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Genome-Wide Survey and Expression Analysis of P_(1B)-ATPases in rice, Maize and Sorghum

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rice science 2018年第4期25卷 208-217页

作者： E Zhiguo LI Tingting CHEN Chen WANG Lei Key laboratory of rice Biology China National Rice Research Institute Key laboratory of Plant Functional genomics Ministry of Education/Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/College of Agriculture Yangzhou University

P1B-type ATPase ion pumps that transport heavy metal ions across cellular membranes are essential for plant growth and development. To date, a genomic comparison overview of the family in rice, maize and sorghum is not yet available. In this study, a total of 31 heavy metal P1B-type ATPase （HMA） genes were identified, including 9 in rice, 11 each from maize and sorghum. They were classified into two distinct subfamilies based on their sequence composition and phylogenetic relationship. Four pairs of HMA genes were expanded via gene duplication with tandemly duplicated. Comprehensive analyses were performed to investigate the expression profiles of HMA genes in various tissues by using quantitative real-time PCR. Some HMA members exhibited abundant and tissue-specific expression patterns. Moreover, most of the genes were found to be differentially expressed under the Cu/Cd treatment. This study will facilitate further studies on P1B-type ATPase family and provide valuable hints for the functional validation in rice, maize and sorghum.

关键词： P1B-type ATPase rice maize sorghum HMA gene family expression pattern analysis

Post-genomics revolution in the design of premiumquality rice in a high-yieldingbackground to meet consumer demands in the 21st century

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Plant Communications 2022年第3期3卷 1-16页

作者： Nese Sreenivasulu Changquan Zhang Rhowell NTiozon Qiaoquan Liu Consumer Driven Grain Quality and Nutrition Unit Rice Breeding and Innovation PlatformInternational Rice Research InstituteLos Ban˜os 4030Philippines Key laboratory of Plant Functional genomics of the Ministry of Education Jiangsu Key Laboratory of Crop Genomics and Molecular BreedingCollege of AgricultureYangzhou UniversityYangzhou 225009China Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops Jiangsu Key Laboratory of Crop Genetics and PhysiologyYangzhou UniversityYangzhou 225009China Max Planck Institute of Molecular Plant Physiology Am M€uhlenberg 114476 Potsdam-GolmGermany

The eating and cooking quality(ECQ)of rice is critical for determining its economic value in the marketplace and promoting consumer *** has therefore been of paramount importance in rice breeding ***,we highlight advances in genetic studies of ECQ and discuss prospects for further enhancement of ECQ in *** in gene-and genome-editing techniques have enabled improvements in rice *** genes and quantitative trait loci(QTLs)have been shown to regulate starch composition,thereby affecting amylose content and thermal and pasting properties.A limited number of genes/QTLs have been identified for other ECQ properties such as protein content and ***-assisted breeding has identified rare alleles in diverse genetic resources that are associated with superior ECQ *** post-genomics-driven information summarized in this review is relevant for augmenting current breeding strategies to meet consumer preferences and growing population demands.

关键词： amylose amylopectin eating and cooking quality genetics genome editing texture

Identification of Potential Zinc Deficiency Responsive Genes and Regulatory Pathways in rice by Weighted Gene Co-expression Network Analysis

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rice science 2022年第6期29卷 545-558页

作者： Blaise Pascal MUVUNYI LU Xiang ZHAN Junhui HE Sang YE Guoyou CAAS-IRRI Joint laboratory for genomics-Assisted Germplasm Enhancement Agricultural Genomics Institute in ShenzhenChinese Academy of Agricultural Sciences(CAAS)Shenzhen 518120China rice Breeding Innovations Platform International Rice Research Institute(IRRI)Metro Manila 1301the Philippines

Zinc(Zn)malnutrition is a major public health *** biofortification of Zn in rice grain can alleviate global Zn ***,elucidating the genetic mechanisms regulating Zn deprivation response in rice is essential to identify elite genes useful for breeding high grain Zn rice ***,a meta-analysis of previous RNA-Seq studies involving Zn deficient conditions was conducted using the weighted gene co-expression network analysis(WGCNA)and other in silico prediction tools to identify modules(denoting cluster of genes with related expression pattern)of co-expressed genes,modular genes which are conserved differentially expressed genes(DEGs)across independent RNA-Seq studies,and the molecular pathways of the conserved modular *** identified 16 modules of co-expressed ***-eight and five modular DEGs were conserved in leaf and crown,and root tissues across two independent RNA-Seq *** enrichment analysis showed that 24 of the 28 conserved modular DEGs from leaf and crown tissues significantly up-regulated 2 Kyoto Encyclopedia of Genes and Genomes(KEGG)pathways and 15 Gene Ontology(GO)terms,including the substrate-specific transmembrane transporter and the small molecule metabolic ***,the well-studied transcription factors(OsWOX11 and OsbHLH120),protein kinase(OsCDPK20 and OsMPK17),and miRNAs(OSA-MIR397A and OSA-MIR397B)were predicted to target some of the identified conserved modular *** of the 24 conserved and up-regulated modular DEGs,19 were yet to be experimentally validated as Zn deficiency responsive *** from this study provide a comprehensive insight on the molecular mechanisms of Zn deficiency response and may facilitate gene and pathway prioritization for improving Zn use efficiency and Zn biofortification in rice.

