基于SSR标记的贵州薏苡种质资源遗传多样性?分析

利用SSR标记研究了22份薏苡种质的遗传多样性,用11对扩增带型稳定的SSR引物从供试材料中检测出105个等位基因变异,每对引物检测等位基因4～20个,平均9.55个。SSR引物的PIC介于0.3048～0.9238,平均多态性信息量为0.8255。利用UPGMA聚类分系法将供试自交系划分为4类,该划分结果与根据地理来源、种质系谱的分类结果基本一致。SSR分子标记辅助的种质改良是薏苡品种改良的重要途径。     

SSR标记用于玉米自交系遗传变异与优势类群划分的研究

采用SSR和杂种优势聚类方法分析我国15个玉米骨干自交系的遗传变异,并初步进行了杂种优势类群划分,从62个SSR引物中筛选的40对有效引物对15个玉米自交系进行了分析,共检测到188个等位基因变异,每个SSR座位的等位基因数2－9个,平均为4．7个,SSR位点的多态信息含量PIC值平均为0．675,分布范围在0．360－0．851之间,根据SSR数据对供试材料进行遗传相似性分析,Nei氏相似性系数分布在0．574－0．777之间,10对多态性高的SSR引物可有效区分15个自交系,应用SSR聚类分析的结果与系谱关系相一致,与杂种优势类法相比较,SSR方法具有效率高,结果可靠,可标准化的特点,对SSR方法在玉米育种实践上的应用进行了初步探讨。     

利用SSR分析山西省玉米地方品种的遗传多样性

采用混合取样方法和SSR分子标记技术,利用48对引物对山西省38个玉米地方品种的遗传多样性进行了分析.共检测出368个等位基因,每个SSR位点的等位基因数为2～14个,平均为7.48个;多态性信息量(PIC)变化范围在0.24～0.89之间,平均为0.66.总共检测出185个稀有等位基因,21个特有等位基因.SSR标记聚类分析把38个品种大体分成了4个群.研究表明,山西地方品种遗传多样性非常丰富,很多品种具有频率很高的独特基因,它们可能具有一定的特异性.因而,山西玉米地方品种对于拓宽玉米种质的遗传基础可能会起很大的作用.     

中国温带糯玉米自交系遗传及品质性状分析

利用SSR标记研究了40份中国温带常用糯玉米自交系的遗传变异,用32对扩增带型稳定的引物,从供试材料中检测出152个等位基因变异,每对引物检测等位基因2～9个,平均4.75个,平均多态信息量0.632;遗传多样性和聚类分析把40份供试糯玉米自交系分为4个类群;对40份糯玉米自交系籽粒的蛋白质、可溶性糖、还原糖、淀粉和赖氨酸含量进行测定,结果表明,糯玉米籽粒营养成分中蛋白质与淀粉之间存在消长关系,可溶性糖与还原糖含量之间存在显著正相关,且随着蛋白质含量的增加,与营养品质密切有关的赖氨酸含量随之增加.     

贵州70份玉米自交系的SSR标记遗传多样性及其杂种优势群分析

从251个SSR标记中筛选出均匀分布在玉米基因组上的88个SSR标记,用以分析评价贵州省2000年以来47个审定品种的70份亲本材料的遗传多样性。SSR标记检测的结果:88个标记共检测出466个等位基因,每个标记可检测等位基因2～18个,平均为5.31个;每个标记位点的多态性信息量(PIC)变化为0.213～0.965,平均为0.586,这表明贵州玉米自交系具有较为丰富的遗传多样性。POPTREE聚类分析结果:70份自交系分为Ⅰ、Ⅱ和Ⅲ类群。Ⅰ类群含8个自交系,以瑞德和兰卡斯特等温带种质为主。Ⅱ类群有11个自交系,以PN78599、瑞德和兰卡斯特等温带种质为主。Ⅲ类群拥有51个自交系,可分为A和B 2个亚群,B亚群还可再分为B1和B2 2个次亚群,A亚群中的10个系以我国地方温带种质为主,B1次亚群中的19个系以贵州地方亚热带种质为主,B2次亚群中的22个系以泰国苏湾热带种质为主。杂种优势利用分析的结果表明,贵州近些年在玉米育种中,主要是利用贵州地方亚热带种质和泰国苏湾热带种质2个杂种优势群,这与其多态位点百分率较高有关,与其群内SSR位点的平均等位数较多有关。贵州玉米育种利用的种质类型较少,有必要加强玉米种...     

