Genetic characteristics of 207 microsatellite markers in the Korean population and in other Asian populations

Microsatellites, short tandem repeats, are useful markers for genetic analysis because of their high frequency of occurrence over the genome, high information content due to variable repeat lengths, and ease of typing. To establish a panel of microsatellite markers useful for genetic studies of the Korean population, the allele frequencies and heterozygosities of 207 microsatellite markers in 119 unrelated Korean, Indian and Pakistani individuals were compared. The average heterozygosity of the Korean population was 0.71, similar to that of the Indian and Pakistani populations. More than 80% of the markers showed heterozygosity of over 0.6 and were valuable as genetic markers for genome-wide screening for disease susceptibility loci in these populations. To identify the allelic distributions of the multilocus genetic data from these microsatellite markers, the population structures were assessed by clustering. These markers supported, with the most probability, three clustering groups corresponding to the three geographical populations. When we assumed only two hypothetical clusters (K), the Korean population was separate from the others, suggesting a relatively deep divergence of the Korean population. The present 207 microsatellite markers appear to reflect the historical and geographical origins of the different populations as well as displaying a similar degree of variation to that seen in previously published genetic data. Thus, these markers will be useful as a reference for human genetic studies on Asians.     

Genetic structure and mating system of Euterpe edulis Mart. Populations: a comparative analysis using microsatellite and allozyme markers

A comparative study between microsatellite and allozyme markers was conducted on the genetic structure and mating system in natural populations of Euterpe edulis Mart. Three cohorts, including seedlings, saplings, and adults, were examined in 4 populations using 10 allozyme loci and 10 microsatellite loci. As expected, microsatellite markers had a much higher degree of polymorphism than allozymes, but estimates of multilocus outcrossing rate ( = 1.00), as well as estimates of genetic structure (F(IS), G(ST)), were similar for the 2 sets of markers. Estimates of R(ST), for microsatellites, were higher than those of G(ST), but results of both statistics revealed a close agreement for the genetic structure of the species. This study provides support for the important conclusion that allozymes are still useful and reliable markers to estimate population genetic parameters. Effects of sample size on estimates from hypervariable loci are also discussed in this paper.     

Population genetics of the yellow fever mosquito in Trinidad: comparisons of amplified fragment length polymorphism (AFLP) and restriction fragment length polymorphism (RFLP) markers

Recent development of DNA markers provides powerful tools for population genetic analyses. Amplified fragment length polymorphism (AFLP) markers result from a polymerase chain reaction (PCR)-based DNA fingerprinting technique that can detect multiple restriction fragments in a single polyacrylamide gel, and thus are potentially useful for population genetic studies. Because AFLP markers have to be analysed as dominant loci in order to estimate population genetic diversity and genetic structure parameters, one must assume that dominant (amplified) alleles are identical in state, recessive (unamplified) alleles are identical in state, AFLP fragments segregate according to Mendelian expectations and that the genotypes of an AFLP locus are in Hardy-Weinberg equilibrium (HWE). The HWE assumption is untestable for natural populations using dominant markers. Restriction fragment length polymorphism (RFLP) markers segregate as codominant alleles, and can therefore be used to test the HWE assumption that is critical for analysing AFLP data. This study examined whether the dominant AFLP markers could provide accurate estimates of genetic variability for the Aedes aegypti mosquito populations of Trinidad, West Indies, by comparing genetic structure parameters using AFLP and RFLP markers. For AFLP markers, we tested a total of five primer combinations and scored 137 putative loci. For RFLP, we examined a total of eight mapped markers that provide a broad coverage of mosquito genome. The estimated average heterozygosity with AFLP markers was similar among the populations (0.39), and the observed average heterozygosity with RFLP markers varied from 0.44 to 0.58. The average FST (standardized among-population genetic variance) estimates were 0.033 for AFLP and 0.063 for RFLP markers. The genotypes at several RFLP loci were not in HWE, suggesting that the assumption critical for analysing AFLP data was invalid for some loci of the mosquito populations in Trinidad. Therefore, the results suggest that, compared with dominant molecular markers, codominant DNA markers provide better estimates of population genetic variability, and offer more statistical power for detecting population genetic structure.     

