Genetic Diversity and Core Collection for Potato (<Emphasis Type="BoldItalic">Solanum tuberosum</Emphasis> L.) Cultivars from Cameroon as Revealed by SSR Markers

Twelve pairs of SSR markers were used to evaluate the genetic diversity of 138 accessions of potato cultivars from the Western Highlands region of Cameroon. The average Polymorphism information content (PIC) value (0.74) and number of alleles (7.08) indicated a high genetic diversity of the potato cultivars tested. Analysis of molecular variance revealed that most of the genetic variations are found within geographic region (≥ 91%), resulting in high gene flow (Nm > 4 individuals). Local varieties had significantly more alleles than exotic varieties. Genetic diversity estimates for accessions from low elevations were significantly lower than those from medium and high elevations. Cluster analysis showed three clusters; the model-based approach inferred two gene pools. Genotypes revealed a high level of admixture between gene pools within locations and elevations. A core collection identified in this study composed of 27 individuals representing 19.57% of the whole collection and captured 99.15% of the total alleles found.     

基于SSR标记关联分析挖掘大豆灰斑病10号生理小种抗病资源

培育灰斑病抗性品种可降低灰斑病对大豆生产的危害。本研究以202份黑龙江省近25年主栽的大豆品种构建关联群体,在人工接种条件下鉴定大豆品种对灰斑病10号生理小种抗病指数。利用187对SSR标记对遗传多样性、群体结构和连锁不平衡位点进行分析,通过GLM 和MLM两种模型对大豆品种的灰斑病抗性与标记进行关联分析,进一步分析抗性关联位点等位变异与抗性表型效应关系。结果表明：202份大豆品种对灰斑病10号生理小种抗性遗传变异系数为14.26%;187个标记在群体中共获得809个等位变异,平均等位变异为4.42个,变幅2~10个,其中17号染色体的平均PIC值最高（0.64）,12号染色体的平均PIC值最低（0.26）;检测到稀有等位变异146个,特有等位变异位点58个;无论共线性组合位点还是非共线性组合位点均存在不同程度LD,连锁不平衡P<0.05支持的对数占总对数的21.65%;202份大豆品种被划分为3个亚群,亚群POP1与POP3之间遗传距离最小（0.03）,亚群POP2与POP3之间遗传距离最大（0.35）;两种模型共同检测到11个SSR标记与灰斑病10号生理小种抗性显著关联,其中位于3号染色体上的Satt549的贡献率最大,可解释表型变异14.74%;具有增效效应的等位变异共有24个,增效效应超过10的等位变异有7个,增效效应最大为Satt703-247（19.62）,典型载体材料为合丰29;其次是Satt587-185（19.58）,典型载体材料为东农50;Satt549位点增效等位变异的平均效应值最高（13.87）,Sat_366位点增效等位变异的平均效应值最低（0.84）。聚合优异等位变异和载体材料可为培育抗灰斑病品种的亲本选配和后代等位条带辅助选择提供依据。     

Genetic Fingerprinting of Potato Varieties from the Northwest Potato Variety Development Program

The Northwest Potato Variety Development (NWPVD) Program has released 45 improved potato varieties since 1985. Thirty-four potato varieties, four breeding clones and two advanced selections from NWPVD Program, and six commonly-grown potato varieties were fingerprinted using 32 simple sequence repeat (SSR) markers and 12,808 single nucleotide polymorphism (SNP) markers. Of 32 SSR markers, 29 exhibited significant polymorphism across all the 46 potato clones studied. A total of 143 alleles were observed with an average of 4.6 alleles per SSR marker. These markers span all 12 chromosomes of potato, with a maximum of five markers from chromosome VIII and minimum of one marker from chromosome VI. The polymorphic information content (PIC) and expected heterozygosity (H_e) of the SSR markers ranges between 0.18 to 0.75 and 0.20 to 0.78, respectively. Based on PIC, H_e, and ease of scoring, we recommend a set of eight SSR markers: STG0016, STI0004, STI0012, STI0023, STI0030, STI0033, STM1016 and STM1104 for fingerprinting NWPVD varieties. Out of 12,808 SNPs, 88.8% resulted in reliable three cluster diploid calling of which 87.8% were polymorphic. Tetraploid calling resulted in 44.2% of SNPs of which 94.5% were polymorphic. Our study provided fingerprinting resources for the NWPVD varieties and can be used in issues related to intellectual property rights, ownership, trademark and diversity analysis.     