糯玉米种质品质性状鉴定和SSR标记遗传多样性分析

对165份来源不同的糯玉米农家种和自交系的穗粒性状和淀粉品质性状进行了鉴定,并利用60对SSR标记进行了遗传多样性分析。结果表明,165份糯玉米种质穗长、秃顶长、行数、行粒数和穗粗变异较大,粗淀粉含量、支链淀粉含量和淀粉糊化特性RVA特征谱带值各指标变异丰富。60 对SSR引物在165份材料间共检测到281个等位基因变异,PCR扩增片段大小介于90～690bp,每对引物检测到2～9个等位基因,平均为4.68个;每对SSR 引物的多态信息量( PIC) 在0.332～0. 860之间,平均为0. 690。利用UPGMA 聚类分析方法将供试种质自交系分为3类,划分结果基本符合品系的来源情况,生产应用的多数糯玉米自交系材料与我国西南地区糯玉米地方品种材料具有较远的亲缘关系。显示出165份糯玉米种质具有丰富的遗传多样性,可为糯玉米杂优利用和遗传改良提供遗传基础。     

利用SSR标记研究不同来源的同名玉米骨干自交系的遗传同一性和遗传差异

从分子水平上阐明不同单位保存的同一份种质资源的遗传同一性和遗传差异对种质资源的保存和利用有重要意义.本研究利用116对SSR引物对不同来源的5个玉米骨干自交系(黄早四、掖478、Mo17、丹340和自330,共39份材料)进行了鉴定,共检测到400个等位变异,每对引物可以检测到1～4个等位变异,平均为3.45个.5个自交系中每个自交系间检测的等位变异在156～228个,5个自交系同名材料之间遗传相似系数变化范围为0.7～0.9.聚类分析结果表明,在供试自交系中黄早四、掖478、Mo17等3个材料的同名自交系能很好地聚为一类,且遗传相似系数很高.丹340和自330的同名材料在聚类时个别材料互有交叉,在利用时需要注意.     

我国西南地区玉米地方品种遗传多样性的SSR分子标记分析

利用微卫星(SSR)标记技术和DNA混合取样方法,选取均匀覆盖玉米染色体组的42对SSR引物,检测了来自我国西南地区54个玉米地方品种的遗传多样性。在54个玉米地方品种中检测到256个等位基因,每个SSR标记的等位基因数为2～9个,平均6.1个,说明我国西南地区玉米地方品种遗传多样性丰富。根据遗传相似系数矩阵做出的树状图,将54个玉米地方品种大致划分成4类,来源于同一地区的多数玉米地方品种划分在同一类中,表明西南地区玉米地方品种的地理分布与其遗传背景存在内在联系。从54个玉米地方品种中选出11个,每个品种选取15个单株,共165个DNA单株样品,分析玉米地方品种的遗传结构及其品种内的遗传多样性。对于检测玉米地方品种的遗传多样性,DNA单株样品分析优于DNA混合样品分析,42对相同的SSR引物在11个玉米地方品种中检测到330个等位基因,平均等位基因数A=7.86,有效等位基因数Ae=3.90,平均期望杂合度He=0.69,实际观察杂合度H0=0.37。据遗传结构分析结果,固定指数(F)为0.25～0.79,表明玉米地方品种是典型的混合繁育系统;由于杂合体不足,玉米地方品种群体间及群体内的遗传结构均偏离了Hardy-Weinberg平衡;杂合性基因多样度比率(Fst)平均为0.07,表明品种间和品种内的遗传变异分别占总遗传变异的7%和93%。玉米地方品种内遗传多样性及品种间遗传距离分析结果表明,在我国西南地区,分布在四川的玉米地方品种具有最丰富的遗传变异。经综合分析推测,我国西南地区玉米地方品种最早引进到四川种植,由此向毗邻地区传播扩散。     