关键词： rice biofortification zinc deficiency gene expression weighted gene co-expression network analysis

A Simple CRISPR/Cas9 System for Multiplex Genome Editing in rice

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Journal of Genetics and genomics 2015年第12期42卷 703-706页

作者： Chun Wang Lan Shen Yaping Fu Changjie Yan Kejian Wang State Key laboratory of rice Biology China National Rice Research Institute Chinese Academy of Agricultural Sciences Key laboratory of Plant Functional genomics Ministry of EducationYangzhou University

Generating mutants bearing multiple gene modifications is essential for determining the functions of gene family members with redundant functions, or for analyzing epistatic re- lationships in genetic pathways. Using conventional methods, mutants with multiple gene mutations are generated by several rounds of intercrossing plants carrying a single mutation and identification of the offspring. This process is both timeconsuming and labor-intensive. Moreover, if the genes of interest are closely linked, multiple mutations can not be generated （Wijnker and de Jong, 2008）.

关键词： A Simple CRISPR/Cas9 System for Multiplex Genome Editing in rice PDS Kpn RNA gene PCR

Conditional and unconditional mapping of quantitative trait loci underlying plant height and tiller number in rice (Oryza sativa L.) grown at two nitrogen levels

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Progress in Natural Science:Materials International 2008年第12期18卷 1539-1547页

作者： Hua Jiang~(a,b) Liang Jiang~b Longbiao Guo~b Zhenyu Gao~b Dali Zeng~b Lihuang Zhu~c Guohua Liang~a Qian Qian~b a State Key laboratory of rice Biology/Key laboratory of Plant Functional Genomies,Ministry of Education of China,Yangzhou University,Yangzhou 225009,China b State Key laboratory of rice Biology,China National rice Research Institute,Hangzhou 310006,China c Institute of Genetics,Chinese Academy of Sciences,Beijing 100101,China State Key laboratory of rice Biology/Key laboratory of Plant Functional genomics Ministry of Education of China Yangzhou University Yangzhou 225009 China State Key laboratory of rice Biology China National Rice Research Institute Hangzhou 310006 China Institute of Genetics Chinese Academy of Sciences Beijing 100101 China

In this study,we used 127 double haploid (DH) lines to analyze agricultural traits of *** DH lines,derived from a ZYQ8 (indica)/JX17 (japonica) cross by anther culture,contained 160 RFLP and 83 SSR *** and conditional quantitative trait loci (QTL) mapping was conducted to analyze plant height (PH) and tillers per plant (TP) at five growth stages that were grown at two nitrogen *** PH and 13 TP unconditional QTL were identified in the different growth stages,including 19 QTL from high-nitrogen (HN) and 14 QTL from low-nitrogen (LN) *** conditional QTL for 14 genomic regions under LN/HN con- ditions showed that there was a significant effect on PH and TP across the different *** one conditional QTL,ph2-3,was unable to be detected in unconditional *** QTL were detected in the first four rice growth stages than in the final ***- more,a line from the DH mapping population,DH78,was identified in extreme phenotypes of PH and TP that exhibited dwarfism and less-tiller (dft) *** gene dft1 was mapped to chromosome 2 using a backcrossed population of DH78/JX17 through a map- based cloning *** location of dft1 coincided with the mapping region of the small-LOD peak,QTL ph2 and tp2,which were identified in plants grown in low-nitrogen *** backcrossing and fine-mapping successfully delimited the dft1 locus to a 91 kb region.

关键词： Oryza sativa Quantitative trait loci Double haploid (DH) population Developmental behavior Nitrogen Map-based cloning

Virus-induced gene silencing and its application in plant functional genomics

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Science China(Life Sciences) 2012年第2期55卷 99-108页

作者： HUANG ChangJun QIAN YaJuan LI ZhengHe ZHOU XuePing State Key laboratory of rice Biology Institute of BiotechnologyZhejiang UniversityHangzhou 310058China

Virus-induced gene silencing is regarded as a powerful and efficient tool for the analysis of gene function in plants because it is simple, rapid and transformation-free. It has been used to perform both forward and reverse genetics to identify plant functional genes. Many viruses have been developed into virus-induced gene silencing vectors and gene functions involved in development, biotic and abiotic stresses, metabolism, and cellular signaling have been reported. In this review, we discuss the development and application of virus-induced gene silencing in plant functional genomics.

