Siberian wild rye (Elymus sibiricus L.): Genetic diversity of germplasm determined using DNA fingerprinting and SCoT markers

Elymus sibiricus is a perennial, self-pollinating, allotetraploid grass native to northern Asia. It is widely used in cultivated pastures and natural grassland due to excellent cold and drought tolerance, good forage quality, and adaptability to a variety of habitats. Information on the genetic diversity and variation among worldwide E. sibiricus germplasm is limited but necessary for germplasm collection, conservation and effective commercial use. In this study we ana lyzed genetic diversity and variation of 69 E. sibiricus accessions from the species range and constructed DNA fingerprinting profiles of 24 accessions using SCoT markers. A total of 173 bands were generated from 16 SCoT primers, 154 of which were polymorphic with 89.0% of polymorphic bands (PPB) occurring at the species level. The PPB within 8 geographical regions ranged from 2.3 to 54.3 %. Genetic variation was greater within geographical regions (57.9%) than between regions (42.1%). The 24 accessions from Qinghai-Tibet Plateau, Mongolia Plateau, Kazakhstan, and Russia were distinguished by their unique fingerprinting. This is the first report using SCoT markers for identifying cultivars and accessions of E. sibiricus. The DNA fingerprinting profiles of E. sibiricus were useful in germplasm collection and identification. The genetic diversity of worldwide E. sibiricus germplasm has been substantially affected by ecogeographical factors. Our results suggest that collecting and evaluating E. sibiricus germplasm from major geographic regions and unique environments broadens the available genetic base and illustrates the range of variation.     

Genetic diversity of Ustilago maydis strains

Thirty wild isolates belonging to five different locations in Mexico plus two laboratory strains of Ustilago maydis were characterized by restriction fragment length polymorphism (RFLP) analysis using 23 different clones as probes derived from a PstI library and two restriction enzymes. All loci analysed presented a high level of polymorphism, including one locus with thirty one different alleles. Geographical grouping of the populations was based on Nei's genetic distance and there was no correlation between genetic and geographic distances among these isolates. Our results suggest that DNA fingerprinting is a useful method for detecting genetic variation in populations of U. maydis. This work demonstrated that considerable genetic variation may be present within field populations of U. maydis.     

小熊猫圈养种群遗传多样性及其影响因子

利用寡核苷酸指纹探针ＬＺＦ－Ｉ检测了成都大熊猫繁育研究基地仿生态圈养场小熊猫种群全部２２只个体的ＤＮＡ指纹,检测结果表明其遗传多样性参数如下：⑴各体间ＤＡＮ指纹图的相似性为０．１７２;个体Ａ的指纹谱带在个体Ｂ中出现的概率为０．１８０６。⑵圈养种群的等位基因频率为０．０９４８,杂合率为９０．５２％,⑶种群中指名亚种亲本个体的引进是影响该种群遗传多样性的主要因子。     

Genetic diversity and species-specific PCR-based markers from AFLP analyses of Thai bananas

A large amount of banana genetic resource has been found in Thailand which is believed to be one of the centers of its origins. To assess genetic diversity and determine genetic relationships of edible bananas in Thailand, 110 accessions of banana species and cultivars collected from villages and natural locations were investigated. UPGMA clustering of numerical data from Amplified Fragment Length Polymorphism (AFLP) patterns showed two large groups which corresponded to genome designations of Musa acuminata (AA) and Musa balbisiana (BB), the known ancestors of most edible cultivars. The AFLP data suggested that among Thai bananas, AA and AAA cultivars were closely related to M. acuminata subsp. malaccensis, while some of ‘B’ genome contained ones closely related to wild M. balbisiana in Thailand and some may have been imported. Eight species-specific PCR-based primer pairs, generated from the AFLP results clearly identify ‘A’ and ‘B’ genomes within cultivars and hybrids. The analyses were useful to readily and easily infer progenitors of these cultivars and pronounce wide genetic diversity of the bananas in Thailand.     