Biodiversity of 52 chicken populations assessed by microsatellite typing of DNA pools

In a project on the biodiversity of chickens funded by the European Commission (EC), eight laboratories collaborated to assess the genetic variation within and between 52 populations from a wide range of chicken types. Twenty-two di-nucleotide microsatellite markers were used to genotype DNA pools of 50 birds from each population. The polymorphism measures for the average, the least polymorphic population (inbred C line) and the most polymorphic population (Gallus gallus spadiceus) were, respectively, as follows: number of alleles per locus, per population: 3.5, 1.3 and 5.2; average gene diversity across markers: 0.47, 0.05 and 0.64; and proportion of polymorphic markers: 0.91, 0.25 and 1.0. These were in good agreement with the breeding history of the populations. For instance, unselected populations were found to be more polymorphic than selected breeds such as layers. Thus DNA pools are effective in the preliminary assessment of genetic variation of populations and markers. Mean genetic distance indicates the extent to which a given population shares its genetic diversity with that of the whole tested gene pool and is a useful criterion for conservation of diversity. The distribution of population-specific (private) alleles and the amount of genetic variation shared among populations supports the hypothesis that the red jungle fowl is the main progenitor of the domesticated chicken.     

Comparative analysis of genetic diversity of sesame (Sesamum indicum L.) from Vietnam and Cambodia using agro-morphological and molecular markers

The purpose of this study was to comparatively analyze the genetic diversity of sesame (Sesamum indicum L.) using agro-morphological and molecular markers. Twelve sesame populations collected from three regions in Cambodia and Vietnam were used in this study. A high genetic variation was revealed both by agro-morphological and RAPD markers within and among the 12 sesame populations. The range of agro-morphological trait based average taxonomic distance among populations (0.02 to 0.47) was wider than that of RAPD based genetic distance (0.06 to 0.27). The mean distance revealed by agro-morphological markers (0.23) and RAPD markers (0.22) was similar. RAPD based analysis revealed a relatively higher genetic diversity in populations from South Vietnam as compared to the other two regions. Interestingly, populations from this region also had higher values for yield related traits such as number of capsules per plant, number of seeds per capsule, and seed yield per plant suggesting positive correlation between the extent of genetic variation within population and yield related traits in sesame. A highly significant positive correlation (r = 0.88, P < 0.001) was found between agro-morphological and RAPD markers in estimating the genetic distance between populations. Both methods suggested the existence of a substantial amount of genetic diversity both in the Vietnamese and Cambodian populations. Although both agro-morphological and RAPD markers were found to be useful in genetic diversity analysis in sesame, their combined use would give superior results.     

Genetic variation and population structure of oriental migratory locust, Locusta migratoria manilensis, in China by allozyme, SSRP-PCR, and AFLP markers

Allozyme analysis, microsatellite primer PCR (SSRP-PCR), and amplified fragment length polymorphism (AFLP) techniques were used to assess genetic diversity and population structure of the Chinese oriental migratory locust, Locusta migratoria manilensis. A total of 299 PCR markers (67 SSRPs and 232 AFLPs) were detected in eight populations, of which 98.7% were polymorphic markers. The proportion of polymorphic loci (95.5-98.8%) by SSRP+AFLP markers indicated no significant differences between populations, and all populations exhibited a similar level of variability; results of the allozyme analysis demonstrated that 19 loci gave rise to a lower level of polymorphism (55.6-66.7%). The genetic distances between the populations were relatively low. Shannon's index and Nei's gene diversity showed low differentiation among the populations. Allozyme analysis, however, reflected greater similarity and smaller differentiation between the populations than those shown by SSRP and AFLP markers. Neighbor-joining dendrograms derived from both the allozyme and SSRP+AFLP markers showed that the genetic distances among Chinese oriental migratory locust populations were not greatly influenced by geographic distance and breeding habitats.     

