Genetic relationships in cultivars of hop, Humulus lupulus L., determined by RAPD analysis

Random amplified polymorphic DNA (RAPD) was used to evaluate the genetic variability and relationship of 65 hop cultivars from all the major hop-growing regions in the world. Twenty-eight selected random primers used in the RAPD reaction generated an average of 38.6%) polymorphic fragments, which was sufficient to produce 47 different RAPD profiles among the cultivars examined. The level of genetic variability was much higher than previously reported. Genetic similarity was estimated and UPGMA cluster analysis was performed using the RAPD data. Cluster analysis separated the cultivars into genetically related RAPD groups which were compared with pedigree data and grouping of the hop cultivars by essential oil type. The RAPD groups, strongly supported by pedigree data, gave more precise information on the level and distribution of genetic variability within hop cultivars than characterization by essential oils. Cultivars were divided into American and European groups, supporting the distinction between two geo-graphically distinct hop germplasms. Five genetically distinct groups revealed differences within the European germplasm, reflecting past hop breeding practices which have been adopted in different regions. The use of RAPD markers for hop germplasm characterization and genetic diversity study is discussed.     

小麦K-CMS保持系的SRAP鉴定及遗传多样性分析

为更好地对小麦K-CMS保持系的遗传背景进行分析,筛选优良亲本,以进一步提高小麦杂交育种的效率。利用SRAP技术,对30份小麦K-CMS保持系的遗传背景进行研究,以SRAP标记在30个品种之间扩增的多态性位点数据,采用Nei和Li的方法,计算品种间的遗传距离;以2年田间试验得到的品种株高、穗长、小穗数、穗下节长、穗粒草重、穗粒数、穗粒重、旗叶长等表现型性状平均数经正态标准化后,采用欧氏距离计算品种间遗传距离,再比较分析。分析表明,82对SRAP引物揭示出多态性,多态率68.3%,获得208条多态性谱带,平均每对引物产生3.68条多态性谱带,表现出较高的多态性。基于分子标记的聚类分析结果与系谱分析结果基本一致。若以整个遗传距离的总平均数作尺度对聚类图的结果进行分类,大致可分为6类。Mantel检测表明,SRAP标记数据计算的遗传距离矩阵和表现型计算的遗传距离矩阵存在极显著的相关性0.8123(t=11.325t0.01)。SRAP标记是检测品种间遗传差异的有效方法,可为小麦K-CMS保持系种质资源遗传差异的研究提供理论依据。研究还证实,一个骨干亲本与由其衍生出来的品种(系)之间的遗传差异一般较小。     

Changes in allelic frequency over time in European bread wheat (Triticum aestivum L.) varieties revealed using DArT and SSR markers

A collection of 189 bread wheat landraces and cultivars, primarily of European origin, released between 1886 and 2009, was analyzed using two DNA marker systems. A set of 76 SSR markers and ~7,000 DArT markers distributed across the wheat genome were employed in these analyses. All of the SSR markers were found to be polymorphic, whereas only 2,532 of the ~7,000 DArT markers were polymorphic. A Mantel test between the genetic distances calculated based on the SSR and DArT data showed a strong positive correlation between the two marker types, with a Pearson’s value (r) of 0.66. We assessed the genetic diversity and allelic frequencies among the accessions based on spring- versus winter-wheat type as well as between landraces and cultivars. We also analyzed the changes in genetic diversity and allelic frequencies in these samples over time. We observed separation based on both vernalization type and release date. Interestingly, we detected a decrease in genetic diversity in wheat accessions released over the period from 1960 to 1980. However, our results also showed that modern plant breeding have succeeded in maintaining genetic diversity in modern wheat cultivars. Studying allelic frequencies using SSR and DArT markers over time revealed changes in allelic frequencies for a number of markers that are known to be linked to important traits, which should be useful for genomic screening efforts. Monitoring changes in the frequency of molecular DNA markers over time in wheat cultivars may yield insight into alleles linked to important traits that have been the subject of positive or negative selection in the past and that may be useful for marker-assisted breeding programs in the future.     

