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PubMed2005

Genetic variation within and among populations of a dominant desert tree Haloxylon ammodendron (Amaranthaceae) in China.

BACKGROUND AND AIMS: China is one of the countries most severely affected by desertification. Haloxylon ammodendron (Amaranthaceae) is an ecologically important component of the desert ecosystem and is one of the main tree species used for restoration, yet we know little about its genetic structure. METHODS: Genetic variation within and between nine populations of H. ammodendron from two regions of China was investigated using ISSR (inter-simple sequence repeat) markers. KEY RESULTS: Eight primers used in this study amplified 219 reproducible bands of which 184 (84 %) were polymorphic. Analysis of molecular variance (AMOVA) revealed high genetic variation within populations (97.63 %) and low genetic differentiation between regions (0.62 %) and among populations (1.75 %). CONCLUSIONS: It is suggested that the present genetic structure could have arisen by high levels of gene flow. The gene flow among populations observed here is probably mainly attributable to pollen movement. The genetic structure also has important implications in ecological restoration practice.

Amaranthaceae↗

PubMed2002

Variations in abundance: genome-wide responses to genetic variation and vice versa.

How do naturally occurring polymorphisms in DNA sequence relate to variation in gene expression? Recent work to map genetic sources of expression variation has shown a surprising balance between cis and trans effects. Other work suggests some chromosomal clustering of genes by expression pattern. A synthesis of approaches may provide new insight in to adaptive mechanisms in evolution and the population basis of complex traits.

Animals↗

PubMed1999

Genetic variation for carbon isotope composition in honey mesquite (Prosopis glandulosa).

Carbon isotope composition (delta(13)C) is a useful surrogate for integrated, plant water-use efficiency (WUE) when measured on plants grown in a common environment. In a variety of species, genetic variation in delta(13)C has been linked to the distribution of genotypes across gradients in atmospheric and soil water. We examined genetic variation for delta(13)C in seedlings of honey mesquite (Prosopis glandulosa Torr.), an invasive grassland shrub that thrives in the southwestern USA. Fifteen maternal families, representing progeny of 15 adult trees, were studied in three common garden experiments in a greenhouse. The 990-km east-west transect along which the adult trees were located encompasses a wide precipitation gradient, and includes mesic grassland, semiarid grassland, and Chihuahuan desert ecosystems. Genetic variation for delta(13)C in mesquite was substantial, with the rank order of half-sib families based on delta(13)C relatively stable across experiments, which were conducted under different environmental conditions. Conversely, rankings of families by mean seedling height (an index of growth rate) varied markedly among experiments. Seedlings derived from Chihuahuan desert adults emerged more quickly and had more negative delta(13)C (indicative of lower WUE) than seedlings derived from the other regions. Although delta(13)C and seedling height were not correlated, these results suggest that mesquite genotypes at the drier, western extreme of the species' range are adapted for quicker emergence and possibly faster growth than genotypes from mesic areas. Together, these traits may facilitate exploitation of infrequent precipitation events.

Journal Article↗

PubMed1998

Genetic variation and causes of genotype-environment interaction in the body size of blue tit (Parus caeruleus).

In several studies of natural populations of birds, the heritability of body size estimated by parent-offspring regression has been lower when offspring have developed in poor feeding regimens than when they developed in good feeding regimens. This has led to the suggestion that adaptation under poor regimens may be constrained by lack of genetic variation. We examined the influence of environmental conditions on expression of genetic variation in body size of nestling blue tits (Parus caeruleus) by raising full sibs in artificially reduced and enlarged broods, corresponding to good and poor feeding regimens, respectively. Individuals grown in the poor regimen attained smaller body size than their sibs grown in the good regimen. However, there was among-family variation in response to the treatments--i.e., genotype-environment interactions (GEIs). Partitioning the GEI variance into contributions attributable to (1) differences in the among-family genetic variance between the treatments and (2) imperfect correlation of genotypic values across treatments identified the latter as the main cause of the GEI. Parent-offspring regressions were not significantly different when offspring were reared in the good environment (h2 = 0.75) vs. when they were reared in the poor environment (h2 = 0.63). Thus, there was little evidence that genetic variance in body size was lower under the poor conditions than under the good conditions. These results do not support the view that the genetic potential for adaptation to poor feeding conditions is less than that for adaptation to good conditions, but they do suggest that different genotypes may be favored under the different conditions.

