiyang Yuan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (D.W.); (W.S.); (Z.Y.)
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China;
| | - Sibin Yu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (D.W.); (W.S.); (Z.Y.)
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China;
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Liu P, He L, Mei L, Zhai W, Chen X, Ma B. Rapid and Directional Improvement of Elite Rice Variety via Combination of Genomics and Multiplex Genome Editing. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:6156-6167. [PMID: 35575308 DOI: 10.1021/acs.jafc.1c08028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
High yield and superior quality are the main goals pursued by breeders for crop improvement. However, both of them are complex agronomic traits controlled by multiple genes, so the simultaneous improvement of these traits via sexual recombination is time-consuming and direction-uncontrolled. In this study, to solve this dilemma, we introduced the comparative genomic analysis based multiplex genome editing system (CG-MGE), a method for rapid and directional improvement of multiple traits. Application of this method, association analysis between genotypes and phenotypes was carried out to mine excellent alleles; subsequently, the rare excellent alleles of Gn1a, GW2, TGW3, and Chalk5 were simultaneously created by multiplex genome editing and successfully improved the plant architecture, grain yield, and quality of a widely cultivated elite rice variety. Overall, this study provides a method for rapid and directional improvement of crops, and the application of the CG-MGE will be helpful to accelerate rational design breeding.
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Affiliation(s)
- Pengcheng Liu
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Lumei He
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Le Mei
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wenxue Zhai
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xifeng Chen
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Bojun Ma
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
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Identification of C-T novel polymorphism in 3rd exon of OsSPL14 gene governing seed sequence in rice. PLoS One 2022; 17:e0264478. [PMID: 35286332 PMCID: PMC8920263 DOI: 10.1371/journal.pone.0264478] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 02/10/2022] [Indexed: 12/13/2022] Open
Abstract
Recently food shortage has become the major flagging scenario around the globe. To resolve this challenge, there is dire need to significantly increase crop productivity per unit area. In the present study, 24 genotypes of rice were grown in pots to assess their tillering number, number of primary and secondary branches per panicle, number of grains per panicle, number of grains per plant, and grain yield, respectively. In addition, the potential function of miR156 was analyzed, regulating seed sequence in rice. Furthermore, OsSPL14 gene for miR156 was sequenced to identify additional mutations within studied region. The results demonstrated Bas-370 and L-77 showed highest and lowest tillers, respectively. Bas-370, Rachna basmati, Bas-2000, and Kashmir Basmati showed high panicle branches whereas, L-77, L-46, Dilrosh, L-48, and L-20 displayed lowest panicle branches. Bas-370 and four other studied accessions contained C allele whereas, L-77 and 18 other investigated accessions had heterozygous (C and T) alleles in their promoter region. C-T allelic mutation was found in 3rd exon of the OsSPL14 gene. The sequence analysis of 12 accessions revealed a novel mutation (C-T) present ~2bp upstream and substitution of C-A allele. However, no significant correlation for novel mutation was found for tillering and panicle branches in studied rice accessions. Taken together present results suggested novel insight into the binding of miR156 to detected mutation found in 3rd exon of the OsSPL14 gene. Nevertheless, L-77, L-46, Dilrosh, L-48, and L-20 could be used as potential breeding resource for improving panicle architecture contributing yield improvement of rice crop.
