Assessing genetic diversity in a sugarcane germplasm collection using an automated AFLP analysis

An assessment of genetic diversity within and between Saccharum, Old World Erianthus sect. Ripidium, and North American E.giganteus (S.giganteum) was conducted using Amplified Fragment Length Polymorphism (AFLP^TM) markers. An automated gel scoring system (GelCompar^TM) was successfully used to analyse the complex AFLP patterns obtained in sugarcane and its relatives. Similarity coefficient calculations and clustering revealed a genetic structure for Saccharum and Erianthus sect. Ripidium that was identical to the one previously obtained using other molecular marker types, showing the appropriateness of AFLP markers and the associated automated analysis in assessing genetic diversity in sugarcane. A genetic structure that correlated with cytotype (2n=30, 60, 90) was revealed within the North American species, E. giganteus (S.giganteum). Complex relationships among Saccharum, Erianthus sect. Ripidium, and North American E.giganteus were revealed and are discussed in the light of a similar study which involved RAPD markers. This revised version was published online in July 2006 with corrections to the Cover Date.     

Genetic diversity in a world germplasm collection of tall fescue

Festuca arundinacea Schreb., commonly known as tall fescue, is a major forage crop in temperate regions. Recently, a molecular analysis of different accessions of a world germplasm collection of tall fescue has demonstrated that it contains different species from the genus Festuca and allowed their rapid classification into the three major morphotypes (Continental, Mediterranean and Rhizomatous). In this study, we explored the genetic diversity of 161 accessions of Festuca species from 29 countries, including 28 accessions of INTA (Argentina), by analyzing 15 polymorphic SSR markers by capillary electrophoresis. These molecular markers allowed us to detect a total of 214 alleles. The number of alleles per locus varied between 5 and 24, and the values of polymorphic information content ranged from 0.627 to 0.840. In addition, the accessions analyzed by flow cytometry showed different ploidy levels (diploid, tetraploid, hexaploid and octaploid), placing in evidence that the world germplasm collection consisted of multiple species, as previously suggested. Interestingly, almost all accessions of INTA germplasm collection were true hexaploid tall fescue, belonging to two eco-geographic races (Continental and Mediterranean). Finally, the data presented revealed an ample genetic diversity of tall fescue showing the importance of preserving the INTA collection for future breeding programs.     

Measurement and classification of genetic diversity in okra (Abelmoschus esculentus)

Eighteen accessions of okra of diverse ecological background were evaluated for genetic variability through the techniques of coefficient of racial likeness (CRL) and principal coordinate analysis (PCO). The variation patterns among the accessions were classified by using the techniques of metroglyph analysis and single-linkage cluster analysis. CRL and PCO produced similar results on the diversity of the accessions but the grouping of the accessions by metroglyph analysis and SLCA produced different results. The usefulness of metroglyph analysis depends on the amount of variation accounted for by the two principal characters on which the two co-ordinate axes are constructed. The techniques are compared.     

Assessment of genetic diversity in a Morus germplasm collection using fluorescence-based AFLP markers

To meet various breeding objectives and to conserve the existing genetic resources of mulberry for future use, the present study was undertaken to investigate the amount of genetic diversity and to establish the relationships between mulberry genotypes using fluorescence-based AFLP markers. Genetic diversity was estimated in 45 mulberry accessions from different eco-geographic regions of Japan and other parts of the world. Five primer combinations amplified an average of 110 AFLP markers per primer combination, ranging in size from 35 to 500 bp. A high degree of polymorphism was revealed by these combinations that ranged from 69.7 to 82.3% across all the genotypes studied. Several rare genotype-specific bands were also identified which could be effectively utilized to distinguish different genotypes. The wide range in genetic similarity coefficients (0.58–0.99) indicated that the mulberry germplasm collection represents a genetically diverse popu-lation. The phenetic dendrogram generated by the UPGMA method grouped 45 accessions into four major clusters, which was in agreement with the results from conventional methods. Clustering of some genotypes into strictly separate groups was not readily apparent and no clear interrelationships could be depicted, in spite of their different geographic origin. In addition, AFLP analysis provided sufficient polymorphism for DNA typing and contributed additional insights into the genetic structure of the mulberry germplasm. These results will help in the formulation of appropriate strategies for conservation and variety improvement in mulberry, for which little or no knowledge of genetic diversity is currently available. Received: 30 December 1999 / Accepted: 14 March 2000     