Comparison of phenotypic and molecular marker-based classifications of hard red winter wheat cultivars

Genetic diversity is the basis for successful crop improvement and can be estimated by different methods. The objectives of this study were to estimate the genetic diversity of 30 ancestral to modern hard red winter wheat (Triticum aestivum L.) cultivars adapted to the Northern Great Plains using pedigree information, morphological traits (agronomic measurements from six environments), end-use quality traits (micro-quality assays on 50 g grain or milled flour samples for the six environments), and molecular markers (seed storage proteins separated using SDS-PAGE, 51 SSRs, and 23 SRAP DNA markers), and to determine the relationships of genetic distance estimates obtained from these methods. Relationships among diversity estimates were determined using simple (Pearson) and rank (Spearman) correlation coefficients between distance estimates and by clustering cultivars using genetic-distances for different traits. All methods found a wide range in genetic diversity. The genetic distance estimates based on pedigree had the highest values due to possible over-estimation arising from model assumptions. The genetic diversity estimates based on seed storage protein were lowest because they were the major determinants of end-use quality, which is a highly selected trait. In general, the diversity estimates from each of the methods were positively correlated at a low level with the exceptions of SRAP diversity estimates being independent of morphologic traits (simple correlation), SDS-PAGE, and SSR diversity estimates (rank correlation). However, SSR markers, thought to be among the most efficient markers for estimating genetic diversity, were most highly correlated with seed storage proteins. The procedures used to accurately estimate genetic diversity will depend largely upon the tools available to the researcher and their application to the breeding scheme.     

Assessment of genetic diversity in bread wheat genotypes for tolerance to drought using AFLPs and agronomic traits

Moisture stress greatly limits the productivity of wheat in many wheat-growing regions of the world. Knowledge of the degree of genetic diversity among parental materials for key selection traits will facilitate the development of high yielding, stress tolerant wheat cultivars. The objectives of this study were to: (i) use amplified fragment length polymorphisms (AFLPs) to assess genetic diversity among bread wheat lines and cultivars with different responses to drought stress in two distinct environments and, (ii) compare genetic diversity estimated by AFLPs with diversity evaluated on agronomic performance under drought stress. Twenty-eight genotypes, 14 from Iran and 14 developed or obtained by CIMMYT, were evaluated in the study. Phenotypic data on the 14 Iranian lines were obtained in Iran, and data on the 14 CIMMYT lines were collected in Mexico. Ten AFLP primer pairs detected 335 polymorphic bands among the 28 cultivars. At the 5th fusion level of the resulting dendrogram, 6 genotype clusters were identified. Thirteen of the 14 CIMMYT genotypes grouped into one cluster while 4 of the remaining groups were comprised only of Iranian genotypes. When the agronomic performance of the Iranian materials was compared with the AFLP diversity analysis, 5 of the 6 drought susceptible genotypes clustered together in the agronomic dendrogram, and were located in the same cluster in the AFLP dendrogram. However, the drought tolerant Iranian materials did not show the same degree of relationship. The CIMMYT materials did not demonstrate a significant association between agronomic performance and genetic diversity determined using AFLPs. Clearly these data show that there are genotypes with similar agronomic performance and different genetic constitutions in this study that can be combined in a breeding program to potentially improve tolerance to drought stress.     

基于SNP分子标记的泰山/泰科麦系列小麦遗传解析

对不同年份育成的21个小麦品种（系）进行全基因组扫描,通过分析遗传距离和染色体区段/位点,明确其亲缘关系远近和遗传差异。分析可知,获得的2029个SNP基因位点在B基因组拥有较高的遗传多样性,其次是A和D基因组;在7个同源群中,第3和第6同源群呈现出较高的遗传多样性,而第1和第4同源群的遗传多样性较低;21条染色体中,3A、1B、6B染色体的遗传多样性较高,而1A、6A的遗传多样性偏低。对21份供试材料依据审定（育成）年份分析其群体的平均遗传距离,不同年份品种间的平均遗传距离先增大后减小,遗传多样性逐渐降低;21份供试材料间的遗传相似系数在0.69~0.99之间,大致可聚为4个类群,同一年份的品种一般聚在一起,与其系谱关系吻合。构建并分析供试材料的基因型图谱发现,00s、10s和现在育成的小麦品种（系）共有SNP和共有染色体区段分别主要在A、D和B基因组,对应已发表性状同不同年份育种目标吻合。同时发现21份供试材料均含有25个共同SNP位点,分布在1A、5A、6A、7A、2B、3B、6B、1D、2D、3D和7D染色体上,且每条染色体上分布的SNP位点数目均不相同,通过对应已发表性状进一步证实在品种（系）组配与选育过程中注重产量、株高、分蘖数、抽穗期、灌浆速率和抗病等性状的选择。以上研究结果可为今后小麦新品种组配和选育提供参考依据。     