Animals↗

PubMed2002

Temporal and geographic genetic variation in Culex nigripalpus theobald (Culicidae: Diptera), a vector of St. Louis encephalitis virus, from Florida.

A field population of Culex (Culex) nigripalpus Theobald from Vero Beach, FL sampled monthly over a period of 24 mo, a colony sample and 10 geographic samples were analyzed for genetic variation at 14 enzyme loci using polyacrylamide gel electrophoresis. The Cx. nigripalpus colony sample showed significantly lower genetic variation than the field-collected samples, measured by mean number of alleles per locus (colony 1.4 +/- 0.1 versus field 2.1 +/- 0.22), percentage of polymorphic loci (colony 35.7% versus field 54.8 +/- 7.7%), but mean observed heterozygosity (Ho = colony 0.16 +/- 0.07 versus field 0.17 +/- 0.03) and mean Hardy-Weinberg expected heterozygosity (He = colony 0.14 +/- 0.06 versus field 0.18 +/- 0.02) did not differ significantly. Three of the 14 loci (Aldox, Gpd, and Gpi) from the Vero Beach field samples showed distinct temporal patterns in the frequency of the most common allele. Higher mean observed heterozygosity (Ho) occurred during months following high rainfall in the Vero Beach field samples than during months following low rainfall. The average Nm value of 3.6 indicated high gene flow among the temporally distributed samples of the Vero Beach population. Genetic variability values between geographic samples from Panhandle, FL and south Florida were not significant. Gene flow estimates based on F(ST) = 0.039 provided a Nm of 6.2 indicating high levels of gene flow among the geographic samples of Cx. nigripalpus. The average Nei's and modified Rogers' genetic distances among the 10 populations were 0.009 +/- 0.001 and 0.081 +/- 0.004, respectively. The cluster analysis did not suggest geographic clustering, Because Cx. nigripalpus is the vector of St. Louis encephalitis (SLE) in Florida, temporal and geographic genetic variation in this species is discussed in relation to the seasonal and geographic SLE virus activity in Florida.

Animals↗

PubMed2025

Genome-wide Parallelism Underlies Rapid Freshwater Adaptation Fueled by Standing Genetic Variation in a Wild Fish.

A fundamental focus of ecological and evolutionary biology is determining how natural populations adapt to environmental changes. Rapid parallel phenotypic evolution can be leveraged to uncover the genetics of adaptation. Using population genomic approaches, we investigated the genetic architecture underlying rapid parallel freshwater adaptation of Neosalanx brevirostris by comparing four freshwater-resident populations with their common ancestral anadromous population. We demonstrated that the rapid parallel adaptation to freshwater followed a complex polygenic architecture and was characterized by genomic-level parallelism, which proceeded predominantly through repeated selection on the preexisting standing genetic variations. Frequencies of the genome-wide adaptive standing variations were moderate in the ancestral anadromous population, which had pre-adapted to fluctuating salinities. Relatively large allele frequency shifts were observed at some adaptive single-nucleotide polymorphisms (SNPs) during parallel adaptation to freshwater environments, with a large fraction of freshwater-favored alleles being fixed or nearly fixed. These adaptive SNPs were involved in multiple biological functions associated with osmoregulation, immunoregulation, locomotion, metabolism, etc., which were highly consistent with the polygenic architecture of adaptive divergence between the two ecotypes involving multiple complex physiological and behavioral traits. This work provides insight into the mechanisms by which natural populations rapidly evolve to changes in the environment and highlights the importance of standing genetic variation for the evolutionary potential of populations facing global environmental changes.

