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Dissection of a rapidly evolving wheat resistance gene cluster by long-read genome sequencing accelerated the cloning of Pm69

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Plant Communications 2024年第1期5卷 69-83页

作者： Yinghui Li Zhen-Zhen Wei Hanan Sela Liubov Govta Valentyna Klymiuk Rajib Roychowdhury Harmeet Singh Chawla Jennifer Ens Krystalee Wiebe Valeria Bocharova Roi Ben-David Prerna B.Pawar Yuqi Zhang Samidha Jaiwar Istvan Molnar jaroslav dolezel Gitta Coaker Curtis J.Pozniak Tzion Fahima Institute of Evolution University of HaifaMt.CarmelHaifa 3498838Israel The Department of Evolutionary and Environmental Biology University of HaifaMt.CarmelHaifa 3498838Israel The Institute of Plant Protection Sichuan Academy of Agricultural SciencesChengdu 610066China Crop Development Centre and Department of Plant Sciences University of Saskatchewan51 Campus DriveSaskatoonSK S7N 5A8Canada Department of Vegetables and Field Crops Institute of Plant SciencesAgricultural Research Organization(ARO)–Volcani CenterRishon Lezion 7505101Israel Department of Crop Genomics and Bioinformatics China Agricultural UniversityBeijing 100094China Institute of Experimental Botany of the Czech Academy of Sciences Centre of the Region Hana´for Biotechnological and Agricultural ResearchSlechtitelu 3177900 OlomoucCzech Republic Plant Pathology Department University of CaliforniaDavisDavisCA 95616USA Present address:Department of Plant Science University of ManitobaWinnipegMB R3T 2N2Canada Present address:Agricultural Institute Centre for Agricultural ResearchELKHMartonvasar 2462Hungary

Gene cloning in repeat-rich polyploid genomes remains ***,we describe a strategy for overcoming major bottlenecks in cloning of the powdery mildew resistance gene(R-gene)Pm69 derived from tetraploid wild emmer wheat.A conventional positional cloning approach was not effective owing to suppressed *** sorting was compromised by insufficient purity.A Pm69 physical map,constructed by assembling Oxford Nanopore Technology(ONT)long-read genome sequences,revealed a rapidly evolving nucleotide-binding leucine-rich repeat(NLR)R-gene cluster with structural variations.A single candidate NLR was identified by anchoring RNA sequencing reads from susceptible mutants to ONT contigs and was validated by virus-induced gene ***69 is likely a newly evolved NLR and was discovered in only one location across the wild emmer wheat distribution range in ***69 was successfully introgressed into cultivated wheat,and a diagnostic molecular marker was used to accelerate its deployment and pyramiding with other R-genes.

关键词： cluster resistance Israel

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Development of oligonucleotide probes for FISH karyotyping in Haynaldia villosa,a wild relative of common wheat

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The Crop Journal 2020年第4期8卷 676-681页

作者： Jia Lei Jiawen Zhou Haojie Sun Wentao Wan Jin Xiao Chunxia Yuan Miroslava Karafiátová jaroslav dolezel Haiyan Wang Xiue Wang State Key Laboratory of Crop Genetics and Germplasm Enhancement Cytogenetics InstituteNanjing Agricultural University/JCIC-MCPNanjing 210095JiangsuChina Institute of Experimental Botany Czech Academy of SciencesCentre of the Region Hana for Biotechnological and Agricultural ResearchŠlechtitelů3177900 OlomoucCzech Republic

Haynaldia villosa is a wild relative of wheat and a valuable gene resource for wheat *** to the limited number of probes available for fluorescence in situ hybridization(FISH),the resolution at which the karyotype of *** can be characterized is poor,hampering accurate characterization of small segmental alien *** designed ten oligonucleotide probes using tandem repeats in DNA sequences derived from the short arm of *** chromosome 6 V(6 VS).FISH with seven of them resulted in clear signals on *** *** these,we constructed FISH karyotypes for *** using oligo-6 VS-1 and oligo-6 VS-35 oligonucleotides and characterized the distribution of the two probes in five different *** *** new FISH probes can efficiently characterize *** introgressions into wheat.

