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rice functional genomics:decades'efforts and roads ahead

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 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.

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

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rice metabolic regulatory network spanning the entire life cycle

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Molecular Plant 2022年第2期15卷 258-275页

作者： Chenkun Yang Shuangqian Shen Shen Zhou Yufei Li Yuyuan Mao Junjie Zhou Yuheng Shi Longxu An Qianqian Zhou Wenju Peng Yuanyuan Lyu Xuemei Liu Wei Chen Shouchuang Wang Lianghuan Qu Xianqing Liu Alisdair R.Fernie Jie Luo National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research(Wuhan) Huazhong Agricultural UniversityWuhan 430070China College of Tropical Crops Hainan UniversityHaikou 570228China Sanya Nanfan Research Institute of Hainan University Hainan Yazhou Bay Seed LaboratorySanya 572025China College of Plant Science and Technology Huazhong Agricultural UniversityWuhan 430070China Max Planck Institute of Molecular Plant Physiology Potsdam-Golm 14476Germany Centre of Plant Systems Biology and Biotechnology Plovdiv 4000Bulgaria

As one of the most important crops in the world,rice(Oryza sativa)is a model plant for metabolome research.Although many studies have focused on the analysis of specific tissues,the changes in metab-olite abundance across the entire life cycle have not yet been determined.In this study,combining both tar-geted and nontargeted metabolite profiling methods,a total of 825 annotated metabolites were quantified in rice samples from different tissues covering the entire life cycle.The contents of metabolites in different tissues of rice were significantly different,with various metabolites accumulating in the plumule and radicle during seed germination.Combining these data with transcriptome data obtained from the same time period,we constructed the rice Metabolic Regulation Network.The metabolites and co-expressed genes were further divided into 12 clusters according to their accumulation patterns,with members within each cluster displaying a uniform and clear pattern of abundance across development.Using this dataset,we established a comprehensive metabolic profile of the rice life cycle and used two independent strategies to identify novel transcription factors-namely the use of known regulatory genes as bait to screen for new networks underlying lignin metabolism and the unbiased identification of new glycerophospholipid metabolism regulators on the basis of tissue specificity.This study thus demonstrates how guilt-by-association analysis of metabolome and transcriptome data spanning the entire life cycle in cereal crops provides novel resources and tools to aid in understanding the mechanisms underlying important agro-nomic traits.

关键词： rice metabolome transcriptome transcription factor co-expression glycerophospholipid

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Effect of metal fractions on rice grain metal uptake and biological parameters in mica mines waste contaminated soils

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Journal of Environmental Sciences 2024年第2期136卷 313-324页

作者： Saibal Ghosh Sandip Mondal Jajati Mandal Abhishek Mukherjee Pradip Bhattacharyya Agricultural and Ecological Research Unit Indian Statistical InstituteGiridihJharkhand 815301India School of Science Engineering&EnvironmentUniversity of SalfordManchester M54WTUK

Heavy metals from mica waste not only deteriorate the soil quality but also results in the uptake of metals in the crop.The present investigation was conducted to evaluate the effects of different fractions of metals on the uptake in rice,soil microbial and biochemical properties in mica waste-contaminated soils of Jharkhand,India.From each active mine,soil samples were randomly collected at distances of100 m(zone 3).Sequential metal extraction was used to determine the fractions of different metals(nickel(Ni),cadmium(Cd),chromium(Cr)and lead(Pb))including water-soluble(Ws)and exchangeable metals(Ex),carbonate-bound metals(CBD),Fe/Mn oxide(OXD)bound metals,organically bound metals(ORG),and residues(RS).The Ni,Cr,Cd and Pb in rice grain were 0.83±0.41,0.41±0.19,0.21±0.14 and 0.17±0.08 mg/kg respectively.From the variable importance plot of the random forest(RF)algorithm,the Ws fraction of Ni,Cr and Cd and Ex fraction of Pb was the most important predictor for rice grain metal content.Further,the partial dependence plots(PDP)give us an insight into the role of the two most important metal fractions on rice grain metal content.The microbial and enzyme activity was significantly and negatively correlated with Ws and Ex metal fractions,indicating that water-soluble and exchangeable fractions exert a strong inhibitory effect on the soil microbiological parameters and enzyme activities.

