SEARCH · PubMed Health

Results for “Genetic Variation”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 523 records · Page 29Linked to original sources

PubMed2005

Effect of moxidectin selection on the genetic variation within Cylicocyclus nassatus based on amplified fragment length polymorphism (AFLP).

Cyathostomins are among the most important intestinal nematodes of horses, yet, the literature on the molecular genetics of these worms is scarce. In this study, the technique of amplified fragment length polymorphism (AFLP) was applied to study the genetic diversity as well as to determine the effect of moxidectin selection on the population genetic diversity for Cylicocyclus nassatus, one of the most common cyathostomin species. Genomic DNAs from 30 individual male worms were used from each of two populations: an avermectin-milbemycin (AM)-naive population (Population-S) and a population derived from Population-S following 21 treatments with moxidectin (Population-Mox). Three selective primer pairs were used for each worm, yielding a total of 229 AFLP markers. Calculation of average pair wise Jaccard indices revealed a high degree of genetic variation within both populations using all three primer combinations. In addition, selection by moxidectin during a 3-year period caused a significant decrease in the level of genetic diversity as evidenced by analysis of AFLP markers for two primer combinations but not for the third. A dendrogram of relationships among individuals based on AFLP markers did not show a clear classification of individuals in separate groups. It was concluded that a high degree of genetic intrapopulation variation exists in C. nassatus and that moxidectin selection has a significant effect on the genetic composition of C. nassatus.

Animals↗

PubMed1989

Electrophoretically detectable genetic variation in natural and hatchery stocks of Atlantic salmon in Finland.

To survey the genetic resources of Atlantic salmon (Salmo salar L.) stocks in Finland, an electrophoretic study was made of natural and hatchery stocks. The stocks were compared with the nearest stocks in the USSR, and the effects of hatchery rearing were evaluated. The genetic variation within and between stocks was measured from 20 samples, of which three (Kola, Neva and Onega) were from the USSR. Twenty-five enzyme loci were examined, of which six were polymorphic: AAT-4, IDH-3, ME-3, MDH-3, PGM-1, and SDH-1. The mean heterozygosity of all the populations was 4.2% (1.0-7.2). For the natural salmon stocks of the Arctic Ocean, the mean heterozygosity was 6.3%, for the natural stocks of Atlantic salmon in the Baltic 4.8%, for the hatchery stocks 3.6%, and for the lake salmon (Salmo salar m. sebago Girard) 1.8%. The results are in agreement with the hypothesis that the amount of variation depends on the effective population size and that culture diminishes variation by decreasing the effective population size. All the stocks originating from different rivers differed from each other with statistical significance. The most unique stocks were the River Kola stock and the lake salmon stock from Lake Saimaa. The genetic distances were consistent with the geographic distance between the rivers from which the stocks originated. Stress is laid on the importance in fish culture of maintaining separate stocks and using larger brood stocks.

Animals↗

PubMed2003

Assessment of genetic variation in timothy (Phleum pratense L.) using RAPD and UP-PCR.

DNA-based fingerprinting technologies including random amplified polymorphic DNA (RAPD) and universally primed PCR (UP-PCR), a novel method for studying genetic variation, were employed as genetic markers for assessing genetic diversity and relationships in timothy (Phleum pratense L.). This study sought to identify the genetic background of the genotypes used in timothy breeding. Thirty eight genotypes from fifteen countries were used as test materials. RAPD and UP-PCR dendrograms based on 132 (from 3 primers) and 44 highly reproducible bands, respectively, were analyzed. The electrophoretic gels showed that the PCR products were informative and polymorphic. Different geographic genotype groups were distinguished according to the combined RADP and UP-PCR results. The results demonstrate that methods based on molecular fingerprinting can be used for timothy identification.

Breeding↗

PubMed2006

Fourteen novel genetic variations and haplotype structures of the TYMS gene encoding human thymidylate synthase (TS).