用SSR标记评估东北三省水稻推广品种的遗传多样性

 利用53个SSR标记和24个表型性状分析东北三省107个水稻推广品种,探讨东北水稻推广品种群体遗传多样性及不同育成年代、省份间的遗传多样性和互补性。结果表明,表型遗传多样性高于DNA水平,年代间表型与微卫星标记的遗传多样性具有较高的相似性,而地区间无明显相似性。东北水稻推广品种遗传多样性比较狭窄,随着时间推移增加的新等位基因多于消失的旧等位基因数。三省水稻推广品种遗传多样性呈现黑龙江>吉林>辽宁的趋势,但由于地区间频繁引种,东北水稻品种在区域上的遗传分化已不明显,其差异主要来源于品种间的基因型差异。不同省份存在较多的互补等位变异,最多的在黑龙江和辽宁之间。不同省份和不同年代间分别拥有各自特有和特缺的等位变异。参试品种可分为5个类群,每一类群均有两个以上年代（省份）品种分布。     

Use of a global wheat core collection for association analysis of flour and dough quality traits

Flour and dough quality are very important breeding traits for wheat (Triticum aestivum L.) the selection of which would benefit from linked molecular markers. Association analysis allows the identification of genes or quantitative trait loci (QTL) related to target traits. The effectiveness of this approach depends on the availability of a densely genotyped population with large genetic variability for the traits of interest. Our objective was to identify chromosomal regions associated with flour and dough quality traits using a core collection built by maximizing the genetic diversity and phenotypic variability. We investigated the association of DArT, SSR and SNP markers with grain protein content, grain hardness, water-extractable arabinoxylan (WEAX) viscosity, wholemeal flour color and dough rheology.Out of 803 markers tested, 130 markers spread over the genome were associated with at least one trait, varying from 20 associated with WEAX viscosity to 60 associated with dough quality. Most chromosome regions known to determine wheat quality from the study of several bi-parental recombinant inbred lines were confirmed here and some new regions were identified. Associations were found for each trait studied, demonstrating that the core collection is a useful tool for QTL association mapping of these and other traits of interest.     

Genetic Diversity of Tropical Hybrid Rice Germplasm Measured by Molecular Markers

Investigation of genetic diversity and relationships among breeding lines is of great importance to facilitate parent selection in hybrid rice breeding programs.In this study,we characterized 168 hybrid rice parents from International Rice Research Institute with 207 simple sequence repeat (SSR) and 353 single nucleotide polymorphism (SNP) markers.A total of 1 267 SSR and 706 SNP alleles were detected with the averages of 6.1 (SSR) and 2.0 (SNP) alleles per locus respectively across all lines.Based on the genetic distances estimated from the SSR and SNP markers separately and combined,the unrooted neighbor-joining cluster and STRUCTURE analyses consistently separated the 168 hybrid rice parents into two major groups:B-line and R-line,which is consistent with known parent pedigree information.The genetic distance matrices derived from the SSR and SNP genotyping were highly correlated (r=0.81,P < 0.001),indicating that both of the SSR and SNP markers have distinguishable power to detect polymorphism and are appropriate for genetic diversity analysis among tropical hybrid rice parents.A subset of 60 SSR markers were also chosen by the Core Hunter with 368 alleles,and the cluster analysis based on the total and subset of SSR markers highly corresponded at r=0.91 (P < 0.001),suggesting that fewer SSR markers can be used to classify and evaluate genetic diversity among parental lines.     

青稞主要性状的差异性与遗传分析

为合理评价110份青稞品种(系)的农艺性状及遗传特性,对参试种质材料的株高、穗长、穗粒数、分蘖数和千粒重进行了调查统计,同时用分布于大麦全基因组的48对SSR标记进行了遗传多样性分析。结果表明,参试材料各农艺性状变异较大,变异系数为2.92%~42.33%,其中株高、穗长、分蘖数、穗粒数和千粒重变化范围分别为53~122cm、2.5~7cm、2~19个、20~90粒和25.46~60.34g。SSR标记共检测到168个等位变异,变化范围为2~6个。110份青稞种质材料分成三大类群。SSR标记的1 128个位点成对组合中,不论是共线性成对组合还是非共线性成对组合,都存在一定的连锁不平衡(linkage disequilibrium,LD)。D′统计概率(P0.01)支持的LD成对位点438个,占全部位点的38.8%,D′的平均值为0.36,整体LD水平较高。较高水平的LD位点(D′0.5)主要分布在2H、4H、6H和7H连锁群上。     