关键词： Metal fractions Microbial parameters Mica waste soil Soil enzymes rice Random forest

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Regulation of rhizosphere microenvironment by rice husk ash for reducing the accumulation of cadmium and arsenic in rice

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Journal of Environmental Sciences 2024年第2期136卷 1-10页

作者： Yi Jiang Ya Liu Xuantao Yi Peng Zeng Bohan Liao Hang Zhou Jiaofeng Gu College of Environmental Science and Engineering Central South University of Forestry and TechnologyChangsha 410004China Hunan Engineering Laboratory for Control of rice Quality and Safety Changsha 410004China

It is important to reduce Cd and As content in brown rice in contaminated paddy soils.We conducted research on the effects of rice husk ash (RHA) on the Cd and As in the rhizosphere microenvironment (soil,porewater,and iron plaque) and measured the Cd,As,and Si content in rice plants.The main elements in RHA were Si (29.64%) and O (69.17%),which had the maximum adsorption capacity for Cd was 42.49 mg/kg and for As was 18.62 mg/kg.Soil pH and available Si content increased,while soil available Cd and As decreased following application of 0.5%–2%RHA.RHA promote the transformation of Cd to insoluble fraction,while As was transformed from a poorly soluble form to a more active one.RHA reduced Cd content and increased Si content in porewater,and reduced As only at the later rice growth stages.RHA increased the amount of iron plaque,thereby decreasing the Cd content in iron plaque,while increased the As content in it.Cd and inorganic As content in brown rice were decreased,to 0.31 mg/kg and 0.18 mg/kg,respectively.The decrease of Cd in brown rice was due to the decrease of Cd mobility in soil,thereby reducing root accumulation,while the decrease of As in brown rice was affected by the transport from roots to stems.Therefore,RHA can be considered as a safe and efficient in-situ remediation amendment for Cd and As co-contaminated paddy soil.

关键词： rice husk ash(rha) Cadmium Arsenic Silicon rice Soil

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OsPDR20 is an ABCG metal transporter regulating cadmium accumulation in rice

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Journal of Environmental Sciences 2024年第2期136卷 21-34页

作者： He Li Chao Li Di Sun Zhi Min Yang Department of Biochemistry and Molecular Biology College of Life SciencesNanjing Agricultural UniversityNanjing 210095China

Cadmium(Cd)is a non-essential toxic heavy metal,seriously posing high environmental risks to human health.Digging genetic resources relevant to functional genes is important for understanding the metal absorption and accumulation in crops and bioremediation of Cd-polluted environments.This study investigated a functionally uncharacterized ATP binding cassette transporter G family(ABCG)gene encoding a Pleiotropic Drug Resistance 20(PDR20)type metal transporter which is localized to the plasma membrane of rice.OsPDR20 was transcriptionally expressed in almost all tissues and organs in lifespan and was strongly induced in roots and shoots of young rice under Cd stress.Ectopic expression of OsPDR20 in a yeast mutant ycf1 sensitive to Cd conferred cellular tolerance with less Cd accumulation.Knockdown of OsPDR20 by RNA interference(RNAi)moderately attenuated root/shoot elongation and biomass,with reduced chlorophylls in rice grown under hydroponic medium with 2 and 10μmol/L Cd,but led to more Cd accumulation.A field trial of rice grown in a realistic Cd-contaminated soil(0.40 mg/kg)showed that RNAi plants growth and development were also compromised compared to wild-type(WT),with smaller panicles and lower spikelet fertility but little effect on yield of grains.However,OsPDR20 suppression resulted in unexpectedly higher levels of Cd accumulation in rice straw including lower leaves and culm and grain.These results suggest that OsPDR20 is actively involved in Cd accumulation and homeostasis in rice crops.The increased Cd accumulation in the RNAi plants has the potential application in phytoremediation of Cd-polluted wetland soils.