Analysis of molecular genetic diversity and population structure in Amaranthus germplasm using SSR markers

We assessed the molecular genetic diversity and population structure of Amaranthus species accessions using 11 simple sequence repeat markers. A total of 122 alleles were detected, and the number of alleles per marker (N_A) ranged from 6 to 21 with an average of 11.1 alleles. The frequency of major alleles per locus ranged from 0.148 to 0.695, with an average value of 0.496 per marker. The overall polymorphic information content values were 0.436–0.898, with an average value of 0.657. The observed heterozygosity (H_O) and expected heterozygosity (H_E) ranged from 0.056 to 0.876 and from 0.480 to 0.907, with average values of 0.287 and 0.698, respectively. The average H_O (0.240) was lower than the H_E and gene flow (Nm), and showed substantial genetic variability among all populations of amaranth accessions. The sample groupings did not strictly follow the geographic affiliations of the accessions. A similar pattern was obtained using model-based structure analysis without grouping by species type. Knowledge of the genetic diversity and population structure of amaranth can be used to select representative genotypes and manage Amaranthus germplasm breeding programs.     

遗传多样性概述

遗传多样性作为生物多样性的重要组成部分,是物种多样性、生态系统多样性和景观多样性的基础。随着研究方法和实验技术的发展,遗传多样性研究从形态学水平、细胞学（染色体）水平、生理生化水平逐渐发展到分子水平。形态标记、细胞学标记、等位酶分析、DNA多态性分析等方法,为我们研究遗传多样性提供了有效的工具。特别是DNA多态性分析是一种更为直接而有效的方法。     

Molecular assessment of genetic diversity in mung bean germplasm

RAPD profiles were used to identify the extent of diversity among 54 accessions of mung bean that included both improved and local land races. Out of the 40 primers screened, seven primers generated 174 amplification products with an average of 24.85 bands per primer. The RAPD profiles were analysed for Jaccard's similarity coefficients that was found to be in the range from 0 to 0.48, indicating the presence of wide range of genetic diversity at molecular level. Cluster analysis was carried out based on distances (1-similarity coefficient) using neighbour-joining method in Free Tree package. The dendrogram resolved all the accessions into two major clusters, I (with 11 accessions) and II (with 43 accessions). However, the cluster was further divided into four subclusters (II A with six, II B with nine, II C with 15 and II D with 13 accessions). The distribution of the accessions in different clusters and subclusters appears to be related to their performance in field conditions for 10 morphological traits that were scored. This study indicated that the RAPD profiles provide an easy and simple technique for preliminary genetic diversity assessment of mung bean accessions that may reflect morphological trait differences among them.     

利用30个微卫星标记分析长江中下游鲢群体的遗传多样性

摘要: 利用30对微卫星分子标记对长江中下游5个鲢群体进行了遗传多样性分析。结果表明: 在30个基因座中, 共检测到144个等位基因, 每个座位检测到的等位基因数为1～10个, 其中有25个座位具有多态性, 多态位点百分率为83.33,5个群体的平均等位基因数A为4.0/4.1, 平均有效等位基因数Ne为2.4445～2.6332, 平均观察杂合度Ho为0.3233～0.3511, 平均期望杂合度He为0.4421～0.4704, 平均多态信息含量PIC为0.4068～0.4286。对数据进行F-检验, Fst值表明群体间的遗传分化程度中等, 并对基因型进行了基于Hardy-Weinberg平衡的卡方检验, 所得P值说明5个群体均一定程度上偏离了平衡。5个群体间的遗传相似系数为0.8466～0.9146,遗传距离为0.0893～0.1665, 并根据Nei氏标准遗传距离用UPGMA方法对5个鲢群体进行亲缘关系聚类。     