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Liu M, Fan F, He S, Guo Y, Chen G, Li N, Li N, Yuan H, Si F, Yang F, Li S. Creation of Elite Rice with High-Yield, Superior-Quality and High Resistance to Brown Planthopper Based on Molecular Design. RICE (NEW YORK, N.Y.) 2022; 15:17. [PMID: 35290527 PMCID: PMC8924342 DOI: 10.1186/s12284-022-00563-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 03/05/2022] [Indexed: 06/14/2023]
Abstract
Breeding rice (Oryza sativa L.) with high yield, superior quality, desired grain shape and high resistance is the goal of breeding to meet the needs of current consumers. It is usually hard to combine multiple complex traits based on traditional breeding methods because they are frequently antagonistic to each other. However, molecular design breeding, as a novel breeding method, is an optional alternative to this challenge. To demonstrate molecular design breeding, 15 favorable genes from five parent lines were pyramided together to develop elite rice with high-yield, superior-quality, desired grain shape and high resistance to brown planthopper (BPH). The parental lines were 9311, the recurrent parent, carrying APO1, Ghd7, Ghd8 and Gn1a for high yield, GS3 and qSW5 for grain shape, and Wx and ALK for eating and cooking quality; 1880 with Gn8.1 for large panicles; Luo-Yu-Xiang carrying GW7 for grain shape and SBE3, SSIV2 and SSIII for eating and cooking quality; Luoyang6 with Bph6 and Luoyang9 with Bph9 for BPH resistance. After careful screening for the 15 targeted genes, desired phenotype and maximum genetic background from 9311, three molecular design lines with desired phenotypes, named as MD1 (Molecular design 1), MD2 and MD3 were developed. MD3 carried all 15 targeted genes, and MD1 and MD2 had 14 of the 15 targeted genes. Only SBE3 was not introgressed into MD1 and MD2 but this had minimal impact on the gel consistency and alkali spreading value. These newly bred lines exhibited higher yield potential, better grain quality with slender grains, low amylose content, high gel consistency and alkali spreading value, and higher BPH resistance compared to the parent 9311. In this study, we successfully created three novel rice lines with high yield, superior quality and improved BPH resistance by rational molecular design. Our results demonstrate molecular design is a powerful strategy to improve multiple complex traits and will provide a reference for the future commercial rice improvement.
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Affiliation(s)
- Manman Liu
- State Key Laboratory of Hybrid Rice, Hongshan Laboratory of Hubei Province, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan, 430072, China
| | - Fengfeng Fan
- State Key Laboratory of Hybrid Rice, Hongshan Laboratory of Hubei Province, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan, 430072, China
| | - Shihao He
- State Key Laboratory of Hybrid Rice, Hongshan Laboratory of Hubei Province, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan, 430072, China
| | - Yu Guo
- State Key Laboratory of Hybrid Rice, Hongshan Laboratory of Hubei Province, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan, 430072, China
| | - Gaili Chen
- State Key Laboratory of Hybrid Rice, Hongshan Laboratory of Hubei Province, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan, 430072, China
| | - Nannan Li
- State Key Laboratory of Hybrid Rice, Hongshan Laboratory of Hubei Province, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan, 430072, China
| | - Nengwu Li
- State Key Laboratory of Hybrid Rice, Hongshan Laboratory of Hubei Province, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan, 430072, China
| | - Huanran Yuan
- State Key Laboratory of Hybrid Rice, Hongshan Laboratory of Hubei Province, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan, 430072, China
| | - Fengfeng Si
- State Key Laboratory of Hybrid Rice, Hongshan Laboratory of Hubei Province, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan, 430072, China
| | - Fang Yang
- State Key Laboratory of Hybrid Rice, Hongshan Laboratory of Hubei Province, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan, 430072, China
| | - Shaoqing Li
- State Key Laboratory of Hybrid Rice, Hongshan Laboratory of Hubei Province, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan, 430072, China.
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38
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Breeding future crops to feed the world through de novo domestication. Nat Commun 2022; 13:1171. [PMID: 35246512 PMCID: PMC8897434 DOI: 10.1038/s41467-022-28732-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 02/09/2022] [Indexed: 01/18/2023] Open
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Ge J, Wang J, Pang H, Li F, Lou D, Fan W, Liu Z, Li J, Li D, Nong B, Zhang Z, Wang Y, Huang J, Xing M, Nie Y, Xiao X, Zhang F, Wang W, Xu J, Kim SR, Kohli A, Ye G, Qiao W, Yang Q, Zheng X. Genome-wide selection and introgression of Chinese rice varieties during breeding. J Genet Genomics 2022; 49:492-501. [DOI: 10.1016/j.jgg.2022.02.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 02/11/2022] [Accepted: 02/16/2022] [Indexed: 11/15/2022]
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40
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Combined Role of Fe Nanoparticles (Fe NPs) and Staphylococcus aureus L. in the Alleviation of Chromium Stress in Rice Plants. Life (Basel) 2022; 12:life12030338. [PMID: 35330089 PMCID: PMC8950458 DOI: 10.3390/life12030338] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 02/18/2022] [Accepted: 02/18/2022] [Indexed: 12/21/2022] Open