Animals↗

PubMed1992

Genetic variation between strains of the Mediterranean fruit fly, Ceratitis capitata, detected by DNA fingerprinting.

DNA fingerprinting has been used to detect genetic variation in the Mediterranean fruit fly, Ceratitis capitata. Three different probes have been identified that can be used to detect DNA restriction fragment length polymorphisms between strains of this species. The strains used in this study differ only in terms of their geographic origin or genetic background. One of the probes used is the bacteriophage vector M13, and the other two are repetitive sequences derived from the medfly genome based on a weak homology to M13. Within a strain, each probe produces a consistent restriction fragment profile that is not affected by the method or timing of DNA extraction. Between strains, when M13 is used as a probe, an average of 10% of the observable bands are polymorphic. Use of the medfly genomic sequences as a probe increases the proportion of polymorphic bands between strains up to 30%. The fact that genetic differences between even such closely related strains can be reliably detected by this method holds great promise for studies of insect pests including the ability to monitor the movements of pest species, determining the extent of genetic variation in pest populations, and in making identifications from otherwise unidentifiable material.

Animals↗

PubMed1995

Assessment of genetic variations within populations of Sika deer in Japan by analysis of randomly amplified polymorphic DNA (RAPD).

Random amplified polymorphic DNA (RAPD) was exploited as a genetic marker to assess the level of genetic variation in populations of Sika deer, Cervus nippon, in Japan. DNA samples were collected from three local populations in Japan, namely, Kinkazan, Goyozan and Ashoro populations. Four arbitrary primers, when used individually, amplified an average of five RAPD fragments in the polymerase chain reaction (PCR). The number of polymorphic bands was scored to calculate band-sharing coefficients within populations. Average band-sharing coefficients revealed a higher degree of homogeneity in the Kinkazan population. Samples collected from larger populations, namely, Ashoro and Goyozan, revealed greater polymorphism than samples from the Kinkazan deer. Our data suggest that RAPD is useful as a marker for detecting genetic variations in populations of Sika deer with reduced levels of genetic diversity.

Animals↗

PubMed1987

Sensitive techniques for the detection of genetic variation in human isozymes.

The principal means by which genetic variation of enzyme proteins has been revealed is the physicochemical separation of isozymes in an electrical field followed by their specific detection. This approach is widely applicable to all types of species and almost every conceivable kind of tissue homogenate or protein secretion. In the human organism alone the products of more than 200 enzyme loci have been investigated by this means and more than 40 genetically determined human isozyme polymorphisms have been identified. Much of this progress has been achieved by the use of conventional gel electrophoresis methods and isozyme detection schemes that depend on enzyme-catalyzed conversion of substrate into chromogens or other types of visible product. However, the functional isozyme detection systems are often of limited sensitivity and are dependent on the good condition of the biological material under analysis and the retention of adequate enzyme activity. Also in some cases, especially where the final product of the detection reaction is not an insoluble compound, the staining may be so diffuse as to offset the high resolving power of the most effective protein separation methods such as isoelectric focusing in ultranarrow pH gradients. The recent development of alternative protein detection methods based on immunoblotting offers a new general approach to isozyme analysis and overcomes some of the limitations of isozyme detection by functional staining methods. The immunoblot methodology is applicable to proteins separated electrophoretically on denaturing gels and on native gels, including proteins separated by isoelectric focusing, and the fidelity of the high-resolution separation techniques appears to be preserved for most proteins by passive or electroblot transfer to nitro-cellulose filters. Furthermore this approach provides considerable flexibility in the sensitivity and the nature of the final reporter signal that is employed. For example, the reporter signal can be amplified by the use of appropriate intermediate reagents to provide a level of detection sensitivity for isozyme proteins which should, even with the present procedures, be far in excess of that which is obtained even by the best functional isozyme staining system. Also the use of an evanescent reporter system such as chemiluminescence may allow multiple analyses of the same immunoblot and hence examination of several different isozyme systems by sequentially using different primary antibodies.

