The relationship between the concepts of genetic diversity and differentiation

Summary Diversity as a measure of individual variation within a population is widely agreed to reflect the number of different types in the population, taking into account their frequencies. In contrast, differentiation measures variation between two or more populations, demes or subpopulations. As such, it is based on the relative frequencies of types within these subpopulations and, ideally, measures the average distance of subpopulations from their respective lumped remainders. This concept of subpopulation differentiation can be applied consistently to a single population by regarding each individual as a deme (subpopulation) of its own, and it results in a measure of population differentiation _T which depends on the relative frequencies of the types and the population size. _T corresponds to several indices of variation frequently applied in population genetics and ecology, and it verifies these indices as measures of differentiation rather than diversity. For any particular frequency distribution of types, the diversity is then shown to be the size of a hypothetical population in which each type is represented exactly once, i. e. for which _T =1. Hence, the diversity of a population is its differentiation effective number of types. This uniquely specifies the link between the two concepts. Moreover, again corresponds to known measures of diversity applied in population genetics and ecology. While population differentiation can always be estimated from samples, the diversity of a population, particularly if it is large, may not be. In such cases, it is recommended that population differentiation is estimated and the corresponding sample diversity merely computed. Finally, a solution to the problem of measuring multi-locus diversities is provided.     

分子标记在猕猴遗传多样性研究中的应用

分子标记目前已成为研究遗传多样性的主要工具,为此,简要综述了几种常用的分子标记(RFLPs、RAPD、mtDNA、微卫星DNA、SNPs)的检测方法及其在猕猴种群遗传多样性研究中的应用,为国内猕猴遗传多样性的研究提供参考。     

分子生物学技术在轮虫遗传多样性和系统发生研究中的应用

分子生物学技术,如等位酶分析、DNA序列分析、限制性片段长度多态性、随机扩增多态、重复DNA序列多态性,在轮虫研究中的应用始于上世纪70年代,研究领域主要是轮虫群体遗传学、生物变异与多样性和系统发生与进化,被研究的轮虫种类主要集中在臂尾轮虫属、晶囊轮虫属和蛭态轮虫的一些种类。着重介绍分子生物学技术在轮虫遗传学和系统学研究中的应用,并对今后的研究热点提出了展望。     

反转录转座子标记及在作物遗传育种中的应用

反转录转座子通过RNA中间体进行反转录而转座,广泛分布于各种植物基因组中,拷贝数多,异质性高,在种内和种间表现出较高的序列差异性和丰富的插入多态性。针对这些特点,开发出了几种基于反转录转座子的分子标记,如SSAP、RIVPI、RAP、REMAP和RBIP等。由于反转录转座子标记能揭示出丰富的多态性,因而在遗传多样性和系谱研究、遗传连锁图谱构建及性状基因定位等方面得到了应用。随着分离技术的不断改进,获取序列信息更加容易,反转录转座子作为分子标记用于作物遗传育种将具有广阔前景。     

分子标记技术在蕨类植物遗传多样性研究中的应用

简要介绍了蕨类植物的生态类型和生殖方式;回顾了近年来分子标记技术在蕨类植物遗传多样性研究中的应用,主要包括种间亲缘关系和分类学的研究、遗传变异和遗传结构的研究,以及系统发育地理学方面的研究.最后,对蕨类植物遗传多样性研究中存在的一些问题进行了讨论和展望.     

金银花五个品系的RAPD分析及DNA指纹图谱的建立

运用RAPD技术,对5个金银花品系进行遗传多样性研究并构建这5个金银花品系的DNA指纹图谱。从80个引物中筛选出25个带纹清晰,多态性好的引物用于实验。其中,引物SBSD06的扩增条带可以清楚明确区分5个品系,建立其DNA指纹图谱。在清晰、稳定出现的170条带中,153条带具有多态性。按UPGMA法进行聚类分析,计算其遗传相似系数,结果显示,金银花5个品系聚为两类,与其形态学分类结果相符。     

扬子鳄分子遗传学与遗传多样性研究现状

扬子鳄 (Alligatorsinensis)是中国特有的珍稀物种 ,其遗传资源的保护已受到广泛关注和重视。本文简要介绍了近年来有关扬子鳄在分子系统学、遗传多样性与种群遗传结构、线粒体基因组、个体识别以及性别决定方面的分子遗传学研究状况。     

Deciphering genetic diversity analysis of saffron (Crocus sativus L.) using RAPD and ISSR markers

The existence of genetic diversity in Crocus sativus has globally remained a mystery till date. The study investigated PCR based DNA amplification profile of saffron using ISSR and RAPD based primers. A total of 38 amplicons were generated by ISSR primers in the range from 7 to 12 with an average of 9.50 bands per primer. 20 bands were found to be polymorphic and 18 were monomorphic with an average percentage of polymorphism as 52.48%. RAPD based amplification revealed a total 161 amplicons, 107 as polymorphic and 54 as monomorphic with an average percentage of polymorphism as 66.44%. Cumulative results of RAPD and ISSR demonstrated that Nei-Li’s similarity index ranged between 0.70 and 0.97. The results of AMOVA has revealed 9% of variance among populations and 91% of variance within populations, Φ PT was found as 0.089, which indicates existence of genetic differences though limited. In conclusion, the results indicate that saffron accessions are minimally genetically differentiated, which could be capitalized in future breeding programmes to ameliorate this precious crop.     

分子遗传标记技术在兔遗传多样性分析中的应用

实验兔是重要的实验动物之一,在医药领域发挥重要作用。各种分子遗传标记的出现为实验兔系统发育、种群遗传结构分析以及质量控制等各个领域提供了更为简便、可靠的研究手段。但目前,国内实验兔遗传质量不稳定,遗传背景不明确,严重制约着实验兔的应用。本文对各种分子标记在兔遗传多样性中的应用进行综述,以为实验兔遗传检测方法的建立提供帮助。     

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.     

