Genetic analysis of fish genomes and populations: allozyme variation within and among Atlantic salmon from Downeast rivers of Maine

Single nucleotide polymorphisms of Ficolin 2 gene in Behçet's disease

CYP19A1 facilitates the bioconversion of estrogens from androgens. CYP19A1 intron single nucleotide polymorphisms (SNPs) may alter mRNA splicing, resulting in altered CYP19A1 activity, and potentially influencing disease susceptibility. Genetic studies of CYP19A1 SNPs have been well documented in populations of European ancestry; however, studies in populations of African ancestry are limited. In the present study, ten ‘candidate’ intronic SNPs in CYP19A1 from 125 African Americans (AA) and 277 European Americans (EA) were genotyped and their frequencies compared. Allele frequencies were also compared with HapMap and ASW 1000 Genomes populations. We observed significant differences in the minor allele frequencies between AA and EA in six of the ten SNPs including rs10459592 (p<0.0001), rs12908960 (p<0.0001), rs1902584 (p = 0.016), rs2470144 (p<0.0001), rs1961177 (p<0.0001), and rs6493497 (p = 0.003). While there were no significant differences in allele frequencies between EA and CEU in the HapMap population, a 1.2- to 19-fold difference in allele frequency for rs10459592 (p = 0.004), rs12908960 (p = 0.0006), rs1902584 (p<0.0001), rs2470144 (p = 0.0006), rs1961177 (p<0.0001), and rs6493497 (p = 0.0092) was observed between AA and the Yoruba (YRI) population. Linkage disequilibrium (LD) blocks and haplotype clusters that is unique to the EA population but not AA was also observed. In summary, we demonstrate that differences in the allele frequencies of CYP19A1 intron SNPs are not consistent between populations of African and European ancestry. Thus, investigations into whether CYP19A1 intron SNPs contribute to variations in cancer incidence, outcomes and pharmacological response seen in populations of different ancestry may prove beneficial.

Data on geographical variation in allele frequencies at enzyme coding loci in Atlantic salmon from the British Isles were collated from published and unpublished sources. Statistically significant differences in allele frequencies were found among samples both within and among river systems, suggesting that the Atlantic salmon in the British Isles is not a panmictic population and that even within major river systems it cannot be treated as a single genetic stock for fisheries management purposes. Although there was some evidence of regional differences in the frequency of some rare alleles, most single‐locus variation did not show strong geographic patterns, with the exception of the AAT‐4* locus at which allele frequencies had a significant latitudinal cline. There was some evidence for the existence of genetically‐distinct celtic and boreal races of Atlantic salmon in the British Isles as previously has been suggested. Multiple regression analyses revealed associations between genetic variation and local environmental conditions (i.e. between variation at MEP‐2* and both temperature and local river gradient), providing additional evidence for adaptive population divergence in the species.

Association of interleukin-10 gene single nucleotide polymorphisms with susceptibility to systemic lupus erythematosus in a Chinese population

Abstract: We studied the barrier effects of various roadways on the genetic subdivision of bank vole (Clethrionomys glareolus) populations. Allele frequencies, genetic variability, and genetic distances of natural populations were calculated based on polymorphism of seven microsatellite markers. We compared bank vole populations in control areas without such barriers with animals from both sides of a country road, a railway, and a highway. Using F and R statistics, we demonstrated significant population subdivision in bank vole populations separated by the highway, but not in populations on either side of the other roadways or in the control area. Correlations between geographic and genetic distances were revealed by an extended method based on a Mantel analysis. This allowed us to measure genetic barrier effects and express them as additional geographic distances. For instance, statistically significant differences in allele frequencies in all seven loci examined existed among populations in southern Germany and Switzerland, which are separated by the Rhine River and Lake Constance. The real geographic distance between bank vole populations in Konstanz and those in Lengwil, Switzerland, was 6 km. According to this analysis the genetic barrier effect of the Rhine could be defined as an additional distance of 7.7 km. This study shows for the first time that not only old geographic barriers but also more recent fragmentation of landscape by, for example, highways has an important effect on gene flow and the genetic substructuring of populations, which should be considered in future environmental impact assessments.