福建不同生态类型鸭种（群）的遗传多样性研究

用40个10碱基随机引物对福建2个生态类型的7个地方鸭种的基因组池DNA进行了RAPD分析,从扩增产物表现为多态的引物筛选出9个特异性强的引物进行个体DNA的RAPD分析,并利用Shannon指数估算了2个生态区域鸭群的遗传多样性,探讨了它们与生态环境之间的关系及其变化规律．结果表明,福建境内的地方鸭种具有较高的遗传多样性,闽东沿海地区鸭群有67．97％的遗传变异来自群体内,32．03％来自于群体间;闽西山地丘陵地区鸭群有59．05％的遗传变异来自群体内,40．95％来自于群体间;闽东地区鸭群的遗传变异明显高于闽西地区鸭群．同时,用非加权组平均法(UPGMA)对各种群的聚类分析表明,闽西地区的连城白鸭、泰宁麻鸭、龙岩山麻鸭和三明麻鸭归为一类;闽东地区的龙海金定鸭和莆田黑鸭聚为一类．不同生态区域内鸭群的遗传变异与地理位置存在一定的相关性．     

Genetic diversity and population structure of Leptosphaeria maculans isolates in Western Canada

Leptosphaeria maculans is a serious concern for canola production worldwide. For effective disease management, knowledge of the pathogen's genetic variability and population structure is a prerequisite. In this study, whole-genome sequencing was performed for 162 of 1590 L. maculans isolates collected in the years 2007–2008 and 2012–2014 in Western Canada. DNA variants in genome-wide and specific regions including avirulence (Avr) genes were characterized. A total of 31,870 high-quality polymorphic DNA variants were used to study L. maculans genetic diversity and population structure. Cluster analysis showed that 150 isolates were clustered into 2 main groups and 4 subgroups by DNA variants located in either Avr or small secreted protein-encoding genes and into 2 main groups and 6 subgroups by genome-wide variants. The analysis of nucleotide diversity and differentiation also confirmed genetic variation within a population and among populations. Principal component analysis with genome-wide variants showed that the isolates collected in 2012–2014 were more genetically diverse than those collected in 2007–2008. Population structure analysis discovered three distinct sub-populations. Although isolates from Saskatchewan and Alberta were of similar genetic composition, Manitoba isolates were highly diverse. Genome-wide association study detected DNA variants in genes AvrLm4-7, Lema_T86300, and Lema_T86310 associated with the years of collection.     

Low-Cot DNA sequences for fingerprinting analysis of germplasm diversity and relationships in Amaranthus

We examined genetic diversity and relationships among 24 cultivated and wild Amaranthus accessions using the total low-Cot DNA and five individual repetitive sequences as probes. These low-Cot DNA probes were obtained by the isolation of various classes of repetitive-DNA sequences, including satellites, minisatellites, microsatellites, rDNA, retrotransposon-like sequences, and other unidentified novel repetitive sequences. DNA fingerprints generated by different types of repetitive-DNA probes revealed different levels of polymorphism in the Amaranthus genomes. A repetitive sequence containing microsatellites was found to be a suitable probe for characterizing intraspecific accessions, whereas more conservative sequences (e.g. rDNA) were informative for resolving phylogenetic relationships among distantly related species.Genetic diversity, measured as restriction fragment length polymorphism (RFLP) and the similarity index at the low-Cot DNA level, was equally high among intraspecific accessions between the two species groups: grain amaranths (A. caudatus, A. cruentus, and A. hypochondriacus) and their putative wild progenitors (A. hybridus, A. powellii, and A. quitensis). At the interspecific level, however, the grain amaranth species are less divergent from each other than their wild progenitors. With the rare exceptions of certain A. caudatus accessions, grain amaranths were found to be closely related to A. hybridus. The results based on low-Cot DNA were comparable with previous RAPD and isozyme studies of the same set of species/accessions of Amaranthus, indicating that low-Cot DNA sequences are suitable probes for a fingerprinting analysis of plant germplasm diversity and for determining phylogenetic relationships. Received: 19 October 1998 / Accepted: 8 January 1999     

Genetic characterization of highly inbred chicken lines by two DNA methods: DNA fingerprinting and polymerase chain reaction using arbitrary primers