半野生大豆种质资源SSR位点遗传多样性分析

利用12对SSR引物对67份半野生大豆种质进行了遗传多样性的检测分析,结果表明,12个位点共检测到184个等位基因变异,平均每个位点等位基因数目为15．41个,平均多态性信息量,平均遗传多样性指数,平均遗传距离分别为0．849,0．706,0．118,根据SSR分析结果,按欧式距离将67份半野生大豆种质聚类并划分为5个组群。     

57株毛头鬼伞遗传多样性分析

运用SRAP、RAPD、ISSR3种分子标记技术对来源不同地区的57株毛头鬼伞Coprinus comatus进行了遗传多样性分析,通过3种分子标记进行聚类分析,当相异系数D为0.48时,可以把57株毛头鬼伞分为4类:Ⅰ类包括Co0001;Ⅱ类包括Co0003;Ⅲ类包括Co0005;Ⅳ类包括其余54个菌种。供试的57个菌株间的相异系数范围从0–0.72,具有一定的遗传多态性。但其中有许多菌株两者之间的相异系数为0,说明毛头鬼伞菌种存在着比较严重的同种异名现象。     

Patterns of genetic diversity in related taxa of Antirrhinum L. assessed using allozymes

Allozyme diversity was studied within and among populations of five related taxa of Antirrhinum L. endemic to the Iberian Peninsula ( A. graniticum Rothm. ssp. graniticum , ssp. brachycalyx Sutton and ssp. ambiguum (Lange) Mateu & Segarra, A. boissieri Rothm. and A. onubensis (Fdez. Casas) Fdez. Casas). All of the studied taxa are obligate outcrossing endemic perennial herbs which form isolated populations. However, the taxa vary in range and population sizes, and are found on different soil types. The level and distribution of allozyme diversity differed widely between taxa: A. graniticum ssp. brachycalyx had the lowest level of allozyme diversity (H_T = 0.09), whilst the highest level was detected in A. boissieri (H_T = 0.25). Total variation was partitioned into within- and among-population variation. The proportion attributable to variation within populations varied from about 67% up to 84.3% and 89.5% in A. graniticum ssp. brachycalyx and A. graniticum ssp. ambiguum , respectively. Both these subspecies also showed little population divergence (G_ST = 0.10 and 0.09, respectively) and had high levels of estimated gene flow (Nm = 2.18 and 2.62, respectively). These results are discussed in relation to geographical proximity of populations and habitat continuity. Isolation by distance was not detected in any of the studied taxa. This result suggests that divergence among populations is due to random genetic drift.  © 2003 The Linnean Society of London . Biological Journal of the Linnean Society , 2003, 79 , 299–307.     

SSR and AFLP based genetic diversity of soybean germplasm differing in photoperiod sensitivity

Forty-four soybean genotypes with different photoperiod response were selected after screening of 1000 soybean accessions under artificial condition and were profiled using 40 SSR and 5 AFLP primer pairs. The average polymorphism information content (PIC) for SSR and AFLP marker systems was 0.507 and 0.120, respectively. Clustering of genotypes was done using UPGMA method for SSR and AFLP and correlation was 0.337 and 0.504, respectively. Mantel's correlation coefficients between Jaccard's similarity coefficient and the cophenetic values were fairly high in both the marker systems (SSR = 0.924; AFLP = 0.958) indicating very good fit for the clustering pattern. UPGMA based cluster analysis classified soybean genotypes into four major groups with fairly moderate bootstrap support. These major clusters corresponded with the photoperiod response and place of origin. The results indicate that the photoperiod insensitive genotypes, 11/2/1939 (EC 325097) and MACS 330 would be better choice for broadening the genetic base of soybean for this trait.     

