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Genomic decoding of breeding history to guide breeding-by-design in rice

National Science Review 2023年第5期10卷 124-137页

作者： Zhuo Chen Qingyun Bu Guifu Liu Maoqing Wang Hongru Wang Huazhao Liu Xiufeng Li Hong Li Jun Fang Yan Liang Zhenfeng Teng Sai Kang Hong Yu Zhukuan Cheng Yongbiao Xue Chengzhi Liang Jiuyou Tang Jiayang Li chengcai chu State Key Laboratory of Plant Genomics Institute of Genetics and Developmental BiologyInnovation Academy for Seed DesignChinese Academy of Sciences Key Laboratory of Soybean Molecular Design Breeding Northeast Institute of Geography and AgroecologyChinese Academy of Sciences Key Laboratory of Crop Biotechnology Breeding of the Ministry of Agriculture and Rural Affairs Beidahuang Kenfeng Seed Co.Ltd Institute of Botany Chinese Academy of Sciences Guangdong Laboratory for Lingnan Modern Agriculture and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources College of AgricultureSouth China Agricultural University University of Chinese Academy of Sciences State Key Laboratory of Plant Cell and Chromosome Engineering Institute of Genetics and Developmental BiologyInnovation Academy for Seed DesignChinese Academy of Sciences Hainan Yazhou Bay Seed Laboratory

Deciphering the intrinsic molecular logic of empirical crop breeding from a genomic perspective is a decisive prerequisite for breeding-by-design(BbD),but remains not well ***,we decoded the historical features of past rice breeding by phenotyping and haplotyping 546 accessions covering the majority of cultivars bred in the history of Northeast China(NEC).We revealed that three groups founded the genetic diversities in NEC rice with distinct evolution patterns and traced and verified the breeding footprints to known or genome-wide association study(GWAS)-detected quantitative trait loci(QTLs),or introgressions from indica sub-species with chronological changes in allele *** we summarized a rice breeding trend/principle in NEC,and combined with the successful example in breeding and application of Zhongkefa5 to demonstrate the guiding value of our conclusion for BbD in *** study provides a paradigm for decoding the breeding history of a specific crop to guide BbD,which may have implications in different crop breeding.

关键词： rice breeding-by-design breeding history genome-wide association study genomic decoding

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A Novel QTL qTGW3 Encodes the GSK3/ SHAGGY-Like Kinase OsGSK5/OsSK41 that Interacts with OsARF4 to Negatively Regulate Grain Size and Weight in Rice

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Molecular Plant 2018年第5期11卷 736-749页

作者： Zejun Hu Sun-Jie Lu Mei-Jing Wang Haohua He Le Sun Hongru Wang Xue-Huan Liu Ling Jiang Jing-Liang sun Xiaoyun Xin Wei Kong chengcai chu Hong-Wei Xue Jinshui Yang Xiaojin Luo Jian-Xiang Liu State Key Laboratory of Genetic Engineering Institute of Plant Biology School of Life Sciences Fudan University Shanghai 200433 China Key Laboratory of Crop Physiology Ecology and Genetic Breeding Ministry of Education Jiangxi Agricultural University Nanchang 330045 China State Key Laboratory of Plant Genomics National Center for Plant Gene Research (Beijing) Institute of Genetics and Developmental Biology Chinese Academy of Sciences Beijing 100101 China National Key Laboratory of Plant Molecular Genetics Institute of Plant Physiology and Ecology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai 200032 China State Key Laboratory of Plant Physiology and Biochemistry College of Life Sciences Zhejiang University Hangzhou 310027 China