SSR分子标记在山茶属观赏资源遗传多样性研究中的应用

采用微卫星(SSR)分子标记的方法,利用20对SSR引物对33份山茶属资源(含种和品种)的DNA样品进行了PCR扩增,从中筛选出10对扩增效果较好的SSR引物,并对33份资源进行了遗传多样性分析。结果显示:10对引物在33个植物材料中共检测出123个等位基因,每个SSR位点的等位基因数为3~22个,SSR2引物检测到的等位基因数量最多,达22个,平均每对引物含有12.3个等位基因,平均多态性信息量为0.74,变化范围为0.06~0.96。利用遗传距离矩阵按UPGMA方法进行聚类,结果表明33份植物材料可分为9个分支,很好的区分了品种间的亲缘关系,可为杂交育种的组合选择提供理论基础。不同花型的山茶属植物在10个微卫星位点上共发现42个特异等位基因,可能与不同的花型性状有关。     

基于SSR标记的荔枝种质遗传多样性分析

从53对本课题组自主开发设计的SSR特异引物对中筛选出22对多态性引物,对46份荔枝材料的基因组DNA进行扩增,共得到54个等位基因,其中每对引物的平均等位基因数为2.4,共获得23个特异性标记,各标记的平均观察杂合度值、平均期望杂合度和PIC值分别为0.451、0.355和0.507。其中L it6位点各数值最高,是最理想的选择标记。利用22对多态性引物对46份荔枝种质进行聚类分析,构建树状图,结果表明:大多数种质相似系数在0.63～0.95之间,说明它们之间的亲缘关系较近,并发现淮枝(广东)与淮枝(海南)两者可能为同名异物品种。     

玉米自交系幼胚培养能力与遗传关系研究(简报)

玉米幼胚培养获得的胚性愈伤组织具有较强的长期继代能力和再生植株能力,常被用于构建转基因受体系统。然而基因型是制约玉米组织培养植株再生的重要因素之一,不同玉米基因型的幼胚培养能力关系到其遗传转化研究的结果[1]。     

Microsatellites in Zea - variability,patterns of mutations,and use for evolutionary studies

To evaluate the performance of microsatellites or simple sequence repeats (SSRs) for evolutionary studies in Zea, 46 microsatellite loci originally derived from maize were applied to diverse arrays of populations that represent all the diploid species of Zea and 101 maize inbreds. Although null phenotypes and amplification of more than two alleles per plant were observed at modest rates, no practical obstacle was encountered for applying maize microsatellites to other Zea species. Sequencing of microsatellite alleles revealed complex patterns of mutation including frequent indels in the regions flanking microsatellite repeats. In one case, all variation at a microsatellite locus came from indels in the flanking region rather than in the repeat motif. Maize microsatellites show great variability within populations and provide a reliable means to measure intraspecific variation. Phylogeographic relationships of Zea populations were successfully reconstructed with good resolution using a genetic distance based on the infinite allele model, indicating that microsatellite loci are useful in evolutionary studies in Zea. Microsatellite loci show a principal division between tropical and temperate inbred lines, and group inbreds within these two broad germplasm groups in a manner that is largely consistent with their known pedigrees. Received: 10 February 2001 / Accepted: 21 May 2001     