基于SSR标记的澳洲坚果种质资源遗传多样性分析

澳洲坚果原产于澳大利亚亚热带雨林,是我国新兴的重要经济作物,其种质资源丰富,但遗传背景复杂,亲缘关系混乱。开展澳洲坚果种质资源遗传多样性分析,可拓展澳洲坚果种质资源创新利用途径,有效加快澳洲坚果育种进程。形态表型分析是最早用于种质鉴定和管理的标记之一,但易受环境因素影响。DNA分子标记技术在种质资源鉴定、遗传多样性分析中克服了传统表型分析易受环境影响的缺点。本研究采用9对高多态性SSR引物对91份国外引进以及自主选育品种(品系)澳洲坚果种质进行遗传多样性分析。结果表明,共扩增出73个等位基因位点,平均等位基因8个,平均基因多样性为0.689,平均杂合度为0.578,多态性信息含量PIC为0.453~0.792,平均值为0.659,表明91份澳洲坚果具有较高的多态性。UPGMA聚类分析表明,在遗传距离为0.33处,将91份澳洲坚果分为2大类,且其亲缘关系与地理来源无显著相关性,与主成分分析、Structure分析结果一致。本研究供试澳洲坚果材料群体内遗传变异显著高于群体间变异,且遗传成分来源单一,遗传结构较为简单。本研究为澳洲坚果种质的有效利用以及核心种质构建提供理论基础,为进一步加速澳洲坚果种质遗传改良以及分子辅助育种奠定基础。     

基于SSR标记的澳洲坚果种质资源遗传多样性分析

澳洲坚果原产于澳大利亚亚热带雨林,是我国新兴的重要经济作物,其种质资源丰富,但遗传背景复杂,亲缘关系混乱。开展澳洲坚果种质资源遗传多样性分析,可拓展澳洲坚果种质资源创新利用途径,有效加快澳洲坚果育种进程。形态表型分析是最早用于种质鉴定和管理的标记之一,但易受环境因素影响。DNA分子标记技术在种质资源鉴定、遗传多样性分析中克服了传统表型分析易受环境影响的缺点。本研究采用9对高多态性SSR引物对91份国外引进以及自主选育品种(品系)澳洲坚果种质进行遗传多样性分析。结果表明,共扩增出73个等位基因位点,平均等位基因8个,平均基因多样性为0.689,平均杂合度为0.578,多态性信息含量PIC为0.453~0.792,平均值为0.659,表明91份澳洲坚果具有较高的多态性。UPGMA聚类分析表明,在遗传距离为0.33处,将91份澳洲坚果分为2大类,且其亲缘关系与地理来源无显著相关性,与主成分分析、Structure分析结果一致。本研究供试澳洲坚果材料群体内遗传变异显著高于群体间变异,且遗传成分来源单一,遗传结构较为简单。本研究为澳洲坚果种质的有效利用以及核心种质构建提供理论基础,为进一步加速澳洲坚果种质遗传改良以及分子辅助育种奠定基础。     

273份水稻种质资源的遗传多样性、群体结构与连锁不平衡分析

[目的]评估273份水稻种质资源的遗传多样性和群体结构,为今后利用这些水稻种质资源进行遗传育种和关联分析提供参考.[方法]利用214个分子标记对来自14个国家的273份水稻地方品种和育种材料进行基因型检测,分析其遗传多样性、群体结构、连锁不平衡程度.[结果]群体结构分析将供试群体划分为2个亚群(SG1、SG2)以及1个...     

梧州茶树种质资源的遗传多样性及亲缘关系分析

基于SSR标记对梧州六堡镇群体种和南渡镇野生大茶树种质资源的遗传多样性和亲缘关系进行了分析,并筛选出用于该种质资源鉴别的核心分子标记。研究结果如下：（1）17对SSR引物在供试材料中共扩增得到98个等位基因,每对SSR引物扩增的等位位点为3~8个,平均每个位点5.764 7个等位基因;（2）从17个SSR分子标记中筛选出8个核心标记组合即可区分每份种质资源;（3）六堡镇茶树种质资源的平均等位基因数（A）、基因型数、基因多样性（H）、多态性信息含量（PIC）分别为4.647 1、7.000 0、0.675 4、0.628 3,高于南渡镇野生大茶树种质资源,与栽培种茶树群体接近;（4）聚类分析表明,六堡镇茶树群体部分种质资源单独聚为一类,部分与云南的大叶种茶树,少量与浙江、贵州地方栽培种聚为一类;而南渡镇野生茶树种质资源单独聚为一类,仅有2个六堡镇的种质材料散落其间。综上所述,梧州茶树种质资源丰富,遗传多样性较高,研究结果为进一步开发和利用该资源奠定了基础。     