Grain size and shape are important determinants of grain weight and yield in rice. Here, we report a new major quantitative trait locus （QTL）, qTGW3, that controls grain size and weight in rice. This locus, qTGW3, encodes OsSK41 （also known as OsGSK5）, a member of the GLYCOGEN SYNTHASE KINASE 3/SHAGGY-like family. Rice near-isogenic lines carrying the loss-of-function allele of OsSK41 have increased grain length and weight. We demonstrate that OsSK41 interacts with and phosphorylates AUXIN RESPONSE FACTOR 4 （OsARF4）. Co-expression of OsSK41 with OsARF4 increases the accumulation of OsARF4 in rice protoplasts. Loss of function of OsARF4 results in larger rice grains. RNA-sequencing analysis suggests that OsARF4 and OsSK41 repress the expression of a common set of downstream genes, including some auxin-responsive genes, during rice grain development. The loss-of-function form of OsSK41 at qTGW3 represents a rare allele that has not been extensively utilized in rice breeding. Suppression of OsSK41 function by either targeted gene editing or QTL pyramiding enhances rice grain size and weight. Thus, our study reveals the important role of OsSK41 in rice grain development and provides new candidate genes for genetic improvement of grain yield in rice and perhaps in other cereal crops.

关键词： QTL mapping GSK3-like family protein OsGSK5 OsARF4 grain size and weight Oryza sativa

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氮铁平衡促进水稻分蘖、提高产量和氮素利用效率

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科学通报 2023年第31期68卷 4073-4075页

作者：孙虎威王威储成才华南农业大学农学院广州510642 华南农业大学农业农村部华南作物资源高效利用重点实验室(部省共建) 广州510642 岭南现代农业科学与技术广东省实验室广州510642

粮食安全攸关国家安全、社会稳定和国民经济的健康持续发展.当今粮食生产严重依赖化肥(尤其是氮肥)投入,然而化肥的大量施用不仅导致土壤酸化板结、水体富营养化,同时化肥也是二氧化碳排放的主要来源^([1]).因此,减少化肥投入不仅有助... 详细信息

粮食安全攸关国家安全、社会稳定和国民经济的健康持续发展.当今粮食生产严重依赖化肥(尤其是氮肥)投入,然而化肥的大量施用不仅导致土壤酸化板结、水体富营养化,同时化肥也是二氧化碳排放的主要来源^([1]).因此,减少化肥投入不仅有助于改善环境,对减少碳排放也极为重要.由此可见,培育氮高效作物品种是现代农业的迫切需求.同时,探索新的施肥技术,保证作物不同养分间的平衡,也是提高作物产量、减少化肥投入的有效途径^([2]).

关键词：健康持续发展化肥投入作物品种二氧化碳排放现代农业氮素利用效率作物产量施肥技术

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The divergence of brassinosteroid sensitivity between rice subspecies involves natural variation conferring altered internal auto-binding of OsBSK2

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Journal of Integrative Plant Biology 2022年第8期64卷 1614-1630页

作者： Wenchao Yin Lulu Li Zhikun Yu Fan Zhang Dapu Liu Hongkai Wu Mei Niu Wenjing Meng Xiaoxing Zhang Nana Dong Yanzhao Yang Jihong Liu Yongqiang Liu Guoxia Zhang Jianlong Xu Shimei Wang chengcai chu Qian Qian Hongning Tong National Key Facility for Crop Gene Resources and Genetic Improvement Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China Rice Research Institute of Anhui Academy of Agricultural Sciences Hefei 230001China State Key Laboratory of Plant Genomics Institute of Genetics and Developmental Biologythe Innovative Academy for Seed DesignChinese Academy of SciencesBeijing 100101China

Japonica/geng and indica/xian are two major rice(Oryza sativa)subspecies with multiple divergent traits,but how these traits are related and interact within each subspecies remains ***(BRs)are a class of steroid phytohormones that modulate many important agronomic traits in ***,using different physiological assays,we revealed that japonica rice exhibits an overall lower BR sensitivity than *** screening of BR signaling genes led to the identification of a set of genes distributed throughout the primary BR signaling pathway with divergent *** these,we demonstrate that the C38/T variant in BR Signaling Kinase2(OsBSK2),causing the amino acid change P13L,plays a central role in mediating differential BR signaling in japonica and indica ***2in indica plays a greater role in BR signaling than OsB SK2in japonica by affecting the auto-binding and protein accumulation of ***,we determined that OsBSK2 is involved in a number of divergent traits in japonica relative to indica rice,including grain shape,tiller number,cold adaptation,and nitrogen-use *** study suggests that the natural variation in OsB SK2 plays a key role in the divergence of BR signaling,which underlies multiple divergent traits between japonica and indica.

