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基于简化基因组技术的啤酒花栽培种和野生种SNP位点开发及遗传结构分析

中国园艺学会2015年学术年会

作者：徐晓美巢娟吴廷全王瑞孙保娟王恒明徐小万李颖广东省农业科学院蔬菜研究所广东省蔬菜新技术研究重点实验室

辣椒疫病是由辣椒疫霉菌(Phytophthora capsici Leonian)引起的一种毁灭性土传病害。辣椒根腐疫病的发生通常直接导致植株不可逆死亡,对辣椒生产的损害最为严重。因此,鉴定并定位辣椒根腐疫病抗性基因,开发其紧密连锁分子标记并构建辣... 详细信息

辣椒疫病是由辣椒疫霉菌(Phytophthora capsici Leonian)引起的一种毁灭性土传病害。辣椒根腐疫病的发生通常直接导致植株不可逆死亡,对辣椒生产的损害最为严重。因此,鉴定并定位辣椒根腐疫病抗性基因,开发其紧密连锁分子标记并构建辣椒抗根腐疫病分子标记辅助育种体系,选育抗性品种是解决辣椒根腐疫病病害的有效途径。以辣椒抗疫病材料‘CM334’和高世代纯合感病材料‘10399’及其子代F、F和BCF为试材。辣椒疫霉菌株BYL1,从广州钟落潭实验基地发病辣椒植株上分离获得。待辣椒幼苗生长至4片真叶时采用灌根法接种,距植株根际1 cm处用注射器小心注入5mL(1×10个·mL)游动孢子悬浮液,黑暗保湿24 h后正常管理。待感病对照10399开始发病时进行调查,每天1次,感病对照全部发病萎焉时(接种后约10d)停止调查。没有出现病症的植株为抗病株,出现病症的植株为感病株。DNA提取及抗、感病混池构建:从436株BCF群体中经表型鉴定筛选出极端抗病和极端感病植株各60株,以常规CTAB法提取各单株DNA,经纯度和完整性检验合格后分别挑选出50个抗病单株和感病单株DNA等量混合成终浓度为40 ng·μL的抗病DNA混池和感病DNA混池,用于slaf-seq。结果表明:接种后3d,感病亲本10399开始发病,接种后11 d,42株全部枯萎死亡,而32株抗病亲本均未感病。F代和反交F代群体的各48株幼苗在接种11 d没有表现出任何病症,表现为抗病;157株F代分离群体中有115株幼苗表现抗病,42株表现感病,抗、感分离比符合3:1(X=0.26,P=0.61)的分离比例;BC(F×P)群体中154株幼苗均表现抗病,BC(F×P)群体中75株幼苗表现抗病,83株表现感病,抗、感分离符合1:1(X1:1=0.41,P=0.52)的分离比例。分析结果表明CM334抗根腐疫病抗性性状由一个显性核基因控制。slaf-seq并结合集群分离分析方法(BSA)对辣椒根腐疫病抗性基因进行定位,结果表明在辣椒第10号染色体末端定位到1个关联区域,大小约为16.0Mb,并在该区域内检测到SNP关联标记139个。随后在关联区域内筛选出10个多态SSR标记,并对636株BCF群体进行基因型分析。结合表型调查,连锁分析表明10个多态标记均与抗性基因连锁并将其定位在标记P52-11-21与P52-11-41之间,与两侧标记的遗传距离分别为1.5 cM和1.1 cM。

关键词：辣椒根腐疫病 slaf-seq 精细定位

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中草药 2021年第20期52卷 6365-6372页

作者：赵亚琴樊丛照张际昭邱远金辛海量李晓瑾张本刚王果平新疆中药民族药研究所新疆乌鲁木齐830002 第二军医大学上海200433 中国医学科学院药用植物研究所北京100193

目的为揭示新疆啤酒花Humulus lupulus野生与栽培个体间的遗传关系、遗传结构及野生资源的遗传潜力。方法利用slaf-seq简化基因组测序技术,对新疆20个野生个体和18个栽培个体的SNP位点进行了开发与鉴定。利用系统发育分析、群体遗传结... 详细信息

