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Sdr4 dominates pre-harvest sprouting and facilitates adaptation to local climatic condition in Asian cultivated rice

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Journal of Integrative Plant Biology 2022年第6期64卷 1246-1263页

作者： Bo Zhao Hui Zhang Tianxiao Chen Ling Ding Liying Zhang Xiali Ding Jun Zhang Qian Qian Yong Xiang shenzhen Branch Guangdong Laboratory for Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518120China Shanxi Key laboratory of Minor Crop Germplasm Innovation and Molecular Breeding College of Life SciencesShanxi Agricultural UniversityTaigu 030801China State Key laboratory of rice Biology China National Rice Research InstituteHangzhou 310006China

Pre-harvest sprouting(PHS),which reduces grain yield and quality,is controlled by seed dormancy genes.Because few dormancy-related genes have been cloned,the genetic basis of seed dormancy in rice(Oryza sativa L.)remains unclear.Here,we performed a genome-wide association study and linkage mapping to dissect the genetic basis of seed dormancy in rice.Our findings suggest that Seed Dormancy4(Sdr4),a central modulator of seed dormancy,integrates the abscisic acid and gibberellic acid signaling pathways at the transcriptional level.Haplotype analysis revealed that three Sdr4 alleles in rice cultivars already existed in ancestral Oryza rufipogon accessions.Furthermore,like the semi-dwarf 1(SD1)and Rc loci,Sdr4 underwent selection during the domestication and improvement of Asian cultivated rice.The distribution frequency of the Sdr4-n allele in different locations in Asia is negatively associated with local annual temperature and precipitation.Finally,we developed functional molecular markers for Sdr4,SD1,and Rc for use in molecular breeding.Our results provide clues about the molecular basis of Sdr4-regulated seed dormancy.Moreover,these findings provide guidance for utilizing the favorable alleles of Sdr4 and Rc to synergistically boost PHS resistance,yield,and quality in modern rice varieties.

关键词： climatic adaptation pre-harvest sprouting Rc rice SD1 Sdr4 seed dormancy

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 issue.Genetic biofortification of Zn in rice grain can alleviate global Zn malnutrition.Therefore,elucidating the genetic mechanisms regulating Zn deprivation response in rice is essential to identify elite genes useful for breeding high grain Zn rice varieties.Here,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 DEGs.WGCNA identified 16 modules of co-expressed genes.Twenty-eight and five modular DEGs were conserved in leaf and crown,and root tissues across two independent RNA-Seq studies.Functional 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 process.Further,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 DEGs.Out of the 24 conserved and up-regulated modular DEGs,19 were yet to be experimentally validated as Zn deficiency responsive genes.Findings 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

GRAIN INCOMPLETE FILLING 2 regulates grain filling and starch synthesis during rice caryopsis development

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Journal of Integrative Plant Biology 2017年第2期59卷 134-153页

作者： Xiangjin Wei Guiai Jiao Haiyan Lin Zhonghua Sheng Gaoneng Shao Lihong Xie Shaoqing Tang Qingguo Xu Peisong Hu State Key laboratory of rice Biology Key Laboratory of Rice Biology and Breeding of Ministry of Agriculture China National Rice Research Institute Hangzhou 310006 China . College of Agronomy Hunan Agricultural University Changsha 410128 China Agricultural Genomes Institute at shenzhen Chinese Academy of Agricultural Sciences Shenzhen 518120 China

rice grain filling determines grain weight, final yield and grain quality. Here, a rice defective grain filling mutant, gif2, was identified. Grains ofgif2 showed a slower filling rate and a significant lower final grain weight and yield compared to wild-type. The starch content in gilt2 was noticeably decreased and its physicochemical properties were also altered. Moreover, gif2 endosperm cells showed obvious defects in compound granule formation. Posi- tional cloning identified GIF2 to encode an ADP-glucose pyrophosphorylase （AGP） large subunit, AGPL2; consequently, AGP enzyme activity in gif2 endosperms was remarkably decreased. GIF2 is mainly expressed in developing grains and the coded protein localizes in the cytosol. Yeast two hybrid assay showed that GIF2 interacted with AGP small subunits OsAGPS% OsAGPS2a and OsAGPS2b. Transcript levels for granule-bound starch synthase, starch synthase, starch branching enzyme and starch debranching enzyme were distinctly elevated in gif2 grains. In addition, the level of nucleotide diversity of the GIF2 locus was extremely low in both cultivated and wild rice. All of these results suggest that GIF2 plays important roles in the regulation of grain filling and starch biosynthesis during caryopsis development, and that it has been preserved during selection throughout domestication of modern rice.