Thirteen highly inbred chicken lines were analysed at the DNA level by DNA fingerprinting (DFP) and by polymerase chain reaction (PCR) using random primers. In general, the DFP patterns of individuals within a line were identical. The DFP band-sharing (BS) values among lines from different breeds (Leghorn, Fayoumi, Spanish) ranged from 0.10 to 0.20. The DFP BS values among Leghorn lines from different genetic backgrounds ranged from 0.42 to 0.79. The DFP BS values among lines selected for different major histocompatibility complex serotypes from a common genetic background ranged from 0.70 to 0.95. Some randomly amplified polymorphic DNA (RAPD) PCR products were specific to a single line, some to all lines from the same genetic base, and some to all lines from the same breed. The RAPD-PCR band-sharing values ranged from 0.66 to 0.99 for all between-line comparisons. Thus, the ability to detect biodiversity at the DNA level was greater in this study for DFP than for RAPD-PCR. The possible origin of line-specific bands, relative advantages of detecting biodiversity by using different molecular screening techniques and uses of highly inbred chicken lines in molecular analysis are discussed.     

犬种布鲁氏菌的遗传多样性分析

【背景】犬种布鲁氏菌是犬种布病的病原菌,主要导致犬流产和繁殖障碍。虽然犬种布鲁氏菌感染人群的病例极为少见,但是犬种布鲁氏菌对人的安全风险仍存在争议。目前,我国犬种布病的流行病学特征及犬种布鲁氏菌的遗传多样性的研究相对缺乏。开展犬种布病的流行特征及遗传多样性调查对加强犬种布病的监测防控具有重要意义。【目的】对犬种布病的流行病学特征和犬种布鲁氏菌的遗传多态性进行调查,为犬种布病的防控提供参考。【方法】采用常规鉴定方法和BCSS-PCR对63株试验菌株进行鉴定。采用HGDI (Hunter and Gaston diversity index)多态性指数调查犬种布鲁氏菌的遗传多态性,用MLVA方法基于BioNumerics5.0软件对菌株进行聚类分析,揭示犬种布病的流行病学特点。此外,基于MLVA-11采用goeBURST软件构建犬种布鲁氏菌的最小生成树(Minimum spanning tree,MST),阐述我国犬种布鲁氏菌的地理起源特征。【结果】常规鉴定方法和BCSS-PCR扩增结果显示63株试验菌株全部为犬种布鲁氏菌。BCSS-PCR与常规鉴定方法的符合率为100%,BCSS-PCR的分析敏感性为10-3 (即50 pg/μL犬种布鲁氏菌DNA)。我国犬种布鲁氏菌具有较高的遗传多样性,基于HGDI分析表明Panel 2B的5个位点具有较高的变异度,等位基因型由高到底依次为bruce09(11) bruce07(8)bruce16(7)bruce04(6)bruce30(5)。MLVA聚类分析表明北京地区出现了3次较小规模的犬种布病暴发流行,其余地区均为零星散发。我国犬种布鲁氏菌可分为5个地理集群,以MLVA-11基因26型克隆群为主导种群,该种群与来自美国、希腊、加拿大、法国、罗马尼亚和韩国等国家的菌株具有共同的地理起源,其余4个种群为中国特有。【结论】我国犬种布鲁氏菌呈现高度的遗传多样性并有广泛的地理来源,表现为输入性和中国特有血统共存的起源进化特征。     

我国部分金莲花种质资源遗传多样性的RAPD研究

用RAPD标记对来自不同产地的24份金莲花种质从分子水平开展遗传多样性研究,为综合评价我国金莲花资源现状及植物资源的合理保护提供参考。结果显示,30条RAPD引物共扩增获得194条清晰可辨条带,其中多态性条带108条,多态性位点百分率为55.67%,金莲花总多样性指数为0.1460,居群内遗传多样性为0.0591,Shannon’s多样性指数为0.2248;通过UPGMA进行聚类分析,将24份金莲花种质划分为3个大类,根据总遗传多样性和居群内遗传多样性计算不同居群间遗传分化系数为0.6902,基因流估计平均值为0.2244。研究结果表明,目前我国金莲花种质资源的遗传多样性指数偏低,应该尽快采取相应措施,对不同金莲花资源进行合理保护。     