关键词： brassinosteroid divergence grain shape natural variation rice

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Towards a Comprehensive Understanding of Brassinosteroid Functional Mechanisms in Rice

Towards a Comprehensive Understanding of Brassinosteroid Fun...

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全国农业生物化学与分子生物学第十五届学术研讨会

作者： Hongning Tong Yunhua Xiao Dapu Liu Ronghui Che chengcai chu Institute of Genetics and Developmental Biology Chinese Academy of Sciences

Brassinosteroids(BRs)are a class of plant hormones having great potential in improvement of plant performance under either normal or adverse ***,the molecular mechanisms underlying their diverse functions were not fully understood,especially in crop *** rice,BRs have significant functions in regulating plant height,lamina inclination and grain size by mainly promoting cell *** have identified a GRAS family protein named DLT,and demonstrated that DLT

关键词： Brassinosteroid Plant architecture Grain size Salt stress Rice

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Rice functional genomics:decades'efforts and roads ahead

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Science China(Life Sciences) 2022年第1期65卷 33-92页

作者： Rongzhi Chen Yiwen Deng Yanglin Ding Jingxin Guo Jie Qiu Bing Wang Changsheng Wang Yongyao Xie Zhihua Zhang Jiaxin Chen Letian Chen chengcai chu Guangcun He Zuhua He Xuehui Huang Yongzhong Xing Shuhua Yang Daoxin Xie Yaoguang Liu Jiayang Li State Key Laboratory of Hybrid Rice College of Life SciencesWuhan UniversityWuhan 430072China National Key Laboratory of Plant Molecular Genetics CAS Center for Excellence in Molecular Plant SciencesShanghai Institute of Plant Physiology&EcologyChinese Academy of SciencesShanghai 200032China State Key Laboratory of Plant Physiology and Biochemistry College of Biological SciencesChina Agricultural UniversityBeijing 100193China State Key Laboratory of Plant Genomics Institute of Genetics and Developmental BiologyInnovation Academy for Seed DesignChinese Academy of SciencesBeijing 100101China State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources South China Agricultural UniversityGuangzhou 510642China National Center for Gene Research Center of Excellence in Molecular Plant SciencesShanghai Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghai 200233China Shanghai Key Laboratory of Plant Molecular Sciences College of Life SciencesShanghai Normal UniversityShanghai 200234China National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research Huazhong Agricultural UniversityWuhan 430070China College of Plant Science Jilin UniversityChangchun 130062China MOE Laboratory of Bioinformatics School of Life SciencesTsinghua UniversityBeijing 100084China

Rice(Oryza sativa L.)is one of the most important crops in the *** 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 *** 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.

关键词： rice omics GWAS phytohormone action nutrient use biotic and abiotic responses photoperiodic flowering reproductive development

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组学技术揭示水稻杂种优势遗传机制

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植物学报 2017年第1期52卷 4-9页

作者：汪鸿儒储成才中国科学院遗传与发育生物学研究所植物基因组学国家重点实验室北京100101

杂种优势是杂交后代在生长或生殖性状上表现出优于亲本的现象。虽然杂种优势在农业生产上已广为应用,但其分子机理仍不清楚。最近,中国科学家通过分析17个代表性杂交稻(Oryza sativa)品种,共10 074个F2个体的全基因组序列和表型,对水稻... 详细信息