Abstract
Chromium (Cr) is a toxic heavy metal whose high concentration in soil badly affects plant growth, photosynthesis, and overall yield. Metal-derived nano-particles and metal-resistant bacteria can strengthen the plant defense system against different abiotic stresses; however, little is known about the use of nanoparticles in conjunction with bacteria. This study examined the combined effect of Fe nanoparticles (Fe NPs) and a chromium-resistant bacterium Staphylococcus aureus, on rice plants grown on chromium saturated medium. Chromium stress reduced rice growth, biomass, and chlorophyll contents by causing oxidative damage leading to overproduction of electrolyte leakage, hydrogen peroxide, and malondialdehyde. Fe NPs significantly improved plant growth, biomass, yield, and photosynthetic activity by enhancing the chlorophyll contents and alleviating oxidative damage. Application of Fe NPs also reduced the uptake and accumulation of Cr in the plants by increasing the bioavailability of micronutrients to the plant. The Fe NPs decreased oxidative damage and enhanced the enzymatic and non-enzymatic activity in the plant to withstand Cr stress compared to the plants without Fe NPs treatments. The inoculation of rice plants with the chromium-resistant bacteria S. aureus further enhanced the positive impact of Fe NPs by transforming the toxic form of chromium (Cr6+) into a less toxic form of chromium (Cr3+). The bacterial inoculation reduced Cr uptake by plants through adsorption of Cr ions, resulting in decreased chromium ion bioavailability. At chromium level 100 mg/kg, the foliar application of Fe NPs from 0 to 20 mg/L increased the total chlorophyll contents from 2.8 to 3.9. The application of S. aureus further enhanced the chlorophyll contents from 4.4 to 5.4, respectively. The current study suggested that combining Fe NPs and S. aureus could be a viable strategy for reducing Cr toxicity and accumulation in rice plants and most likely other plants.
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41
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Liu D, Zhao H, Xiao Y, Zhang G, Cao S, Yin W, Qian Y, Yin Y, Zhang J, Chen S, Chu C, Tong H. A cryptic inhibitor of cytokinin phosphorelay controls rice grain size. MOLECULAR PLANT 2022; 15:293-307. [PMID: 34562665 DOI: 10.1016/j.molp.2021.09.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 08/21/2021] [Accepted: 09/19/2021] [Indexed: 06/13/2023]
Abstract
Plant hormone cytokinin signals through histidine-aspartic acid (H-D) phosphorelay to regulate plant growth and development. While it is well known that the phosphorelay involves histidine kinases, histidine phosphotransfer proteins (HPs), and response regulators (RRs), how this process is regulated by external components remains unknown. Here we demonstrate that protein phosphatase with kelch-like domains (PPKL1), known as a signaling component of steroid hormone brassinosteroid, is actually a cryptic inhibitor of cytokinin phosphorelay in rice (Oryza sativa). Mutation at a specific amino acid D364 of PPKL1 activates cytokinin response and thus enlarges grain size in a semi-dominant mutant named s48. Overexpression of PPKL1 containing D364, either with the deletion of the phosphatase domain or not, rescues the s48 mutant phenotype. PPKL1 interacts with OsAHP2, one of authentic HPs, and D364 resides in a region resembling the receiver domain of RRs. Accordingly, PPKL1 can utilize D364 to suppress OsAHP2-to-RR phosphorelay, whereas mutation of D364 abolishes the effect. This function of PPKL1 is independent of the phosphatase domain that is required for brassinosteroid signaling. Importantly, editing of the D364-residential region produces a diversity of semi-dominant mutations associated with variously increased grain sizes. Further screening of the edited plants enables the identification of two genotypes that confer significantly improved grain yield. Collectively, our study uncovers a noncanonical cytokinin signaling suppressor and provides a robust tool for seed rational design.
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Affiliation(s)
- Dapu Liu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, the Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - He Zhao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, the Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Yunhua Xiao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, the Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Guoxia Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, the Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Shouyun Cao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, the Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Wenchao Yin
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yangwen Qian
- Biogle Genome Editing Center, Changzhou, Jiangsu Province 213125, China
| | - Yanhai Yin
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
| | - Jinsong Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, the Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Shouyi Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, the Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Chengcai Chu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, the Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China.
