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

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 *** centromeres are crucial for chromosome segregation,and contain some unreported *** to the diverse and complex centromere region,a comprehensive understanding of rice centromere structure and function at the population level is *** 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 *** showed that rice centromeres have diverse satellite repeat CentO,which vary across chromosomes and subpopulations,reflecting their distinct evolutionary *** 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 ***,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 *** 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 *** 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

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CRISPR/Cas9-mediated knockout of E4 gene promotes maturation in soybean

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Oil crop Science 2024年第3期9卷 170-176页

作者： Shuiqing Wu Li Chen Mengwei guo Yupeng Cai Yang Gao Shan Yuan Shi Sun Yuxian Zhang Wensheng Hou Tianfu Han College of Agriculture Heilongjiang Bayi Agricultural UniversityDaqing163316China Ministry of Agriculture key Laboratory of Soybean Biology(beijing) Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing100081China College of Agriculture Northeast Agricultural UniversityHarbin150030China State key Laboratory of crop Germplasm Innovation and Molecular Breeding Syngenta Biotechnology(China)Co.LtdBeijing100081China

Soybean is a broadly popular and extensively cultivated crop,however,many high-yield and high-quality varieties require specific growth conditions,restricting their widespread *** appropriate light conditions and photoperiod must be attained for these varieties to thrive in new *** this study,we employed CRISPR/Cas9 to design two sgRNAs aimed at knocking out the maturity-related gene E4 in a major American soybean variety called''Jack'',which belongs to maturity group MGII.E4 gene is primarily involved in the photoperiodic flowering and maturity in soybean,making it an ideal candidate for genetic *** successfully obtained 1 homozygous E4-SG1 mutant type with 1-bp insertion,and 4 homozygous E4-SG2 mutants type with 2-bp deletion,7-bp deletion,61-bp deletion,and 1-bp insertion,*** homozygous e4 mutant plants contained early termination codons devoid of transgenic ***,no potential offtarget sites of the E4 gene were detected.A comparative analysis revealed that,unlike the wild-type,the maturity time of homozygous e4 mutants was early under both short-day and long-day *** mutants offer novel germplasm resources that may be used to modify the photoperiod sensitivity and maturity of soybean,enhancing its adaptability to high-latitude regions.

关键词： Soybean E4 CRISPR/Cas9 Maturity

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A complete reference genome assembly for foxtail millet and Setaria-db, a comprehensive database for Setaria

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Molecular Plant 2024年第2期17卷 219-222页

作者： Qiang He Chunchao Wang Qiang He Jun Zhang Hongkai Liang Zefu Lui Kun Xie Sha Tang Yuhan Zhou Bin Liu Hui Zhi Guanqing Jia Ganggang guo Huilong Du Xianmin Diao State key Laboratory of crop gene resources and Breeding Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China School of Life Sciences Institute of Life Sciences and Green DevelopmentHebei UniversityBaoding 071000China State key Laboratory of Rice Biology&Breeding Zhejang Provincial Key Laboratory of Crop GermplasmThe Advanced Seed InstituteZhejiang UniversityHangzhouChina

Dear Editor,,Foxtail millet(Setaria italica)and its wild ancestor green foxtail(***),are two C4 genetic model plants known for their desirable traits,such as small size,short life cycle,ease of transformation,and a compact genome size(~420 Mb)(He et al.,2023).Foxtail millet stands out as the only cultivated species within the Setaria *** a foundational crop for ancient east Asian agriculture civilization,it possesses remarkable drought and soil-nutrient deficiency tolerance.

关键词： comprehensive soil cultivated

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Development and utilization of a new chemically-induced soybean library with a high mutation density

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Journal of Integrative Plant Biology 2017年第1期59卷 60-74页

作者： Zhongfeng Li Lingxue Jiang Yansong Ma Zhongyan Wei Huilong Hong Zhangxiong Liu Jinhui Lei Ying Liu Rongxia Guan Yong guo Longguo Jin lijuan Zhang Yinghui Li Yulong Ren Wei He Ming Liu Nang Myint Phyu Sin Htwe Lin Liu bingfu guo Jian Song Bing Tan Guifeng Liu Maiquan Li Xianli Zhang Bo Liu Xuehui Shi Sining Han Sunan Hua Fulai Zhou Lili Yu Yanfei Li Shuang Wang Jun Wang Ruzhen Chang lijuan qiu national key facility for gene resources and genetic improvement/key Laboratory of crop Germplasm Utilization Ministry of AgricultureInstitute of Crop ScienceChinese Academy of Agricultural Science Soybean Research Institute Heilongjiang Academy of Agricultural Sciences College of Agriculture Yangtze University