杂种优势是杂交后代在生长或生殖性状上表现出优于亲本的现象。虽然杂种优势在农业生产上已广为应用,但其分子机理仍不清楚。最近,中国科学家通过分析17个代表性杂交稻(Oryza sativa)品种,共10 074个F2个体的全基因组序列和表型,对水稻产量杂种优势相关位点进行了系统定位和解析。此外,中国另一个科研小组通过整合杂交稻亲本和杂交种的表型组、转录组及基因组等多层次数据,深入研究了超级杂交稻两优培九产量的杂种优势基础。这些研究不仅为杂种优势理论的建立提供了新数据,也为水稻育种实践提供了有益的指导。

关键词：水稻杂种优势基因组学全基因组关联分析

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Modulation of nitrate-induced phosphate response by the MYB transcription factor RLI1/HINGE1 in the nucleus

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Molecular Plant 2021年第3期14卷 517-529页

作者： Zhihua Zhang Zhao Li Wei Wang Zhimin Jiang Liping Guo Xiaohan Wang Yangwen Qian Xiahe Huang Yongqiang Liu Xiujie Liu Yahong Liu Aifu Li Yu Yan Junpeng Xie Shouyun Cao Stanislav Kopriva Legong Li Fanjiang Kong Baohui Liu Yingchun Wang Bin Hu chengcai chu State Key Laboratory of Plant Genomics Institute of Genetics and Developmental Biologythe Innovative Academy for Seed DesignChinese Academy of SciencesBeijingChina School of Life Sciences Guangzhou University.GuangzhouChina College of Plant Science Jilin UniversityChangchunChina Biogle Genome Editing Center ChangzhouChina State Key Laboratory of Molecular Developmental Biology Institute of Genetics and Developmental Biologythe Innovative Academy for Seed DesignChinese Academy of SciencesBeijingChina College of Advanced Agricultural Science University of Chinese Academy of SciencesBeijingChina Botanical Institute Cluster of Excellence on Plant SciencesUniversity of CologneCologneGermany College of Life Sciences Capital Normal UniversityBeijingChina

The coordinated utilization of nitrogen(N)and phosphorus(P)is vital for plants to maintain nutrient balance and achieve optimal ***,we revealed a mechanism by which nitrate induces genes for phosphate utilization;this mechanism depends on NRT1.1B-facilitated degradation of cytoplasmic SPX4,which in turn promotes cytoplasmic-nuclear shuttling of PHR2,the central transcription factor of phosphate signaling,and triggers the nitrate-induced phosphate response(NIPR)and N-P coordinated utilization in *** this study,we unveiled a fine-tuning mechanism of NIPR in the nucleus regulated by Highly Induced by Nitrate Gene 1(HINGE1,also known as RLI1),a MYB-transcription factor closely related to ***1/HINGE1,which is transcriptionally activated by PHR2 under nitrate induction,can directly activate the expression of phosphate starvation-induced *** importantly,RLI1/HINGE1 competes with PHR2 for binding to its repressor proteins in the nucleus(SPX proteins),and consequently releases PHR2 to further enhance phosphate ***,RLI1/HINGE1 amplifies the phosphate response in the nucleus downstream of the cytoplasmic SPX4-PHR2 cascade,thereby enabling fine-tuning of N-P balance when nitrate supply is sufficient.

关键词： rice NIPR RLI1/HINGE1 PHR2 SPXs nucleus

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The OsWRKY72-OsAAT30/OsGSTU26 module mediates reactive oxygen species scavenging to drive heterosis for salt tolerance in hybrid rice

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Journal of Integrative Plant Biology 2024年第4期66卷 709-730页

