scholarly journals Hardy-Weinberg Equilibrium in the Large Scale Genomic Sequencing Era

2019 ◽  
Author(s):  
Nikita Abramovs ◽  
Andrew Brass ◽  
May Tassabehji
Keyword(s):  
Allele Frequency ◽  
Large Scale ◽  
Large Population ◽  
Heterozygote Advantage ◽  
Weinberg Equilibrium ◽  
Genome Data ◽  
Population Sizes ◽  
Hardy Weinberg Equilibrium ◽  
High Level ◽  
Autosomal Recessive Diseases

AbstractHardy-Weinberg Equilibrium (HWE) is used to estimate the number of homozygous and heterozygous variant carriers based on its allele frequency in populations that are not evolving. Previously, deviation from HWE in large population databases were investigated to detect genotyping errors, which can result in extreme heterozygote excess (HetExc). However, HetExc might also be a sign of natural selection since recessive disease causing variants are expected to occur less frequently in a homozygous state in the general population, but might reach high allele frequency, especially if they are advantageous, in a heterozygote state. We developed a filtering strategy to detect these variants and applied it on genome data from 137,842 individuals. We found that the main limitations of this approach were quality of genotype calls and insufficient population sizes, whereas population structure and high level of inbreeding could reduce sensitivity, but not precision, in certain populations. Nevertheless, we identified 365 HetExc variants in 326 genes, most of which were specific to African/African American populations (~84.7%). Although the majority of them were not associated with known diseases, or were classified as “benign”, they were enriched in genes associated with autosomal recessive diseases. The resulting dataset also contained two known recessive disease causing variants with evidence of heterozygote advantage in the genes HBB and CFTR. Finally, we provide in silico evidence of a novel heterozygote advantageous variant in the CHD6 gene (involved in influenza virus replication). We anticipate that our approach will allow the detection of rare recessive disease causing variants in the future.

scholarly journals Microsatelite diversity of Bosnian-Herzegovinian-Croatian shepherd dog Tornjak

Genetika ◽  
2016 ◽  
Vol 48 (1) ◽  
pp. 49-56
Author(s):  
Almira Softic ◽  
Katica Velija ◽  
Jasmin Ramic ◽  
Kasim Bajrovic ◽  
Gabrijela Radosavljevic ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Allele Frequency ◽  
Bosnia And Herzegovina ◽  
Microsatellite Loci ◽  
Weinberg Equilibrium ◽  
Major Allele Frequency ◽  
Hardy Weinberg Equilibrium ◽  
Major Allele ◽  
High Level ◽  
Diversity Studies

This paper presents the first estimation of polymorphism of the Bosnian-Herzegovinian-Croatian Shepherd dog Tornjak in Bosnia and Herzegovina using 10 microsatellite loci, which are an integral part of StockMarks? for Canine Genotyping Kit (Applied Biosystems, Foster City, CA, USA). Ten microsatellite loci used in this study are appropriate for assessing the genetic diversity for this breed. Measures of genetic diversity were estimated based on allelic and genotypic calculations, observed (HO) and expected (HE) heterozygosities, deviations from Hardy-Weinberg equilibrium and polymorphism information content (PIC). The lowest genetic diversity was estimated for locus PEZ20, and the highest for PEZ6 locus. Observed and expected mean heterozygosities were 0.7261 and 0.7392, respectively. Statistically significant deviation (p<0.05) from Hardy-Weinberg equilibrium was found for PEZ1, PEZ12, PEZ3 and PEZ6 loci. The PIC values suggested that all markers (100%) are very informative (PIC > 0.5) in terms of their suitability for genetic diversity studies. When all observed parameters are taken into account (observed and expected heterozygosities, PIC, number of detective and effective alleles, number of detected and maximum possible genotypes, major allele frequency and major allele frequency index), we can conclude that PEZ6 locus shows the highest genetic diversity while PEZ3 displays the lowest. However, assuming values of observed and expected heterozygosities, as well as PIC, we consider loci PEZ20 to be the least diverse, but this locus has more effective alleles and more genotypes present than PEZ3. These preliminary results are the first genetic diversity survey of the Bosnian-Herzegovinian-Croatian Shepherd dog Tornjak in Bosnia and Herzegovina and could be useful to the dog breeders in designing and managing breeding strategies. Summarizing the information above, we can conclude that the population of the Bosnian-Herzegovinian-Croatian Shepherd dog Tornjak from B&H is not affected by substantial loss of genetic diversity. Results of our study indicate presence of reasonably high level of genetic variability and lead to a better understanding of this dog breed.