| | - Hongning Tong
- 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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42
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Wu L, Chang Y, Wang L, Wang S, Wu J. The aquaporin gene PvXIP1;2 conferring drought resistance identified by GWAS at seedling stage in common bean. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:485-500. [PMID: 34698878 DOI: 10.1007/s00122-021-03978-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 10/16/2021] [Indexed: 06/13/2023]
Abstract
A whole-genome resequencing-derived SNP dataset used for genome-wide association analysis revealed 12 loci significantly associated with drought stress based on survival rate after drought stress at seedling stage. We further confirmed the drought-related function of an aquaporin gene (PvXIP1;2) located at Locus_10. A variety of adverse conditions, including drought stress, severely affect common bean production. Molecular breeding for drought resistance has been proposed as an effective and practical way to improve the drought resistance of common bean. A genome-wide association analysis was conducted to identify drought-related loci based on survival rates at the seedling stage using a natural population consisting of 400 common bean accessions and 3,832,340 SNPs. The coefficient of variation ranged from 40.90 to 56.22% for survival rates in three independent experiments. A total of 12 associated loci containing 89 significant SNPs were identified for survival rates at the seedling stage. Four loci overlapped in the region of the QTLs reported to be associated with drought resistance. According to the expression profiles, gene annotations and references of the functions of homologous genes in Arabidopsis, 39 genes were considered potential candidate genes selected from 199 genes annotated within all associated loci. A stable locus (Locus_10) was identified on chromosome 11, which contained LEA, aquaporin, and proline-rich protein genes. We further confirmed the drought-related function of an aquaporin (PvXIP1;2) located at Locus_10 by expression pattern analysis, phenotypic analysis of PvXIP1;2-overexpressing Arabidopsis and Agrobacterium rhizogenes-mediated hairy root transformation systems, indicating that the association results can facilitate the efficient identification of genes related to drought resistance. These loci and their candidate genes provide a foundation for crop improvement via breeding for drought resistance in common bean.
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Affiliation(s)
- Lei Wu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yujie Chang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Lanfen Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Shumin Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jing Wu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Anwar K, Joshi R, Morales A, Das G, Yin X, Anten NPR, Raghuvanshi S, Bahuguna RN, Singh MP, Singh RK, Zanten M, Sasidharan R, Singla‐Pareek SL, Pareek A. Genetic diversity reveals synergistic interaction between yield components could improve the sink size and yield in rice. Food Energy Secur 2022. [DOI: 10.1002/fes3.334] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- Khalid Anwar
- Stress Physiology and Molecular Biology Laboratory School of Life Sciences Jawaharlal Nehru University New Delhi India
| | - Rohit Joshi
- Stress Physiology and Molecular Biology Laboratory School of Life Sciences Jawaharlal Nehru University New Delhi India
- Division of Biotechnology CSIR‐Institute of Himalayan Bioresource Technology Palampur India
| | - Alejandro Morales
- Centre for Crop Systems Analysis Plant Sciences Group Wageningen University & Research Wageningen The Netherlands
- Molecular Plant Physiology Institute of Environmental Biology Utrecht University Utrecht The Netherlands
- Plant Ecophysiology Institute of Environmental Biology Utrecht University Utrecht The Netherlands
| | - Gourab Das
- Stress Physiology and Molecular Biology Laboratory School of Life Sciences Jawaharlal Nehru University New Delhi India
| | - Xinyou Yin
- Centre for Crop Systems Analysis Plant Sciences Group Wageningen University & Research Wageningen The Netherlands
| | - Niels P. R. Anten
- Centre for Crop Systems Analysis Plant Sciences Group Wageningen University & Research Wageningen The Netherlands
| | - Saurabh Raghuvanshi
- Department of Plant Molecular Biology University of Delhi South Campus New Delhi India
| | - Rajeev N. Bahuguna
- Stress Physiology and Molecular Biology Laboratory School of Life Sciences Jawaharlal Nehru University New Delhi India
- Center for Advance Studies on Climate Change Dr. Rajendra Prasad Central Agricultural University, Pusa Samastipur India
| | - Madan Pal Singh
- Division of Plant Physiology Indian Agricultural Research Institute PUSA New Delhi India
| | - Rakesh K. Singh
- Crop Diversification and Genetics International Center for Biosaline Agriculture Academic City Dubai United Arab Emirates
| | - Martijn Zanten
- Molecular Plant Physiology Institute of Environmental Biology Utrecht University Utrecht The Netherlands
| | - Rashmi Sasidharan
- Plant Ecophysiology Institute of Environmental Biology Utrecht University Utrecht The Netherlands
| | - Sneh L. Singla‐Pareek