Forty genetic variations including 14 novel ones were found in the human TYMS gene, which encodes thymidylate synthase, in 263 Japanese cancer patients who received 5-fluorouracil (FU)-based chemotherapy. Three novel variations were located within the 28-bp tandem repeat sequence in the 5'-untranslated region (UTR) and were designated 5Rc, 3Rc-ins and 4Rc. Allele frequencies were 0.021 for 5Rc, 0.006 for 3Rc-ins and 0.002 for 4Rc. Other novel variations included -133G>C and -125G>C in the 5'-UTR; IVS1-278G>A, IVS2-68C>T, IVS2-23T>C, IVS4+122_+123insATTG, IVS4-141G>A, IVS5-100A>T and IVS6-111G>A in the introns; and 1244(*302)A>G and 1264(*322)G>A in the 3'-UTR. The allele frequencies were 0.34 for IVS4+122_+123insATTG, 0.042 for -133G>C, 0.011 for IVS4-141G>A, 0.006 for -125G>C, 0.004 for IVS1-278G>A, IVS2-68C>T, 1244(*302)A>G and 1264(*322)G>A, and 0.002 for IVS2-23T>C, IVS5-100A>T and IVS6-111G>A. Using the detected polymorphisms, linkage disequilibrium (LD) analysis was performed, which divided the TYMS gene into three LD blocks. The 28-bp tandem repeat sequence in the 5'-UTR was assigned as Block 2 with a total of 7 alleles. In Blocks 1 and 3, 7 and 19 haplotypes were determined/inferred, respectively. Our findings provide fundamental and useful information for genotyping TYMS in the Japanese and probably other Asian populations.

3' Untranslated Regions↗

PubMed2001

The midbrain dopaminergic system: anatomy and genetic variation in dopamine neuron number of inbred mouse strains.

The mesotelencephalic dopamine system is genetically variable and affects motor behavior, motivation, and learning. Here we examine the genetic variation of mesencephalic DA neuron number in a quasi-congenic RQI mouse strain and its background partner and in a recombinant inbred strain with different levels of mesencephalic tyrosine hydroxylase activity (TH/MES). We used B6.Cb4i5-alpha6/Vad, C57BL/6By, and CXBI, which are known to express high, intermediate, and low levels of TH/MES, respectively. Unbiased stereological sampling with optical disector counting methods were employed to estimate the number of TH-positive neurons in the A8-A9-A10 cell groups. Morphometric studies on the mesencephalic dopamine cell groups indicated that male mice of the B6.Cb4i5-alpha6/Vad strain were endowed with a significantly lower number of TH-positive cells than CXBI mice. In all strains studied, the right retrorubral field (A8 area) had a higher number of dopamine neurons compared to the left A8 area. The results suggest an inverse relationship between TH/MES and number of dopamine neurons in the A9-A10 cell groups and significant lateral asymmetry in the A8 cell group. A detailed anatomical atlas of the mesencephalic A8-A9-A10 dopaminergic cell groups in the mouse is also presented to facilitate the assignment of TH-positive neurons to specific cell groups.

Animals↗

PubMed1991

Determination of genetic variation within Plasmodium falciparum by using enzymatically amplified DNA from filter paper disks impregnated with whole blood.

A new method which allows the enzymatic amplification of DNA extracted from whole blood dried on filter paper disks is presented. The method was used to study heterogeneity within an erythrocyte-binding antigen (EBA-175) of Plasmodium falciparum. Blood specimens from malaria-infected patients in Southeast Asia and Africa were spotted onto filter paper, dried, and transported for processing. P. falciparum DNA was extracted by boiling the filter paper disks in the presence of Chelex-100 ion-chelating resin, amplified by the polymerase chain reaction, and analyzed for the presence of genetic variation. In all cases examined, plasmodial DNA was successfully amplified and characterized from filter paper disks. Hybridization of the polymerase chain reaction products with internal probes demonstrated simultaneous infection with two strains of P. falciparum in two patients. This technique represents a sensitive and practical field method for the determination of genetic variation within P. falciparum and the study of molecular epidemiology.

Animals↗

PubMed2004

Genetic variation in primary metabolites of Pastinaca sativa; can herbivores act as selective agents?

Although insect herbivory has been shown to act as a selective agent on plant secondary metabolism, whether primary metabolites contribute to resistance and can respond to selection by herbivores remains untested. In the wild parsnip (Pastinaca sativa), its principal herbivore, Depressaria pastinacella, acts as a selective agent on furanocoumarin resistance factors. In this study, we determined whether webworms can, by causing differential reductions in fitness, act as selective agents on parsnip primary metabolites. Estimates of narrow-sense heritabilities were significantly different from zero for C18 fatty acids in buds and developing fruits, fructose and sorbitol in buds, fructose, myo-inositol, bergapten, and psoralen in fruits. Wild parsnips protected from webworms by insecticide produced 2.5 times as much seed biomass as unsprayed plants; that webworms accounted for this difference in plant fitness was indicated by a significant negative relationship between reproductive effort and an index of webworm damage. Only a handful of metabolites influenced resistance to webworms; these included osthol, sorbitol, and protein in developing fruits as well as previously documented furanocoumarins. Osthol, a coumarinic compound, enhanced resistance, as did protein content, while sorbitol lowered resistance. Other primary metabolites may affect resistance to webworms, but their effect was context-dependent, that is, their effect depended on concentrations of other metabolites (epistasis). Susceptible plant phenotypes were found to have average chemical compositions. Although there was genetic variation in some of the primary metabolites in parsnips, the epistatic nature of their involvement in resistance and the lack of genetic variation in some suggest that selection on them from webworms will be either inconsistent or ineffective.