目的为揭示新疆啤酒花Humulus lupulus野生与栽培个体间的遗传关系、遗传结构及野生资源的遗传潜力。方法利用slaf-seq简化基因组测序技术,对新疆20个野生个体和18个栽培个体的SNP位点进行了开发与鉴定。利用系统发育分析、群体遗传结构分析和主成分分析(principal component analysis,PCA)等方法,从基因组水平揭示了野生种与栽培种之间的遗传结构。结果结果表明,通过slaf-seq测序共获得863 228个slaf标签,其中多态性slaf标签有443 922个,共获得2 867 140个SNP位点。系统发育分析表明,野生个体和栽培个体整体上可各自分为2个聚类簇。总的Shanon-Wiener指数平均为0.397,其中野生个体为0.455,栽培个体为0.398;总的Nei多样性指数平均为0.249,其中野生个体为0.293,栽培个体为0.250。AMOVA分析表明,啤酒花的主要遗传变异主要来源于群体间,野生个体与栽培个体之间具有较大的遗传分化。结论新疆分布的野生啤酒花个体与栽培个体之间存在较大的遗传分化,但是野生啤酒花个体具有较高的遗传多样性,说明新疆啤酒花的野生资源具有较高的遗传育种潜力。

关键词：啤酒花简化基因组测序技术 slaf-seq 野生个体栽培个体遗传结构

药用芍药栽培品种的SNP标记开发及品种鉴定

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中草药 2025年第1期 239-247页

作者：刘宇辰张振宇尹旻臻储姗姗彭华胜黄璐琦安徽中医药大学药学院中国中医科学院中药资源中心道地药材品质保障与资源持续利用全国重点实验室

目的基于简化基因组，建立一种准确鉴定药用芍药Paeonia lactiflora栽培品种的单核苷酸多态性（single nucleotide polymorphism,SNP）分子标记方法。方法利用特异位点扩增片段测序（specific-locus smplified fragment sequencing,SL... 详细信息

目的基于简化基因组，建立一种准确鉴定药用芍药Paeonia lactiflora栽培品种的单核苷酸多态性（single nucleotide polymorphism,SNP）分子标记方法。方法利用特异位点扩增片段测序（specific-locus smplified fragment sequencing,slafseq）技术对浙江、安徽、四川和湖南的13个药用芍药栽培品种进行SNP标记开发。通过多个指标如杂合率、缺失率和多态性来筛选候选标记，并通过遗传多样性、群体结构和主成分分析等方法进一步评估候选标记。最后采用能够区分药用芍药栽培品种的最简SNP组合绘制指纹图谱。结果通过slaf-seq测序共获得3 703 329个slaf标签，其中多态性标签有60 749个，共获得412 873个群体SNP标记，最后筛选的47个核心SNP标记位点表现出高多态性，可以很好地区分药用芍药栽培品种。结论基于简化基因组，建立了主要药用芍药栽培品种的SNP标记开发和指纹图谱绘制的方法，为药用芍药的品种鉴定和白芍药材的临床应用提供借鉴。

关键词：药用芍药栽培品种 slaf-seq 单核苷酸多样性指纹图谱

克氏原螯虾养殖群体的slaf测序及遗传多样性分析

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南方农业学报 2021年第12期52卷 3265-3273页

作者：刘亚楠刘洁魏上李亚琳李明肖俊邱高峰陆颖上海海洋大学水产种质资源发掘与利用教育部重点实验室上海201306 上海海洋大学海洋生物科学国际联合研究中心上海201306 金华市水产技术推广站浙江金华321017 广西水产科学研究院/广西水产遗传育种与健康养殖重点实验室南宁530021

【目的】探究克氏原螯虾养殖群体内和群体间的遗传多样性,为引种和群体间杂交以改善养殖群体种质提供参考依据。【方法】以湖北、江西、安徽、浙江和江苏5省克氏原螯虾主产地14个养殖群体的120个个体为研究对象,采用简化基因组测序技术... 详细信息

【目的】探究克氏原螯虾养殖群体内和群体间的遗传多样性,为引种和群体间杂交以改善养殖群体种质提供参考依据。【方法】以湖北、江西、安徽、浙江和江苏5省克氏原螯虾主产地14个养殖群体的120个个体为研究对象,采用简化基因组测序技术——特定区点扩增片段测序技术(slaf-seq)进行基因组测序,获得基因组SNP基因型数据,构建群体系统发育进化树,并进行群体结构、主成分和遗传多样性分析。【结果】共鉴定出741147个单核苷酸多态性(SNP)位点,群体系统进化分析表明,14个群体的种源主要来自浙江金华和江苏宿迁,然后再向各地引种迁徙。群体结构分析结果与系统进化分析结果相吻合。主成分分析结果揭示了安徽长丰和滁州群体、湖北荆州龙口及和平2个群体,以及浙江东阳群体等5个群体与其他群体间存在相对较远的亲缘关系,是杂交引种的潜在种源。群体遗传多样性分析显示,14个群体的Ho介于0.2171~0.2801,平均值为0.2476,He介于0.3424~0.3598,平均值为0.3534,PIC介于0.2750~0.2878,群体间相差不大,接近0.25,各群体均接近遗传多样性中等水平的下限。【结论】14个克氏原螯虾养殖群体内的遗传多样性较低,群体间的亲缘关系较接近,品种单一、长期内交迹象明显。通过群体的基因组重测序,能以较低的成本实现对养殖群体遗传多样性的定期监测。