scholarly journals A Genome-Wide Identification Study Reveals That HmoCYP76AD1, HmoDODAα1 and HmocDOPA5GT Involved in Betalain Biosynthesis in Hylocereus

Genes ◽  
2021 ◽  
Vol 12 (12) ◽  
pp. 1858
Author(s):  
Qingzhu Hua ◽  
Canbin Chen ◽  
Fangfang Xie ◽  
Zhike Zhang ◽  
Rong Zhang ◽  
...  
Keyword(s):  
Large Scale ◽  
Water Soluble ◽  
Soluble Nitrogen ◽  
Genome Data ◽  
Genome Wide ◽  
A Genome ◽  
Red Color ◽  
Hylocereus Undatus ◽  
High Level ◽  
Cytochrome P 450

Betalains are water-soluble nitrogen-containing pigments with multiple bioactivities. Pitayas are the only at large-scale commercially grown fruit containing abundant betalains for consumers. Currently, the key genes involved in betalain biosynthesis remain to be fully elucidated. Moreover, genome-wide analyses of these genes in betalain biosynthesis are not available in betalain-producing plant species. In this study, totally 53 genes related to betalain biosynthesis were identified from the genome data of Hylocereus undatus. Four candidate genes i.e., one cytochrome P-450 R gene (HmoCYP76AD1), two L-DOPA 4,5-dioxygenase genes (HmoDODAα1 and HmoDODAα2), and one cyclo-DOPA 5-O glucosyltransferase gene (HmocDOPA5GT) were initially screened according to bioinformatics and qRT-PCR analyses. Silencing HmoCYP76AD1, HmoDODAα1, HmoDODAα2 or HmocDOPA5GT resulted in loss of red pigment. HmoDODAα1 displayed a high level of L-DOPA 4,5-dioxygenase activity to produce betalamic acid and formed yellow betaxanthin. Co-expression of HmoCYP76AD1, HmoDODAα1 and HmocDOPA5GT in Nicotiana benthamiana and yeast resulted in high abundance of betalain pigments with a red color. These results suggested that HmoCYP76AD1, HmoDODAα1, and HmocDOPA5GT play key roles in betalain biosynthesis in Hylocereus. The results of the present study provide novel genes for molecular breeding programs of pitaya.

scholarly journals Population genetic data of the 21 autosomal STRs included in GlobalFilerTM kit of a population sample from the Kingdom of Bahrain

2019 ◽  
Author(s):  
Noora R. Al-Snan ◽  
Safia Messaoudi ◽  
Saranya R. Babu ◽  
Moiz Bakhiet
Keyword(s):  
Genetic Structure ◽  
Allele Frequency ◽  
Population Genetic ◽  
Population Parameters ◽  
Autosomal Strs ◽  
Genetic Studies ◽  
Weinberg Equilibrium ◽  
Str Loci ◽  
Hardy Weinberg Equilibrium ◽  
Bahraini Population