5-Methoxypsoralen↗

PubMed2001

Genetic variation of the second exon of ELA-DRB genes in Argentine Creole horses.

Genetic variation in the equine leucocyte antigen-DRB (ELA-DRB) second exon was investigated using polymerase chain reaction (PCR) amplification, restriction fragment length polymorphism (RFLP) of PCR products (PCR-RFLP) and deoxyribonucleic acid (DNA) sequencing. Eight distinct PCR-RFLP patterns could be identified in the studied Argentine Creole (AC) horses. The number of observed patterns per individual ranged from four to six, thus confirming the presence of multiple DRB copies in AC horses. Three PCR-RFLP alleles and three new sequences were identified. The estimated rates of synonymous and non-synonymous substitutions among ELA-DRB exon 2 sequences were higher within the antigen recognition site (ABS) than on the non-ABS. Phylogenetic analysis showed that the nucleotide sequences clustered in two main groups, while some sequences were not included in either group. Finally, the identification of the number of alleles per animal, the phylogenetic and segregation analyses allowed us to explain the number of ELA-DRB loci. However, it was not possible to identify specific alleles with specific loci.

Alleles↗

PubMed2001

Genetic variations in five genes involved in the excitement of cardiomyocytes.

We provide here 29 genetic variations, including 28 novel ones, in five genes that are potentially involved in the excitement of cardiomyocytes: we found 4 in KCNA10, 2 in KCNK1, 8 in KCNK6, 11 in SLC18A1 (VMAT1), and 4 in SLC6A2 (norepinephrine transporter). We also examined their allelic frequencies in a Japanese population of long QT syndrome-affected and nonaffected individuals. These data would be useful for genetic association studies designed to investigate acquired arrhythmias.

Amino Acid Substitution↗

PubMedDate not supplied

Genetic variation in number of pituitary PAS-purple cells in the house mouse.

A genetic variation in the number of pituitary PAS-purple cells in the house mouse is described. C57BL/K1 mice have low and DBA/2/K1 mice have high numbers of these cells in both peripheral and central parts of the anterior pituitary gland. The variation may be due to a single locus with incomplete dominance for the low-number allele. There is no correlation with glucuronidase or galactosidase activities and no association with the b and d loci.

Animals↗

PubMed2002

Phylogeographic analysis of the brooding brittle star Amphipholis squamata (Echinodermata) along the coast of New Zealand reveals high cryptic genetic variation and cryptic dispersal potential.

Direct development in benthic marine invertebrates is usually associated with narrow geographical range, low rates of colonization, and low levels of gene flow. Paradoxically, the small brittle star Amphipholis squamata broods its larvae to a crawl-away juvenile stage, yet has a cosmopolitan distribution. Using sequence and restriction-fragment-length-polymorphisms (RFLP) analyses of nuclear and mitochondrial DNA from 16 coastal populations throughout New Zealand, we tested whether the species is indeed a poor disperser, as may be expected from its brooding habit. We predicted that local and regional populations would be genetically structured according to isolation by distance. We also suspected that this ubiquitous "species" is composed of a variety of cryptic taxa in different geographic areas, as has been discovered in an increasing number of marine invertebrates. We found evidence of four genetically divergent and reproductively isolated lineages that can exist in syntopy. Lineages vary in abundance, haplotype diversity, and geographic distribution. The partitioning of genetic variation within the most common lineage, as well as the geographic distribution of the four lineages, suggest a north/south split. This pattern is consistent with known New Zealand marine biogeographic zones and appears to be linked to the regime of oceanic circulation, which is characterized by subtropical, southward-moving water masses in the north, and sub-Antarctic, northward-moving water in the south. We conclude that the dispersal ability of A. squamata is regionally restricted but with sporadic long-distance dispersal, which serves to increase local genetic variation. Our results support the idea that dispersal occurs through passive transport by drifting or rafting on macroalgae, which A. squamata commonly inhabits, and emphasize that poor dispersal ability is not necessarily a corollary of direct development.