关键词：克氏原螯虾 slaf-seq SNP 遗传多样性群体遗传学

利用SALF-seq简化基因组测序分析茄子种质资源遗传多样性

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分子植物育种 2022年第23期20卷 7940-7949页

作者：冯恩友肖熙鸥林文秋莫定鸣冯晓赓马飞骏湛江市农业科学研究院湛江524094 中国热带农业科学院南亚热带作物研究所湛江524091

为研究茄子种质资源的亲缘关系,本研究利用slaf-seq (Specific-Locus Amplified Fragment sequencing)简化基因组测序对40份茄子高代自交系进行简化基因组测序,利用获得的SNP (Single nucleotide polymorphism)标记进行遗传结构分析。... 详细信息

为研究茄子种质资源的亲缘关系,本研究利用slaf-seq (Specific-Locus Amplified Fragment sequencing)简化基因组测序对40份茄子高代自交系进行简化基因组测序,利用获得的SNP (Single nucleotide polymorphism)标记进行遗传结构分析。本研究共获得700 639个slaf标签和1 248 593 SNPs。结果表明,SNP数量在每条染色体上和同一条染色上的不同位置差异较大,注释结果表明SNP和InDel主要发生在基因间隔区。利用获得的SNPs多样性可以将40份材料分为3个类群。SNP分类结果与根据青枯病抗性分类结果基本一致,而与根据果形果色分类结果不一致,通过筛选,获得了高质量的122个perfect SNPs。本研究结果为杂组合的选配提供了参考,同时所开发的SNP位点为KSAP高通量基因分型奠定了良好的基础。

关键词：茄子 slaf-seq 遗传多样性 SNP位点

Identification and Physical Mapping of New PCR-Based Markers Specific for the Long Arm of Rye(Secale cereale L.) Chromosome 6

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Journal of Genetics and Genomics 2016年第4期43卷 199-206页

作者： Meng Li Zongxiang Tang Ling Qiu Yangyang Wang Shuyao Tang Shulan Fu Province Key Laboratory of Plant Breeding and Genetics Sichuan Agricultural University Agronomy College Sichuan Agricultural University

To effectively use elite genes on the long arm of rye chromosome 6（the 6RL arm） in wheat breeding programs,precise and fast identification of 6RL chromatin in wheat backgrounds is ***-based 6RL-specific markers can facilitate the detection of elite genes on 6RL in wheat ***,only a limited number of 6RL-specific markers have been *** the present study.300 new PCR-based 6RL-specific markers were identified using specific length amplified fragment sequencing（slaf-seq） technology,and were further physically mapped to four regions on the 6RL arm using 6R and 6RL deletion ***,127 of the 300 markers were physically localized to a region from the site between 2.3 and 2.5 to the telomere,the same region where the powdery mildew resistance gene was *** addition,95 of the 300 markers exhibit polymorphisms,which can be used to investigate the diversity of rye 6RL *** markers developed in this study can be used to identify given segments of 6RL in wheat backgrounds and accelerate the utilization of elite genes on 6RL in wheat breeding.

关键词： Wheat Rye 6RL-specific marker Physical mapping slaf-seq Powdery mildew

Construction of a high-density genetic linkage map and identification of flowering-related QTL in erect milkvetch(Astragalus adsurgens)

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The Crop Journal 2022年第4期10卷 1141-1150页

作者： Wenlong Gong Lin Ma Qiu Gao Bao Wei Jiangui Zhang Xiqiang Liu Pan Gong Zan Wang Guiqin Zhao College of Pratacultural Science Gansu Agricultural UniversityLanzhou 730070GansuChina College of Grassland Science and Technology China Agricultural UniversityBeijing 100193China Institute of Animal Sciences Chinese Academy of Agricultural SciencesBeijing 100193China National Animal Husbandry Service Beijing 100125China