EST-derived single nucleotide polymorphism markers for assembling genetic and physical maps of the barley genome

In a panel of seven genotypes, 437 expressed sequence tag (EST)-derived DNA fragments were sequenced. Single nucleotide polymorphisms (SNPs) that were polymorphic between the parents of three mapping populations were mapped by heteroduplex analysis and a genome-wide consensus map comprising 216 EST-derived SNPs and 4 InDel (insertion/deletion) markers was constructed. The average frequency of SNPs amounted to 1/130 bp and 1/107.8 bp for a set of randomly selected and a set of mapped ESTs, respectively. The calculated nucleotide diversities (π) ranged from 0 to 40.0 × 10⁻³ (average 3.1 × 10⁻³) and 0.52 × 10⁻³ to 39.51 × 10^–3 (average 4.37 × 10⁻³) for random and mapped ESTs, respectively. The polymorphism information content value for mapped SNPs ranged from 0.24 to 0.50 with an average of 0.34. As expected, combination of SNPs present in an amplicon (haplotype) exhibited a higher information content ranging from 0.24 to 0.85 with an average of 0.50. Cleaved amplified polymorphic sequence assays (including InDels) were designed for a total of 87 (39.5%) SNP markers. The high abundance of SNPs in the barley genome provides avenues for the systematic development of saturated genetic maps and their integration with physical maps. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. Both R. Kota and R.K. Varshney contributed equally to this work.     

SSR analysis of 38 genotypes of soybean (Glycine Max (L.) Merr.) genetic diversity in India

Sixteen polymorphic Simple sequence repeat (SSR) markers were used to determine the genetic diversity and varietal identification among 38 soybean (Glycine max (L.) Merr.) genotypes which are at present under seed multiplication chain in India. A total of 51 alleles with an average of 2.22 alleles per locus were detected. The polymorphic information content (PIC) among genotypes varied from 0.049 (Sat_243 and Satt337) to 0.526 (Satt431) with an average of 0.199. The pair wise genetic similarity between soybean varieties varied from 0.56 to 0.97 with an average of 0.761. These 16 SSR markers successfully distinguished 12 of the 38 soybean genotypes. These results suggest that used SSR markers are efficient for measuring genetic diversity and relatedness as well as identifying varieties of soybeans. Diverse genetic materials may be used for genetic improvements of soybean genotypes.     

Genetic diversity assessment in Somali sorghum (<Emphasis Type="Italic">Sorghum bicolor</Emphasis> (L.) Moench) accessions using microsatellite markers

In the north-western region of Somalia, bordering Ethiopia, sorghum represents an important resources for human and animal nutrition. The critical situation of Somalia is threatening the preservation of this valuable resource and it becomes urgent to develop a strategy of correct evaluation of the sorghum germplasm in order to promote conservation and preservation programs. Microsatellites, also known as Simple Sequence Repeats (SSRs), are reproducible molecular markers useful in assessing the level of genetic diversity of plants. A total of 5 sorghum SSR-specific primer pairs were used to assess the genetic diversity of Somali sorghum landraces. Extensive variation was found at the microsatellite loci analysed, except for a locus that resulted in a monomorphic for some accessions. Considerable differences were found between total and effective number of alleles indicating non uniform allele frequency. Moreover allele frequency at a single locus significantly changed among accessions. Total gene diversity calculated for each locus ranged from 0.44 to 0.79. Most of the genetic diversity occurred within accessions demonstrating that accessions are not under selection processes and/or there is a continuous exchange of genes between sorghum populations. In any case, the patterns of clustering were significantly affected by the presence/absence of some alleles with high discriminant weight. Accessions Carabi, Abaadiro, Masego Cas and Masego Cad represent distinct genotypes confirming finding observed in previous phenotypic studies. The results highlight the central role of local farmers in maintaining and shaping local germplasm.     

Biotechnological approaches for conservation and improvement of rare and endangered plants of Saudi Arabia

Genetic variation is believed to be a prerequisite for the short-and long-term survival of the plant species in their natural habitat. It depends on many environmental factors which determine the number of alleles on various loci in the genome. Therefore, it is important to understand the genetic composition and structure of the rare and endangered plant species from their natural habitat to develop successful management strategies for their conservation. However, rare and endangered plant species have low genetic diversity due to which their survival rate is decreasing in the wilds. The evaluation of genetic diversity of such species is very important for their conservation and gene manipulation. However, plant species can be conserved by in situ and in vitro methods and each has advantages and disadvantages. DNA banking can be considered as a means of complimentary method for the conservation of plant species by preserving their genomic DNA at low temperatures. Such approach of preservation of biological information provides opportunity for researchers to search novel genes and its products. Therefore, in this review we are describing some potential biotechnological approaches for the conservation and further manipulation of these rare and endangered plant species to enhance their yield and quality traits.     

产喜树碱喜树内生真菌的筛选及喜树内生真菌的SRAP分析

生活在宿主植物里的内生真菌是很重要的药用资源。喜树是中国的传统药用植物。从喜树植物中分离得到了大约50种菌株,其中一株产喜树碱的菌株通过形态学鉴定为青霉属,这是首次在喜树植物中发现产喜树碱的青霉属菌株。为研究简单序列重复相关序列扩增多态性(SRAP)方法在喜树内生真菌中应用的可行性,选择了十株喜树内生真菌进行SRAP多态性分析。SRAP引物共扩增出1 295条带,而这些菌株也被分为三大类。这些结果表明,SRAP研究喜树内生真菌具有高效性,是讨论喜树内生真菌的遗传多样性的有效方法。     

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.