基于ISSR标记的猕猴桃品种 遗传多样性分析及指纹图谱构建

采用ISSR标记对中华猕猴桃(Actinidia chinensis Planch.)、美味猕猴桃〔A.chinensis var.deliciosa(A.Chev.)A.Chev.〕、软枣猕猴桃〔A.arguta(Sieb.et Zucc.)Planch.ex Miq.〕和毛花猕猴桃(A.eriantha Benth.)的32个样本进行了遗传多样性分析,并以ISSR标记为基础构建了DNA指纹图谱.结果表明:筛选的10个多态性高且条带清晰的引物共扩增出200个条带(位点),其中,多态性位点195个,多态性位点百分率(PPL)达97.50%;各引物的多态性信息含量(PIC)以及供试样本的观测等位基因数(Na)、有效等位基因数(Ne)、Nei's基因多样性指数(H)和Shannon's多样性指数(I)的总均值分别为0.9080、1.9800、1.3569、0.2255和0.3613,4个猕猴桃种间的遗传分化系数(Gst)为0.4146,基因流(Nm)为0.7059,且32个样本间的Na、Ne、H和I值差异极显著(P<0.001).供试32个样本间的遗传相似系数(GS)为0.5650~0.9650,平均值为0.7164;基于GS值进行UPGMA聚类分析,在GS值为0.76处将32个样本分为4组,基本对应供试的4个猕猴桃种类,其中,第Ⅰ组的大多数样本属于美味猕猴桃品种,第Ⅱ组的样本均属于中华猕猴桃品种,第Ⅲ组的样本属于毛花猕猴桃品种,第Ⅳ组的样本均属于软枣猕猴桃品种.分子方差分析结果表明:4个猕猴桃的种间变异占总变异的40.84%,种内变异占总变异的59.16%.研究结果表明:供试的猕猴桃品种间遗传分化程度较高,基因交流频率较低,且总遗传变异的近60%存在于种内,说明供试的猕猴桃品种具有较丰富的遗传多样性.另外,根据10个ISSR引物的扩增结果,筛选出引物UBC818、UBC824、UBC854和UBC895扩增的15个多态性位点构建的DNA指纹图谱可用于供试32个猕猴桃样本的鉴定.     

Genetic diversity and relationships of diploid and tetraploid cottons revealed using AFLP

Gossypium species (± 49) represent a vast resource of genetic diversity for the improvement of cultivated cotton. To determine intra- and inter-specific genetic relationships within a diverse collection of Gossypium taxa, we employed 16 AFLP primer combinations on three diploid species, Gossypium herbaceum L. (A1), Gossypium arboreum L. (A2) and Gossypium raimondii Ulbrich (D5), and 26 AD allotetraploid accessions (Gossypium barbadense L. and Gossypium hirsutum L.). A total of 1180 major AFLP bands were observed; 368 of these (31%) were polymorphic. Genetic similarities among all taxa ranged from 0.21 (between the diploid species G. arboreum and G. raimondii) up to 0.89 (within G. barbadense). Phenetic trees based on genetic similarities (UPGMA, N-J) were consistent with known taxonomic relationships. In some cases, well-supported phylogenetic relationships, as well as evidence of genetic reticulation, could also be inferred. UPGMA trees and principal coordinate analysis based on genetic similarity matrices were used to identify genetically distinct cultivars that are potentially important sources of germplasm for cotton improvement, particularly of fiber quality traits. We show that AFLP is useful for estimating genetic relationships across a wide range of taxonomic levels, and for analyzing the evolutionary and historical development of cotton cultivars at the genomic level. Received: 17 January 2000 / Accepted: 4 May 2000     

基于粪便DNA的东北马鹿遗传多样性

东北马鹿(Cervus canadensis xanthopygus)为国家二级重点保护野生动物,近些年其种群数量急剧下降、分布区不断退缩、种群基因交流受阻,很多地区更是难觅其踪迹。亟需对其种群的遗传变化,特别是遗传多样性和近交衰退等种群遗传信息开展进一步评价,增强保护与管理的针对性。本研究在大、小兴安岭和长白山脉的6个重点研究区域,共收集409份疑似马鹿粪便样本。首先基于mtDNA Cyt b基因测序技术进行物种鉴定,并对鉴定为马鹿的阳性样本利用微卫星技术进行个体识别。结果共识别出172只东北马鹿个体;Cyt b基因序列共检测出14个变异位点和11个单倍型,单倍型多样性为0.849 (0.105～0.732),核苷酸多样性为0.678%(0.099%～0.775%)。10个微卫星位点检测出种群平均等位基因数为5.7 (5.2～7.2),有效等位基因数为3.3 (2.5～4.1),观测杂合度为0.687 (0.644～0.725),期望杂合度为0.619 (0.564～0.689),近交系数为-0.113 (-0.160～-0.037)。结果表明,东北马鹿种群遗传多样性处于中等水平,其...     

