Hardy-Weinberg Expectations Research Articles

Associations of the genetic polymorphisms in CYP11B2 gene with nonfamilial structural atrial fibrillation

To investigate whether polymorphisms in CYP11B2 gene are associated with nonfamilial structural atrial fibrillation (AF) in Chinese Han population. A fine-designed pair-matched hospital based case-control study was performed in 297 cases and 297 controls. We investigated two tagging single nucleotide polymorphisms (tSNPs)-rs4545, rs3802228 in CYP11B2 gene by using GenomeLab SNPstream technique. Two tSNPs were consistent with Hardy-Weinberg expectations in case and control groups. Compared with controls, the left atrial diameter of cases was significantly higher (P < 0.0001). No significant difference in genotype or allele frequencies of tSNPs in CYP11B2 gene was observed. However, at the site of rs3802228 in 3'UTR of the case group, the left atrial diameter in AF patients with GG genotype was significantly higher than others. After adjusted for covariates age, smoking, Body mass index and hypertension, we did not observe the association of rs4545, rs3802228 with AF. Our result suggested that polymorphisms of rs4545 in CYP11B2 gene might not be associated with atrial fibrillation but polymorphism of 3'UTR rs3802228 locus in CYP11B2 gene might be associated with atrial structural remodeling.

Low Genetic Differentiation in the Populations of the Malabar Carp Labeo dussumieri as revealed by Allozymes, Microsatellites and RAPD

The population structure of Labeo dussumieri, an endangered and endemic cyprinid from three riverine locations in the Western Ghats, India was investigated using allozyme, microsatellite and RAPD markers. L. dussumieri samples were obtained from Meenachil, Manimala and Pamba River basins, Kerala. Fourteen (46.7%) out of 30 allozyme loci, seven microsatellite loci and 12 RAPD Operon decamers gave polymorphic pattern. Six allozyme loci (AAT-2*, EST-4*, GLDH*, GPI-2*, G6PDH* and LDH-2*) and three microsatellite loci (LdussG1, MFW19 and Bgon22) exhibited consistent significant deviation from Hardy-Weinberg Equilibrium expectations in different populations after probability level (P<0.05) was adjusted for sequential Bonferroni correction. All the three marker types demonstrated concordant results and various estimates revealed genetic variability within the subpopulations but surprisingly low level (= 0.0034 to 0.0081) of genetic differentiation among L. dussumieri from different river samples. AMOVA analysis also indicated low differentiation among subpopulations. No evidence for a recent genetic bottleneck was observed in L. dussumieri populations based on allozyme and microsatellite data set analysis. Meenachil, Manimala and Pamba Rivers open in to the southern end of Vembanad Lake in Kerala and are connected to each other in the lower reaches through an extensive network of natural canals. Common ancestry in the prehistoric period; and possible mixing of fish populations resulting in high gene flow across the rivers through the lake and interconnecting canals could have been responsible for the lack of significant allelic heterogeneity among the L. dussumieri populations. The stocks from the three rivers do not require different management strategies and for propagation assisted river ranching programme of this species, large effective breeding population can be developed by mixing individuals from three rivers

Levels of gene flow among populations of a wolf spider in a recently fragmented habitat: current versus historical rates

Gene flow among populations is important for countering the deleterious effects of random genetic drift and inbreeding, as well as spreading beneficial mutations. Wind-driven aerial dispersal is known to occur in numerous plants and invertebrates. Its evolution suggests that historically, suitable habitat patches were dense enough to make such undirected dispersal evolutionarily advantageous. Using microsatellite markers we assessed the population genetic structure of seven populations of a wolf spider (Rabidosa rabida) capable of ballooning. Historically, each spider population received a mean of 1.5 migrants per generation from the other six populations. Over the past several generations the number of migrants reaching a population is only 0.2. This statistically significant reduction in gene flow coincides with high levels of habitat fragmentation and suggests that undirected aerial dispersal is ineffective in this fragmented landscape. Further, individuals within populations showed signficantly elevated levels of homozygosity relative to Hardy–Weinberg expectations, suggesting that cursorial dispersal may be very limited and genetic structure within populations exists. Inbreeding coefficients averaged 0.18 over all seven populations with very little variation among populations (s = 0.02). Fitness was lower in smaller populations relative to larger ones. Altered landscapes pose evolutionary dilemmas for many metapopulations and species that depend on undirected movement for dispersal may be particularly vulnerable to habitat fragmentation.