Analysis of Variance↗

PubMed2005

Stress responses and genetic variation in bacteria.

Under stressful conditions mechanisms that increase genetic variation can bestow a selective advantage. Bacteria have several stress responses that provide ways in which mutation rates can be increased. These include the SOS response, the general stress response, the heat-shock response, and the stringent response, all of which impact the regulation of error-prone polymerases. Adaptive mutation appears to be process by which cells can respond to selective pressure specifically by producing mutations. In Escherichia coli strain FC40 adaptive mutation involves the following inducible components: (i) a recombination pathway that generates mutations; (ii) a DNA polymerase that synthesizes error-containing DNA; and (iii) stress responses that regulate cellular processes. In addition, a subpopulation of cells enters into a state of hypermutation, giving rise to about 10% of the single mutants and virtually all of the mutants with multiple mutations. These bacterial responses have implications for the development of cancer and other genetic disorders in higher organisms.

Adaptation, Biological↗

PubMed2026

Climate Gradients and Habitat Discontinuity Structure Genetic Variation in a Spring-Specialist Plant.

BACKGROUND AND AIMS: Groundwater-dependent ecosystems support disproportionate biodiversity in arid regions, yet the population genetics of spring-specialist plants remains poorly understood. Here, we present the first species-wide genetic dataset for crimson monkeyflower (Mimulus verbenaceus, Phrymaceae), a spring-specialist plant distributed in seeps, springs, and associated riparian areas across desert regions of North America. We aim to relate landscape features and climate gradients to the spatial genetic structuring within this system. METHODS: Using genome-wide reduced representation sequencing data consisting of 10,760 SNPs from 175 individuals across 17 populations, we characterized the patterns of genetic differentiation and diversity. Population structure was assessed using ADMIXTURE and Principal Component Analysis. We examined the contributions of climate to range-wide genetic variation in crimson monkeyflower using redundancy analysis. KEY RESULTS: Patterns of genetic differentiation were more consistent with those of spring-specialist animal taxa than those of upland plants or generalist riparian plants. We found strong population structure at both broad regional scales and at fine local scales. While geographic and spatial structuring was a primary driver of genetic structure across all scales, riparian connectivity influenced local patterns of diversity, and adaptation to local climatic variation was more influential at regional scales, with temperature, relative humidity, and a monsoon-driven climate gradient contributing to genetic differentiation. CONCLUSIONS: Our findings highlight the distinctive association with isolated perennial groundwater sources, as well as climate gradients, with genetic variation in this spring-specialist plant. These findings suggest that spring-specialist plants deserve special consideration in ecological theory, management, and conservation.

Mimulus↗

PubMed1982

Genetic variation of pepsinogen 1 in the rat.

A pepsinogen (Pg 1) polymorphism was observed in gastric mucosal samples of Wistar rats by polyacrylamide slab gel electrophoresis. Three phenotypes were observed: S (a slow-moving band), F (a fast-moving band), and FS (both bands). Pg 1 variation was controlled by a pair of codominant alleles at a single autosomal locus. Interstrain variation of Pg 1 was studied in five strains of laboratory rats. Genetic variation of Pg 1 was detected only in the Wistar strain.

Alleles↗

PubMed1997

Genetic variation in the expression of the six hsp genes in the presence of heat shock in Drosophila melanogaster.

Genetic variation in total mRNA level of the six hsp genes (hsp22, hsp23, hsp26, hsp27, hsp70 and hsp82) in the presence of heat shock was investigated by using seventy-four second- and seventy third-chromosome lines of Drosophila melanogaster which have the same genetic background derived from a highly inbred stock. There was significant variation in all the six hsp genes for both the second- and third-chromosome lines except for the hsp22 gene of the third-chromosome lines. Although all the structural genes of the heat shock proteins are localized on the third chromosome, the estimates of genetic variance for the second-chromosome lines were larger than those for the third-chromosome lines. Highly significant correlations between total mRNA level of the different hsp genes in all the combinations of the six hsp genes using the second-chromosome lines were found, but some of correlations for the third-chromosome lines were not significant. These results suggest that some second chromosome variants have similar effects on the expression of the different genes.