关键词： Chromosome identification Haynaldia villosa Oligonucleotide probes Tandem DNA repeats

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Sequence analysis of Erianthus arundinaceus chromosome 1 isolated by flow sorting after genomic in situ hybridization in suspension

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The Crop Journal 2022年第6期10卷 1746-1754页

作者： Shan Yang Petr Cápal jaroslav dolezel Xueting Li Wang Qian Zhiqiang Wang Kai Zeng Peiting Li Hongkai Zhou Rui Xia Muqing Zhang Zuhu Deng National Engineering Research Center for Sugarcane&State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources Fujian Agriculture and Forestry UniversityFuzhou 350002FujianChina State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources&Guangxi Key Laboratory of Sugarcane Biology Guangxi UniversityNanning 530004GuangxiChina Institute of Experimental Botany of the Czech Academy of Sciences Center of the Region Hanáfor Biotechnological and Agricultural ResearchOlomouc CZ-77900Czech Republic College of Coastal Agricultural Sciences Guangdong Ocean UniversityZhanjiang 524088GuangdongChina State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources South China Agricultural UniversityGuangzhou 510642GuangdongChina

Erianthus arundinaceus is a wild relative of sugarcane(Saccharum officinarum L.)with many desirable agronomic traits for sugarcane genetic ***,limited knowledge of the complex genome of hexaploid *** has impeded the development of required molecular *** complex genomes into single chromosomes can simplify *** flow-cytometric sorting of a single chromosome of *** in a Saccharum-Erianthus introgression line is reported.A novel approach called genomic in situ hybridization in suspension was used to discriminate the alien chromosome from sugarcane chromosomes at the same size.A total of 218,000 *** chromosome 1(EaC1)were sorted to>97%purity and amplified DNA was sequenced using Illumina and Pac Bio *** resulting assembly had a 70.93 Mb contig sequence with an N50 of 19.62 kb.A total of 56.69 Mb repeat sequences were predicted,accounting for 79.1%of the chromosome and 2646 genes having a total length of 1.84 Mb that represented 2.59%of the *** these genes,1877(70.9%)genes were functionally *** phylogenetic relationship of *** with other species using the chromosome1 sequence revealed that *** was distantly related to Oryza sativa and Zea mays,followed by Sorghum bicolor,and was closely related to *** and Saccharum *** study provides the first insights into the characteristics of EaC1,and the results will provide tools to support molecular improvement and alien introgression breeding of sugarcane.

关键词： Flow cytometry GISHIS Chromosome sorting Genome analysis Sugarcane

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Chromosome sorting and its applications in common wheat (Triticum aestivum) genome sequencing

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Chinese Science Bulletin 2010年第15期55卷 1463-1468页

作者： WU SuoWei XIAO Yang ZHENG Xu CAI YingFan dolezel jaroslav LIU Bing Hua YANG Li SONG MeiFang ZHOU Peng ZHOU Yang MENG FanHua WANG ShanHong LIU HongWei HAI HuQu YANG JianPing Institute of Crop Sciences Chinese Academy of Agricultural Sciences Beijing 100081 China Graduate School Chinese Academy of Agricultural Sciences Beijing 100081 China College of Bio-information Chongqing University of Posts and Telecommunication Chongqing 400065 China Laboratory of Molecular Cytogenetics and Cytometry Institute of Experimental Botany Olomouc CZ-77200 Czech Republic Institute of Vegetable Research Shandong Academy of Agricultural Sciences Jinan 250100 China

The large genome size (～17000 Mb) and complicated DNA structures of common wheat (Triticum aestivum) hamper its genome *** means of flow cytometry,systematic investigations on individual chromosome sorting have been carried out to construct chromosome-specific bacterial artificial chromosome (BAC) libraries since the *** wheat chromosome-specific BAC libraries,such as chromosome 3B,three D genome chromosomes (1D,4D and 6D),and the short arm of chromosome 1B,have been developed,and the physical map of chromosome 3B was established in *** same chromosome-based strategy is being employed by the International Wheat Genome Sequencing Consortium (IWGSC) to establish the physical maps of the other 20 common wheat chromosomes (*** Spring).Several projects on wheat genome sequencing are currently *** availability of new sequencing technologies provides new choices for sequencing of gene space of the wheat *** applications of flow-sorted chromosomes in wheat genome studies present some examples to analyze the complex genomes of cereals.