普通野生稻（Oryza rufipogon Griff．）的SSR遗传多样性研究

利用SSR标记对分布在我国7个省的17个居群普通野生稻(Oryza rufipogon Griff．)的种质资源进行研究,结果表明：17个居群普通野生稻的遗传多样性有着显著的差异,从UPGMA聚类结果可以看出普通野生稻的遗传多样性与其生态地理分布有显著的相关性,遗传多样性指数高的地区极有可能是栽培稻的起源中心;用筛选出的7对SSR引物对336份：DNA样品进行扩增,得到60条特异条带,在分子水平上进一步证明普通野生稻的起源为两广地区;本研究也表明SSR是进行遗传资源多样性研究的一种切实有效的研究方法。     

SSR标记在毛木耳种质资源遗传多样性研究中的应用

本研究利用基于毛木耳全基因组开发的SSR标记对27份毛木耳菌株（野生14株、栽培13株）的遗传多样性进行分析。首先随机选取3个菌株（2个野生菌株、1个栽培菌株）的DNA为模板,从144对SSR引物中筛选出扩增条带清晰、稳定性强、多态性丰富的引物24对。24对SSR引物共检测到116个多态性SSR片段,每对引物的多态性片段有3-7个,引物平均检测效率为4.83个,Shannon’s遗传多样性指数范围是0.866-1.885,多态性位点比率100%。供试菌株遗传相似系数范围是0.618-0.971,说明毛木耳种质资源具有丰富的遗传多样性。野生菌株与栽培菌株间平均遗传相似系数分别为0.746、0.779,说明毛木耳野生菌株遗传多样性更为丰富。经聚类分析,在遗传相似系数为0.680时,可将供试菌株分为无色（白色）类群Ⅰ和有色（浅黄色到红褐色）类群Ⅱ。遗传相似系数为0.704时,可将供试菌株中栽培菌株和野生菌株明显区分（14株野生菌株均在类群Ⅱ-2中,13株栽培菌株分别在类群Ⅰ和Ⅱ-1中）。本研究表明基于全基因组的SSR标记能从分子水平上揭示各菌株间的遗传差异,丰富毛木耳遗传多样性的研究手段,并为进一步进行毛木耳的品种选育、遗传学研究等提供有力手段。     

Importance of genetic characterization and conservation of plant genetic resources: The breeding system and genetic diversity of wild soybean (Glycine soja)

Abstract Plant genetic resources play an important role in the improvement of cultivated plants. To characterize and evaluate the ecological and reproductive features of wild soybean ( Glycine soja Sieb. et Zucc.), which is the most probable ancestor of cultivated soybean ( G. max (L) Merr.), the breeding system and genetic diversity of G. soja were investigated. The extent of natural cross-pollination of G. soja was estimated in four populations along the Omono River in Akita Prefecture, Japan by examining allozyme variation. Although it has been previously believed that G. soja is autogamous, as is cultivated soybean, the mean multilocus outcrossing rate ( t m) estimate was 13%. These values are much higher than the outcrossing rate previously reported for both G. soja and G. max . Frequent visits by honeybees and carpenter bees to flowers were also observed, which supported this conjecture. Furthermore, to evaluate the genetic variation of G. soja as a genetic resource, the genetic structure of 447 populations over Japan were analyzed. Wild soybean populations had a higher degree of variation of isozyme loci. The G ST coefficient of gene differentian values among the sites within the district were particularly high, revealing that the isozyme genotype was greatly different among site populations and homogeneous within the sites. The genetic differentiation among nine districts was observed in the allele frequencies of a few loci, indicating that geographic isolation in the wild soybean population was effectively created through the distance between the districts. The difference in the allele frequency among the districts may be produced under genetic drift. Finally, the importance of the preservation of natural plant populations and the habitats of wild progenitors (i.e. the in situ conservation of plant genetic resources) was emphasized.     