A survey of allozymic alleles and genetic diversity was made for 151 accessions of the American Barley Core Collection. A total of 25 alleles at ten loci were observed. Two loci were monomorphic. The average diversity index for individual loci ranged between 0.026 and 0.649. Most significant differences in allelic frequency and genetic diversity value were found between spring and winter barley. Spring barley showed a greatly higher average diversity than winter barley (t=2.124, P=0.071). The smallest differences in allelic frequencies and diversity values were observed between the two geographical regions, North and South America. Rare alleles were detected only in a few accessions. Seven rare alleles were associated with spring barley. The genetic similarities among the 151 accessions ranged from 0.20 to 1.00, which showed that a high level of genetic variability exists in this set of core accessions. Cluster analysis and principal coordinate analysis did not give clear-cut separation of different types of barley, but most of the winter barley accessions were closely associated.

Genetic protein variation in Atlantic salmon in Scotland: comparison of wild and farmed fish

A laboratory population of Heliothis virescens (F.) reared on a lima bean diet is compared with a population reared on a soybean-wheat germ diet. Significant differences in allele frequencies are observed at 3 loci: alphaglycerophosphate dehydrogenase (α-GPHD), hexokinase-a (HEX-A) and hexokinase-b (HEX-B). Experimental populations were established to test the influence of diet and population density on allele frequency changes at these loci. Significant differences in HEX-A allele frequencies are observed between a population maintained for 3 generations on a lima bean and one on a soybean-wheat germ diet. A population maintained for 3 generations on a lima bean diet at normal density and one at a high density show significant differences between HEX-B allele frequencies. Changes at both hexokinase loci are related to a difference in sucrose content of the diets. The cause of α-GPDH allele frequency differences between the 2 laboratory populations was not identified. The different diets cause allele frequency changes at specific loci but do not affect the mean heterozygosity of 19 enzyme loci: 0.247 on lima bean and 0.231 on soybean-wheat germ diets.

ObjectiveTo investigate the relationship between L-type calcium channel α1C subunit (CACNA1C) gene polymorphism and schizophrenia (SCZ) and cognitive function in the Han nationality, the main nationality in China.MethodsGenotyping of CACNA1C SNP (rs1006737, rs1024582, rs2007044) in SCZ patients (n = 312) and healthy controls (n = 305) was performed. Cognitive function was assessed in the SCZ patients using Repeatable Battery for the Assessment of Neuropsychological Status (RBANS). Then, the correlation between SNP and SCZ, as well as cognition, was calculated.ResultsThere was no significant difference in allele frequency and genotype distribution frequency of the three polymorphic loci of CACNA1C gene between the two groups. In cognitive tests, delayed memory scores in RBANS were significantly lower in rs1006737 “A” risk allele carriers than in non-carriers.ConclusionThere is no significant difference in allele and genotype frequency of CANCA1C Gene rs1006737, rs1024582 and rs2007044 between the schizophrenia patients and healthy controls. The cognitive function of schizophrenia patients is correlated with the rs1006737, and the delayed memory of “A” allele carriers is significantly reduced.

Isolates of Cryphonectria parasitica were sampled from American chestnut trees in 13 locations in eastern North America to study genetic differentiation and gene flow among subpopulations of this pathogen. Using data from six unlinked restriction fragment length polymorphism loci, we found significant differences in allele frequencies at all loci among the 13 subpopulations. Thirty-one percent of the total gene diversity was attributed to differences among subpopulations (G ST = 0.31). Genetic differentiation was examined for two subsets of data: one from between two subpopulations in Michigan, which were outside the natural range of the host, and the other from among nine subpopulations from ecologically similar sites (disturbed sites resulting from clearcutting and burning were eliminated). There were significant differences in allele frequencies at two loci between the two Michigan subpopulations, even though these sites were only 16 km apart. Differentiation was high between these subpopulations because two loci were fixed or nearly fixed for different alleles (G ST = 0.81). There was also differentiation among the nine subpopulations from ecologically similar sites (G ST = 0.20); significant differences in allele frequencies were found at five of the six loci. We attribute this level of differentiation to restricted gene flow among subpopulations. We did not, however, estimate gene flow quantitatively from these data because populations did not appear to be at equilibrium. There was no correlation between the estimated average number of migrants per generation between each pair of nine subpopulations and geographic distance. This correlation would be expected to be negative if populations were at equilibrium and gene flow was restricted to short distances (isolation by distance). The lack of correlation was interpreted as non-equilibrium conditions; therefore, gene flow would be overestimated