Gene Amplification↗

PubMed2000

Genetic variation in coronary heart disease and myocardial infarction: methodological overview and clinical evidence.

The precise molecular mechanisrms that lead to coronary artery disease (CAD) and myocardial infarction (MI) are not understood, despite a wealth of knowledge on predisposing risk factors and pathomechanisms. CAD and MI are complex genetic diseases; neither the environment alone nor a single gene cause disease, but a mix of environmental and genetic factors lead to atherosclerosis of the coronary arteries and subsequent manifestation of clinical disease. The biological complexity of atherosclerotic disease results from unknown or unpredictable interactions of many genetic and environmental factors which, by themselves, have only been partially identified. According to current knowledge, genetic variations in causative or susceptihility genes form the basis of molecular mechanisms that, together with environmental impact, lead to CAD/MI and determine its clinical course. Linkage analysis, which follows 'disease' alleles in families, or genetic association in a population of unrelated individuals are tools used in the search for chromosomal loci and candidate genes that are involved in these complex diseases. Progress in sequencing and mapping of the human genorne and efforts to identify all of the expected one million single nucleotide polymorphisms (SNPs) expected to be present in mankind will allow new approaches such as genome-wide association studies. The contribution of the current state of knowledge on genetic variation in man towards the dissection of CAD/MI as complex traits is sobering. Raised expectations with regard to the power of molecular genetic studies as compared to the traditional pathophysiological experimental approaches, lack of precise clinical phenotyping, lack of functional characterisation of gene variants, and the vast number of yet undetected genes may provide some explanation. Except for certain polymorphisms in lipid genes (i.e., apolipoprotein E [apo E]) or rare genetic variations (i.e., LDL receptor), which have a causal effect on both the intermediate (LDL-cholesterol level in plasma) and the clinical phenotypes (CAD/MI), the role of most gene polymorphisms is controversial or unknown. Despite the enormous progress in sequencing the human genome and in molecular genetic and bioinformatic techniques during the past decade, the progress in mapping and identifying genes responsible for complex traits such as CAD/MI has been modest and presents a formidable challenge to medical research in the 21st century.

Coronary Disease↗

PubMed1991

Quantitative genetic variation and developmental clocks.

It is well-known that most genetic variation affects quantitative traits, and natural or artificial selection can act to change quantitative features of organisms more rapidly than qualitative ones. Surprisingly, variability is not confined to outbred species, but also occurs in inbred mice at a much higher rate than expected from known mutation rates. The size and shape of organisms and their constituent parts are, at least in part, controlled by the number of cell divisions, and there is published evidence for the existence of developmental clocks, which may count cell divisions. A molecular model for a developmental clock was previously proposed. It depends on the DNA methylation of repeated sequences of DNA, where the methylation of each additional sequence is tied to DNA synthesis and therefore cell division. The number of repeats specifies the number of divisions which will occur before a signal is produced which can activate or inactivate one or more genes. It is known that crossing over occurs between sister chromatids, and where tandemly repeated sequences occur unequal exchange can generate a larger or smaller number of repeats. An example of this is seen in the well-known variability of "minisatellite" sequences in human DNA. Unequal sister chromatid exchange can occur in mitotic and meiotic cells in the germ line, and in the case of developmental clock sequences could generate variation in clock length which in turn would directly affect quantitative traits. These events can be regarded as a special case of molecular drive during evolution.

Animals↗

PubMedDate not supplied

Genetic variation in two land snails, Cepaea nemoralis and Succinea putris (Gastropoda, Pulmonata), from sites differing in heavy metal content.