Molecular marker diversity among current and historical maize inbreds

Advanced-cycle pedigree breeding has caused maize (Zea mays L.) inbreds to become more-elite but more-narrow genetically. Our objectives were to evaluate the genetic distance among current and historical maize inbreds, and to estimate how much genetic diversity has been lost among current inbreds. We selected eight maize inbreds (B14, B37, B73, B84, Mo17, C103, Oh43 and H99) that largely represented the genetic background of current elite inbreds in the U.S. seed industry. A total of 32 other inbreds represented historical inbreds that were once important in maize breeding. Cluster analysis of the inbreds, using data for 83 SSR marker loci, agreed well with pedigree information. Inbreds from Iowa Stiff Stalk Synthetic (BSSS), Reid Yellow Dent, and Lancaster clustered into separate groups with only few exceptions. The average number of alleles per locus was 4.9 among all 40 inbreds and 3.2 among the eight current inbreds. The reduction in the number of alleles per locus was not solely due to sample size. The average genetic distance (D _ij ) was 0.65 among the eight current inbreds, 0.67 among the 32 historical inbreds, and 0.67 among all 40 inbreds. These differences were statistically insignificant. We conclude that genetic diversity among current inbreds has been reduced at the gene level but not at the population level. Hybrid breeding in maize maintained, rather than decreased, genetic diversity, at least during the initial subdivision of inbreds into BSSS and non-BSSS heterotic groups. We speculate, however, that exploiting other germplasm sources is necessary for sustaining long-term breeding progress in maize. Received: 21 August 2000 / Accepted: 5 January 2001     

Variation of DNA fingerprints among accessions within maize inbred lines and implications for identification of essentially derived varieties.

Genetic distances (GDs) based on molecular markers are important parameters for identifying essentially derived varieties (EDVs). In this context information about the variability of molecular markers within maize inbred lines is essential. Our objectives were to (1) determine the variation in the size of simple sequence repeat (SSR) fragments among different accessions of maize inbreds and doubled haploid (DH) lines, (2) attribute the observed variation to genetic and marker system-specific sources, and (3) investigate the effect of SSR fragment size differences within maize lines on the GD between maize lines and their consequences for the identification of essentially derived varieties. Two to five accessions from nine inbred lines and five DH lines were taken from different sources or drawn as independent samples from the same seed lot. Each accession was genotyped with 100 SSR markers that evenly covered the whole maize genome. In total, 437 SSR fragments were identified, with a mean of 4.4 alleles per locus. The average polymorphic information content (PIC) was 0.58. GD estimates between two accessions of the same genotype ranged from 0.00 to 0.12 with an average of 0.029 for inbred lines and 0.001 for DH lines. An average of 11.1 SSRs was polymorphic between accessions of the same inbred line due to non-amplification (8.1 SSRs), heterogeneity (4.0 SSRs) or unknown alleles (2.6 SSRs). In contrast to lab errors, heterogeneity contributed considerably to the observed variation for GD. In order to decrease the probability to be suited for infringing an EDV threshold by chance, we recommend to increase the level of homogeneity of inbred lines before applying for plant variety protection.     

Variation of DNA fingerprints among accessions within maize inbred lines and implications for identification of essentially derived varieties: II. Genetic and technical sources of variation in AFLP data and comparison with SSR data

Accuracy and reproducibility of genetic distances (GDs) based on molecular markers are crucial issues for identification of essentially derived varieties (EDVs). Our objectives were to investigate (1) the amount of variation for amplified fragment length polymorphism (AFLP) markers found among different accessions within maize inbreds and doubled haploid (DH) lines, (2) the proportion attributable to genetic and technical components and marker system specific sources, (3) its effect on GDs between maize lines and implications for identification of EDVs, and (4) the comparison to published SSR data from the same plant materials. Two to five accessions from nine inbred lines and five DH lines were taken from different sources of maintenance breeding or drawn as independent samples from the same seed lot. Each of the 41 accessions was genotyped with 20 AFLP primer combinations revealing 988 AFLP markers. Map positions were available for 605 AFLPs covering all maize chromosomes. On average, six (0.6%) AFLP bands were polymorphic between different accessions of the same line. GDs between two accessions of the same line averaged 0.013 for inbreds and 0.006 for DH lines. The correlation of GDs based on AFLPs and SSRs was tight (r = 0.97**) across all 946 pairs of accessions but decreased (r = 0.55**) for 43 pairs of accessions originating from the same line. On the basis of our results, we recommend specific EDV thresholds for marker systems with different degree of polymorphism. In addition, precautions should be taken to warrant a high level of homogeneity for DNA markers within maize lines before applying for plant variety protection.     