Contrasting genetic diversity and differentiation of populations of two successional stages in a Neotropical pioneer tree (Eremanthus erythropappus, Asteraceae)

Eremanthus erythropappus, commonly known as "candeia", is an abundant pioneer tree species, forming dense populations known as "candeial", but it is also found in forests at middle stages of succession. Trees from forests are bigger and occur in lower density than in the "candeial". The objectives of the present study were to investigate if the decrease in population density during successional process is accompanied by 1) changes in within-population genetic diversity, and 2) differentiation of populations. Eight populations, four of early successional stage ("candeial") and four of middle successional stages (forest), were analyzed with RAPD markers. The genetic diversity found was high compared to other tree species analyzed with RAPD markers. AMOVA revealed that most of the genetic variations of E. erythropappus were found within populations (85.7%), suggesting that this species is predominantly outcrossing. The relatively low differentiation among the populations can be attributed to small distances among the populations analyzed (0.2 to 10.8 km). No indication that populations from middle successional habitats show lower genetic variation than populations from early successional stages was found. The percentage of polymorphic fragments (82.8 and 84.8%) and the Shannon indexes (0.442 and 0.455) were similar in "candeial" and forest, respectively. These results suggest that if an increase in selection intensity occurred during succession, it did not result in a decrease in genetic diversity or that the selection effect was balanced by other factors, such as gene flow. Higher significant differentiation among E. erythropappus populations from "candeial" in relation to that among populations from forest was also not detected.     

Genetic Variation and Population Structure of Oriental Migratory Locust, Locusta migratoria manilensis, in China by Allozyme, SSRP-PCR, and AFLP Markers

Allozyme analysis, microsatellite primer PCR (SSRP-PCR), and amplified fragment length polymorphism (AFLP) techniques were used to assess genetic diversity and population structure of the Chinese oriental migratory locust, Locusta migratoria manilensis. A total of 299 PCR markers (67 SSRPs and 232 AFLPs) were detected in eight populations, of which 98.7% were polymorphic markers. The proportion of polymorphic loci (95.5–98.8%) by SSRP+AFLP markers indicated no significant differences between populations, and all populations exhibited a similar level of variability; results of the allozyme analysis demonstrated that 19 loci gave rise to a lower level of polymorphism (55.6–66.7%). The genetic distances between the populations were relatively low. Shannon’s index and Nei’s gene diversity showed low differentiation among the populations. Allozyme analysis, however, reflected greater similarity and smaller differentiation between the populations than those shown by SSRP and AFLP markers. Neighbor-joining dendrograms derived from both the allozyme and SSRP+AFLP markers showed that the genetic distances among Chinese oriental migratory locust populations were not greatly influenced by geographic distance and breeding habitats.     

Development and use of EST-SSR markers for assessing genetic diversity in the brown planthopper (Nilaparvata lugens Stål)

To assess genetic diversity in populations of the brown planthopper (Nilaparvata lugens St?l) (Homoptera: Delphacidae), we have developed and applied microsatellite, or simple sequence repeat (SSR), markers from expressed sequence tags (ESTs). We found that the brown planthopper clusters of ESTs were rich in SSRs with unique frequencies and distributions of SSR motifs. Three hundred and fifty-one EST-SSR markers were developed and yielded clear bands from samples of four brown planthopper populations. High cross-species transferability of these markers was detected in the closely related planthopper N. muiri. The newly developed EST-SSR markers provided sufficient resolution to distinguish within and among biotypes. Analyses based on SSR data revealed host resistance-based genetic differentiation among different brown planthopper populations; the genetic diversity of populations feeding on susceptible rice varieties was lower than that of populations feeding on resistant rice varieties. This is the first large-scale development of brown planthopper SSR markers, which will be useful for future molecular genetics and genomics studies of this serious agricultural pest.     