Genetic diversity in soybean as determined by RAPD and microsatellite analysis

The random amplified polymorphic DNA (RAPD) and microsatellite techniques were used to evaluate the genetic diversity among 18 soybean genotypes selected for a breeding programme to increase the protein content of varieties adapted for central European growing conditions. Out of 33 random primers used in RAPD reactions, only 12 showed polymorphism useful for characterization of these genotypes. In contrast, all 12 microsatellite primer pairs used in this study detected polymorphism with 2–6 alleles per locus. Similarity measures and cluster analysis were made using RAPD and simple sequence repeat (SSR) data, separately and together. The resulting dendrograms were compared with each other and with the available pedigree information as a control. The dendrogram derived from RAPD data showed some divergence from the pedigree information available for the lines. The dendrograms based on SSR data and SSR data combined with RAPD gave very good agreement with pedigree information. It can be concluded that the combined use of a limited number of RAPD and SSR markers is a useful and reliable means of evaluating genetic relationships of genotypes in the absence of pedigree data.     

用RAPD、ISSR和AFLP标记分析系谱关系明确的甘薯品种的亲缘关系

用RAPD、ISSR和AFLP标记对系谱关系明确的7个甘薯品种进行了亲缘关系分析。24个RAPD引物、14个ISSR引物和9对AFLP引物分别扩增出173、174和168条多态性带。3种分子标记在检测甘薯品种间遗传差异上相关程度高，其中RAPD与ISSR之间的相关系数最大为0.9328。用ISSR标记估计的品种间遗传距离为0.1286~1.0932，平均0.4883，大于其余2个标记的估计值。3种分子标记皆可揭示甘薯品种的亲缘关系，其中ISSR标记产生的聚类图与系谱图最吻合，认为ISSR标记更适于分析甘薯品种的亲缘关系。     

Genetic diversity in mustard (Brassica juncea L.) germplasm from Pakistan as determined by RAPDs

The genetic diversity and the relationships among a collection of mustard (B. juncea) germplasm, including 41 accessions collected from Pakistan, 6 oilseed cultivars/ lines and 5 Japanese vegetable cultivars, were evaluated using random amplified polymorphic DNA (RAPD) markers. A total of 198 polymorphic amplified products were obtained from 30 decamer primers. Of these, 14 were unique to the accession PAK-85835 and 37 were specific to PAK-85839. Based on pair-wise comparisons of RAPD amplification products, genetic similarity was estimated using similarity coefficients of Nei & Li (1979) and a dendrogram was constructed using the unweighted pair-group method with arithmetic averages (UPGMA). Cluster analysis based on these genetic similarities placed most of the collected germplasm and oilseed cultivars/lines close to each other, showing a low level of polymorphism between the oilseed accessions collected in Pakistan. However, the clusters formed by the oilseed collections and cultivars were distinct from those formed by the vegetable cultivars. A low level of genetic variability of oilseed mustard in Pakistan was attributed to the selection for similar traits and horticultural uses. The farmers' preference for more remunerative crops and perhaps the close parentage of these accessions further contributed towards their little diversity. The study demonstrated that the RAPD is a simple and fast technique to compare the genetic relationships and the patterns of variation among accessions of this crop. This revised version was published online in August 2006 with corrections to the Cover Date.     

Study of genetic diversity in safflower genotypes using agro-morphological traits and RAPD markers

This research was conducted to study the genetic diversity in safflower (Carthamus tinctorius L.) using agro-morphological traits and RAPD markers. Sixteen selected lines derived from landraces growing in various agro-climatic regions of Iran along with four exotic genotypes were evaluated in a randomized complete block design with three replications under field conditions. Days to emergence, days to initial flowering, days to flowering, days to maturity, plant height, branches per plant, capitula per plant, seeds per capitulum, 1,000-seed weight, seed yield per plant, seed yield, and reaction to powdery mildew (Leveillula taurica Arnaud) were evaluated in this study. Genetic diversity of the genotypes was assessed by RAPD markers. The results indicated significant differences among genotypes for the agro-morphological traits and clustering based on these traits classified the genotypes into five groups. Analysis of the RAPD markers revealed 15 polymorphic primers out of 50 used primers. Based on RAPD data, the highest genetic similarity was observed between the cultivars of “AC Sunset,” “AC Sterling” from Canada and the lowest relatedness observed between a local breeding line “E₂₄₂₈” and genotype “GE₆₂₉₂₃” from Germany. Cluster analysis based on RAPD markers and 54% coefficient of similarity divided the genotypes into five distinct groups. Comparing the clusters based on agro-morphological traits with those from molecular markers showed slight similarities. The finding of high genetic variation for agro-morphological traits and polymorphism at DNA level reveal that agronomic traits can be improved by selection programs.     