Mutagenized populations have provided important materials for introducing variation and identifying gene function in plants. In this study, an ethyl methanesulfonate（EMS）-induced soybean（Glycine max） population,consisting of 21,600 independent M_2 lines, was *** 1,000 M_（4（5））families, with diverse abnormal phenotypes for seed composition, seed shape, plant morphology and maturity that are stably expressed across different environments and generations were identified. Phenotypic analysis of the population led to the identification of a yellow pigmentation mutant, gyl, that displayed significantly decreased chlorophyll（Chl） content and abnormal chloroplast development. Sequence analysis showed that gyl is allelic to Minn Gold, where a different single nucleotide polymorphism variation in the Mg-chelatase subunit gene（ChlI1a） results in golden yellow leaves. A cleaved amplified polymorphic sequence marker was developed and may be applied to marker-assisted selection for the golden yellow phenotype in soybean breeding. We show that the newly developed soybean EMS mutant population has potential for functional genomics research and genetic improvement in soybean.

关键词： soybean mutant yellow chemically golden phenotype genomics mutation Glycine chloroplast

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Development of a rice phenomics facility equipped with agricultural photonics

Development of a rice phenomics facility equipped with agric...

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第十三届全国植物基因组学大会

作者： Wanneng Yang~1,Lingfeng Duan~(2,3),Chenglong Huang~(2,3),Ni Jiang~(2,3),Wei Fang~(2,3),Hui Feng~(2,3), guoxing Chen~1,Lizhong Xiong~1,Qian Liu~(2,3,*) 1 national key Laboratory of crop genetic improvement and national Center of Plant gene Research,,Huazhong Agricultural University,Wuhan,430070,china. 2 Britton Chance Center for Biomedical Photonics,Wuhan national Laboratory for Optoelectronics-Huazhong University of Science and Technology,1037 Luoyu Rd.,Wuhan 430074,P.R.china. 3 key Laboratory of Biomedical Photonics of Ministry of Education,College of Life Science and Technology,Huazhong University of Science and Technology,1037 Luoyu Rd.,Wuhan 430074,P.R.china.

As genome sequencing of rice and other crops varieties completed, terabytes of sequence information have been presented and needed to be linked with *** genetic analysis,precise and rapid quantification of phenotypic data are ***,the conventional methods of extracting rice phenotypic traits are still manual,which is time consuming,subjective,wearisome and lack- *** aimed to develop a rice phenomics facility for high-throughput phenotyping morphological and yield-related traits,which mainly includes plant height, tillers,dry weight,leaf area,leaf temperature,the number of total spikelets(NTS),the number of filled spikelets(NFS),the 1000-grain weight(TGW),the grain length(GL), and the grain width(GW).After test under industrial condition,the facility was capable of evaluating phenotyping morphological and yield-related traits with mean absolute percent error less than 5%.And the efficiency is 2880 and 1440 plants per continuous 24 h workday for phenotyping morphological and yield-related traits, *** facilities will be also used for phenotyping conditional traits,such as stress resistance and nutrition use *** with agri-photonics,the rice phenomics facility can be used to determine rice phenotypic traits with four advantages over conventional method:objectivity,high efficiency,repeatability,and ***,the high-throughput facility provides plant scientists and breeders a novel tool to bridge genomics and phenomics.

