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OcBSA:An NGS-based bulk segregant analysis tool for outcross populations

Molecular Plant 2024年第4期17卷 648-657页

作者： lingkui zhang Yanfeng Duan Zewei zhang Lei zhang Shumin Chen Chengcheng Cai Shaoguang Duan Kang zhang Guangcun Li Feng Cheng State Key Laboratory of Vegetable Biobreeding Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural AffairsKey Laboratory of Biology and Genetic Improvement of Tuber and Root Crop of Ministry of Agriculture and Rural AffairsSino-Dutch Joint Laboratory of Horticultural GenomicsInstitute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijing 100081China

Constructing inbred lines for self-incompatible species and species with long generation times is challenging,making the use of F1 outcross/segregating populations the main strategy for genetic studies of such ***,there is a lack of dedicated algorithms/tools for rapid quantitative trait locus(QTL)mapping using the F1 *** this end,we have designed and developed an algorithm/tool called OcBSA specifically for QTL mapping of F1 *** transforms the four-haplotype inheritance problem from the two heterozygous diploid parents of the F1 population into the two-haplotype inheritance problem common in current genetic studies by removing the two haplotypes from the heterozygous parent that do not contribute to phenotype segregation in the F1 *** of OcBSA on 1800 simulated F1 populations demonstrated its advantages over other currently available tools in terms of sensitivity and *** addition,the broad applicability of OcBSA was validated by QTL mapping using seven reported F1 populations of apple,pear,peach,citrus,grape,tea,and *** also used OcBSA to map the QTL for flower color in a newly constructed F1 population of potato generated in this *** OcBSA mapping result was verified by the insertion or deletion markers to be consistent with a previously reported locus harboring the ANTHOCYANIN 2 gene,which regulates potato flower *** together,these results highlight the power and broad utility of OcBSA for QTL mapping using F1 populations and thus a great potential for functional gene mining in outcrossing *** ease of use,we have developed both Windows and Linux versions of OcBSA,which are freely available at:https://***/Bioinformaticslab/OcBSA.

关键词： outcross BSA self-incompatible F1 population QTL mapping potato

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Improved genome annotation of Brassica oleracea highlights the importance of alternative splicing

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Horticultural Plant Journal 2024年第4期10卷 961-970页

作者： Yinqing Yang Lei zhang Qi Tang lingkui zhang Xing Li Shumin Chen Kang zhang Ying Li Xilin Hou Feng Cheng State Key Laboratory of Crop Genetics and Germplasm Enhancement College of HorticultureNanjing Agricultural UniversityNanjing 210095China State Key Laboratory of Vegetable Biobreeding Institute of Vegetables and FlowersChinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural AffairsSino-Dutch Joint Laboratory of Horticultural GenomicsBeijing 100081China

Brassica oleracea has been developed into many important crops,including cabbage,kale,cauliflower,broccoli and so *** genome and gene annotation of cabbage(cultivar JZS),a representative morphotype of ***,has been widely used as a common reference in biological *** its genome assembly has been updated twice,the current gene annotation still lacks information on untranslated regions(UTRs)and alternative splicing(AS).Here,we constructed a high-quality gene annotation(JZSv3)using a full-length transcriptome acquired by nanopore sequencing,yielding a total of 59452 genes and 75684 ***,we re-analyzed the previously reported transcriptome data related to the development of different tissues and cold response using JZSv3 as a reference,and found that 3843 out of 11908 differentially expressed genes(DEGs)underwent AS during the development of different tissues and 309 out of 903 cold-related genes underwent AS in response to cold ***,we also identified many AS genes,including BolLHCB5 and BolHSP70,that displayed distinct expression patterns within variant transcripts of the same gene,highlighting the importance of JZSv3 as a pivotal reference for AS ***,JZSv3 provides a valuable resource for exploring gene function,especially for obtaining a deeper understanding of AS regulation mechanisms.