The formation of a sporadic abdominal aortic aneurysm (AAA) is explained by the remodeling of the extracellular matrix (ECM) and breakdown of structural components of the vascular wall. Matrix metalloproteinases are the principal matrix-degrading proteases and are known to play a major role in the remodeling of the extracellular matrix in arterial vessels. Their activity is controlled by tissue inhibitors of metalloproteinases (TIMPs). Decreased TIMP-1 and TIMP-2 expression in the extracellular matrix of the walls of AAAs has been shown in several studies. This case control study was designed to investigate the possible impact of genetic variants of the TIMP-1 gene in the etiology of AAA. TIMP-1 single nucleotide polymorphisms (SNPs) were analyzed in a primary study sample of 50 patients with AAA and 44 controls. Differences in genotype and allele frequencies of identified polymorphisms were determined after sequencing the entire coding region and selected parts of the promoter using the automated laser fluorescence technique. A second sample (96 patients vs. 89 controls) was investigated by single-base sequencing to confirm significant results. Three polymorphisms were identified, one of which, described for the first time in this article, is located in intron 4 (TIMP-1: 328 + 16C > T). A statistically significant difference in allele frequencies for SNP TIMP-1 372T>C was detected in the primary study group. The C allele was more frequent in male patients with AAA than in the control group [23 vs. 4, p = 0.029, OR (95% CI) 4.38 (1.13-20.47)]. However, this result could not be confirmed in a second sample of males [52 vs. 45, p = 0.624, OR (95% CI) 1.16 (0.65-2.06)]. There were no statistically significant differences in genotype or allele frequencies of the other detected SNPs between the two groups. Our analysis of the entire coding region and selected parts of the promoter of the TIMP-1 gene failed to show an association between genetic polymorphisms and AAA, suggesting that variations in the TIMP-1 gene do not contribute to the development of AAA.

Levels of genetic diversity, population genetic structure, and gene flow in six Korean populations of Eurya emarginata were investigated based on allozyme variation using starch gel electrophoresis. Although most Korean populations are relatively small and isolated, with respect to their habitats, they maintain high levels of genetic variation. Fourteen of the 18 putative isozyme loci surveyed were polymorphic in at least one population. Overall, mean genetic diversity within populations (Hep = 0.296) was higher than those for most species with very similar life history traits. Analysis of fixation indices showed an overall slight deficiency of heterozygotes relative to Hardy-Weinberg expectations (54% were positive). Although significant differences in allele frequencies among populations were found for all 14 polymorphic loci (P < 0.05), about 92% of the total variation in the species is common to all populations (GST=0.079). Indirect estimates of the number of migrants per generation (Nm) (2.02, calculated from the mean GST; 1.10, calculated from the mean frequency of six private alleles) indicate that gene movement among populations of E. emarginata is comparable with those for plants with similar life history traits. It is likely that factors such as dioecy, high fecundity, long generation time, and occurrence in late-successional forests may contribute to maintain high levels of genetic diversity within populations and low levels of genetic divergence between adjacent populations of the species.