AbstractIntroductionBahrain’s population consists mainly of Arabs, Baharna and Persians leading Bahrain to become ethnically diverse. The exploration of the ethnic origin and genetic structure within the Bahraini population is fundamental mainly in the field of population genetics and forensic science.AimThe purpose of the study was to investigate and conduct genetic studies in the population of Bahrain to assist in the interpretation of DNA-based forensic evidence and in the construction of appropriate databases.Materials and Methods24 short-tandem repeats in the GlobalFiler™ PCR Amplification kit including 21 autosomal STR loci and three gender determination loci were amplified to characterize different genetic and forensic population parameters in a cohort of 543 Bahraini unrelated healthy men. Samples were collected during the year 2017.ResultsThe genotyping of the 21 autosomal STRs showed that most loci were in Hardy-Weinberg Equilibrium (HWE) except for three markers; D3S1358, D19S433 and D5S818 which showed deviation from HWE. We also found out no significant deviations from LD between pairwise STR loci in Bahraini population except when plotting for D3S1358-CSF1PO, CSF1PO-SE33, D19S433-D12S391, FGA-D2S1338, FGA-SE33, FGA-D7S820 and D7S820-SE33. The SE33 locus was the most polymorphic for the studied population and THO1 locus was the less polymorphic. The Allele 8 in TPOX scored the highest allele frequency of 0.496. The SE33 locus showed the highest power of discrimination (PD) in Bahraini population, whereas TPOX showed the lowest PD value. The 21 autosomal STRs showed a value of combined match probability (CMP) equal to 4.5633E-27, and a combined power of discrimination (CPD) of 99.99999999%. Off-ladders and tri-allelic variants were observed in various samples at D12S391, SE33 and D22S1045 loci.ConclusionOur study indicated that the twenty-one autosomal STRs are highly polymorphic in the Bahraini population and can be used as a powerful tool in forensics and population genetic analyses including paternity testing and familial DNA searching.Author SummaryKingdom of Bahrain is a country of 33 islands located in the Arabian Peninsula. The location of Bahrain had affected the diversity of its population, which is mainly divided into four main ethnic groups: Arabs, Baharna and Persians. Genetic studies on Bahraini population are very limited and little has been done to characterize population structure within Kingdom of Bahrain. Here, we used 21 autosomal STRs included in the GlobalFiler™ Amplification Kit to amplify DNA from 543 non-related males from Bahraini population. We conducted statistical analysis using two main different software such as STRAF and GenAlEx. Different forensic and population parameters were obtained to characterize Bahraini population. Some of the significant results obtained were the following: most of the loci were in Hardy-Weinberg Equilibrium, the most polymorphic and informative marker was SE33. Allele 8 in TPOX presented the highest allele frequency for the studied population. We also found out some of the rare variants which were recorded in STRbase website. Bahraini population was correspondingly compared to the genetic structure of the region. Our study indicated the usefulness of the 21 autosomal STRs in the GlobalFiler ™ in establishing databases, analyzing paternity and reviewing DNA-based evidences.

scholarly journals Canine POMC deletion (P187fs) allele frequency in Labrador Retrievers in Brazil

2019 ◽  
Vol 39 (11) ◽  
pp. 909-914 ◽  
Author(s):  
Natalia O. Lourenço ◽  
Ana Luísa H. Albuquerque ◽  
Roberta M. Basso ◽  
Anelize S. Trecenti ◽  
Lukas G. Albertino ◽  
...  
Keyword(s):  
Prospective Study ◽  
Allele Frequency ◽  
Body Condition Score ◽  
Ideal Body Weight ◽  
Labrador Retriever ◽  
Food Motivation ◽  
Allele Distribution ◽  
Weinberg Equilibrium ◽  
Hardy Weinberg Equilibrium ◽  
Labrador Retrievers

ABSTRACT: The Labrador Retriever is among the main breeds with the greatest predisposition to obesity. Several factors, especially the interrelationships between food management, exercise and social factors; influence the likelihood of a dog becoming obese. Furthermore, genetic factors are also responsible for obesity in dogs, and in Labrador Retriever, a frameshift mutation (P187fs) in pro-opiomelanocortin (POMC) gene is strongly associated with obesity. There is no knowledge of studies that have previously evaluated the prevalence of the canine POMC deletion (P187fs) in Brazilian Labrador Retriever. Therefore, the objective of this study was to investigate this mutation in Labrador Retriever dogs in Brazil. Of the 108 Labrador Retrievers that were assessed in this study, 59 were from a previous study, composed by animals assisted in a veterinary hospital with unknown lineage, and 49 were from a prospective study, composed of 19 pet and 30 assistance/rescue Labrador Retriever dogs. The obesity risk and appetite questionnaire were applied, with some modifications, to tutors of the animals used in the prospective study. Fragments of the DNA, containing the mutation, were amplified by PCR and submitted to direct gene sequencing. The allele frequency of the mutation was 21.3% and was out of Hardy-Weinberg equilibrium (P<0.05). Using only the data of animals with known lineage, the presence of the mutated allele was higher in the Assistance/rescue Group than Pet Group (P<0.01), furthermore, the allele frequencies observed in Assistance Group (31.7%) was out of Hardy-Weinberg equilibrium (P<0.05), while that in the Pet Group (18.4%) was in equilibrium (P>0.05). Although the mutation has increased the food-motivation in the assistance/rescue dogs, other variables, especially frequent exercising, favored that these animals maintained the ideal body weight (body condition score = 5). In summary, the Hardy-Weinberg disequilibrium observed in the allele distribution of the deletion POMC_P187fs in this study, independently of the Labrador Retriever group assessed, suggesting the possibility of positive selection of the mutated allele, which may lead to the maintenance of this deleterious allele in the studied population.