关键词： Brassica oleracea Oxford nanopore technologies Gene annotation Alternative splicing

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Genome Assembly and Population Resequencing Reveal the Geographical Divergence of Shanmei(Rubus corchorifolius)

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Genomics, Proteomics & Bioinformatics 2022年第6期20卷 1106-1118页

作者： Yinqing Yang Kang zhang Ya Xiao lingkui zhang Yile Huang Xing Li Shumin Chen Yansong Peng Shuhua Yang Yongbo Liu Feng Cheng Institute of Vegetables and Flowers Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Horticultural CropsMinistry of Agriculture and Rural AffairsSino-Dutch Joint Laboratory of Horticultural GenomicsBeijing 100081China Biotechnology Research Center Xiangxi Academy of Agricultural SciencesJishou 416000China Lushan Botanical Garden Chinese Academy of SciencesJiujiang 332900China State Environmental Protection Key Laboratory of Regional Eco-process and Function Assessment Chinese Research Academy of Environmental SciencesBeijing 100012China

Rubus corchorifolius(Shanmei or mountain berry,2n=14)is widely distributed in China,and its fruits possess high nutritional and medicinal ***,we reported a highquality chromosome-scale genome assembly of Shanmei,with contig size of 215.69 Mb and 26,696 *** comparison among Rosaceae species showed that Shanmei and Fupenzi(Rubus chingii Hu)were most closely related,followed by blackberry(Rubus occidentalis),and that environmental adaptation-related genes were expanded in the Shanmei *** resequencing of 101 samples of Shanmei collected from four regions in the provinces of Yunnan,Hunan,Jiangxi,and Sichuan in China revealed that among these samples,the Hunan population of Shanmei possessed the highest diversity and represented the more ancestral ***,the Yunnan population underwent strong selection based on the nucleotide diversity,linkage disequilibrium,and historical effective population size ***,genes from candidate genomic regions that showed strong divergence were significantly enriched in the flavonoid biosynthesis and plant hormone signal transduction pathways,indicating the genetic basis of adaptation of Shanmei to the local *** high-quality assembled genome and the variome dataset of Shanmei provide valuable resources for breeding applications and for elucidating the genome evolution and ecological adaptation of Rubus species.

关键词： Rubus corchorifolius Genome assembly Resequencing Divergence Genome evolution

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Segmental Translocation Contributed to the Origin of the Brassica S-locus

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Horticultural Plant Journal 2020年第3期6卷 167-178页

作者： Yinan Cui Mu Zhuang Jian Wu Jisheng Liu Yiyue zhang lingkui zhang Yile Huang Xu Cai Jianli Liang Kang zhang Xiaowu Wang Feng Cheng Institute of Vegetables and Flowers Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of AgricultureSino-Dutch Joint Laboratory of Horticultural GenomicsBeijing 100081China

Self-incompatibility(SI),which has recurred during the evolution of plants,is one of the most important cross-pollination mating *** S-loci have been reported in Brassicaceae,namely,Arabidopsis lyrata(Al),Brassica(Br),and Leavenworthia alabamica(La)***,through multi-genomic comparative analysis of 20 species,we revealed that the most ancient S-locus was formed prior to the divergence of Brassicaceae lineage I and *** retained and inherited by Arabidopsis,as the Al S-locus in Brassicaceae lineage ***,we found that the Br S-locus,which has been widely used in the breeding of Brassica crops to generate hybrid seeds,was formed through segmental translocation(ST)in the hexaploid ancestor of Brassica in Brassicaceae lineage *** Br S-locus was evolved through a ST from one of the triplicated ancestral S-locus paralogs in the Brassica hexaploidy ancestor,while the other two S-locus paralogs were *** with the previous discovery that the La S-locus was formed through a secondary origin in Brassicaceae lineage I,we conclude the monophyletic origin of Al and Br S-loci and clarify the evolutionary route of S-loci in the Brassicaceae *** findings will contribute to evolutionary studies and breeding applications of the S-locus in Brassicaceae.