Genetic association study of selected candidate genes (ApoB, LPL, Leptin) and telomere length in obese and hypertensive individuals

BackgroundA genetic study was carried out among obese and hypertensive individuals from India to assess allelic association, if any, at three candidate loci: Apolipoprotein B (ApoB) minisatellite and two tetranucleotide repeat loci; LPL (Lipoprotein lipase) and Leptin. Attempt has also been made to find out whether telomere length attrition is associated with hypertension and obese individuals.MethodsVenous blood samples were collected from 37 normal, 35 obese and 47 hypertensive individuals. Genomic DNA was extracted from peripheral blood mononuclear cells (PBMC) and PCR amplifications were achieved using locus specific primers. Genotyping of ApoB minisatellite was performed using 4% polyacrylamide gel electrophoresis (PAGE) followed by silver staining, whereas LPL and Leptin loci were genotyped using ALF Express™ DNA sequencer. Telomere length was determined using a recently developed real time based quantitative PCR, where the relative telomere length was determined by calculating the relative ratio of telomere (T) and single copy gene (S) PCR products which is expressed as T/S ratio.ResultsAll the three loci are highly polymorphic, display high heterozygosity and conform to Hardy-Weinberg's equilibrium expectations. ApoB minisatellite displayed 14 alleles, whereas LPL and Leptin tetranucleotide loci were having 9 and 17 alleles, respectively. Interestingly two new alleles (9 and 11 repeats) were detected at ApoB locus for the first time. The alleles at Leptin locus were classified as Class I (lower alleles: 149-200 bp) and Class II alleles (higher alleles: >217 bp). Higher alleles at ApoB (>39 repeats), predominant allele 9 at LPL and alleles 164 bp and 224 bp at Leptin loci have shown allelic association with hypertensive individuals. After adjusting the influence of age and gender, the analysis of co-variance (ANCOVA) revealed the relative telomere length (T/S ratio) in hypertensive individuals to be (1.01 ± 0.021), which was significantly different (P < 0.001) from obese (1.20 ± 0.023) and normal (1.22 ± 0.014) individuals. However, no significant difference in the relative telomere length was observed among male and female individuals, although age related decrease in telomere length was observed in these limited sample size.ConclusionThe present study revealed that allelic association at ApoB, LPL, Leptin loci and loss of telomere length may have strong genetic association with hypertensive individuals. However, further study on larger sample size is needed to draw firm conclusions.

Genetic diversity status of White shrimp Penaeus (Litopenaeus) vannamei broodstock in Mexico

The Mexican shrimp culture industry is based upon Penaeus (Litopenaeus) vannamei broodstock with a presumed common genetic origin and more than 10 generations of closed breeding. This has raised concerns about the low level of genetic diversity and accumulated inbreeding in these broodstock. Inbreeding depression can lead to low performance of hatchery-reared shrimp, and an evaluation of the genetic diversity can significantly enhance broodstock management. In this study, we evaluated the genetic composition and diversity of broodstock from six hatcheries from Northwestern Mexico, and estimated their inbreeding levels based on DNA microsatellite markers. A total of 658 individuals were analyzed with six microsatellite loci. Medium mean genetic diversity values (8.98 alleles per locus) and heterozygosity (0.57) were higher than anticipated. There was significant variation in the genetic composition of broodstock from different hatcheries. All the hatchery broodstock were significantly different from a wild population from the state of Sinaloa. The most common alleles were the same in broodstock from all six hatcheries. None of the hatchery stocks has uniquely distinctive alleles. Broodstock management appears to have maintained genetic diversity, because mean allele numbers were similar to the pooled values from a single hatchery sampled between 2000 and 2002. However, with an observed heterozygosity ( H o) below Hardy–Weinberg expectations and a high mean inbreeding coefficient (26.5%) it would be timely to introduce cross breeding among hatcheries to reduce the risk of inbreeding depression.