关键词： rice ABCG transporter Cadmium accumulation Phytoremediation

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

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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 established.Here,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 frequencies.Then 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 practice.Our 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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The transcription factor HBF1 directly activates expression of multiple flowering time repressors to delay rice flowering

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aBIOTECH 2023年第3期4卷 213-223页

作者： Cong Li Liya Zhang Xin Wang Chunsheng Yu Tao Zhao Bin Liu Hongyu Li Jun Liu Chunyu Zhang Institute of Crop Science Chinese Academy of Agricultural SciencesBeijing 100081China Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement and Guangdong Provincial Key Laboratory of Applied Botany South China Botanical GardenChinese Academy of SciencesGuangzhou 510650China Institute of Nanfan and Seed Industry Guangdong Academy of SciencesGuangzhou 510316China

Flowering time(or heading date)is an important agronomic trait that determines the environmental adaptability and yield of many crops,including rice(Oryza sativa L.).Hd3a BINDING REPRESSOR FACTOR 1(HBF1),a basic leucine zipper transcription factor,delays flowering by decreasing the expression of Early heading date 1(Ehd1),Heading date 3a(Hd3a),and rice FLOWERING LOCUS T 1(RFT1),but the underlying molecular mechanisms have not been fully elucidated.Here,we employed the hybrid transcriptional factor(HTF)strategy to enhance the transcriptional activity of HBF1 by fusing it to four copies of the activation domain from Herpes simplex virus VP16.We discovered that transgenic rice lines overexpressing HBF1-VP64(HBF1V)show significant delays in time to flower,compared to lines overexpressing HBF1-MYC or wild-type plants,via the Ehd1–Hd3a/RFT1 pathway,under both long-day and short-day conditions.Transcriptome deep sequencing analysis indicated that 19 WRKY family genes are upregulated in the HBF1V overexpression line.We demonstrate that the previously unknown gene,OsWRKY64,is a direct downstream target of HBF1 and represses flowering in rice,whereas three known flowering repressor genes,Days to heading 7(DTH7),CONSTANS 3(OsCO3),and OsWRKY104,are also direct target genes of HBF1 in flowering regulation.Taking these results together,we propose detailed molecular mechanisms by which HBF1 regulates the time to flower in rice.

关键词： HBF1 bZIP transcription factor OsWRKY64 Flowering time rice

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Generation of low-cadmium rice germplasms via knockout of OsLCD using CRISPR/Cas9

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Journal of Environmental Sciences 2023年第4期126卷 138-152页

作者： Huamei Chen Rong Ye Ying Liang Shuchang Zhang Xiulian Liu Chongjun Sun Fangbai Li Jicai Yi College of Life Sciences South China Agricultural UniversityGuangzhou 510642China Institute of Eco-environmental and Soil Sciences Guangdong Academy of SciencesGuangzhou 510650China

The OsLCD gene,which has been implicated in cadmium (Cd) accumulation in rice,might be a useful target for CRISPR/Cas9 editing.However,the effects of Os LCD gene editing on Cd accumulation,plant growth,and yield traits remain unknown.Here,we used CRISPR/Cas9to generate oslcd single mutants from indica and japonica rice cultivars.We also generated osnramp5 single mutants and oslcd osnramp5 double mutants in the indica background.When grown in Cd-contaminated paddy soils,all oslcd single mutants accumulated less Cd than the wild types (WTs).Consistent with this,oslcd single mutants grown in Cd-contaminated hydroponic culture accumulated significantly less Cd in the shoots as compared to WTs.This decrease in accumulation probably resulted from the reduction of Cd translocation under Cd stress.Oxidative damage also decreased,and plant growth increased in all oslcd single mutant seedlings as compared to WTs in the presence of Cd.Plant growth and most yield traits,as well essential element concentrations in rice seedling shoots,brown rice,and rice straw,were similar between oslcd single mutants and WTs.In the presence of Cd,Cd concentrations in the brown rice and shoots of oslcd osnramp5 double mutants were significantly decreased compared with WTs as well as osnramp single mutants.Our results suggested that OsL CD knockout may reduce Cd accumulation alone or in combination with other knockout mutations in a variety of rice genotypes;unlike Os Nramp5 mutations,Os LCD knockout did not reduce essential element contents.Therefore,Os LCD knockout might be used to generate low-Cd rice germplasms.