西南地区麻疯树天然种群遗传多样性的等位酶变异

为了揭示麻疯树(Jatropha curcas)天然种群的遗传多样性和遗传结构, 采用聚苯烯酰胺凝胶垂直平板电泳技术, 对采自四川、云南、贵州3个省的10个麻疯树天然种群的叶片样本进行了同工酶分析。7个酶系统10个位点的检测结果表明: 麻疯树种群水平上的遗传多样性较高, 每位点平均等位基因数为2.428 6, 多态位点百分率为97.14%, 平均期望杂合度为0.396 4。种群间遗传分化系数为0.041 3, 种群间总的基因流较高, 为5.808 9, 种群间遗传一致度较高(Shannon信息指数为0.921 7- 0.995 3)。非加权类平均法(UPGMA)聚类结果显示, 10个种群的遗传距离与地理距离相关性不显著。麻疯树天然种群具有较低程度的遗传分化、较高的基因流, 种内及种群内多样性丰富, 这为麻疯树优良品种的选育提供了良好的遗传基础。     

走马胎种质资源遗传多样性的ISSR分析

走马胎( Ardisia gigantifolia)是紫金牛科( Myrsinaceae)紫金牛属( Ardisia)多年生小灌木植物。走马胎作为我国传统中药材,已有多年的药用历史。目前,走马胎不再局限于临床药用,在食疗和保健方面的开发利用崭露头角,大大扩展了其应用范围。随着走马胎市场需求量的增大,野生走马胎植物被过度采挖,导致野生走马胎资源几乎枯竭。人工栽培走马胎逐渐成为供应药用市场的主力军,但是人工栽培走马胎种质、种子来源混杂,常会造成质量和疗效的不稳定,而利用分子标记技术可以从分子水平上对走马胎进行种质的区分和评价。该研究利用ISSR分子标记技术,对来自广西地区的36份走马胎种质资源进行了遗传多样性分析,采用POPGEN32软件进行数据分析,用UPGMA软件绘制聚类图。结果表明：14条ISSR引物共检测到136个清晰的扩增位点,多态性位点112个,多态位点百分率为82.35％;Nei’ s基因多样性指数( H)为0.2965,Shannon多样性指数(I)为0.4417,基因分化系数(Gst)为0.8558。个体间的遗传相似系数为0.6678~0.8382,平均为0.7391。基于聚类分析可知,所有的个体被划分为5类,其中绝大多数来自相同或者邻近地区的个体严格按照地理位置聚为相同的一类或者亚类,只有少数个体在归类上与地理位置相悖。研究证明ISSR分子标记技术在评价走马胎种质资源亲缘关系和遗传变异等方面有很好的适用。该研究结果为该药用植物的种质资源评估和引种栽培提供了科学依据。     

Determination of genetic diversity among Saccharina germplasm using ISSR and RAPD markers

Various species of genus Saccharina are economically important brown macroalgae cultivated in China. The genetic background of the conserved Saccharina germplasm was not clear. In this report, DNA-based molecular markers such as inter simple sequence repeats (ISSR) and random amplified polymorphic DNA (RAPD) were used to assess the genetic diversity and phylogenetic relationships among 48 Saccharina germplasms. A total of 50 ISSR and 50 RAPD primers were tested, of which only 33 polymorphic primers (17 ISSR and 16 RAPD) had an amplified clear and reproducible profile, and could be used. Seventeen ISSR primers yielded a total of 262 bands, of which 256 were polymorphic, and 15.06 polymorphic bands per primer were amplified from 48 kelp gametophytes. Sixteen RAPD primers produced 355 bands, of which 352 were polymorphic, and 22 polymorphic bands per primer were observed across 48 individuals. The simple matching coefficient of ISSR, RAPD and pooled ISSR and RAPD dendrograms ranged from 0.568 to 0.885, 0.670 to 0.873, and 0.667 to 0.862, revealing high genetic diversity. Based on the unweighted pair group method with the arithmetic averaging algorithm (UPGMA) cluster analysis and the principal components analysis (PCA) of ISSR data, the 48 gametophytes were divided into three main groups. The Mantel test revealed a similar polymorphism distribution pattern between ISSR and RAPD markers, the correlation coefficient r was 0.62, and the results indicated that both ISSR and RAPD markers were effective to assess the selected gametophytes, while matrix correlation of the ISSR marker system (r = 0.78) was better than that of the RAPD marker system (r = 0.64). Genetic analysis data from this study were helpful in understanding the genetic relationships among the selected 17 kelp varieties (or lines) and provided guidance for molecular-assisted selection for parental gametophytes of hybrid kelp breeding.