- Plant Stress Biology International Centre for Genetic Engineering and Biotechnology New Delhi India
| | - Ashwani Pareek
- Stress Physiology and Molecular Biology Laboratory School of Life Sciences Jawaharlal Nehru University New Delhi India
- National Agri‐Food Biotechnology Institute Mohali India
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44
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Chen DG, Zhou XQ, Chen K, Chen PL, Guo J, Liu CG, Chen YD. Fine-mapping and candidate gene analysis of a major locus controlling leaf thickness in rice ( Oryza sativa L.). MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:6. [PMID: 35103045 PMCID: PMC8792131 DOI: 10.1007/s11032-022-01275-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 01/13/2022] [Indexed: 05/16/2023]
Abstract
UNLABELLED Leaf thickness is an important trait in rice (Oryza sativa L.). It affects both photosynthesis and sink-resource efficiency. However, compared to leaf length and length width, reports seldom focused on leaf thickness due to the complicated measurement and minor difference. To identify the quantitative trait loci (QTL) and explore the genetic mechanism regulating the natural variation of leaf thickness, we crossed a high leaf thickness variety Aixiuzhan (AXZ) to a thin leaf thickness variety Yangdao No.6 (YD 6) and evaluated 585 F2 individuals. We further use bulked sergeant analysis with whole-genome resequencing (BSA-seq) to identify five genomic regions, including chromosomes 1, 6, 9, 10, and 12. These regions represented significant allele frequency differentiation between thick and thin leaf thickness among the mixed pool offspring. Moreover, we conducted a linkage mapping using 276 individuals derived from the F2 population. We fine-mapped and confirmed that chromosome 9 contributed the primary explanation of phenotypic variance. We fine-mapped the candidate regions and confirmed that the chromosome 9 region contributed to flag leaf thickness in rice. We observed the virtual cellular slices and found that the bundle sheath cells in YD 6 flag leaf veins are fewer than AXZ. We analyzed the potential regions on chromosome 9 and narrowed the QTL candidate intervals in the 928-kb region. Candidate genes of this major QTL were listed as potentially controlled leaf thickness. These results provide promising evidence that cloning leaf thickness is associated with yield production in rice. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s11032-022-01275-y.
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Affiliation(s)
- Da-gang Chen
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 People’s Republic of China
| | - Xin-qiao Zhou
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 People’s Republic of China
| | - Ke Chen
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 People’s Republic of China
| | - Ping-li Chen
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 People’s Republic of China
| | - Jie Guo
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 People’s Republic of China
| | - Chuan-guang Liu
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 People’s Republic of China
| | - You-ding Chen
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 People’s Republic of China
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Meng T, Zhang X, Chen X, Ge J, Zhou G, Wei H, Dai Q. Trends in grain quality and responses to nitrogen application of
japonica
inbred rice released after the 1980s in east China. Cereal Chem 2021. [DOI: 10.1002/cche.10512] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Tianyao Meng
- Institutes of Agricultural Science and Technology Development/Joint International Research Laboratory of Agriculture and Agri‐Product Safety The Ministry of Education of China Yangzhou University Yangzhou China
| | - Xubin Zhang
- Jiangsu Key Laboratory of Crop Cultivation and Physiology/Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Co‐Innovation Center for Modern Production Technology of Grain Crops/Research Institute of Rice Industrial Engineering Technology Yangzhou University Yangzhou China
| | - Xi Chen
- Institutes of Agricultural Science and Technology Development/Joint International Research Laboratory of Agriculture and Agri‐Product Safety The Ministry of Education of China Yangzhou University Yangzhou China
| | - Jialin Ge
- Jiangsu Key Laboratory of Crop Cultivation and Physiology/Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Co‐Innovation Center for Modern Production Technology of Grain Crops/Research Institute of Rice Industrial Engineering Technology Yangzhou University Yangzhou China
| | - Guisheng Zhou
- Institutes of Agricultural Science and Technology Development/Joint International Research Laboratory of Agriculture and Agri‐Product Safety The Ministry of Education of China Yangzhou University Yangzhou China
| | - Huanhe Wei
- Jiangsu Key Laboratory of Crop Cultivation and Physiology/Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Co‐Innovation Center for Modern Production Technology of Grain Crops/Research Institute of Rice Industrial Engineering Technology Yangzhou University Yangzhou China
| | - Qigen Dai
- Institutes of Agricultural Science and Technology Development/Joint International Research Laboratory of Agriculture and Agri‐Product Safety The Ministry of Education of China Yangzhou University Yangzhou China