关键词：细菌人工染色体基因组测序普通小麦应用排序 BAC文库物理图谱基因组大小

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基于纤毛鹅观草特异的卫星重复序列开发寡核苷酸探针

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南京农业大学学报 2022年第3期45卷 442-452页

作者：程梦豪 Miroslava Karafiatova 孙昊杰 Kate Arina Holušva jaroslav dolezel 宋新颖王海燕王秀娥南京农业大学作物遗传与种质创新国家重点实验室/细胞遗传研究所/现代作物生产省部共建协同创新中心江苏南京210095 捷克科学院实验植物学研究所/哈纳地区生物技术和农业研究中心捷克共和国奥洛穆茨77900

[目的]本文旨在开发纤毛鹅观草特异的寡核苷酸(oligonucleotide,oligo)探针,进一步完善纤毛鹅观草染色体鉴定技术。[方法]利用前期选育的普通小麦-纤毛鹅观草异附加系DA2S^(c)L和DA6S^(c),通过流式分拣和基因组二代测序获得纤毛鹅观草... 详细信息

[目的]本文旨在开发纤毛鹅观草特异的寡核苷酸(oligonucleotide,oligo)探针,进一步完善纤毛鹅观草染色体鉴定技术。[方法]利用前期选育的普通小麦-纤毛鹅观草异附加系DA2S^(c)L和DA6S^(c),通过流式分拣和基因组二代测序获得纤毛鹅观草染色体6S^(c)和染色体臂2S^(c)长臂的基因组序列,利用Repeatexplorer2/TAREAN软件从中鉴定出卫星重复序列并设计成oligo探针,通过荧光原位杂交(fluorescence in situ hybridization,FISH)分析所开发oligo探针的应用价值。[结果]从6S^(c)和2S^(c)L基因组序列中共鉴定出11个卫星重复序列并开发成11个oligo探针,oligo-FISH结果表明,其中6个探针可以在纤毛鹅观草染色体上产生明显杂交信号,而在小麦染色体上未产生明显杂交信号,可用于特异鉴定小麦背景中的纤毛鹅观草染色体或片段。对1套普通小麦-纤毛鹅观草异附加系oligo-FISH分析发现,oligo-2S^(c)L^(-1)63和oligo-6S^(c)-111仅在S^(c)基因组染色体上产生明显信号,可作为纤毛鹅观草S^(c)组特异探针;将oligo-2S^(c)L-161和oligo-2S^(c)L-163组合,对1整套二体异附加系进行双色oligo-FISH,构建了纤毛鹅观草染色体的oligo-FISH核型。[结论]本研究提供了纤毛鹅观草重复序列组成的初步信息,开发的探针能特异鉴定纤毛鹅观草染色体,阐明纤毛鹅观草2个基因组的来源和分化,对推动纤毛鹅观草优异基因的转移和利用有重要意义。

关键词：纤毛鹅观草普通小麦-纤毛鹅观草异附加系染色体分拣卫星重复序列寡聚核苷酸探针荧光原位杂交

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Pm21 from Haynaldia villosa Encodes a CC-NBS- LRR Protein Conferring Powdery Mildew Resistance in Wheat

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Molecular Plant 2018年第6期11卷 874-878页

作者： Liping Xing Ping Hu Jiaqian Liu Kamil Witek Shuang Zhou Jiefei Xu Weihao Zhou Li Gao Zhenpu Huang Ruiqi Zhang Xiue Wang Peidu Chen Haiyan Wang Jonathan D.G. Jones Miroslava Karafiatova Jan Vrana Jan Baros jaroslav dolezel Yuanchun Tian Yufeng Wu Aizhong Cao National Key Laboratory of Crop Genetics and Germplasm Enhancement Cytogenetics Institute Nanjing Agricultural University/JGIC-MCP Nanjing 210095 China The Sainsbury Laboratory Norwich Research Park Norwich NR4 7UH UK Institute of Experimental Botany Centre of the Region Hana for Biotechnological and Agricultural Research Slechtitelu 31 78371 OlomoucCzech Republic

Dear Editor Wheat powdery mildew, caused by Blumeria graminis f. sp. tritici （Bgt）, is a destructive disease of wheat throughout the world. One of the most important environmental-friendly and economical methods to reduce wheat loss caused by Bgt is to develop highly resistant varieties （Kuraparthy et al., 2007）. Pm21 from the wild species Haynaldia villosa （also known as Dasypyrum villosum） confers high resistance to Bgt in wheat throughout all growth stages. It has now become one of the most highly effective genetic loci introgressed into wheat from wild species, and the commercial varieties harboring Pm21 have been widely used in wheat production with more than 4 million hectares in China.