Isolation and characterization of 18 new polymorphic microsatellite loci for the swordfish, Xiphias gladius

Eighteen microsatellite loci (13 di- and 5 tri-repeats) were isolated from swordfish and characterized in two populations from the Atlantic Ocean and Mediterranean Sea. The number of alleles per locus ranged from two to 29 and the observed heterozygosity from 0.302 to 0.953. All but one locus conformed to Hardy-Weinberg expectations and there was no evidence for linkage disequilibrium between loci.

Twelve tetranucleotide microsatellite loci for westslope cutthroat trout Oncorhynchus clarki lewisi (Salmonidae)

We isolated 12 tetra-nucleotide microsatellite loci from westslope cutthroat trout (Oncorhynchusclarkilewisi). These loci were tested against 58 individuals from a single creek for polymorphism. The number of alleles ranged from 2 to 8, with an average of 4.3. The expected heterozygosity ranged from 0.12 to 0.79, with an average of 0.52. Ten of the twelve loci conformed to Hardy–Weinberg expectations. These microsatellite loci will be useful for describing population structure in westslope cutthroat trout.

Polymorphism and forensic applications of miniSTR loci &lt;I&gt;D10S1248, D2S441, D1S1677, D9S1122&lt;/I&gt;, and &lt;I&gt;D10S1435&lt;/I&gt; in Northwestern Han population

To investigate the polymorphism, genetic stability and the value for analysis degraded samples of D10S1248/ D2S441/D1S1677/D9S1122/D10S1435 five loci in northwestern Han population. The lengths of fragments were analyzed by fluorescence PCR and ABI310 Genetic Analyzer. Samples from 154 unrelated northwestern Han individuals, 10 genealogies and 10 highly degraded specimens were genotyped. Among the 154 unrelated northwestern Han individuals, we discovered 8, 7, 7, 6, and 7 alleles in the five miniSTR loci, respectively. The frequency distributions in the loci showed no deviations from Hardy-Weinberg equilibrium expectations. The H is at 0.662-0.792, PD is at 0.869-0.915, PE is at 0.382-0.585, and PIC is at 0.650-0.750.The research of genetic stability and the value for analysis degraded sample indicated that the five miniSTR loci had high genetic stability and could analysis the degraded samples effectively. Therefore, these 5 miniSTR loci can be used as genetic markers of Northwestern Han populations in forensic practice involving individual identification and paternity testing from degraded DNA samples.

Genetic profiling of the Azores Islands (Portugal): Data from 10 X‐chromosome STRs

The populations from the Azores islands have been the target of several genetic studies, using data derived from monoparental and recombining genetic systems. These studies have provided a complex picture of the genetic landscape of the three groups of Azorean islands, and further data are required to assess its genetic profile. We present a study of the polymorphism in 10 X-chromosome STR loci (DSXS8378, DXS9898, DXS7133, GATA31E08, GATA172D05, DXS7423, DXS6809, DXS7132, DXS9902, DXS6789) conducted on a total of 304 chromosomes (97 females and 110 males) of unrelated individuals with Azorean ancestry. Average gene diversity was 74.47%, ranging from 66.21% (DXS7133) to 81.19% (GATA172D05). No shared haplotypes were found. Genotype frequencies among females displayed conformity with Hardy-Weinberg expectations for all loci. Pairwise linkage disequilibrium tests did not reveal evidences of association between the studied markers. Significant differences in allelic frequencies between the Western and the Eastern group of islands are in agreement with previous results from mitochondrial DNA and Y chromosome studies, providing further evidence that the Azores cannot be considered an homogeneous population. Moreover, differences between the Western group and the North of Portugal are also reported, supporting the pertinence of a specific database for the Azores populations, on what concerns the genetic markers analyzed.

Frequency data for 12 mini STR loci in Argentina

Allele frequencies and forensic parameters for twelve miniSTR autosomal loci (D10S1248, D14S1434, D22S1045, D4S2364, D2S441, D1S1677, D20S480, D6S2439, D6S1056, D9S1118, D4S2639 and D17S1290) were calculated from a sample of 506 unrelated individuals from the Central-East Region of Argentina. No significant deviations from Hardy–Weinberg expectations were found. Furthermore, comparisons with other previously studied populations were made. These twelve miniSTR markers may help forensic laboratories in solving parentage testing as well as in typing degraded DNA samples.