- Jiangsu Key Laboratory of Crop Cultivation and Physiology/Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Co‐Innovation Center for Modern Production Technology of Grain Crops/Research Institute of Rice Industrial Engineering Technology Yangzhou University Yangzhou China
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Rice functional genomics: decades' efforts and roads ahead. SCIENCE CHINA. LIFE SCIENCES 2021; 65:33-92. [PMID: 34881420 DOI: 10.1007/s11427-021-2024-0] [Citation(s) in RCA: 100] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/01/2021] [Indexed: 12/16/2022]
Abstract
Rice (Oryza sativa L.) is one of the most important crops in the world. Since the completion of rice reference genome sequences, tremendous progress has been achieved in understanding the molecular mechanisms on various rice traits and dissecting the underlying regulatory networks. In this review, we summarize the research progress of rice biology over past decades, including omics, genome-wide association study, phytohormone action, nutrient use, biotic and abiotic responses, photoperiodic flowering, and reproductive development (fertility and sterility). For the roads ahead, cutting-edge technologies such as new genomics methods, high-throughput phenotyping platforms, precise genome-editing tools, environmental microbiome optimization, and synthetic methods will further extend our understanding of unsolved molecular biology questions in rice, and facilitate integrations of the knowledge for agricultural applications.
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47
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Gu Z, Zhu Z, Li Z, Zhan Q, Feng Q, Zhou C, Zhao Q, Zhao Y, Peng X, Dai B, Sun R, Li Y, Lu H, Zhang L, Huang T, Gong J, Lv D, Huang X, Han B. Cytoplasmic and nuclear genome variations of rice hybrids and their parents inform the trajectory and strategy of hybrid rice breeding. MOLECULAR PLANT 2021; 14:2056-2071. [PMID: 34390871 DOI: 10.1016/j.molp.2021.08.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 07/06/2021] [Accepted: 08/06/2021] [Indexed: 06/13/2023]
Abstract
The male sterility (MS) line is a prerequisite for efficient production of hybrid seeds in rice, a self-pollinating species. MS line breeding is pivotal for hybrid rice improvement. Understanding the historical breeding trajectory will help to improve hybrid rice breeding strategies. Maternally inherited cytoplasm is an appropriate tool for phylogenetic reconstruction and pedigree tracing in rice hybrids. In this study, we analyzed the cytoplasmic genomes of 1495 elite hybrid rice varieties and identified five major types of cytoplasm, which correspond to different hybrid production systems. As the cytoplasm donors for hybrids, 461 MS lines were also divided into five major types based on cytoplasmic and nuclear genomic architecture. Specific core accessions cooperating with different fertility-associated genes drove the sequence divergence of MS lines. Dozens to hundreds of convergent and divergent selective sweeps spanning several agronomic trait-associated genes were identified among different types of MS lines. We further analyzed the cross patterns between different types of MS lines and their corresponding restorers. This study systematically analyzed the cytoplasmic genomes of rice hybrids revealed their relationships with nuclear genomes of MS lines, and illustrated the trajectory of hybrid rice breeding and the strategies for breeding different types of MS lines providing new insights for future improvement of hybrid rice.
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Affiliation(s)
- Zhoulin Gu
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhou Zhu
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhen Li
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233, China; College of Life Sciences, Anhui Normal University, Wuhu, Anhui 241000, China
| | - Qilin Zhan
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233, China
| | - Qi Feng
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233, China
| | - Congcong Zhou
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233, China
| | - Qiang Zhao
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233, China
| | - Yan Zhao
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233, China
| | - Xiaojian Peng
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233, China; School of Life Sciences, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Bingxin Dai
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233, China; School of Life Science and Technology, Shanghai Tech University, Shanghai 201210, China
| | - Rongrong Sun
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan Li
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233, China
| | - Hengyun Lu
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233, China
| | - Lei Zhang
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233, China
| | - Tao Huang
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233, China
| | - Junyi Gong
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Danfeng Lv
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233, China
| | - Xuehui Huang
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Bin Han
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233, China.