关键词： Cadmium rice OsLCD Crispr/Cas9 editing

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Molecular bases of rice grain size and quality for optimized productivity

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Science Bulletin 2023年第3期68卷 314-350,M0004页

作者： Deyong Ren Chaoqing Ding Qian Qian State Key Laboratory of rice Biology China National Rice Research InstituteHangzhou 310006China

The accomplishment of further optimization of crop productivity in grain yield and quality is a great challenge.Grain size is one of the crucial determinants of rice yield and quality;all of these traits are typical quantitative traits controlled by multiple genes.Research advances have revealed several molecular and developmental pathways that govern these traits of agronomical importance.This review provides a comprehensive summary of these pathways,including those mediated by G-protein,the ubiquitin–proteasome system,mitogen-activated protein kinase,phytohormone,transcriptional regulators,and storage product biosynthesis and accumulation.We also generalize the excellent precedents for rice variety improvement of grain size and quality,which utilize newly developed gene editing and conventional gene pyramiding capabilities.In addition,we discuss the rational and accurate breeding strategies,with the aim of better applying molecular design to breed high-yield and superior-quality varieties.

关键词： rice Grain size Grain quality Genetic control Molecular networks Variety improvement

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OsNAC5 orchestrates OsABI5 to fine-tune cold tolerance in rice

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Journal of Integrative Plant Biology 2024年第4期66卷 660-682页

作者： Ruiqing Li Yue Song Xueqiang Wang Chenfan Zheng Bo Liu Huali Zhang Jian Ke Xuejing Wu Liquan Wu Ruifang Yang Meng Jiang College of Agronomy Anhui Agricultural UniversityHefei 230036China Hainan Institute Yazhou Bay Sci-Tech CityZhejiang UniversitySanya 572025China National Key Laboratory of rice Biology Advanced Seed InstituteZhejiang UniversityHangzhou 311225China State Key Laboratory of rice Biology and Chinese National Center for rice Improvement China National Rice Research InstituteHangzhou 311401China Key Laboratory of Germplasm Innovation and Genetic Improvement of Grain and Oil Crops(Co-Construction by Ministry and Province) Ministry of Agriculture and Rural AffairsCrop Breeding and Cultivation Research InstituteShanghai Academy of Agricultural SciencesShanghai 201106China

Due to its tropical origins,rice(Oryza sativa)is susceptible to cold stress,which poses severe threats to production.OsNAC5,a NAC-type transcription factor,participates in the cold stress response of rice,but the detailed mechanisms remain poorly understood.Here,we demonstrate that OsNAC5 positively regulates cold tolerance at germination and in seedlings by directly activating the expression of ABSCISIC ACID INSENSITIVE 5(OsABI5).Haplotype analysis indicated that single nucleotide polymorphisms in a NAC-binding site in the OsABI5 promoter are strongly associated with cold tolerance.OsNAC5 also enhanced OsABI5 stability,thus regulating the expression of cold-responsive(COR)genes,enabling fine-tuned control of OsABI5 action for rapid,precise plant responses to cold stress.DNA affinity purification sequencing coupled with transcriptome deep sequencing identified several OsABI5 target genes involved in COR expression,including DEHYDRATION-RESPONSIVE ELEMENT BINDING FACTOR 1A(OsDREB1A),OsMYB20,and PEROXIDASE 70(OsPRX70).In vivo and in vitro analyses suggested that OsABI5 positively regulates COR gene transcription,with marked COR upregulation in OsNAC5-overexpressing lines and downregulation in osnac5 and/or osabi5 knockout mutants.This study extends our understanding of cold tolerance regulation via OsNAC5 through the OsABI5-CORs transcription module,which may be used to ameliorate cold tolerance in rice via advanced breeding.

关键词： ABA signaling ABI5 cold tolerance DREB NAC5 rice

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