Analysis of genetic variation in grass carp (Ctenopharyngodon idellus) from native and colonized regions using ISSR markers

The grass carp (Ctenopharyngodon idella), a freshwater species native to China, have been introduced in more than 100 countries. In this paper, inter simple sequence repeat (ISSR) markers were used to evaluate genetic variation within and among grass carp populations sampled from its native (China) and colonized habitats (USA, Hungary, and Japan). Twenty-two ISSR primers were used to generate 207 bands, of which 82 (39.61 %) were polymorphic. The highest genetic diversity was observed in the Yangtze River population, whereas the lowest diversity was found in the Tone River population (Japan). Compared with colonized populations, the native populations possess approximately twice as much genetic diversity. The AMOVA analysis showed a relatively high level of genetic variation within populations. Significant genetic differences were revealed both among the native populations and between pooled native and colonized populations.     

Genetic Markers and Quantitative Genetic Variation in Medicago Truncatula (Leguminosae): A Comparative Analysis of Population Structure

Two populations of the selfing annual Medicago truncatula Gaertn. (Leguminoseae), each subdivided into three subpopulations, were studied for both metric traits (quantitative characters) and genetic markers (random amplified polymorphic DNA and one morphological, single-locus marker). Hierarchical analyses of variance components show that (1) populations are more differentiated for quantitative characters than for marker loci, (2) the contribution of both within and among subpopulations components of variance to overall genetic variance of these characters is reduced as compared to markers, and (3) at the population level, within population structure is slightly but not significantly larger for markers than for quantitative traits. Under the hypothesis that most markers are neutral, such comparisons may be used to make hypotheses about the strength and heterogeneity of natural selection in the face of genetic drift and gene flow. We thus suggest that in these populations, quantitative characters are under strong divergent selection among populations, and that gene flow is restricted among populations and subpopulations.     

濒危灌木长叶红砂遗传多样性的RAPD分析

应用RAPD分子标记对濒危灌木长叶红砂(Reaumuria trigyna)种群遗传多样性进行了分析.应用18条随机引物对长叶红砂5个种群的95个个体进行扩增,检测到118个位点,其中多态位点105个.结果表明:长叶红砂种群的多态位点比率(P)为88.98%,显示出长叶红砂种群存在较高的遗传多样性.Shannon多样性指数(0.4966)、Nei基因多样性指数(0.3303)和基因分化系数(Gst=0.1425)的分析结果显示,长叶红砂种群遗传变异大多存在于种群内,种群间的遗传分化占14.25%.聚类分析表明,长叶红砂种群遗传距离与地理距离之间无直接相关关系.遗传多样性水平与物种特性和所处不同群落有关,濒危植物并不一定表现为遗传变异水平的降低.     

Genetics of Caucasian population: distribution of various immunological and biochemical markers in western Georgia

The distribution of genetic markers of blood groups (ABO, Rhesus, MNSs, P, Duffy, Kell-Cellano), plasma proteins (Hp, Gc, Tf, C'3) and red-cell enzymes (AcP, EstD, GLO-1), and also ABH secretion among 10 populations of Western Georgia has been studied. The common characteristic of distribution of gene frequencies for the markers studied was obtained as a whole in Georgia. The Georgians were compared for these markers with some populations of the Caucasus, Europe and West Asia. Among Caucasian populations, Georgians are most similar to Abkhasians. According to some systems, Georgians are close to European groups (ABO, Dubby, GLO-1, EstD), while they are similar to West-Asian groups, as judged by other systems (ABH secretion, AcP). According to Rhesus and MNSs systems, Georgians differ both from populations of Europe and from populations of West Asia.     