关键词： GIF GRAIN INCOMPLETE FILLING 2 regulates grain filling and starch synthesis during rice caryopsis development Figure AGPS RNAi

A centromere map based on super pan-genome highlights the structure and function of rice centromeres

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Journal of Integrative Plant Biology 2024年第2期66卷 196-207页

作者： Yang Lv Congcong Liu Xiaoxia Li Yueying Wang Huiying He Wenchuang He Wu Chen Longbo Yang Xiaofan Dai Xinglan Cao Xiaoman Yu Jiajia Liu Bin Zhang Hua Wei Hong Zhang Hongge Qian Chuanlin Shi Yue Leng Xiangpei Liu Mingliang Guo Xianmeng Wang Zhipeng Zhang Tianyi Wang Bintao Zhang Qiang Xu Yan Cui Qianqian Zhang Qiaoling Yuan Noushin Jahan Jie Ma Xiaoming Zheng Yongfeng Zhou Qian Qian Longbiao Guo Lianguang Shang State Key laboratory of rice Biology China National Rice Research InstituteHangzhou 310006China 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 SciencesShenzhen 518120China Yazhouwan National laboratory No.8 Huanjin RoadYazhou DistrictSanya City 572024China National Key Facility for Crop Gene Resources and Genetic Improvement Institute of Crop ScienceChinese Academy of Agricultural SciencesBeijing 100081China

rice(Oryza sativa)is a significant crop worldwide with a genome shaped by various evolutionary factors.rice centromeres are crucial for chromosome segregation,and contain some unreported genes.Due to the diverse and complex centromere region,a comprehensive understanding of rice centromere structure and function at the population level is needed.We constructed a high-quality centromere map based on the rice super pangenome consisting of a 251-accession panel comprising both cultivated and wild species of Asian and African rice.We showed that rice centromeres have diverse satellite repeat CentO,which vary across chromosomes and subpopulations,reflecting their distinct evolutionary patterns.We also revealed that long terminal repeats(LTRs),especially young Gypsy-type LTRs,are abundant in the peripheral CentO-enriched regions and drive rice centromere expansion and evolution.Furthermore,high-quality genome assembly and complete telomere-to-telomere(T2T)reference genome enable us to obtain more centromeric genome information despite mapping and cloning of centromere genes being challenging.We investigated the association between structural variations and gene expression in the rice centromere.A centromere gene,OsMAB,which positively regulates rice tiller number,was further confirmed by expression quantitative trait loci,haplotype analysis and clustered regularly interspaced palindromic repeats(CRISPR)/CRISPR-associated protein9 methods.By revealing the new insights into the evolutionary patterns and biological roles of rice centromeres,our finding will facilitate future research on centromere biology and crop improvement.

关键词： centromere super pan-genome CentoO satellite repeat rice

Genomic prediction using composite training sets is an effective method for exploiting germplasm conserved in rice gene banks

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The Crop Journal 2022年第4期10卷 1073-1082页

作者： Sang He Hongyan Liu Junhui Zhan Yun Meng Yamei Wang Feng Wang Guoyou Ye CAAS-IRRI Joint laboratory for Genomics-Assisted Germplasm Enhancement Agricultural Genomics Institute in ShenzhenChinese Academy of Agricultural SciencesShenzhen 518120GuangdongChina rice Breeding Innovations Platform International Rice Research InstituteDAPO Box 7777Metro ManilaPhilippines Guangdong Provincial Key laboratory of New Technology in rice Breeding Rice Research InstituteGuangdong Academy of Agricultural SciencesGuangzhou 510640GuangdongChina Hainan Key laboratory for Sustainable Utilization of Tropical Bioresource College of Tropical CropsHainan UniversityHaikou 570228HainanChina

Germplasm conserved in gene banks is underutilized,owing mainly to the cost of characterization.Genomic prediction can be applied to predict the genetic merit of germplasm.Germplasm utilization could be greatly accelerated if prediction accuracy were sufficiently high with a training population of practical size.Large-scale resequencing projects in rice have generated high quality genome-wide variation information for many diverse accessions,making it possible to investigate the potential of genomic prediction in rice germplasm management and exploitation.We phenotyped six traits in nearly 2000 indica(XI)and japonica(GJ)accessions from the rice 3K project and investigated different scenarios for forming training populations.A composite core training set was considered in two levels which targets used for prediction of subpopulations within subspecies or prediction across subspecies.Composite training sets incorporating 400 or 200 accessions from either subpopulation of XI or GJ showed satisfactory prediction accuracy.A composite training set of 600 XI and GJ accessions showed sufficiently high prediction accuracy for both XI and GJ subspecies.Comparable or even higher prediction accuracy was observed for the composite training set than for the corresponding homogeneous training sets comprising accessions only of specific subpopulations of XI or GJ(within-subspecies level)or pure XI or GJ accessions(across-subspecies level)that were included in the composite training set.Validation using an independent population of 281 rice cultivars supported the predictive ability of the composite training set.Reliability,which reflects the robustness of a training set,was markedly higher for the composite training set than for the corresponding homogeneous training sets.A core training set formed from diverse accessions could accurately predict the genetic merit of rice germplasm.