关键词： Pm21 小麦粉蛋白质编码环境友好生长阶段小麦生产还原剂

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NLR1-V,a CC-NBS-LRR encoding gene,is a potential candidate gene of the wheat powdery mildew resistance gene Pm21

NLR1-V,a CC-NBS-LRR encoding gene,is a potential candidate g...

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第八届全国小麦基因组学及分子育种大会

作者： Liping Xing Ping Hu Jiaqian Liu Yufeng Wu jaroslav dolezel Ruiqi Zhang Xiue Wang Peidu Chen Aizhong Cao National Key Laboratory of Crop Genetics and Germplasm Enhancement Cytogenetics InstituteNanjing Agricultural University/JCIC-MCP Institute of Experimental Botany

Wheat powdery mildew,caused by Blumeria graminis ***,is one of the most destructive diseases all over the ***21,transferred from the wild Haynaldia villosa to wheat,confers broad spectrum resistance throughout the whole growth stage,and this gene has been widely used in wheat production for more than 20 *** the candidate gene of Pm21 is the prerequisite for elucidating the resistance mechanism,and is a valuable attempt to clone the target genes from the evohitionarily distant wild *** this study,an innovative approach,which combined cytogenetic stocks development,mutagenesis,RenSeq(R gene enrichment sequencing) and PacBio approaches,was tried successfully to clone an NBS-LRR type gene NLR1-V from the Pm21 *** Stocks and Mutants ***,a new cryptic alien introgression line NAU427 with very small introgression segment of 6 VS but still containing Pm21 gene was identified by molecular markers analysis and resistance phenotype evaluation,and the line showed no fluorescent signal when detected by *** enables us to narrow the Pm21 locus into an extremely small region ***,6 independent susceptible M3 mutants of T6 VS·6 AL was identified from more than 20,000 M2 EMS treated lines,which could help us to anchoring the mutant ***-PacBio and NLR Gene ***,the transcriptome of *** was obtained by NGS and the full-length NBS-LRR gene database was constructed by *** the following study,45 individual NLR-carrying contigs showing >80%identity with 6 A/6 B/6 D/6 H NLR homologous were obtained which were identified as the putative NLRs located on the 6 V chromosome,but only two expressed NLR genes were located to the Pm21 locus using the NAU427 as the mapping material,and only NLR1-V showed polymorphism between the wild T6 VS-6 AL and its six ***21 Candidate Gene ***,both the genomic and cDNA sequences of NLR1-V were cloned and *** f

关键词： NLR1-V CC-NBS-LRR Pm21 Mutagenesis RenSeq-Pacbio Chromosome sorting Chicago Hi-C

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Social networks of reintroduced Przewalski's horses in the Great Gobi B Strictly Protected Area (Mongolia)

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Current Zoology 2024年第2期70卷 182-194页

作者： Anna Bernatkova Ganbaatar Oyunsaikhan jaroslav Simek Martina Komarkova Francisco Ceacero Faculty of Tropical AgriSciences Czech University of Life Sciences PragueCzech Republic Great Gobi B Strictly Protected Area Takhin TalMongolia Zoo Praha U Trojského zamku 120/3PragueCzech Republic

Analyzing social networks is a powerful tool for understanding the ecology of social *** most studies focus on the role of each group member,few compare groups with different *** current population of Przewalski's horses Equus ferus przewalskii at the Great Gobi B Strictly Protected Area(Mongolia)includes groups of wild-born and captive-bred individuals with different experiences with the area(acclimatizing,long-term reintroduced,and wild-born),therefore serving as an ideal natural behavioral *** filmed 11 groups for 141.5 hours in summer 2018(July),late spring 2019(May,June),and autumn 2019(September,October).Affiliative and agonistic interactions were recorded,and social networks were *** tested the influence of origin,experience,season,sex,age,relative time belonging to the group,relat-edness,and dominance rank on different network indices at the individual and group *** found that groups with greater experience in the area are generally better connected than members of the newly formed ***,these strong networks were created by wild-born individuals with very low interaction *** the contrary,inexperienced groups composed of captive-bred individuals displayed many inter actions but created weak social *** results show a trend of behavioral transition from acclimatizing through long-term reintroduced to wild-born groups,supporting that the newly formed groups of released Przewalski's horses need time to display the typical social behavior patterns of wild-born ***-term monitoring of released Przewalski's horses is recommended to promote the success of this reintroduction program.