Genetic structure among and within peripheral and central populations of three endangered floodplain violets

Understanding the partitioning of genetic variance in peripheral and central populations may shed more light on the effects of genetic drift and gene flow on population genetic structure and, thereby, improve attempts to conserve genetic diversity. We analysed genetic structure of peripheral and central populations of three insect-pollinated violets (Viola elatior, Viola pumila, Viola stagnina) to evaluate to what extent these patterns can be explained by gene flow and genetic drift. Amplified fragment length polymorphism was used to analyse 930 individuals of 50 populations. Consistent with theoretical predictions, peripheral populations were smaller and more isolated, differentiation was stronger, and genetic diversity and gene flow lower in peripheral populations of V. pumila and V. stagnina. In V. elatior, probably historic fragmentation effects linked to its specific habitat type were superimposed on the plant geographic (peripheral-central) patterns, resulting in lower relative importance of gene flow in central populations. Genetic variation between regions (3-6%), among (30-37%) and within populations (60-64%) was significant. Peripheral populations lacked markers that were rare and localized in central populations. Loss of widespread markers in peripheral V. stagnina populations indicated genetic erosion. Autocorrelation within populations was statistically significant up to a distance of 10-20 m. Higher average genetic similarity in peripheral populations than in central ones indicated higher local gene flow, probably owing to management practices. Peripheral populations contributed significantly to genetic variation and contained unique markers, which made them valuable for the conservation of genetic diversity.     

Comparative Assessment of Genetic Variability in the Populations of Endemic and Endangered Yellow Catfish, Horabagrus brachysoma (Teleostei: Horabagridae), Based on Allozyme, RAPD, and Microsatellite Markers

The comparative assessment of genetic diversity using allozymes, random amplified polymorphic DNA (RAPD), and microsatellite markers was conducted in endemic and endangered yellow catfish (Horabagrus brachysoma) sampled from three locations in Western Ghats river systems of India. Among the three markers, microsatellites show more polymorphism, having 100% polymorphic loci, whereas allozymes show the least (56%). In RAPD, 60.5% of fragments were polymorphic. Observed heterozygosity and F(ST) values were very high in microsatellites, compared with the other markers. Microsatellite and RAPD markers reported a higher degree of genetic differentiation than allozymes among the populations depicted by pairwise F(ST)/G(ST), AMOVA, Nei's genetic distance, and UPGMA dendrogram. The three classes of markers demonstrated striking genetic differentiation between pairs of H. brachysoma populations. The data emphasize the need for fishery management, conservation, and rehabilitation of this species.     

Concordance of genetic divergence among sockeye salmon populations at allozyme, nuclear DNA, and mitochondrial DNA markers

Abstract.— We examined genetic variation at 21 polymorphic allozyme loci, 15 nuclear DNA loci, and mitochondrial DNA in four spawning populations of sockeye salmon ( Oncorhynchus nerka ) from Cook Inlet, Alaska, to test for differences in the patterns of divergence among different types of markers. We were specifically interested in testing the suggestion that natural selection at allozyme loci compromises the effectiveness of these markers for describing the amount and patterns of gene flow among populations. We found concordance among markers in the amount of genetic variation within and among populations, with the striking exception of one allozyme locus ( sAH ), which exhibited more than three times the amount of among-population differentiation as other loci. A consideration of reports of discordance between allozymes and other loci indicates that these differences usually result from one or two exceptional loci. We conclude that it is important to examine many loci when estimating genetic differentiation to infer historical amounts of gene flow and patterns of genetic exchange among populations. It is less important whether those loci are allozymes or nuclear DNA markers.     