山东省近期育成小麦品种(系)的遗传多样性及其与产量性状的关联分析

为了解山东省近年来育成品种(系)的遗传多样性,并筛选出与产量性状相关的分子标记及其等位变异,选用58对分布于小麦21条染色体上的SSR标记,对109个山东省近年来育成的品种(系)进行遗传多样性和关联分析。SSR标记多态性分析表明,本研究共检测到176个等位位点,各标记等位位点变化范围为2~6个,平均为3.034个;SSR标记多态性信息量(PIC)变化范围为0.111~0.829,平均为0.552。聚类分析显示,同一育种单位育成的或具有共同亲本的品种往往聚为一类。关联分析表明,与产量性状显著关联(P0.01)的标记有18对。对相对稳定的等位变异作进一步分析,发掘了一批与产量性状相关的优异等位变异,如增加产量的等位变异barc187-A240和cfd11-A270,降低株高的等位变异barc21-A110、cfd53-A240和Xwmc765-A190,增加穗粒数的等位变异barc181-A190,增加总茎数的等位变异cfd27-A220和swes247-A200,提高越冬率的等位变异barc177-A110。     

黑龙江省大豆推广品种农艺和品质性状优异等位变异的发掘

发掘推广品种的农艺和品质性状优异等位变异和载体材料可为培育优质大豆品种提供遗传信息和育种资源。本研究以200份黑龙江省近年大豆推广品种为试验材料,利用187对SSR标记进行全基因组扫描,分析群体结构,采用TASSEL软件的GLM方法对标记与3个农艺性状、蛋白质含量及油分含量进行关联分析。结果表明：10 个SSR标记与百粒重关联,其中表型效应值最大的优异等位变异为Sat-149-192,载体材料为东农57;8个SSR标记 与株高关联,表型效应值最大的等位变异是Satt413-206,载体材料为赤豆1号;13个SSR标记与生育期关联,表型 效应值最大的等位变异是Satt631-180,载体材料为黑农61;5个SSR标记与油分含量关联,表型效应值最大的等位 变异是Satt234-138,载体材料为合丰55;9个SSR标记与蛋白质含量关联,表型效应值最大的等位变异是Satt632- 293,其载体材料为东农43。上述等位变异的信息为培育提供了亲本选配和后代等位条带辅助选择的依据。     

糙柱花草遗传多样性SSR分析

为鉴定糙柱花草种质的遗传背景和亲缘关系,提高其利用效率,利用来自不同柱花草种中的16个SSR标记对14份糙柱花草种质进行遗传多样性和聚类分析。结果表明：在16个SSR标记中,10个SSR标记在14份糙柱花草种质间具有多态性。10个多态性SSR标记共检测到32个等位基因,每个标记可检测到2～8个等位基因,平均为3.20个;每个SSR标记的Shannon信息指数(I)和多态性信息含量(PIC)分别为0.191～0.796和0.173～0.769,平均为0.474和0.411。14份糙柱花草种质间的遗传相似系数为0.438～0.938,平均为0.733。聚类分析结果显示,在遗传相似系数为0.74处,14份供试糙柱花草种质可明显被分为3类,其中III类中的CPI 93116柱花草与其他种质遗传关系较远。     

Genetic Diversity and Redundancy Among Potato Accessions in the Montenegrin Collection as Revealed by Microsatellite Markers

Potato was introduced in Montenegro in the middle of the eighteenth century. Since then it has become the most important crop in plant production. During the period between 2008 and 2010 a total of 52 potato accessions was collected across Montenegro and stored in a national gene bank. In the study reported here 23 accessions from the collection were examined using microsatellite (also known as simple sequence repeats or SSRs) molecular markers with the aim to explore genetic diversity and redundancy within the germplasm. The accessions were selected on the basis of preliminary characterization of all 52 accessions for 11 lightsprout traits. Molecular characterization of 23 accessions by 12 SSR markers was carried out at SASA (Science and Advice for Scottish Agriculture) that manages a database of more than 3000 genetic profiles of potato from Europe and abroad. Comparison of SSR genetic profiles of Montenegrin collection against the existing SASA database allowed us to test the authenticity of the Montenegrin accessions. Out of the 23 accessions examined, 13 showed distinct genetic profiles of which seven showed perfect matching with known cultivars, two profiles showed strong similarity to another two cultivars, and four profiles were found unique with regards to the SASA database. Application of microsatellite markers in this study provided valuable information on the extent of genetic diversity residing within Montenegrin potato germplasm; it gave clear indications of the scale of redundancy within the collection; and helped clarify the identity of the accessions. Four accessions within the collection might incorporate unique variation and will be subjected to further agronomical examinations to assess their potential for breeding purposes.     