利用RAPD标记鉴定大豆种质

本研究以５７个中国大豆祖先吕系及育成品种和１８个美国大豆祖先品系为ＤＮＡ样品来源，通过随机引物ＰＣＲ扩增基因组ＤＮＡ的多态性，探索利用ＲＡＰＤ标记鉴定和相关种质的可能性。研究结果表明，５０个１０摩尔随机引物共扩增可分辩产物２４６个，其中８２．４％的随机引物可产生多态性产物，所扩增产物的５４．４％至少在两个基因毒草境存在差异。上ＰＣＲ扩增产物分别以１和０记录存在与否。扩增产物间的成对比较可产生非相似     

Cultivar identification and genetic relationship among selected breeding lines and cultivars in chickpea (Cicer arietinum L.)

Twenty two RAPD and 22 ISSR markers were evaluated for their potential use in determination of genetic relationships in chickpea (Cicer arietinum L.) cultivars and breeding lines. We were able to identify six chickpea cultivars/breeding lines by cultivar-specific markers. All of the cultivars tested displayed a different phenotype generated either by the RAPD or ISSR primers. Though ISSR primers generated less markers than RAPD primers, the ISSR primers produced higher levels of polymorphism (% of polymorphic markers per primer) than RAPD primers. A high level of within cultivar homogeneity was observed in chickpea. Cultivars/breeding lines originating from a common genetic background showed closer genetic relationship. Chickpea lines with similar seed type(kabuli or desi) had a tendency to cluster together. This revised version was published online in August 2006 with corrections to the Cover Date.     

Amplified fragment length polymorphism as a tool for molecular characterization of almond germplasm: genetic diversity among cultivated genotypes and related wild species of almond,and its relationships with agronomic traits

Amplified fragment length polymorphism (AFLP) analysis is a rapid and efficient method for producing DNA fingerprints and molecular characterization. Our objectives were to: estimate genetic similarities (GS), marker indices, and polymorphic information contents (PICs) for AFLP markers in almond cultivars; assess the genetic diversity of almond cultivars and wild species, using GS estimated from AFLP fingerprints and molecular characterization; and facilitate the use of markers in inter-specific introgression and cultivar improvement. The genetic diversity of 45 almond cultivars from Iran, Europe, and America, were studied assaying 19 primer combinations. In addition, several agronomic traits were evaluated, including flowering and maturity times, self-incompatibility, and kernel and fruit properties. Out of the 813 polymerase chain reaction fragments that were scored, 781 (96.23%) were polymorphic. GS ranged from 0.5 to 0.96, marker indices ranged from 51.37 to 78.79, and PICs ranged from 0.56 to 0.86. Results allowed the unique molecular identification of all assayed genotypes. However, the correlation between genetic similarity clustering as based on AFLP and clustering for agronomic traits was low. Cluster analysis based on AFLP data clearly differentiated the genotypes and wild species according to their origin and pedigree, whereas, cluster analysis based on agronomic data differentiated according the pomological characterization. Our results showed the great genetic diversity of the almond cultivars and their interest for almond breeding.     

利用RAPD、ISSR标记分析国兰种质资源遗传多样性的研究

旨在分析不同地区国兰间的亲缘关系,为国兰资源的开发及新品种的选育提供分子水平的参考依据。利用RAPD和ISSR分子标记技术,对7种国兰的21个品种资源进行遗传多样性和亲缘关系分析。结果表明：39个RAPD和ISSR引物在供试材料中共扩增出96条带型清晰的谱带,其遗传中31条为多态性条带;通过UPGMA聚类分析表明,21个国兰品种资源间遗传距离在1.91~6.60之间,其中春兰资源的遗传距离在1.91~4.38之间,建兰资源的遗传距离在2.60~6.20之间,寒兰资源的遗传距离在2.20~5.80之间,墨兰资源的遗传距离在3.52~6.60之间,表现出了较高的遗传多样性。聚类分析结果与传统的形态学分类结果基本一致,也说明分子标记可以在分子水平反映遗传资源的遗传多样性,具有灵敏度高、结果真实可靠等优点。本研究结果显示国兰品种间的亲缘关系与地理位置分布相关,为兰属植物的分类及遗传多样性研究提供了一定的理论支撑。     