Allozyme variation was determined in two land snail species (Cepaea nemoralis and Succinea putris) from four localities in northern Belgium. In each locality we selected a polluted and a nearby, less-polluted, reference plot. We examined whether (i) genetic variability differed between the polluted and reference plots, (ii) populations from polluted plots experienced recent bottlenecks, and (iii) certain allele or genotype frequencies were associated with the pollution. Our results suggest that (i) about 13% of the genetic differentiation in C. nemoralis and 5% in S. putris was due to differences among polluted and reference plots, (ii) polluted and reference plots had comparable levels of genetic variation, but in C. nemoralis observed heterozygosities were higher in polluted plots, (iii) most plots showed significant evidence for recent bottlenecks, irrespective of the degree of pollution, so that bottlenecks seem poor indicators of pollution-induced stress in land snails, and (iv) mutagenic or pollution-induced modifications did not seem to account for new allozyme variants in polluted sites. The observed patterns of genetic variation may be explained by the action of genetic drift, pollution-mediated selection, restricted gene flow, or a combination of these processes.

Alleles↗

PubMed1989

Biochemical correlates of genetic variation in marine lower invertebrates.

In this paper extensive data on enzyme variation in 23 species of coelenterates and sponges were used to investigate the possible correlation of levels of genetic variation with various parameters of enzyme molecular structure and function. The data provide an opportunity not only to look for such correlations for the first time in lower invertebrates, but also to study organisms with far higher average levels of genetic variability than those used in any previous work. A clear inverse relationship was found between enzyme subunit number and levels of polymorphism, with monomers being more variable than dimers or tetramers. No significant difference in polymorphism could be found in enzymes of the functional groups I and II of Gillespie and Langley (1974). Regulatory enzymes appeared to be significant relationship was observed between regulatory power and subunit structure which could bias this result. The results suggest that both neutralist and selectionist ideas may have a useful role to play in the understanding of the factors which can influence or limit levels of genetic variation.

Animals↗

PubMed2003

Genetic variation and hematology: single-nucleotide polymorphisms, haplotypes, and complex disease.

In the course of generating a draft sequence of the human genome, we now recognize the enormous scope of genetic variation among humans, which can be used to probe the genetics of complex diseases such as leukemia or thrombosis. There is already mounting evidence of new susceptibility genes and genes that interact with environmental factors. Genetic variants, especially single-nucleotide polymorphisms (SNPs), also can be utilized to investigate potential modifiers of disease. Genetic variation can be applied to study pharmacogenomics, which could eventually drive the choice of therapeutic and interventional strategies. The genomic revolution ultimately should give insights into key mechanisms in hematological disorders that can be translated into targeted therapies.

Genetic Predisposition to Disease↗

PubMedDate not supplied

Identification and analysis of genetic variation among rose cultivars using random amplified polymorphic DNA.

Identified germplasm is an important component for efficient and effective management of plant genetic resources. Traditionally, cultivars or species identification has relied on morphological characters like growth habit or floral morphology like flower colour and other characteristics of the plant. Studies were undertaken for identification and analysis of genetic variation within 34 rose cultivars through random amplified polymorphic DNA (RAPD) markers. Analysis was made by using twenty five decamer primers. Out of twenty five, ten primers were selected and used for identification and analysis of genetic relationships among 34 rose cultivars. A total of 162 distinct DNA fragments ranging from 0.1 to 3.4 kb was amplified by using 10 selected random decamer primers. The genetic similarity was evaluated on the basis of presence or absence of bands. The cluster analysis indicated that the 34 rose cultivars form 9 clusters. The first cluster consists of eight hybrid cultivars, three clusters having five cultivars each, one cluster having four cultivars, two clusters having three cultivars each and two clusters having one cultivar each. The genetic distance was very close within the cultivars. Thus, these RAPD markers have the potential for identification of clusters and characterization of genetic variation within the cultivars. This is also helpful in rose breeding programs and provides a major input into conservation biology.

Base Sequence↗

PubMed2004

Genetic variation in eleven phase I drug metabolism genes in an ethnically diverse population.