关键词： virus-induced gene silencing gene function gene expression

OsbZIP53 Negatively Regulates Immunity Response by Involving in Reactive Oxygen Species and Salicylic Acid Metabolism in rice

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rice science 2024年第2期31卷 190-202,I0022-I0028页

作者： WU Lijuan HAN Cong WANG Huimei HE Yuchang LIN Hai WANG Lei CHEN Chen E Zhiguo State Key laboratory of rice Biology and Breeding China National Rice Research InstituteHangzhou 310006China Jiangsu Key laboratory of Crop Genetics and Physiology/Key laboratory of Plant Functional genomics of the Ministry of Education/Jiangsu Key laboratory of Crop genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops Agricultural College of Yangzhou UniversityYangzhou 225009China

The basic region/leucine zipper(bZIP)transcription factors play important roles in plant development and responses to abiotic and biotic ***53 regulates resistance to Magnaporthe oryzae in rice by analyzing APIP5-RNAi transgenic *** further investigate the biological functions of OsbZIP53,we generated osbzip53 mutants using CRISPR/Cas9 editing and also constructed OsbZIP53 over-expression transgenic *** analysis of phenotypical,physiological,and transcriptional data showed that knocking-out OsbZIP53 not only improved disease resistance by inducing a hypersensitivity response in plants,but also regulated the immune response through the salicylic acid ***,disrupting OsbZIP53 increased H2O2 accumulation by promoting reactive oxygen species generation through up-regulation of several respiratory burst oxidase homologs(Osrboh genes)and weakened H2O2 degradation by directly targeting *** addition,the growth of osbzip53 mutants was seriously impaired,while OsbZIP53 over-expression lines displayed a similar phenotype to the wild type,suggesting that OsbZIP53 has a balancing effect on rice immune response and growth.

关键词： OsbZIP53 hypersensitive response reactive oxygen species metabolism rice immunity salicylic acid transcription factor

Recent Advances in Cloning and Characterization of Disease Resistance Genes in rice

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Journal of Integrative Plant Biology 2007年第1期49卷 112-119页

作者： Liang-Ying Dai Xiong-Lun Liu Ying-Hui Xiao Guo-Liang Wang rice genomics laboratory Hunan Agricultural University Changsha 410128 China Department of Plant Pathology The Ohio State University Columbus OH 43210 USA

rice diseases caused by fungi, bacteria and viruses are one of the major constraints for sustainable rice （Oryza sativa L.） production worldwide. The use of resistant cultivars is considered the most economical and effective method to control rice diseases. In the last decade, a dozen resistance genes against the fungal pathogen Magnaporthe grisea and the bacterial pathogen Xanthomonas oryzae pv. oryzae have been cloned. Approximately half of them encode nuclear binding site （NBS） and leucine rich repeat （LRR）-containing proteins, the most common type of cloned plant resistance genes. Interestingly, four of them encode novel proteins which have not been identified in other plant species, suggesting that unique mechanisms might be involved in rice defense responses. This review summarizes the recent advances in cloning and characterization of disease resistance genes in rice and presents future perspectives for in-depth molecular analysis of the function and evolution of rice resistance genes and their interaction with avirulence genes in pathogens.

关键词： rice blast bacterial blight Oryza sativa Magnaporthe grisea Xanthomonas oryzae pv. oryzae

A pan-TE map highlights transposable elements underlying domestication and agronomic traits in Asian rice

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National Science Review 2024年第6期11卷 105-118页

作者： Xiaoxia Li Xiaofan Dai Huiying He Yang Lv Longbo Yang Wenchuang He Congcong Liu Hua Wei Xiangpei Liu Qiaoling Yuan Xianmeng Wang Tianyi Wang Bintao Zhang Hong Zhang Wu Chen Yue Leng Xiaoman Yu Hongge Qian Bin Zhang Mingliang Guo Zhipeng Zhang Chuanlin Shi Qianqian Zhang Yan Cui Qiang Xu Xinglan Cao Dandan Chen Yongfeng Zhou Qian Qian Lianguang Shang Shenzhen Branch Guangdong Laboratory of Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural Sciences rice Research Institute Shenyang Agricultural University Yazhouwan National laboratory State Key laboratory of rice Biology China National Rice Research Institute National Key laboratory of Tropical Crop Breeding Tropical Crops Genetic Resources InstituteChinese Academy of Tropical Agricultural Sciences

Transposable elements(TEs) are ubiquitous genomic components and hard to study due to being highly repetitive. Here we assembled 232 chromosome-level genomes based on long-read sequencing *** the 232 genomes with 15 existing assemblies, we developed a pan-TE map comprising both cultivated and wild Asian rice. We detected 177 084 high-quality TE variations and inferred their derived state using outgroups. We found TEs were one source of phenotypic variation during rice domestication and differentiation. We identified 1246 genes whose expression variation was associated with TEs but not single-nucleotide polymorphisms(SNPs), such as Os Rboh B, and validated Os Rboh B's relative expression activity using a dual-Luciferase(LUC) reporter assays system. Our pan-TE map allowed us to detect multiple novel loci associated with agronomic traits. Collectively, our findings highlight the contributions of TEs to domestication, differentiation and agronomic traits in rice, and there is massive potential for gene cloning and molecular breeding by the high-quality Asian pan-TE map we generated.

关键词： transposable element super pan-genome pan-TE rice