Animals↗

PubMed1999

Intraspecific genetic variation of striped red mullet (Mullus surmuletus L.) in the mediterranean sea assessed by allozyme and random amplified polymorphic DNA (RAPD) analysis

Allozyme analysis on 20 putative enzyme-coding loci and RAPD analysis on 154 markers, amplified by eight decamer random primers, were used to assess the genetic variation of striped red mullet, Mullus surmuletus L., collected from six locations in the Mediterranean Sea. Both methods were able to detect a high degree of genetic polymorphism. For both methods, estimates of variance of allele frequencies (FST), and chi2 analyses, revealed significant differences (P < 0.05) among samples. Nei's genetic distance (D) among samples was low (mean D=0.011 for allozymes; mean D=0.018 for RAPDs) with data from both approaches revealing the sample from France to be most distinct from the Greek samples. Nevertheless, although most of the genetic variation in allozymes was not correlated with geographical distance, a correlation between genetic affinities and geographical area was found with RAPDs. It seems therefore that the RAPD method showed a more pronounced effect of isolation-by-distance in comparison with allozymes, probably because of the different number of markers of the red mullet genome examined with each method. Overall, the RAPD technique can be introduced as a complementary tool in the population genetics of marine fishes, providing supplementary information in their genetic stock structure analysis.

Journal Article↗

PubMed2002

Geographic pattern of genetic variation in the European globeflower Trollius europaeus L. (Ranunculaceae) inferred from amplified fragment length polymorphism markers.

The distribution of genetic variation and the phylogenetic relationships between 18 populations of the arctic-alpine plant Trollius europaeus were analysed in three main regions (Alps, Pyrenees and Fennoscandia) by using dominant AFLP markers. Analysis of molecular variance revealed that most of the genetic variability was found within populations (64%), although variation among regions (17%) and among populations within regions (19%) was highly significant (P < 0.001). Accordingly, the global fixation index FST averaged over loci was high (0.39). The among-population differentiation indicates restricted gene flow, congruent with limited dispersal of specific globeflower's pollinating flies (Chiastocheta spp.). Within-population diversity levels were significantly higher in the Alps (mean Nei's expected heterozygosity HE = 0.229) than in the Pyrenees (HE= 0.197) or in Fennoscandia (HE = 0.158). This finding is congruent with the species-richness of the associated flies, which is maximum in the Alps. We discuss the processes involved in shaping observed patterns of genetic diversity within and among T. europaeus populations. Genetic drift is the major factor acting on the small Pyrenean populations at the southern edge of T. europaeus distribution, while large Fennoscandian populations result probably from a founder effect followed by demographic expansion. The Alpine populations represent moderately fragmented relics of large southern ancestral populations. The patterns of genetic variability observed in the host plant support the hypothesis of sympatric speciation in associated flies, rather than recurrent allopatric speciations.

France↗

PubMed2005

Genetic variation of the Y chromosome in Chibcha-speaking Amerindians of Costa Rica and Panama.

Genetic variation of the Y chromosome in five Chibchan tribes (Bribri, Cabecar, Guaymi, Huetar, and Teribe) of Costa Rica and Panama was analyzed using six microsatellite loci (DYS19, DYS389A, DYS389B, DYS390, DYS391, and DYS393), the Y-chromosome-specific alphoid system (alphah), the Y-chromosome Alu polymorphism (YAP), and a specific pre-Columbian transition (C-->T) (M3 marker) in the DYS 199 locus that defines the Q-M3 haplogroup. Thirty-nine haplotypes were found, resulting in a haplotype diversity of 0.937. The Huetar were the most diverse tribe, probably because of their high levels of interethnic admixture. A candidate founder Y-chromosome haplotype was identified (15.1% of Chibchan chromosomes), with the following constitution: YAP-, DYS199*T, alphah-II, DYS19*13, DYS389A*17, DYS389B*10, DYS390*24, DYS391*10, and DYS393*13. This haplotype is the same as the one described previously as one of the most frequent founder paternal lineages in native American populations. Analysis of molecular variance indicated that the between-population variation was smaller than the within-population variation, and the comparison with mtDNA restriction data showed no evidence of differential structuring between maternally and paternally inherited genes in the Chibchan populations. The mismatch-distribution approach indicated estimated coalescence times of the Y chromosomes of the Q-M3 haplogroup of 3,113 and 13,243 years before present; for the mtDNA-restriction haplotypes the estimated coalescence time was between 7,452 and 9,834 years before present. These results are compatible with the suggested time for the origin of the Chibchan group based on archeological, linguistic, and genetic evidence.

Analysis of Variance↗