关键词： Self incompatibility SRK,SCR Gene evolution Brassicaceae

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The genome of Orychophragmus violaceus provides genomic insights into the evolution of Brassicaceaepolyploidizationandits distinct traits

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Plant Communications 2023年第2期4卷 77-92页

作者： Kang zhang Yinqing Yang Xin zhang lingkui zhang Yu Fu Zhongwei Guo Shumin Chen Jian Wu James C.Schnable Keke Yi Xiaowu Wang Feng Cheng Institute of Vegetables and Flowers Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of AgricultureSino-Dutch Joint Laboratory of Horticultural GenomicsBeijing 10008China Department of Agronomy and Horticulture University of NebraskaLincolnNE 68588USA Key Laboratory of Plant Nutrition and Fertilizer Ministry of AgricultureInstitute of Agricultural Resources and Regional PlanningChinese Academy of Agricultural SciencesBeijing 100081China

Orychophragmus violaceus,referred to as‘‘eryuelan’’(February orchid)in China,is an early-flowering ornamental *** high oil content and abundance of unsaturated fatty acids in *** seeds make it a potential high-quality oilseed ***,we generated a whole-genome assembly for *** using Nanopore and Hi-C sequencing *** assembled genome of *** was~1.3 Gb in size,with 12 pairs of *** investigation of ancestral genome evolution,we determined that the genome of *** experienced a tetraploidization event from a diploid progenitor with the translocated proto-Calepineae *** between the reconstructed subgenomes of *** identified indicators of subgenome dominance,indicating that subgenomes likely originated via *** was phylogenetically close to the Brassica genus,and tetraploidy in *** occurred approximately 8.57 million years ago,close in time to the whole-genome triplication of Brassica that likely arose via an intermediate tetraploid ***,the tetraploidization in Orychophragmus was independent of the hexaploidization in Brassica,as evidenced by the results from detailed phylogenetic analyses and comparisons of the break and fusion points of ancestral genomic ***,identification of multi-copy genes regulating the production of high-quality oil highlighted the contributions of both tetraploidization and tandem duplication to functional innovation in *** findings provide novel insights into the polyploidization evolution of plant species and will promote both functional genomic studies and domestication/breeding efforts in ***.

关键词： Orychophragmus violaceus eryuelan genome assembly polyploidization subgenome differentiation function innovation

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The gap-free potato genome assembly reveals large tandem gene clusters of agronomical importance in highly repeated genomic regions

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Molecular Plant 2023年第2期16卷 314-317页

作者： Xiaohui Yang lingkui zhang Xiao Guo Jianfei Xu Kang zhang Yinqing Yang Yu Yang Yinqiao Jian Daofeng Dong Sanwen Huang Feng Cheng Guangcun Li Institute of Vegetables Shandong Academy of Agricultural SciencesJinan 250100China Institute of Vegetables and Flowers Chinese Academy of Agricultural SciencesBeijing100081China Institute of Vegetables and Flowers Chinese Academy of Agricultural Sciences/State Key Laboratory of Vegetable Biobreeding/Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop of Ministry of Agriculture and Rural Affairs/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural AffairsBeijing100081China Institute of Vegetables Shandong Academy of Agricultural Sciences/Molecular Biology Key Laboratory of Shandong Facility Vegetable/National Vegetable Improvement Center Shandong Sub-CenterJinan 250100China Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural SciencesShenzhen518120China Chinese Academy of Tropical Agricultural Sciences Haikou 571101China

Dear Editor,Potato is a vital food security crop and is ranked as the world’s third most important food crop after rice and *** 2011,the first genome assembly of a doubled monoploid potato DM1-3516 R44(DM)was released(Potato Genome Sequencing Consortium,2011),which has been widely used as one of the most popular reference genomes in the last decade and served as a valuable resource in plant genomics and potato genetics community(Leisner et al.,2018;Yang et al.,2020;Zheng et al.,2020).

关键词： agronomic doubled potato

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解析五星级酒店职业安全健康实践

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安全 2009年第10期30卷 30-33页

作者：张令奎上海明天广场金威万豪酒店

万豪酒店首先落实各级安全责任制,发动全体员工在职业安全健康方面发挥积极作用,用先进的风险管理理论对酒店员工伤害进行事故可能性分析,评估事故严重程度,科学地建立事故风险矩阵表,按危害的不同级别,列成清单,对滑倒、坠落、割伤、碰... 详细信息

万豪酒店首先落实各级安全责任制,发动全体员工在职业安全健康方面发挥积极作用,用先进的风险管理理论对酒店员工伤害进行事故可能性分析,评估事故严重程度,科学地建立事故风险矩阵表,按危害的不同级别,列成清单,对滑倒、坠落、割伤、碰(压)伤等常见危害制定了事故风险控制方案。在对危害进行辨识时,采用了"四维集合"的分析方法。本文就上述内容和酒店采取的干预措施进行了详细阐述和评估。