关键词： Przewalski's horses reintroduction social behavior soft-release.

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小麦7DL染色体参考序列/人工分子(pseudomolecule)组装

小麦7DL染色体参考序列/人工分子(pseudomolecule)组装

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第六届全国小麦基因组学及分子育种大会

作者：王乐聂小军童维 Simkova Hana Safar Jan dolezel jaroslav Rudi Apples Mingcheng Luo 宋卫宁旱区作物逆境生物学国家重点实验室

基于国际小麦基因组测序协作组织的合作,我们构建了小麦7DL染色体物理图谱,挑选出了4457个MTP克隆,contigN50为348KB。对这些克隆采用二代测序,组装获得了1454个scaffold,最长scaffold达到2.1Mb,scaffold的N50达到391kb,N90为108kb,拼... 详细信息

基于国际小麦基因组测序协作组织的合作,我们构建了小麦7DL染色体物理图谱,挑选出了4457个MTP克隆,contigN50为348KB。对这些克隆采用二代测序,组装获得了1454个scaffold,最长scaffold达到2.1Mb,scaffold的N50达到391kb,N90为108kb,拼接序列总长为391Mb,覆盖了整个染色体臂的82%,基本完成了小麦7DL的序列草图。为了验证BAC组装的正确性和准确性,我们应用了单分子测序(PacBio),确认了二者组装结果的可靠性。我们对这些scaffold用遗传标记进行了锚定。对组装序列的注释表明,7DL染色体重复序列占整个组装序列的62%以上,进一步的序列分析工作正在进行中。

关键词：小麦基因组

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Corrigendum to“Introgression of sharp eyespot resistance from Dasypyrum villosum chromosome 2VL into bread wheat”[Crop J.11(2023)1512–1520]

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The Crop Journal 2023年第6期11卷 1949-1949页

作者： Caiyun Liu Wei Guo Yang Wang Bisheng Fu jaroslav dolezel Ying Liu Wenling Zhai Mahmoud Said István Molnár Katerina Holušová Ruiqi Zhang Jizhong Wu Institute of Germplasm Resources and Biotechnology/Jiangsu Provincial Key Laboratory of Agrobiology Jiangsu Academy of Agricultural SciencesNanjing 210014JiangsuChina College of Agronomy/JCIC-MCP/National Key Lab of Crop Genetics and Germplasm Enhancement Nanjing Agricultural UniversityNanjing 210095JiangsuChina Institute of Experimental Botany Centre of the HanáRegion for Biotechnological and Agricultural ResearchŠlechtitelu 31CZ-783671 OlomoucCzech Republic Field Crops Research Institute Agricultural Research Centre9 Gamma StreetGiza12619 CairoEgypt Agricultural Institute Centre for Agricultural ResearchELKHMartonvásár 2462Hungary Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops Yangzhou UniversityYangzhou 225009JiangsuChina Zhongshan Biological Breeding Laboratory Nanjing 210014JiangsuChina

The authors regret to report some missing information in the authorship and associated changes of the *** page 1512,the author information reads:“Caiyun Liu a,Wei Guo a,Yang Wang b,Bisheng Fu a,jaroslav dolezel c,Ying Liu a,Wenling Zhai a,Mahmoud Said c,d,István Molnár c,d,e,Katerina Holušovác,Ruiqi Zhang b,*,Jizhong Wu a,f,g,*”.It should be changed to“Caiyun Liu a,1,Wei Guo a,1,Yang Wang b,Bisheng Fu a,jaroslav dolezel c,Ying Liu a,Wenling Zhai a,Mahmoud Said c,d,István Molnár c,d,e,Katerina Holušovác,Ruiqi Zhang b,*,Jizhong Wu a,f,g,*”.On page 1512 in the footnote,the following sentence should be added below the corresponding authors’information:1 These authors contributed equally to this *** correction has been updated *** authors would like to apologize for any inconvenience caused.

关键词： sharp correction bread

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