Characterization of microsatellite loci for the Australian sea urchin Heliocidaris erythrogramma

We report 16 polymorphic microsatellite loci from Heliocidaris erythrogramma, a common sea urchin endemic to temperate Australian waters. These microsatellites were tested in a minimum of 30 individuals, which yielded between five and 14 alleles per locus. Expected heterozygosity ranged from 0.52 to 0.92 with four loci deviating from Hardy-Weinberg expectations. These markers are expected to be useful for experimental studies involving paternity analysis and for quantifying population structure in H. erythrogramma across its geographic range.

Isolation and characterization of 11 tetranucleotide microsatellite loci in the Egyptian mongoose (Herpestes ichneumon)

We report the isolation of 11 polymorphic tetranucleotide microsatellite loci in the Egyptian mongoose (Herpestes ichneumon). In a sample of 27 individuals, we observed between 4 and 7 alleles per locus and their observed and expected heterozygosities ranged from 0.37 to 0.85 and from 0.44 to 0.79, respectively. All genotypic frequencies conformed to Hardy-Weinberg equilibrium expectations and there were no instances of linkage disequilibrium detected between pairs of loci.

Impact of temporal changes and host factors on the genetic structure of a population ofOpisthorchis viverrini sensu latoin Khon Kaen Province (Thailand)

The population genetics of 317 individual Opisthorchis viverrini from Khon Kaen Province Thailand, from 4 different years and 4 cyprinid fish species was examined using multilocus enzyme electrophoresis of enolase (Enol), phosphoglucomutase (Pgm) and triose phosphate isomerase (Tpi). Allele and genotype frequencies for Enol and Pgm were consistent irrespective of year or host species. No heterozygote deficiency was detected for Enol. Significant heterozygote deficiencies were detected in 3 of 4 years for Pgm. For Tpi, allele frequencies of the most common allele and genotype frequency varied between years and among individuals from different host species. Heterozygote deficiencies for Tpi were detected in 2 years. No significant heterozygous deficiencies were detected among O. virerrini from different fish species in 2005, except at Pgm and Tpi from Puntioplites protozsron. There was no statistical significance in pairwise FST values between O. viverrini from Cyclocheilichthys armatus in different years or different host species in 2005. Significant departures from Hardy-Weinberg expectations and a high rate of gene flow in a population of O. viverrini are discussed in terms of self- and cross-fertilisation, natural selection, non-random mating, the Wahlund effect, presence of null alleles, intensity of infection, biology and ecology of their intermediate cyprinid hosts.

Microsatellite loci isolated from the lowland tapir (Tapirus terrestris), one of the largest Neotropical mammal

We describe ten microsatellite loci from the lowland tapir (Tapirus terrestris), one of the last members of the Neotropical megafauna and considered a vulnerable species. A total of 74 alleles were detected, ranging from four to thirteen alleles per locus. The expected heterozygosity ranged from 0.34 to 0.88, with a mean of 0.635. All but one locus conformed to the Hardy–Weinberg expectations. These microsatellite loci can be used in population genetic studies of the genus Tapirus, in which all species are threatened globally.

Population Data for 15 Short Tandem Repeat Loci from Wallachia Region, South Romania

To determine allele frequencies' distribution for 15 short tandem repeat (STR) loci in a population sample of 1910 unrelated individuals from the region of Wallachia, South Romania. DNA was isolated using Chelex 100 method and an adapted version of AGOWA mag DNA Isolation Kit Sputum. Polymerase chain reaction amplification was done using AmpFlSTR Identifiler kit (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818, and FGA). For DNA typing, ABI PRISM 3100 Genetic Analyzer was used. Genetic parameters of forensic interest were calculated and comparisons with geographically close populations were performed. With the exception of vWA locus (P=0.001), no other significant deviations from Hardy-Weinberg expectations were found. Single locus comparisons with data on geographically close populations showed significant differences between the population of Wallachia and the population of Bucharest area, Greece, Turkey, Italy, Hungary, Belarus, and Poland, but no differences were found from the population from Croatia and Serbia. According to 15 analyzed STR loci, the population of Wallachia region was found to be genetically more similar to Slavic populations of Croatia and Serbia than to other surrounding populations.