Genetic diversity of maize inbred lines within and among heterotic groups revealed by RFLPs

Summary The objectives of this study were (1) to investigate genetic diversity for RFLPs in a set of important maize inbreds commonly used in Italian breeding programs, (2) to compare genetic similarities between unrelated lines from the same and different heterotic groups, and (3) to examine the potential of RFLPs for assigning maize inbreds to heterotic groups. Forty inbreds were analyzed for RFLPs with two restriction enzymes (EcoRI and HindIII) and 82 DNA clones uniformly distributed over the maize genome. Seventy clone-enzyme combinations gave single-banded RFLP patterns, and 79 gave multiple-banded RFLP patterns. The average number of RFLP patterns detected per clone-enzyme combination across all inbreds was 5.8. RFLP data revealed a wide range of genetic diversity within the two heterotic groups assayed, Iowa Stiff Stalk Synthetic (BSSS) and Lancaster Sure Crop (LSC). Genetic similarity (GS) between lines was estimated from binary RFLP data according to the method of Nei and Li (1979). The mean GS for line combinations of type BSSS × LSC (0.498) was substantially smaller than for unrelated line combinations or type BSSS × BSSS (0.584) but almost as great as for un-related line combinations of type LSC × LSC (0.506). Principal coordinate and cluster analyses based on GS values resulted in the separate groupings of lines, which is consistent with known pedigree information. A comparison between both methods for multivariate analyses of RFLP data is presented.     

An evaluation of the utility of SSR loci as molecular markers in maize (Zea mays L.): comparisons with data from RFLPS and pedigree

 The utility of 131 simple sequence repeat (SSR) loci to characterize and identify maize inbred lines, validate pedigree, and show associations among inbred lines was evaluated using a set of 58 inbred lines and four hybrids. Thirteen sets of inbred parent-progeny triplet pedigrees together with four hybrids and their parental lines were used to quantify incidences of scoring that departed from expectations based upon simple Mendelian inheritance. Results were compared to those obtained using 80 restriction fragment length polymorphism (RFLP) probes. Over all inbred triplets, 2.2% of SSRs and 3.6% of RFLP loci resulted in profiles that were scored as having segregated in a non-Mendelian fashion. Polymorphic index content (PIC, a measure of discrimination ability) values ranged from 0.06 to 0.91 for SSRs and from 0.10 to 0.84 for RFLPs. Mean values for PIC for SSRs and RFLPs were similar, approximately 0.62. However, PIC values for nine SSRs exceeded the maximum PIC for RFLPs. Di-repeats gave the highest mean PIC scores for SSRs but this class of repeats can result in “stutter” bands that complicate accurate genotyping. Associations among inbreds were similar for SSR and RFLP data, closely approximating expectations from known pedigrees. SSR technology presents the potential advantages of reliability, reproducibility, discrimination, standardization and cost effectiveness over RFLPs. SSR profiles can be readily interpreted in terms of alleles at mapped loci across a broad range of maize germ plasm. Consequently, SSRs represent the optimum approach for the identification and pedigree validation of maize genotypes compared to other currently available methods. Received: 15 January 1997 / Accepted: 28 February 1997     

Microsatellite marker-based genetic diversity assessment among exotic and native maize inbred lines of Bangladesh