Genetic analysis of 12 X-short tandem repeats loci in a northern Thai population

2020 ◽  
pp. 002580242096500
Author(s):  
Supakit Khacha-ananda ◽  
Phatcharin Mahawong
Keyword(s):  
Genetic Polymorphism ◽  
Allele Frequency ◽  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Thai Population ◽  
Weinberg Equilibrium ◽  
Hardy Weinberg Equilibrium ◽  
Forensic Genetic ◽  
Short Tandem ◽  
Forensic Parameters

Short tandem repeats (STRs) are widely used as DNA markers in paternity testing and criminal investigations because of their high genetic polymorphism among individuals in population. However, many factors influence genetic variations of STRs. Therefore, understanding STR information within individual populations could provide database and scientifically reliable STR genotyping for forensic genetic purposes. We aimed to examine allele frequencies of X-STRs, including some forensic parameters, in a northern Thai population. A retrospective descriptive study was conducted by collecting X-STR data from unrelated individuals living in a northern region of Thailand. The allele frequency and forensic parameters – for example polymorphism information content (PIC), power of discrimination in females and males (PDf and PDm), mean exclusion chance (MEC) and haplotype frequency – were calculated. The Hardy–Weinberg equilibrium was analysed. A total of 132 alleles were observed, with corresponding allele frequency ranging from 0.0064 to 0.4904. The PIC of all loci was >0.6, representing high genetic polymorphism, except DXS8378 and DXS7423. Notably, DXS10135 was the most diverse loci with the highest PD and MEC, while DXS7423 was the least polymorphic marker with the lowest PD and MEC. The highest haplotype diversity in male data was on linkage group III (DXS10101-DXS10103-HPRTB) by 0.9895. The genetic distance analysis demonstrated that the northern Thai population had a close relationship with Taiwanese (DA = 0.023). There are no significant deviations among the Hardy–Weinberg equilibrium except DXS10148. This study has established a northern Thai X-STRs reference database to be used as a tool for forensic genetic purposes.

β-lactoglobulin variability in Argentinian Holstein cattle

1998 ◽  
Vol 131 (1) ◽  
pp. 97-101
Author(s):  
A. G. BONVILLANI ◽  
M. A. DI RENZO ◽  
A. MONTILLA ◽  
I. N. TIRANTI
Keyword(s):  
Allele Frequency ◽  
Average Frequency ◽  
Genetic Distances ◽  
Fixation Index ◽  
Weinberg Equilibrium ◽  
Holstein Breed ◽  
Great Homogeneity ◽  
Total Genetic Diversity ◽  
Hardy Weinberg Equilibrium ◽  
Β Lactoglobulin

To determine the genetic variability and population structure of the β-lactoglobulin (LGB) locus in the Argentinian Holstein breed, milk samples from 12 herds at four locations in Córdoba, Argentina, were analysed. Allelic and genotypic frequencies of LGB variants were compared by contingency tables. A G-test was applied to detect Hardy–Weinberg equilibrium. LGB A allele frequency was 0·43 and B allele frequency was 0·57. Allelic and genotypic frequencies indicated great homogeneity among populations. Most of the populations were in Hardy–Weinberg equilibrium. According to the fixation index, populations were panmictics. The partition of the F-statistic demonstrated that mating was at random, although there was a slight excess of heterozygotes, and there were no genetic differences among populations. The Shannon–Weaver index showed that more than 96% of the total genetic diversity for this locus is attributable to the differences within each herd. The diversity among herds within locations and among locations accounted for <4% of the total variation. Phenograms obtained by the Nei procedure for genetic distances disclosed the separation of the herds into two groups, one with an average frequency of LGB B of 0·61 and the other with an LGB B frequency of 0·53. Locations defined two clusters, but the divergence among populations was not important. These results indicated that the Argentinian Holstein breed from Córdoba constitutes one population.