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Involvement of sulfur assimilation in the low β subunit content of soybean seed storage protein revealed by comparative transcriptome analysis

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The crop Journal 2019年第4期7卷 504-515页

作者： Xi Zhang Ruixin Xu Wei Hu Wan Wang Dezhi Han Fan Zhang Yongzhe Gu Yong guo Jun Wang lijuan qiu College of Agriculture Yangtze University Jingzhou 434025 Hubei China national key facility for gene resources and genetic improvement Institute of Crop Sciences Chinese Academy of Agricultural Sciences Beijing 100081 China Soybean Research Center Heihe Institute Heilongjiang Academy of Agricultural Sciences Heihe 100142 Helongjiang China

The β subunit of soybean [Glycine max (L.) Merr.] seed storage protein is of great significance in sulfur-containing amino acid balance and soybean processing properties. The objective of this study was to elucidate the relationship between the β subunit and sulfur-containing amino acid composition, and the potential regulatory mechanism. The β subunit was independently accumulated in comparison with other major subunits (α/α′, acidic, basic, and A3) during seed filling, and a low level of β subunit content (BSC) was formed during the accumulation process. In low-BSC mature seeds, crude protein, oil content, and fatty acid composition were not changed, but sulfur-containing amino acids (Cys + Met) in the low- BSC seeds increased significantly (by 31.5%), suggesting that an internal regulatory mechanism within seed might be responsible for the rebalance of seed protein composition and that sulfur assimilation might be deeply involved in β subunit accumulation. Transcriptomic analysis revealed that genes involved in anabolism of cysteine, methionine, and glutathione were up-regulated but those involved in the catabolism of these compounds were down-regulated, suggesting a relationship between the elevation of methionine and glutathione and low BSC. Our study sheds light on seed composition in low BSC lines and on the potential molecular regulatory mechanism of β subunit accumulation, broadening our understanding of soybean seed protein synthesis and its regulation.

关键词： Soybean β subunit Transcriptome analysis Sulfur-containing amino acids Sulfur assimilation

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MiR1511 co-regulates with miR1511* to cleave the GmRPL4a gene in soybean

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Chinese Science Bulletin 2012年第28期57卷 3804-3810页

作者： LUO ZhongQin JIN Longguo qiu lijuan The national key Faeility for crop gene resources and genetic improvement(NFCRI) Institute of Crop ScienceChinese Academy of Agricultural SeiencesBeijing 100081China

MicroRNA1511(miR1511) is a small RNA with unknown function identified in several plants by deep *** this study,we showed that this small RNA is an authentic miRNA by analyzing the structure of the precursor stem-loop containing the newly identified miR1511 * *** confirmed this result by Northern blotting *** used 5'RACE to identify one of the target genes(GmRPL4a) cleaved by both miR1511 and miR1511 *.The site cleaved by miR1511 * was located in the first exon of GmRPL4a,and the site cleaved by miR1511 was located in the second *** expression level of miR1511/1511 * was higher in leaves than in roots and *** contrast,the lowest level of GmRPL4a expression was in the leaves and the highest in the *** results indicate that an miRNA can co-regulate with an miRNA * to cleave the same target gene in plants,and that the level of GmRPL4a mRNA is regulated by miR1511/1511 *.

关键词：靶基因切割 miRNA Northern 大豆 blot分析小RNA RACE

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genetic dissection of and genomic selection for seed weight, pod length,and pod width in soybean

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The crop Journal 2023年第3期11卷 832-841页

作者： Yijie Chen Yajun Xiong Huilong Hong Gang Li Jie Gao Qingyuan guo Rujian Sun Honglei Ren Fan Zhang Jun Wang Jian Song lijuan qiu College of Agriculture Yangtze UniversityJingzhou 434025HubeiChina College of Life Sciences Yangtze UniversityJingzhou 434025HubeiChina national key facility for gene resources and genetic improvement/Institute of crop Sciences Chinese Academy of Agricultural SciencesBeijing 100081China Soybean Research Institute Heilongjiang Academy of Agricultural SciencesHarbin 150086HeilongjiangChina Engineering Research Center of Ecology and Agricultural Use of Wetland Ministry of EducationJingzhou 434025HubeiChina Hulunbuir Institute of Agriculture and Animal Husbandry Hulunbuir 021000Inner MongoliaChina