Hybrid development is basically dependent on the variability among available genetic resources. Polymorphism among the maize inbreds is essentially needed for maize hybridization. This study aimed at the assessment of diversity among 22 maize inbreds by 18 microsatellite markers. The study identified 187 alleles at 18 SSR loci. The amplified allele frequency per microsatellite locus was 10.4 and the highest allele per locus was 17 in SSR primer pair phi026. SSR primer set p-umc1292, phi074 and phi090 showed the lowest 6 alleles per genotype per locus. The locus phi026 showed the highest degree of gene diversity (0.92), and the locus p-umc1292 had the lowest of gene diversity (0.77) with a mean value of 0.862 among the microsatellites. At each site, the most prevalent allele varied between 0.14 (bnlg371) and 0.36. (p-umc1292). At any given locus, an average of 0.22 out of the 22 selected maize inbred lines had a common major allele. The average value of the polymorphic information content (PIC) was 0.85, within the range of 0.74 at the lowest to 0.92 at the highest. The higher PIC values of phi026 and nc013 established them to be the best markers for maize inbred lines. The UPGMA clustering generated seven distinct groups having 12.5% of similarity coefficient. The results revealed that inbred lines E10, E27, E19, E34, E35, E4, E43, E28, E11, E21, E17, E38, E25, E34, E14, E16, E39 and E3 were more diversified. These lines are promising to be used as parent materials for hybrid maize development in the future.     

Multiple methods for the identification of polymorphic simple sequence repeats (SSRs) in sorghum [Sorghum bicolor (L.) Moench]

Simple sequence repeats (SSRs), also known as microsatellites, are highly variable DNA sequences that can be used as markers for the genetic analysis of plants. Three approaches were followed for the development of PCR primers for the amplification of DNA fragments containing SSRs from sorghum [Sorghum bicolor (L.) Moench]: a search for sorghum SSRs in public DNA databases; the use of SSR-specific primers developed in the Poaceae species maize (Zea mays L.) and seashore paspalum grass (Paspalum vaginatum Swartz); and the screening of sorghum genomic libraries by hybridization with SSR oligonucleotides. A total of 49 sorghum SSR-specific PCR primer pairs (two designed from GenBank SSR-containing sequences and 47 from the sequences of genomic clones) were screened on a panel of 17 sorghum and one maize accession. Ten primer pairs from paspalum and 90 from maize were also screened for polymorphism in sorghum. Length polymorphisms among amplification products were detected with 15 of these primer pairs, yielding diversity values ranging from 0.2 to 0.8 with an average diversity of 0.56. These primer pairs are now available for use as markers in crop improvement and conservation efforts.     

Genetic structure and diversity among maize inbred lines as inferred from DNA microsatellites

Two hundred and sixty maize inbred lines, representative of the genetic diversity among essentially all public lines of importance to temperate breeding and many important tropical and subtropical lines, were assayed for polymorphism at 94 microsatellite loci. The 2039 alleles identified served as raw data for estimating genetic structure and diversity. A model-based clustering analysis placed the inbred lines in five clusters that correspond to major breeding groups plus a set of lines showing evidence of mixed origins. A "phylogenetic" tree was constructed to further assess the genetic structure of maize inbreds, showing good agreement with the pedigree information and the cluster analysis. Tropical and subtropical inbreds possess a greater number of alleles and greater gene diversity than their temperate counterparts. The temperate Stiff Stalk lines are on average the most divergent from all other inbred groups. Comparison of diversity in equivalent samples of inbreds and open-pollinated landraces revealed that maize inbreds capture <80% of the alleles in the landraces, suggesting that landraces can provide additional genetic diversity for maize breeding. The contributions of four different segments of the landrace gene pool to each inbred group's gene pool were estimated using a novel likelihood-based model. The estimates are largely consistent with known histories of the inbreds and indicate that tropical highland germplasm is poorly represented in maize inbreds. Core sets of inbreds that capture maximal allelic richness were defined. These or similar core sets can be used for a variety of genetic applications in maize.