The extent of genetic variation found in drug metabolism genes and its contribution to interindividual variation in response to medication remains incompletely understood. To better determine the identity and frequency of variation in 11 phase I drug metabolism genes, the exons and flanking intronic regions of the cytochrome P450 (CYP) isoenzyme genes CYP1A1, CYP1A2, CYP2A6, CYP2B6, CYP2C8, CYP2C9, CYP2C19, CYP2D6, CYP2E1, CYP3A4 and CYP3A5 were amplified from genomic DNA and sequenced. A total of 60 kb of bi-directional sequence was generated from each of 93 human DNAs, which included Caucasian, African-American and Asian samples. There were 388 different polymorphisms identified. These included 269 non-coding, 45 synonymous and 74 non-synonymous polymorphisms. Of these, 54% were novel and included 176 non-coding, 14 synonymous and 21 non-synonymous polymorphisms. Of the novel variants observed, 85 were represented by single occurrences of the minor allele in the sample set. Much of the variation observed was from low-frequency alleles. Comparatively, these genes are variation-rich. Calculations measuring genetic diversity revealed that while the values for the individual genes are widely variable, the overall nucleotide diversity of 7.7 x 10(-4) and polymorphism parameter of 11.5 x 10(-4) are higher than those previously reported for other gene sets. Several independent measurements indicate that these genes are under selective pressure, particularly for polymorphisms corresponding to non-synonymous amino acid changes. There is relatively little difference in measurements of diversity among the ethnic groups, but there are large differences among the genes and gene subfamilies themselves. Of the three CYP subfamilies involved in phase I drug metabolism (1, 2, and 3), subfamily 2 displays the highest levels of genetic diversity.

Asia, Southeastern↗

PubMed2005

Chromosome 5q candidate genes in coeliac disease: genetic variation at IL4, IL5, IL9, IL13, IL17B and NR3C1.

Genetic predisposition to coeliac disease (CD) is determined primarily by alleles at the HLA-DQB locus, and evidence exists implicating other major histocompatibility complex-linked genes (6p21) and the CTLA4 locus on chromosome 2q33. In addition, extensive family studies have provided strong, reproducible evidence for a susceptibility locus on chromosome 5q (CELIAC2). However, the gene responsible has not been identified. We have assayed genetic variation at the IL4, IL5, IL9, IL13, IL17B and NR3C1 (GR) loci, all of which are present on chromosome 5q and have potential or demonstrated involvement in autoimmune and/or inflammatory disease, in a sample of 409 CD cases and 355 controls. Thirteen single nucleotide polymorphisms were chosen on the basis of functional relevance, prior disease association and, where possible, prior knowledge of the haplotype variation present in European populations. There were no statistically significant allele or haplotype frequency differences between cases and controls. Therefore, these results provide no evidence that these loci are associated with CD in this sample population.

Case-Control Studies↗

PubMed1981

Genetical variation for enzyme activity in a population of Drosophila melanogaster. VI. Molecular variation in the control of alcohol dehydrogenase (ADH) activity.

Four characters, ADH activity at 25 degrees, immunologically determined ADH protein level, total protein and body weight were measured upon 72 hour old adult female and male Drosophila melanogaster from 16 highly inbred lines, derived from the laboratory population, "Texas" (established 1966). The highest levels of ADH activity and ADH protein level were observed in the 2 lined homozygous for the AdhF allele. Amongst the 14 AdhS/S lines variation for ADH protein level was associated with genetical variation for ADH activity (r = 0.6). The genetical association between ADH activity or ADH protein level and either body weight or total protein in the 16 inbred lines was not statistically significant. A study of ADH activity, ADH protein and total protein in 8 lines representing all homozygous combinations of chromosomes I, II and III and derived from two inbred AdhS/S lines, chosen for their respective high and low ADH activities, showed that ADH activity was considerably modified by a post-translational event controlled from chromosome III. Total protein was controlled by different chromosomal effects from those controlling ADH activity. Michaelis constants for crude fly extracts of the two AdhF/F and the above two AdhS/S lines showed clear differences in affinity for isopropanol.

Alcohol Oxidoreductases↗