A biparental soybean population of 364 recombinant inbred lines(RILs)derived from Zhongdou 41×ZYD02.878 was used to identify quantitative trait loci(QTL)associated with hundred-seed weight(100-SW),pod length(PL),and pod width(PW).100-SW,PL,and PW showed moderate correlations among one another,and 100-SW was correlated most strongly with PW(0.64–0.74).Respectively 74,70,75 and19 QTL accounting for 38.7%–78.8%of total phenotypic variance were identified by inclusive composite interval mapping,restricted two-stage multi-locus genome-wide association analysis,3 variancecomponent multi-locus random-SNP-effect mixed linear model analysis,and conditional genome-wide association *** these QTL,189 were novel,and 24 were detected by multiple *** loci were associated with 100-SW,PL,and PW and may be pleiotropic loci.A total of 284 candidate genes were identified in colocalizing QTL regions,including the verified gene Seed thickness 1(ST1).Eleven genes with functions involved in pectin biosynthesis,phytohormone,ubiquitin-protein,and photosynthesis pathways were prioritized by examining single nucleotide polymorphism(SNP)variation,calculating genetic differentiation index,and inquiring gene *** prediction accuracies of genomic selection(GS)for 100-SW,PL,and PW based on single trait-associated markers reached 0.82,0.76,and 0.86 respectively,but selection index(SI)-assisted GS strategy did not increase GS efficiency and inclusion of trait-associated markers as fixed effects reduced prediction *** results shed light on the genetic basis of 100-SW,PL,and PW and provide GS models for these traits with potential application in breeding programs.

关键词： Soybean Seed weight Pod size genetic analysis Genomic selection

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OsPRMT6a-mediated arginine methylation of OsJAZ1 regulates jasmonate signaling and spikelet development in rice

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Molecular Plant 2024年第6期17卷 900-919页

作者： Kun Dong Fuqing Wu Siqi Cheng Shuai Li Feng Zhang Xinxin Xing Xin Jin Sheng Luo Miao Feng Rong Miao Yanqi Chang Shuang Zhang Xiaoman You Peiran Wang Xin Zhang Cailin Lei Yulong Ren Shanshan Zhu Xiuping guo Chuanyin Wu Dong-Lei Yang Qibing Lin Zhijun Cheng Jianmin Wan State key Laboratory of crop gene resources and Breeding National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China State key Laboratory for crop genetics and Germplasm Enhancement Nanjing Agricultural UniversityNanjing 210095China

Although both protein arginine methylation(PRMT)and jasmonate(JA)signaling are crucial for regulating plant development,the relationship between these processes in the control of spikelet development remains *** this study,we used the CRISPR/Cas9 technology to generate two OsPRMT6a loss-of-function mutants that exhibit various abnormal spikelet ***,we found that OsPRMT6a can methylate arginine residues in JA signal repressors OsJAZ1 and *** showed that arginine methylation of OsJAZ1 enhances the binding affinity of OsJAZ1 with the JA receptors OsCOI1a and OsCOI1b in the presence of JAs,thereby promoting the ubiquitination of OsJAZ1 by the SCF^(OsCOI1a/OsCOI1b) complex and degradation via the 26S *** process ultimately releases OsMYC2,a core transcriptional regulator in the JA signaling pathway,to activate or repress JA-responsive genes,thereby maintaining normal plant(spikelet)***,in the osprmt6a-1 mutant,reduced arginine methylation of OsJAZ1 impaires the interaction between OsJAZ1 and OsCOI1a/OsCOI1b in the presence of *** a result,OsJAZ1 proteins become more stable,repressing JA responses,thus causing the formation of abnormal spikelet ***,we discovered that JA signaling reduces the OsPRMT6a mRNA level in an OsMYC2-dependent manner,thereby establishing a negative feedback loop to balance JA *** further found that OsPRMT6a-mediated arginine methylation of OsJAZ1 likely serves as a switch to tune JA signaling to maintain normal spikelet development under harsh environmental conditions such as high ***,our study establishes a direct molecular link between arginine methylation and JA signaling in rice.

关键词： protein arginine methylation jasmonate signaling negative feedback loop spikelet development adaptation to heat stress rice

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Genome wide analysis of the Dof transcription factor gene family reveals soybean-specific duplicable and functional characteristics

Genome wide analysis of the Dof transcription factor gene fa...

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第十四届全国植物基因组学大会

作者： Yong guo lijuan qiu The national key facility for crop gene resources and genetic improvement(NFCRI) Institute of Crop ScienceChinese Academy of Agricultural Sciences

Dof domain protein family represents a classic plant-specific zinc-finger transcription factor family involved in a variety of biological processes in ***,there are only very limited reports on the characterization of... 详细信息

关键词： Dof soybean duplication gene expression phylogenetic analysis cis-regulatory element

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