Genetic diversity of golden takin (Budorcas taxicolor bedfordi) population from Qinling Mountains in China revealed by sequence analysis of mitochondrial DNA control region

The golden takin is an endangered species, listed as a First Grade Protected animal and found only in the Qinling Mountains in China. A great deal of research on the golden takin's living habitat, population size, and home range has been conducted. Here, we employed sequence analysis of the mitochondrial DNA control region to study the genetic diversity of the golden takin from three separate nature reserve parks in the Qinling Mountains. We also compared the results of our study with previously published data on the genetic diversity of mixed takin species located in the Qinling Mountains and the Minshan area. Based on 62 sampled golden takin individuals, we found an overall mean genetic haplotype diversity of 0.687. There is no significant geographic genetic diversity across different golden takin populations within the Qinling Mountains. However, we did show significant diversity between golden takin from the Qinling Mountains and from Minshan. These original data provide a foundation for the genetic diversity of golden takin, and will yield comprehensive information for better supporting the management in the national reserve parks.     

Genetic diversity and structure of the noxious alien grass Praxelis clematidea in southern China

Praxelis clematidea (Asteraceae), a plant species native to South America, is a noxious weed in southern China. We examined the genetic variation and population structure of 12 populations (76 individuals) of P. clematidea from Fujian, Guangdong, and Hainan Provinces in China using inter-simple sequence repeat (ISSR) analysis. From an initial set of 69 ISSR primers, 10 were selected which yielded 80 reproducible bands. Polymorphic bands (P) were 100%, Shannon's information index (I) was 0.4226, and Nei's gene diversity (H) was 0.2791. We infer that the high levels of genetic diversity exhibited by P. clematidea may have contributed to its invasiveness. Gene flow among populations was 2.4930, which has led to homogenization. The coefficient of population differentiation (Gst = 0.1671) indicated low levels of genetic variation among populations and high levels of genetic polymorphism within populations. There was a negative correlation between population elevation and genetic diversity, while there was a significant positive correlation between genetic distance and geographic distance based on a Mantel test (r = 0.5820, P < 0.01). Some populations from different provinces clustered together in principal coordinate and UPGMA analyses indicating that human-mediated events may have contributed to the dispersal of the species.     

松杨栅锈菌遗传多样性初步分析

采用ITS-nrDNA-RELP、测序技术、RAPD(随机扩增多态性DNA)分子标记技术,对我国松杨栅锈菌不同地域的5个生理小种11个菌系进行了遗传多样性分化研究.结果表明,该菌在我国的遗传分化与地理来源相关,可分为西部地理群和北方地理群.西部地理群又可分为高山森林生态型(HMF)和平原生态型(WPL).小种遗传分化不一定与致病性分化一致.t检验表明,各生理小种RAPD遗传多样性指数无明显差异,高山森林小种遗传多样性指数(0.5172)略高于平原小种遗传多样性指数(0.5089).核糖体基因转录间隔区高度保守,不适合该菌种内群体遗传多样性分化研究.     