作者： Citao Liu Bigang Mao Yanxia Zhang Lei tian Biao Ma Zhuo Chen Zhongwei Wei Aifu Li Ye Shao Gongye Cheng Lingling Li Wenyu Li Di Zhang Xiaoping Ding Jiangxiang Peng Yulin Peng Jiwai He Nenghui Ye Dingyang Yuan chengcai chu Meijuan Duan Hunan Provincial Key Laboratory of Stress Biology College of AgricultureHunan Agricultural UniversityChangsha 410128China State Key Laboratory of Hybrid Rice Hunan Hybrid Rice Research CenterChangsha 410125China College of Agriculture South China Agricultural UniversityGuangzhou 510642China State Key Laboratory of Wheat and Maize Crop Science Center for Crop Genome EngineeringCollege of AgronomyHenan Agricultural UniversityZhengzhou 450002China College of Horticulture Fujian Agriculture and Forestry UniversityFuzhou 350002China Department of Computational Medicine and Bioinformatics University of MichiganAnn ArborMI 48109 USA Biobin Data Science Co. Ltd.Changsha 410221China

Hybrid rice(Oryza sativa)generally outperforms its inbred parents in yield and stress tolerance,a phenomenon termed heterosis,but the underlying mechanism is not completely ***,we combined transcriptome,proteome,physiological,and heterosis analyses to examine the salt response of super hybrid rice Chaoyou1000(CY1000).In addition to surpassing the mean values for its two parents(mid-parent heterosis),CY1000 exhibited a higher reactive oxygen species scavenging ability than both its parents(over-parent heterosis or heterobeltiosis).Nonadditive expression and allele-specific gene expression assays showed that the glutathione S-transferase gene OsGSTU26 and the amino acid transporter gene OsAAT30 may have major roles in heterosis for salt tolerance,acting in an overdominant fashion in ***,we identified OsWRKY72 as a common transcription factor that binds and regulates OsGSTU26 and *** salt-sensitive phenotypes were associated with the OsWRKY72^(paternal)genotype or the OsAAT30^(maternal)genotype in core rice germplasm ***72^(paternal)specifically repressed the expression of OsGSTU26 under salt stress,leading to salinity sensitivity,while OsWRKY72^(maternal)specifically repressed OsAAT30,resulting in salinity *** results suggest that the OsWRKY72-OsAAT30/OsGSTU26 module may play an important role in heterosis for salt tolerance in an overdominant fashion in CY1000 hybrid rice,providing valuable clues to elucidate the mechanism of heterosis for salinity tolerance in hybrid rice.

关键词： allele-specific gene expression(ASE) heterosis hybrid rice nonadditive effect(NAE) salt tolerance transcriptome and proteome

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Studies of Improving the Frequency of Indica Rice Transformation by Biolistic Bombardment

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High Technology Letters 2003年第1期9卷 6-10页

作者：易自力 Wang Li Cao Shouyun Yuan Longping Guan chunyun Zhau Puhan Tian Wenzhang chu chengcai Hunan Agricultural University Changsha 410128P.R.China Institute of Genetics Chinese Academy of Sciences Beijing 100101 P.R.China Institute of Genetics Chinese Academy of Sciences Beijing 100101 P.R.China Hunan Agricultural University Changsha 410128P.R.China

In order to improve the frequency of indica rice transformation by biolistic bombardment, suitable culture conditions for embryonic calli,an optimal selection scheme for resistant calli and seedlings, and optimum bombardment parameters a investigated by using 14 commercially important indica rice cultivars. The main results show that the CC medium with 36g/L mannitol is a scheme subculture medium in which the browning of indica rice calli can be mitigated significantly; The concentration of 30～40mg/L Hyg or 150～200mg/L G418 or 10～20 mg/L Basta is suitable for selection of resistant calli; The transformation parameters of 100μg gold powder absorbing 0.2μg DNA per shot and 900 psi helium pressure and 6 cm bombardment distance and bombarded twice for each plate give the best result; Keeping the target calli on osmotic medium containing 60g/L mannitol from 12 ～24h before bombardment to 24～48h after it can increase the efficiencies of transformation . Furthermore, some transgenic indica rice plants are obtained using this optimized transformation system.

关键词： indica rice biolistic bombardment transformation callus

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