Isolation of microsatellites via enrichment and a sequence tagged method in a South American lizard with suspected parental care, Liolaemus leopardinus

We used an enrichment and a sequence tagged microsatellite method (STM) to isolate 11 novel di and tri microsatellites for the high altitude living lizard Liolaemus leopardinus. These loci were trialled in 61 individuals from a single population. Seven loci conformed to Hardy–Weinberg expectations and were in linkage equilibrium. The 7 loci displayed intermediate levels of polymorphism exhibiting between 2 and 10 alleles per locus, with observed heterozygosity values ranging from 0.328 to 0.745. These markers will be useful in population level analyses and in the potential identification of complex social structure and parental care in this species.

Microsatellite DNA markers for comparative phylogeography analysis in the Korean field mouse (Apodemus peninsulae) and large-eared field mouse (Apodemus latronum)

The sympatric Apodemus species are excellent models for studying comparative phylogeography of organisms. On basis of the microsatellite development of three Apodemus species, we describe in this paper the isolation and characterization of microsatellite DNA markers in the two Apodemus species (Apodemus peninsulae and Apodemus latronum) from genomic DNA-enriched libraries. Ten and eight polymorphic loci were found in A. peninsulae and A. latronum, respectively. These loci were highly polymorphic with numbers of alleles per locus ranging from 11–20 and 6–16, and expected heterozygosity from 0.891–0.947 and 0.714–0.950 for A. peninsulae and A. latronum, respectively. Seven and six loci followed Hardy–Weinberg expectations for A. peninsulae and A. latronum, respectively. No significant linkage association was found among all these loci. These polymorphic microsatellite loci will be useful in studying comparative phylogeography of the sympatric Apodemus species.

Genome-wide association study of plasma lipoprotein(a) levels identifies multiple genes on chromosome 6q

Plasma lipoprotein(a) (Lp[a]) level is an independent risk factor of cardiovascular disease that is under strong genetic control. We conducted a genome-wide association study of plasma Lp(a) in 386 members of a founder population that adheres to a communal lifestyle, proscribes cigarette smoking, and prepares and eats meals communally. We identified associations with 77 single nucleotide polymorphisms (SNPs) spanning 12.5 Mb on chromosome 6q26-q27 that met criteria for genome-wide significance (P <or= 1.3 x 10(-7)) and were within or flanking nine genes, including LPA. We show that variation in at least six genes in addition to LPA are significantly associated with Lp(a) levels independent of each other and of the kringle IV repeat polymorphism in the LPA gene. One novel SNP in intron 37 of the LPA gene was also associated with Lp(a) levels and carotid artery disease number in unrelated Caucasians (P = 7.3 x 10(-12) and 0.024, respectively), also independent of kringle IV number. This study suggests a complex genetic architecture of Lp(a) levels that may involve multiple loci on chromosome 6q26-q27.

Isolation and characterization of 14 microsatellite loci for the Chevrier's field mouse (Apodemus chevrieri)

We describe the isolation and characterization of 14 microsatellite loci in the Chevrier's field mouse from genomic DNA-enriched libraries. The 14 loci were highly polymorphic with numbers of alleles per locus in 24 individuals ranging from three to 13, observed heterozygosity from 0.381 to 0.867 and expected heterozygosity from 0.448 to 0.931. All loci followed Hardy-Weinberg expectations except for CFM3, CFM10 and CFM12 loci. No significant linkage association was found among all these loci. The 14 polymorphic microsatellite loci will be useful in studying phylogeography and population genetics of the Chevrier's field mouse.

Microsatellite DNA markers for population‐genetic studies of blue mackerel (Scomber australasicus) and cross‐specific amplification in S. japonicus

Blue mackerel (Scomber australasicus) is targeted by large-scale purse-seiners in the western North Pacific, and its stock structure is still contentious. Herein, we described 10 polymorphic microsatellite loci for blue mackerel. The number of alleles among 32 individuals surveyed ranged from five to 27 (average of 16.2 alleles per locus). Departures from Hardy-Weinberg expectation were observed at two loci. Cross-specific amplification in the congener, S. japonicus, was successful, except for one locus, revealed to be diagnostic for these congeners. These microsatellite loci will be useful tools to address queries in population genetic structure, fishery management unit and taxonomic species status in the genus Scomber.