关键词： Genomic prediction Composite training set rice germplasm Gene bank Reliability criterion

Chlorophyllide-a Oxygenase 1(OsCAO1) Over-Expression Affects rice Photosynthetic Rate and Grain Yield

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rice science 2023年第2期30卷 87-91,I0002-I0006页

作者： HU Ping MA Jie KANG Shujing LI Sanfeng WU Xianmei ZENG Longjun LU Caolin HE Rui HE Huiying SHANG Lianguang RAO Yuchun ZHU Xudong XIONG Guosheng QIAN Qian GUO Longbiao WANG Yuexing State Key laboratory of rice Biology China National Rice Research InstituteHangzhou 310006China shenzhen Branch Guangdong Laboratory for Lingnan Modern Agriculture/Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs/Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518120China Plant Phenomics research Center Nanjing Agricultural UniversityNanjing 210095China College of Chemistry and Life Sciences Zhejiang Normal UniversityJinhua 321004China

Leaf color and photosynthesis are important factors for rice growth and development.Hence,improving the photosynthetic rate is an effective approach for increasing rice yield.We isolated a gene,chlorophyllide-a oxygen... 详细信息

关键词： OsCAO1 development Oxygen

Xiaowei, a New rice Germplasm for Large-Scale Indoor research

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Molecular Plant 2018年第11期11卷 1418-1420页

作者： Shikai Hu Xingming Hu Jiang Hu Lianguang Shang Guojun Dong Dali Zeng Longbiao Guo Qian Qian State Key laboratory of rice Biology China National Rice Research instituteChinese Academy of Agricultural SciencesHangzhou 310006China Agricultural Genomics institute at shenzhen Chinese Academy of Agricultural SciencesShenzhen 518120China

Dear Editor,rice (Oryza sativa)is a model monocot plant for biological studies due to its relatively small genome,rich germplasm resources,and high-efficiency transformation methods.Although significant progress has been made in rice genomics and functional genomics research (Li et al.,2018),large-scale indoor research toward better understanding of rice biology is hampered by its long growth period and extreme dependence on the natural environment for cultivation.There are some rice germplasms that have a short growth period and short plant height,such as Kitaake.

关键词： rice period plant growth

GAEP:a comprehensive genome assembly evaluating pipeline

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Journal of Genetics and Genomics 2023年第10期50卷 747-754页

作者： Yong Zhang Hong-Wei Lu Jue Ruan 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 SciencesShenzhenGuangdong 518120China State Key laboratory of rice Biology and Breeding China National Rice Research InstituteChinese Academy of Agricultural SciencesHangzhouZhejiang 311401China

With the rapid development of sequencing technologies,especially the maturity of third-generation sequencing technologies,there has been a significant increase in the number and quality of published genome assemblies.The emergence of these high-quality genomes has raised higher requirements for genome evaluation.Although numerous computational methods have been developed to evaluate assembly quality from various perspectives,the selective use of these evaluation methods can be arbitrary and inconvenient for fairly comparing the assembly quality.To address this issue,we have developed the Genome Assembly Evaluating Pipeline(GAEP),which provides a comprehensive assessment pipeline for evaluating genome quality from multiple perspectives,including continuity,completeness,and correctness.Additionally,GAEP includes new functions for detecting misassemblies and evaluating the assembly redundancy,which performs well in our testing.GAEP is publicly available at https://***/zyoptimistic/GAEP under the GPL3.0 License.With GAEP,users can quickly obtain accurate and reliable evaluation results,facilitating the comparison and selection of high-quality genome assemblies.

关键词： Genome assembly Assembly quality Assembly metrics Assembly evaluation pipeline Misassembly detection Misassembly breakpoint Assembly redundancy

A prolific and robust whole-genome genotyping method using PCR amplification via primer-template mismatched annealing

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Journal of Integrative Plant Biology 2023年第3期65卷 633-645页

作者： Sheng Zhao Cuicui Zhang Liqun Wang Minxuan Luo Peng Zhang Yue Wang Waqar Afzal Malik Yue Wang Peng Chen Xianjin Qiu Chongrong Wang Hong Lu Yong Xiang Yuwen Liu Jue Ruan Qian Qian Haijian Zhi Yuxiao Chang National Key laboratory for Crop Genetics and Germplasm Enhancement National Center for Soybean ImprovementNanjing Agricultural UniversityNanjing 210095China Guangdong laboratory of Lingnan Modern Agriculture Genome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518120China College of Agriculture Yangtze UniversityJingzhou 434023China Guangdong Provincial Key laboratory of New Technology in rice Breeding Rice Research InstituteGuangdong Academy of Agricultural SciencesGuangzhou 510640China

Whole-genome genotyping methods are important for breeding.However,it has been challenging to develop a robust method for simultaneous foreground and background genotyping that can easily be adapted to different genes and species.In our study,we accidently discovered that in adapter ligation-mediated PCR,the amplification by primertemplate mismatched annealing(PTMA)along the genome could generate thousands of stable PCR products.Based on this observation,we consequently developed a novel method for simultaneous foreground and background integrated genotyping by sequencing(FBI-seq)using one specific primer,in which foreground genotyping is performed by primer-template perfect annealing(PTPA),while background genotyping employs PTMA.Unlike DNA arrays,multiple PCR,or genome target enrichments,FBI-seq requires little preliminary work for primer design and synthesis,and it is easily adaptable to different foreground genes and species.FBI-seq therefore provides a prolific,robust,and accurate method for simultaneous foreground and background genotyping to facilitate breeding in the postgenomics era.

关键词： background selection foreground genotyping primer-template mismatched annealing marker-assisted breeding whole-genome genotyping