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Xiong Y, Zhang C, Zhou H, Sun W, Wang P, Wang D, Qiu X, Ali J, Yu S. Identification of Heterotic Loci with Desirable Allelic Interaction to Increase Yield in Rice. RICE (NEW YORK, N.Y.) 2021; 14:97. [PMID: 34826005 PMCID: PMC8626550 DOI: 10.1186/s12284-021-00539-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 11/17/2021] [Indexed: 05/27/2023]
Abstract
Heterosis denotes the superiority of a hybrid plant over its parents. The use of heterosis has contributed significantly to yield improvement in crops. However, the genetic and molecular bases on heterosis are not fully understood. A large number of heterotic loci were identified for 12 yield-related traits in one parental population of chromosome segment substitution lines (CSSLs) and two test populations, which were interconnected by CSSLs derived from two rice genome-sequenced cultivars, Nipponbare and Zhenshan 97. Seventy-five heterotic loci were identified in both homozygous background of Zhenshan 97 and heterogeneous background of an elite hybrid cultivar Shanyou 63. Among the detected loci, at least 11 were colocalized in the same regions encompassing previously reported heterosis-associated genes. Furthermore, a heterotic locus Ghd8NIP for yield advantage was verified using transgenic experiments. Various allelic interaction at Ghd8 exhibited different heterosis levels in hetero-allelic combinations of five near-isogenic lines that contain a particular allele. The significant overdominance effects from some hetero-allelic combinations were found to improve yield heterosis in hybrid cultivars. Our findings support the role of allelic interaction at heterotic loci in the improvement of yield potential, which will be helpful for dissecting the genetic basis of heterosis and provide an optional strategy for the allele replacement in molecular breeding programs in hybrid rice.
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Affiliation(s)
- Yin Xiong
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chaopu Zhang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hongju Zhou
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wenqiang Sun
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Peng Wang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Dianwen Wang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xianjin Qiu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jauhar Ali
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Sibin Yu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
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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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50
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Song T, Das D, Ye NH, Wang GQ, Zhu FY, Chen MX, Yang F, Zhang JH. Comparative transcriptome analysis of coleorhiza development in japonica and Indica rice. BMC PLANT BIOLOGY 2021; 21:514. [PMID: 34736393 PMCID: PMC8567703 DOI: 10.1186/s12870-021-03276-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 10/18/2021] [Indexed: 05/12/2023]
Abstract
BACKGROUND Coleorhiza hairs, are sheath-like outgrowth organs in the seeds of Poaceae family that look like root hair but develop from the coleorhiza epidermal cells during seed imbibition. The major role of coleorhiza hair in seed germination involves facilitating water uptake and nutrient supply for seed germination. However, molecular basis of coleorhiza hair development and underlying genes and metabolic pathways during seed germination are largely unknown and need to be established. RESULTS In this study, a comparative transcriptome analysis of coleorhiza hairs from japonica and indica rice suggested that DEGs in embryo samples from seeds with embryo in air (EIA) as compared to embryo from seeds completely covered by water (CBW) were enriched in water deprivation, abscisic acid (ABA) and auxin metabolism, carbohydrate catabolism and phosphorus metabolism in coleorhiza hairs in both cultivars. Up-regulation of key metabolic genes in ABA, auxin and dehydrin and aquaporin genes may help maintain the basic development of coleorhiza hair in japonica and indica in EIA samples during both early and late stages. Additionally, DEGs involved in glutathione metabolism and carbon metabolism are upregulated while DEGs involved in amino acid and nucleotide sugar metabolism are downregulated in EIA suggesting induction of oxidative stress-alleviating genes and less priority to primary metabolism. CONCLUSIONS Taken together, results in this study could provide novel aspects about the molecular signaling that could be involved in coleorhiza hair development in different types of rice cultivars during seed germination and may give some hints for breeders to improve seed germination efficiency under moderate drought conditions.
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Affiliation(s)
- Tao Song
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, 518057, China
| | - Debatosh Das
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, 518057, China
| | - Neng-Hui Ye
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, College of Agriculture, Hunan Agricultural University, Changsha, 410128, China
| | - Guan-Qun Wang
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong
| | - Fu-Yuan Zhu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China
| | - Mo-Xian Chen
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Feng Yang
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, 518057, China.
| | - Jian-Hua Zhang
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, 518057, China.
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong.
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong.
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