关键词：酒店职业安全健康伤害预防

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7种茄科植物染色体的演化关系研究

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园艺学报 2023年第5期50卷 1009-1024页

作者：付钰张令奎黄议乐杨印庆陈姝敏张亢李良俊程锋扬州大学园艺与植物保护学院江苏扬州225000 中国农业科学院蔬菜花卉研究所北京100081

为了追溯茄科(Solanaceae)物种染色体的演化关系,对7种茄科物种进行了系统的比较基因组学分析,利用模式植物番茄的基因组为参考模板,全面鉴定7个物种间的基因组共线性关系,以此为基础建立了茄科的基因组片段单元系统,并基于该系统重建... 详细信息

为了追溯茄科(Solanaceae)物种染色体的演化关系,对7种茄科物种进行了系统的比较基因组学分析,利用模式植物番茄的基因组为参考模板,全面鉴定7个物种间的基因组共线性关系,以此为基础建立了茄科的基因组片段单元系统,并基于该系统重建了具有12条染色体的祖先基因组,阐明祖先基因组主要通过基因组片段的易位和倒位逐步形成目前的茄科基因组结构,且这些重排事件多发生在着丝粒等重复序列富集的区域。研究结果为深入认识茄科以及其他植物的基因组进化和物种分化等提供理论参考。

关键词：茄科比较基因组祖先基因组染色体重排着丝粒重复序列

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酵母菌及其衍生物抗菌功能研究进展

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食品科学 2023年第21期44卷 405-416页

作者：马悦单嘉宇蒋耀东黄俊楠王旭张凌魁杨朔董庆利上海理工大学健康科学与工程学院上海200093

致腐和致病的微生物污染食品基质后,会严重影响食品质量并威胁食品安全。利用理化抗菌技术可有效抑制食品中有害微生物的生长繁殖,但可能对食品品质造成不可逆的负面影响。某些酵母菌可以通过拮抗作用或者搭载抗菌药物的方式实现对有害... 详细信息

致腐和致病的微生物污染食品基质后,会严重影响食品质量并威胁食品安全。利用理化抗菌技术可有效抑制食品中有害微生物的生长繁殖,但可能对食品品质造成不可逆的负面影响。某些酵母菌可以通过拮抗作用或者搭载抗菌药物的方式实现对有害微生物的有效防控。本文从以上两个方面系统且全面地归纳了酵母菌及其衍生物的抗菌效果及机制的研究进展。在拮抗作用方面,总结讨论了拮抗酵母菌的种类、来源、与其他抗菌技术的联合抗菌效果及其拮抗作用的主要机制;在搭载抗菌药物方面,分析了酵母菌作为天然药物载体与多种化学抗菌剂组合的优势及局限性。本文旨在为以酵母菌为基础的新型抗菌剂的开发提供参考,以期更好地提高食品质量并保障食品微生物安全。

关键词：酵母菌拮抗作用载药防控方法抗菌

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基于用户需求的地球仪制作最佳方案选取技术研究

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测绘工程 2018年第9期27卷 59-63页

作者：马俊李珂张令奎闫鹤西安测绘总站陕西西安710054

用户对地球仪方面的需求呈现多元化、精准、美观,且日益纷繁复杂。鉴于此情况,文中在分析地球仪制作的两个关键因素和目前地球仪制作方法优缺点的基础上,提出基于用户需求的地球仪制作最佳方案选取技术,对此技术的本质和优点进行详细表... 详细信息

用户对地球仪方面的需求呈现多元化、精准、美观,且日益纷繁复杂。鉴于此情况,文中在分析地球仪制作的两个关键因素和目前地球仪制作方法优缺点的基础上,提出基于用户需求的地球仪制作最佳方案选取技术,对此技术的本质和优点进行详细表述,阐述其应用流程,并通过相关实验证明此技术能够得出满足用户功能需求的最佳制作方案,即此方案具有最贴合用户功能需求、制作速度快、成本低、用户满意度高、具有一定辅助决策能力等优点。

关键词：地球仪 3D打印贴片法高斯投影

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