A Century of Hardy–Weinberg Equilibrium

2008 ◽  
Vol 11 (3) ◽  
pp. 249-256 ◽  
Author(s):  
Oliver Mayo
Keyword(s):  
Gene Locus ◽  
Human Genetics ◽  
Random Mating ◽  
Large Population ◽  
Autosomal Gene ◽  
Genotypic Frequency ◽  
Gene Frequencies ◽  
Weinberg Equilibrium ◽  
Discrete Generation ◽  
Hardy Weinberg Equilibrium

AbstractHardy–Weinberg equilibrium (HWE) is the state of the genotypic frequency of two alleles of one autosomal gene locus after one discrete generation of random mating in an indefinitely large population: if the alleles areAandawith frequenciespandq(=1-p), then the equilibrium gene frequencies are simplypandqand the equilibrium genotypic frequencies forAA,Aaandaaarep2, 2pqandq2. It was independently identified in 1908 by G. H. Hardy and W. Weinberg after earlier attempts by W. E. Castle and K. Pearson. Weinberg, well known for pioneering studies of twins, made many important contributions to genetics, especially human genetics. Existence of this equilibrium provides a reference point against which the effects of selection, linkage, mutation, inbreeding and chance can be detected and estimated. Its discovery marked the initiation of population genetics.

scholarly journals Large-scale assessment of olfactory preferences and learning inDrosophila melanogaster: behavioral and genetic measures

2015 ◽  
Author(s):  
Elisabetta Versace ◽  
Julia Katharina Reisenberger
Keyword(s):  
Large Scale ◽  
Evolutionary Dynamics ◽  
Association Studies ◽  
Large Population ◽  
Olfactory Learning ◽  
Genome Wide Association Studies ◽  
Large Scale Assessment ◽  
Laboratory Selection ◽  
Population Sizes ◽  
Olfactory Preferences

In the Evolve and Resequence method (E&R), experimental evolution and genomics are combined to investigate evolutionary dynamics and the genotype-phenotype link. This approach requires many replicates with large population sizes, which imposes severe restrictions on the analysis of behavioral phenotypes. Aiming to use E&R for investigating the evolution of behavior inDrosophila, we have developed a simple and effective method to assess spontaneous olfactory preferences and learning in large samples of fruit flies using a T-maze. We tested this procedure on (a) a large wild-caught population and (b) 11 isofemale lines ofDrosophila melanogaster. Compared to previous methods, this procedure reduces the environmental noise and allows for the analysis of large population samples. Consistent with previous results, we show that flies have a spontaneous preference for orangevs.apple odor. With our procedure wild-derived flies exhibit olfactory learning in the absence of previous laboratory selection. Furthermore, we find genetic differences in the olfactory learning with relatively high heritability. We propose this large-scale method as an effective tool for E&R and genome-wide association studies on olfactory preferences and learning.

Microbial experimental evolution

2009 ◽  
Vol 297 (1) ◽  
pp. R17-R25 ◽  
Author(s):  
Albert F. Bennett ◽  
Bradley S. Hughes
Keyword(s):  
Experimental Evolution ◽  
Large Scale ◽  
Large Population ◽  
Competitive Fitness ◽  
Experimental Feature ◽  
Generation Times ◽  
Evolutionary Studies ◽  
Direct Competition ◽  
Population Sizes ◽  
Experimental Subjects

Microbes have been widely used in experimental evolutionary studies because they possess a variety of valuable traits that facilitate large-scale experimentation. Many replicated populations can be cultured in the laboratory simultaneously along with appropriate controls. Short generation times and large population sizes make microbes ideal experimental subjects, ensuring that many spontaneous mutations occur every generation and that adaptive variants can spread rapidly through a population. Another highly useful experimental feature is the ability to preserve and store ancestral and evolutionarily derived clones. These can be revived in parallel to allow the direct measurement of the competitive fitness of a descendant compared with its ancestor. The extent of adaptation can thereby be measured quantitatively and compared statistically by direct competition among derived groups and with the ancestor. Thus, fitness and adaptation need not be matters of qualitative speculation, but are quantitatively measurable variables in these systems. Replication allows the quantification of heterogeneity in responses to imposed selection and thereby statistical distinction between changes that are systematic responses to the selective regimen and those that are specific to individual populations.

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