Genetic diversity in the parental lines and heterosis of the tropical rice hybrids

Genetic diversity within and between the maintainer (B) and restorer (R) lines used in hybrid breeding programs of the Philippine was investigated with information from analysis of pedigree record, quantitative traits and SSR assays. Mean coefficients of coancestry were calculated as 0.11 within R lines, 0.27 within B lines, and 0.04 between R and B lines, indicating greater diversity among R lines than among B lines, and the significant divergence between B and R lines. These results are consistent with those obtained from quantitative trait analysis and SSR marker assays. Relative gene diversity for 37 random SSR markers averaged 0.20 within B lines,0.28 within R lines, and 0.52 between two groups of lines. There were no consistent associations among various genetic diversity measures. Random sets of SSR marker and pedigree based diversity measures had no significant correlation with mid-parent heterosis for grain yield and biomass, indicating that prediction of heterosis for complex traits based on these two genetic diversity estimates is difficult. This revised version was published online in August 2006 with corrections to the Cover Date.     

利用RAPD和SSR分析36个贵州主要玉米种质的比较研究

利用RAPD和SSR两种标记方法研究了36个玉米自交系的遗传多样性,并对这两种分子标记系统进行了比较.利用筛选出的22条RAPD引物,检测到了148条有多态性的带;利用筛选出的34对SSR引物,检测到158个等位基因.RAPD和SSR分子标记均有很高的多态性,RAPD多态性带比例为95.95%,SSR位点检测出的平均等位基因数位4.65.RAPD分子标记结果将36个玉米自交系划分为6大类,SSR分子标记将其划分为5大类.与系谱分析基本一致,两种分子标记划分的结果也相似.研究认为,RAPD、SSR两种分子标记系统均适合于玉米种质的遗传多样性研究,但SSR更可取.     

克新系列马铃薯遗传多样性的RAPD分析

利用RAPD标记技术对19份克新系列马铃薯品种进行了遗传多样性分析,分别提取19份马铃薯品种的DNA,进行随机引物多态性扩增,从1000条随机引物中初步筛选出7条有多态性的引物进行详细研究,每条RAPD引物扩增出4~9条带,共获得52条带,其中多态性条带为43条;19份马铃薯品种的遗传距离介于0.17~0.72之间,平均值为0.39,平均遗传距离介于0.31~0.51之间;聚类分析结果在GS=0.53处可将克新系列马铃薯品种划分为三类,聚类结果与系谱分析基本相符,同时也说明克新系列马铃薯的遗传基础有所拓宽。研究表明：RAPD标记简便、快速、成本低,适用于分析马铃薯遗传多样性,指导马铃薯育种实践中的亲本组配。     

RAPD和AFLP标记分析中国马铃薯主要品种的遗传多样性

采用RAPD 和AFLP两种方法分析71份中国各地马铃薯主要品种,均可将其完全区分,并可对其进行分子鉴定;证明中国马铃薯主要品种遗传组成上差异小,遗传多样性差。由于标记方法的原理差异和栽培马铃薯遗传组成复杂性,用2种方法分类的结果有所差异。AFLP标记检测获得的Shannon-weaver指数和Simpson指数均高于RAPD标记检测的结果,AFLP标记检测多态性的能力远高于RAPD标记。AFLP标记平均每个引物组合检测到100.1个位点,其中54.9条为多态性位点,而RAPD标记的相应数据分别为12.5和9.8个。不同的标记方法在马铃薯遗传多样性研究中存在差异,聚类结果从分子水平反映了中国现有主要马铃薯品种遗传基础的狭窄。     

Location and transmission of QTL for multiple traits in the pedigree of soybean cultivars

In silico mapping for single trait was extended to analyze many agronomic traits in the pedigree of soybean. 26 agronomic traits were measured and 477 polymorphic markers chosen on public genetic map were genotyped on 14 inbreeding lines in the pedigree of Suinong14. We firstly determined 6 principal components from 26 agronomic traits using the principal component analysis and then constructed 6 “super traits” by the multiplication of the vector of the standardized original traits by the eigenvectors corresponding to the principle components. With in silico mapping, a total of 24 markers distributing on 13 linkage groups were detected separately as QTL responsible for 6 “super traits” and of which 14 QTL performed pleiotrpy. Tracing the transmission of functional genes in the pedigree, it was found that some genes were capable to explain the genetic mechanism for the contribution of exotic germplasms and domestic founders to soybean cultivars in the improvement of the performance and quality.