Assessment of genetic diversity and chemical composition among seven black locust populations from Northern China

Black locust (Robinia pseudoacacia L.) is one of the important biomass sources used to produce bioenergy and bioethanol. In this study, we examined variations in chemical composition as well as genetic diversity and differentiation among 165 black locust plants from seven populations in five provinces (Beijing, Hebei, Gansu, Shanxi, Shandong) of Northern China using microsatellite markers(SSR). The contents of cellulose, hemicellulose, lignin varied widely among seven populations. Of the microsatellite markers analysed, 14 showed polymorphisms, and 45 alleles were identified. The polymorphism information content (PIC) ranged from 0.2885 (Rops4) to 0.6837 (Rp200), and most of the microsatellite loci had PIC values > 0.5. Expected heterozygosity (He), observed heterozygosity (Ho), and Shannon's information index (I) detected relatively high genetic variation among populations. The percentage of polymorphic loci in three populations was 100%, and the average among all populations were 95.92%. Analysis of molecular variance (AMOVA) indicated that the degree of genetic differentiation among the seven populations was low (G_ST = 0.058; N_m = 4.05), and chemical compositions had no relationship with genetic or geographic distance. This study demonstrates that microsatellite markers efficiently assess of genetic diversity and genetic differentiation in black locust populations, and all seven populations exhibit high genetic diversity. The population from Feixian has the potential to be lingo-cellulosic biomass for bioenergy and bioethanol.     

Randomly Amplified Polymorphic DNA Variation in Populations of Eastern Australian Koalas, Phascolarctos cinereus

Randomly amplified polymorphic DNA (RAPD) variation in populations of the koala, Phascolarctos cinereus, was investigated, revealing significant differences in the level of diversity between southern and northern regions of eastern Australia. Of the 20 polymorphic RAPD markers identified in koalas, 4-7 were polymorphic in southern populations, while 12-17 were polymorphic in northern populations. Analysis of molecular variance revealed a significant difference in the estimated variance between koalas from northern and those from southern regions (P < 0.001), where populations from the north were greater than twice as variable as their southern cousins. The total genetic diversity observed was attributed to regional differences (30.91%), population differences within a region (11.77%), and differences among individuals within a population (57.32%). For the within-region analyses, a large proportion of the genetic diversity was attributable to individual differences within a population, 80.34% for the north and 91.23% for the south. These results demonstrate that RAPD markers are useful for determining population structure among koalas.     

利用17个微卫星标记分析鳙鱼的遗传多样性

选用本实验室克隆的17个鳙鱼微卫星分子标记分析四川泸州和江西鄱阳湖的两个种群鳙鱼的遗传多样性及种质特性,计算和统计了杂合度、多态信息含量（PIC）、有效等位基因数、等位基因频率、遗传距离、遗传相似系数、Hardy-Weinberg平衡偏离指数等方面内容。结果表明：选择使用17个微卫星标记,其中有4个为单态标记,13个为多态标记。江西和四川鳙鱼群体每个微卫星位点的平均等位基因数分别为3.325及3.882,平均有效等位基因数分别为3.531及2.676,多态位点百分率分别为82.4及70.5, 17个微卫星标记共有等位基因71个,多态微卫星位点的PIC在0.114~0.960之间变动,平均为0.417 ,两群体位点平均观测杂合度为0.385和0.452,平均期望杂合度为0.360和0.422,两个群体间的遗传相似系数为0.897,群体间的遗传距离为0.109。     

Genetic experiments with model populations: Fallacies in genetic analysis performed from samples of recombinants selected for two markers

Abstract: Samples selected for two markers (one from each parent) from the progeny of a genetic cross are altered both in the genotype and in the frequency distribution as compared to the original progeny population. The consequences of these alterations were analyzed in selected samples obtained from model progeny populations of hypothetical genetic crosses. In complete progeny populations, distribution of genotypes (pattern of genotypes), sequence of markers, and frequency distribution of individual genotypes exhibit genetically intelligent relationship to each other only under a sole condition: at the correct sequence of markers. In selected samples, the singularity of the interrelationship is relaxed. Consequences of the relaxation in the genetic analysis are multiple, the most striking of which is an insinuation of circularity for the linear gene map.