Erect milkvetch(Astragalus adsurgens)is a perennial legume forage crop with economic and ecological value in livestock grazing and soil-erosion control in arid and semiarid areas *** information and molecular tools to support breeding and research in the species are *** objectives of this investigation were to map its genome using DNA markers and to identify quantitative trait loci(QTL)in the *** F1 mapping population of 250 plants was developed from a cross between two parents with differing flowering-related traits.A high-density genetic linkage map containing 4821 markers on eight linkage groups(LGs)with a total genetic length of 1395 cM and a mean interval of 0.29 cM between adjacent markers was constructed with slaf-seq *** genomic analyses revealed the highest genome sequence similarity(8.71%)between erect milkvetch and Medicago truncatula,followed by Glycine max(7.65%),Cicer arietinum(7.53%),and Lupinus angustifolius(5.21%).A total of 64 significant QTL for flowering-related traits on six LGs were detected,accounting for 9.38 to 19.1%of the associated phenotype *** and 48 key candidate genes for floret number and inflorescence length were identified based on the Glycyrrhiza uralensis *** candidate genes were involved in ubiquitination/degradation,pollen development,cell division,cytokinin biosynthetic process,and plant *** findings shed light on the regulation of flowering traits in erect milkvetch and provide genomic resources for future molecular breeding of the crop.

关键词： Erect milkvetch Genetic map Flowering-related traits QTL mapping slaf-seq

High-density genetic mapping identified a major locus for environmental sex expression in pumpkin(Cucurbita moschata Duch.)

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Horticultural Plant Journal 2022年第5期8卷 593-601页

作者： Hafiz Muhammad Khalid Abbas Hexun Huang Tingquan Wu Rui Wang Hu Du Sen Lu Shudan Xue Chunpeng Yao Qingmin Jin Yujuan Zhong Guangdong Key Laboratory for New Technology Research of Vegetables Vegetable Research InstituteGuangdong Academy of Agricultural SciencesGuangzhou 510640China

Long-day length and high temperature inhibit sex expression in pumpkin(Cucurbita moschata Duch.),and therefore directly impact the production *** this study,female flowering patterns in photoperiod-insensitive(PPIS)and photoperiod-sensitive(PPS)germplasms differed significantly in a moderately long day and high temperature ***,both germplasms exhibited a similar response in short day with either low temperature or high temperature *** sensitivity led to this difference in sex expression between the *** the traits of 1st female flowering node(FFFN)and number of female flowers(NFF),high-density linkage map construction and quantitative trait locus(QTL)mapping were performed using slaf-seq technology and 162 F_(2) individuals generated from PPIS and *** total,4655 slafs were selected and mapped on 20 linkage groups(LGs).The total map length was 2502.01 cM with an average interval distance of 0.75 *** QTLs for both FFFN and NFF were detected on LG6 with intervals of 7.89 and 17.67 cM and PVE values of 30.5%and 22.9%,*** analyses of the major locus for FFFN revealed 73 protein-coding *** them,4 were related to sex expression,photoperiod flowering,and hormone *** InDel(insertion and deletion)marker partially correlated with FFFN of the F_(2) population was also *** study identified the QTL for the sex expression response to environmental factors using the high-density linkage *** identified candidate genes and markers will provide useful information about the molecular interaction between the environment and sex expression and for marker-assisted selection of pumpkin environment-insensitive resources.

关键词： Pumpkin Photoperiod sensitivity Sex expression High-density genetic map slaf-seq QTL mapping

Comparative Study of Genetic Structure and Genetic Diversity betweenWild and Cultivated Populations of Taxus cuspidata,Northeast China

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Phyton-International Journal of Experimental Botany 2024年第2期93卷 355-369页

作者： Dandan Wang Xiaohong Li Yanwen Zhang School of Science Liaodong UniversityDandong118003China

Taxus cuspidata is a rare plant with important medicinal and ornamental *** at the obvious differences between wild and cultivated populations of *** from Northeast China,a total of 61 samples,that is,33 wild yews and 28 cultivated yews were used to analyze the differences and correlations of the kinship,genetic diversity,and genetic structure between them by specific length amplified fragment sequencing(slaf-seq).Finally,470725 polymorphic slaf tags and 58622 valid SNP markers were *** analysis showed that 61 samples were classified into 2 clusters:wild populations and cultivated populations,and some wild yews were categorized into the cultivated populations;the genetic diversity analysis showed that the Nei diversity index of wild populations(0.4068)was smaller than that of cultivated populations(0.4414),and the polymorphic information content(PIC)of wild populations(0.2861)was smaller than that of cultivated populations(0.3309).The genetic differentiation analysis showed that the total populations of gene diversity(H_(t))of cultivated and wild populations were respectively 0.8159 and 0.5685,the coefficient of gene differentiation(G_(st))of cultivated and wild populations was respectively 0.3021 and 0.1068,and the gene flow(N_(m))(2.4967)of wild populations was larger than cultivated populations(0.8199).The molecular variance(AMOVA)revealed that inter-population variation accounted for 29.57%of the total genetic variation,while intra-population variation accounted for 70.42% of the total genetic variation(pslaf-seq technolog

关键词： T.cuspidata slaf-seq SNP wild population cultivated population genetic structure