Genetic diversity of natural populations of Larix principis-rupprechtii in Shanxi Province,China

Prince Rupprecht's Larch (Larix principis-rupprechtii Mayr.) is one of dominant components of middle and high elevation forests in North China. Shanxi Province is well known as “the Hometown of Prince Rupprecht's Larch” in China. In this study, six natural populations of this species across Shanxi were selected to investigate the genetic variation of the species using amplified fragment length polymorphism (AFLP) markers. Results showed that in comparison with some other species of Larix, higher genetic diversity was revealed at the species level for L. principis-rupprechtii (percentage of polymorphic loci PPL = 71.9%, Nei's gene diversity H_E = 0.225, Shannon information index I = 0.341). Most of genetic variation existed within populations (80.5%), while the genetic differentiation among populations was significant (p < 0.001) and higher (G_st = 0.194) than most other species of Larix. The differentiation can be attributed to the limited gene flow (N_m = 1.035) among populations, which could be due to the spatial isolation and habitat fragmentation. The six populations can be divided into three groups based on the Nei's genetic distances between populations (from 0.033 to 0.076). There was no significant correlation (r = 0.268, p > 0.05) between genetic distance and geographic distance among populations. The measures for in-situ or ex-situ conservation should be taken to preserve the genetic diversity of this species.     

Genetic evolution and diversity of common carp Cyprinus carpio L.

Knowledge of genetic variation and population structure of existing strains of both farmed and wild common carp Cyprinus carpio L. is absolutely necessary for any efficient fish management and/or conservation program. To assess genetic diversity in common carp populations, a variety of molecular markers were analyzed. Of those, microsatellites and mitochondrial DNA were most frequently used in the analysis of genetic diversity and genome evolution of common carp. Using microsatellites showed that the genome evolution in common carp exhibited two waves of rearrangements: one whole-genome duplication (12–16 million years ago) and a more recent wave of segmental duplications occurring between 2.3 and 6.8 million years ago. The genome duplication event has resulted in tetraploidy since the common carp currently harbors a substantial portion of duplicated loci in its genome and twice the number of chromosomes (n = 100–104) of most other cyprinid fishes. The variation in domesticated carp populations is significantly less than that in wild populations, which probably arises from the loss of variation due to founder effects and genetic drift. Genetic differentiation between the European carp C.c. carpio and Asian carp C.c. haematopterus is clearly evident. In Asia, two carp subspecies, C.c. haematopterus and C.c. varidivlaceus, seem to be also genetically distinct.     

Genetic diversity and methylation polymorphism analysis of Chrysanthemum nankingense

The diploid species Chrysanthemum nankingense (Anthemideae, Asteraceae) is closely related to the commercially important hexaploid ornamental species Chrysanthemum morifolium and is well adapted to poor environments. In this study, phenotypic variants of C. nankingense were first identified by morphological traits. Using EST-SSR (simple sequence repeat) analysis, we detected some absent EST-SSRs. The percentage of AFLP (amplified fragment length polymorphism) polymorphic fragments was 78.2%, indicating high genetic diversity. To evaluate the genome methylation level and methylation polymorphism, we used the MSAP (methylation-sensitive amplification polymorphism) technique to analyze the 30 C. nankingense lines. The total DNA methylation level ranged from 54.6% to 62.6%. Most of the MSAP-methylated fragments (97%) were polymorphic in the lines. The U-values associated with hemi-methylation were larger than those associated with full methylation in four of the 30 lines, and six individual values were statistically significant (U > 1.96). The high genomic diversity as well as the high methylation polymorphism may be responsible for the morphological polymorphism. There was no significant correlation between the phenotypic and genetic diversity among the lines.     

牛鞭草品种EST-SSR指纹图谱构建及遗传多样性分析

为探讨牛鞭草(Hemarthria spp.)品种间的遗传多样性,从86对EST-SSR引物中筛选出8对引物对牛鞭草属6个品种进行指纹图谱的构建及遗传多样性分析。结果表明,8对EST-SSR引物对牛鞭草属6个品种共扩增出193条清晰条带,多态性条带161条,多态性比例为83.4%。每条引物的多态信息含量(PIC)为0.480~0.695,平均为0.602。UPGMA聚类分析表明,牛鞭草属6个品种在相似系数为0.652处可分为两大类群。8对EST-SSR引物均能将6个品种完全区分开,以3对EST-SSR引物扩增的电泳图谱为基础,建立了牛鞭草属6个品种的指纹图谱标准模式图,每个品种都有唯一的指纹图谱。牛鞭草属6个品种的平均Nei’s基因多样性指数为0.333,平均Shannon信息指数为0.496,品种间的相似系数介于0.399~0.782之间。可见,牛鞭草属植物品种的遗传多样性较丰富,种间差异明显。