乌龙茶品种（系）遗传多样性与亲缘关系的SSR分析

利用40对具有多态性的SSR引物对我国46份乌龙茶品种（系）的遗传多样性和亲缘关系进行了研究。结果表明,40对引物在供试材料中共检测到179个等位基因,329个基因型,平均检测4.48个等位基因,8.23个基因型,平均多态性信息量（PIC）为0.52。46份供试品种（系）的基因多样性指数（H）为0.57,观测杂合度（Ho）为0.40,遗传距离为0.59。按照地理来源分组分析表明,地区间乌龙茶品种（系）的遗传多样性以广东最高,其次为福建,最低的为台湾。亲缘关系分析表明,大部分品种（系）都按照其地理来源和遗传背景进行了聚类。根据育种方式分组的分析表明,杂交选育的品种（系）遗传多样性水平较其他方式选育的品种（系）低。     

Evaluation of Simple Sequence Repeat (SSR) Markers Established in Europe as a Method for the Identification of Potato Varieties Grown in Canada

The correct identification of potato varieties is crucial to maintaining the quality level of seeds produced under the Canadian Seed Potato Certification Program. During inspection of in vitro potato plant propagation centres or seed potato production field lots, morphological characteristics may not be sufficient for the identification of plantlets or tubers and therefore molecular identification is sought by inspectors for variety confirmation. With international harmonization of testing methods in mind, we proposed to evaluate further the microsatellite (SSR) markers established successfully by Reid et al. (2009, Euphytica 182: 239–249, 2011), using the reference potato variety DNA collection at the Canadian Food Inspection Agency (CFIA) established and currently used for Amplified Fragment Length Polymorphism (AFLP) genotyping. The SSR markers developed by the European community laboratories were successfully validated by and established within the CFIA laboratory. Most genotypes generated for a set of 34 varieties were identical between the 2 laboratories with only 3 discrepancies due to the different interpretation of the presence/absence of the alleles. When used with potato reference DNAs of the CFIA collection, the method successfully differentiated 217 varieties apart but 10 groups, which are most likely clonal variants, were not discriminated. The SSR markers were successfully used to address 5 potato variety verification requests from CFIA inspectors during field inspections for seed potato certification. The markers successfully confirmed the presence of rogue varieties in 4 of these requests, therefore fulfilling the CFIA’s mandate towards stakeholders of the Canadian potato industry in preserving the quality of certified seeds.     

33个育成花生品种遗传多样性分析

利用75对SSR标记引物对33个育成花生品种进行遗传多样性分析,结果表明,其中有10对标记引物扩增出多态性,共检测到33个多态等位点,每对引物分别检测出4～8个等位点变异,平均为6.0个,33个花生品种间的遗传相似系数在0.242～1.000之间,平均为0.621。聚类分析结果表明33个参试花生品种在遗传相似系数0.600处分为2个类群,亲本来源相近的品种优先聚在一起。     

应用形态、等位酶和SSR标记研究水稻矮仔占衍生品种的遗传差异

选取我国水稻矮仔占衍生品种24份,应用形态学、等位酶和微卫星(SSR)标记,分析矮仔占衍生品种的遗传差异。聚类分析表明3种方法在鉴别品种的遗传差异上存在较大差异。形态性状和SSR标记均能有效地鉴别24份衍生品种,而等位酶仅能鉴别其中17份。从形态学性状看,以香药糯与其他品种的遗传差异最大,SSR分析以香药糯、珍珠矮11和辐陆选与其他品种的遗传差异较大,而等位酶分析,则以团结1号与其他品种的差异最大。三类标记的遗传距离间虽存在有一定的相关性,但相关系数较小（0.217~0.494）,其中,形态学性状与SSR标记间相关极显著（r= 0.494,P= 0.002）,等位酶与其他两类标记的相关性均不显著。研究结果还表明,系统选育和辐射选育的品种与亲本间有可能存在较大的遗传差异。     

大麦亲本材料性状鉴定及多样性分析

为了给大麦育种亲本组配提供理论依据,对44个大麦亲本进行SSR标记分析并鉴定其农艺性状,结果表明,44个大麦材料的农艺性状存在不同程度差异,株高最高的为苏盐3号,最矮的为E14;SCAR-LETT的穗型较理想。SSR分析结果表明,分布于大麦1H～7H染色体的32个SSR位点有23个位点(71.88%)具有多态性。这32个位点共检测到127个等位变异,每个SSR位点能检测到1～6个,平均为3.9个。品种间遗传相似系数(GS)变幅为0.457～0.984,平均值为0.720。聚类分析表明,这32个SSR标记能将44个亲本材料相互区分开,在GS值0.610水平上可以聚为2个大类。