Management of game species requires an understanding not just of population abundance, but also the structure of and connections between populations. Like other large-bodied carnivores, the cougar (Puma concolor) exhibits density –dependent dispersal and is capable of long-distance movement; in the absence of barriers to movement, these traits should lead to high connectivity between individuals and a lack of genetic differentiation across areas of continuous habitat. Previous research has suggested that cougar movement may be influenced by landscape variables such as forest cover, elevation, human population density, and highways. I assessed the population structure of cougars (Puma concolor) in Washington and southern British Columbia by examining patterns of genetic variation in 17 microsatellite loci, and the contribution of landscape variables to this genetic variation. I evaluated population structure using genetic clustering algorithms and spatial principal components analysis. I quantified the effect of distance on genetic variation by calculating the correlation between the genetic distance and geographic distance between every pair of individuals, as well as the spatial autocorrelation of genetic distances. To compare the observed pattern of genetic differentiation with that which would arise solely from isolation by distance, I simulated allele frequencies across the study area where the cost to movement between individuals was proportional to the distance between them. I also evaluated the support for evidence of male-biased dispersal in allele frequencies. Bayesian clustering analyses identified four populations in the study area, corresponding to the Olympic Peninsula, Cascade Mountains, northeastern Washington and Blue Mountains; these clusters were supported by patterns of genetic differentiation revealed with spatial PCA. v Although I found a significant relationship between the geographic and genetic distance between individuals, simulated allele frequencies displayed no meaningful spatial pattern of differentiation, suggesting that male dispersal would be adequate within the scale of the study area to prevent genetic isolation from occurring if the only factor to affect dispersal was geographic distance. While cougars are capable of long-distance dispersal movements, dispersal in heterogeneous landscapes may be mediated by the resistance of the landscape to movement. I derived resistance surfaces for forest canopy cover, elevation, human population density and highways based on GIS data and estimated the landscape resistance between pairs of individuals using circuit theory. I quantified the effect of the resistance to movement due to each landscape factor on genetic distance using multiple regression on distance matrices and boosted regression tree analysis. Both models indicated that only forest canopy cover and the geographic distance between individuals had an effect on genetic distance, with forest cover exhibiting the greatest relative influence. The boundaries between the genetic clusters I found largely corresponded with breaks in forest cover, showing agreement between population structure and landscape variable selection. The greater relative influence of forest cover may also explain why a significant relationship was found between geographic and genetic distance, yet geographic distance alone could not explain the observed pattern of allele frequencies. While cougars inhabit unforested areas in other parts of their range, forested corridors appear to be important for maintaining population connectivity in the northwest.

We investigated levels of genetic diversity, population genetic structure, and gene flow in Eurya japonica, a widespread and broad‐leaved evergreen dioecious tree native to Japan, China, Taiwan, and the southern and southwestern coast of the Korean Peninsula. Starch‐gel electrophoresis was conducted on leaves collected from 1,000 plants in 20 Korean populations. All 12 loci examined were polymorphic in at least one population, and the mean number of alleles per locus was 3.79. In addition, mean observed population heterozygosity (Hop = 0.425), expected heterozygosity (Hep = 0.462), and total genetic diversity (HT = 0.496) were substantially higher than average values for species with similar life history traits. Although significant differences in allele frequency were detected between populations at all loci (P &lt; 0.001), &lt;7% of the genetic variation was found among populations (FST = 0.069). There was a significant negative correlation between genetic identity and distance between populations (r = ‐0.341; P &lt; 0.05), but this explained only a small amount of the diversity among populations. Indirect estimates of the number of migrants per generation (Nm) (3.37, calculated from FST; 3.74, calculated from the mean frequency of eight private alleles) indicate that gene flow is extensive among Korean populations of E. japonica. Factors contributing to the high levels of genetic diversity found within populations of E. japonica include large and contiguous populations, obligating outcrossing (dioecious plant), high fecundity, and long generation time. Occasional seed dispersal by humans and pollen movement by domesticated honey bees may further enhance gene flow within the species.

Melatonin is reported to be an anti-inflammatory agent. No genetic study concerning the association between melatonin and inflammatory disease has yet been reported. Here we performed a polymorphism study on the melatonin receptor type 1B (MTNR1B) in Korean rheumatoid arthritis (RA) patients and controls. The polymorphism of MTNR1B located in 3'-untranslated region (rs 1562444) was selected for its higher rate of heterozygosity among other single nucleotide polymorphisms (SNPs) in both MTNR1A and MTNR1B genes and investigated in RA patients (n = 173) and healthy controls (n = 195) by polymerase chain reaction-restriction fragment length polymorphism assay using NlaIII restriction enzyme. No statistically significant difference in either genotype distribution or allele frequency was observed between RA patients and controls. The genotype distributions and allele frequencies of rheumatoid factor negative [RF(-)] patients were similar to those of controls. However, statistical analysis of genotype revealed a significant association (chi2 = 6.42, P = 0.04) is present between RF(+) and MTNR1B SNP (rs 1562444). Although no statistically significant difference in allele frequency between RF(+) and controls was observed (chi2 = 2.75, P = 0.10), the results might suggest that MTNR1B SNP (rs 1562444) is associated with the presence of RF in RA. This is the first study, to our knowledge, to report a positive genetic relationship between melatonin and RA.