SIGNIFICANT LINKAGE DISEQUILIBRIUM AND HIGH GENETIC DIVERSITY IN A POPULATION OF PLASMODIUM FALCIPARUM FROM AN AREA (REPUBLIC OF THE CONGO) HIGHLY ENDEMIC FOR MALARIA

2003 ◽  
Vol 68 (3) ◽  
pp. 345-349 ◽  
Author(s):  
P. DURAND ◽  
M. TIBAYRENC ◽  
F. RENAUD ◽  
M.C. LECLERC ◽  
B. OURY ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Plasmodium Falciparum ◽  
Linkage Disequilibrium ◽  
Significant Linkage Disequilibrium ◽  
High Genetic Diversity ◽  
Republic Of The Congo ◽  
Significant Linkage

scholarly journals Lack of Geospatial Population Structure Yet Significant Linkage Disequilibrium in the Reservoir of Plasmodium falciparum in Bongo District, Ghana

2017 ◽  
Vol 97 (4) ◽  
pp. 1180-1189 ◽  
Author(s):  
Shazia Ruybal-Pesántez ◽  
Karen P. Day ◽  
Anita Ghansah ◽  
Kathryn E. Tiedje ◽  
Kwadwo A. Koram ◽  
...  
Keyword(s):  
Plasmodium Falciparum ◽  
Population Structure ◽  
Linkage Disequilibrium ◽  
Significant Linkage Disequilibrium ◽  
Significant Linkage

Microsatellite markers for Cattleya walkeriana Gardner, an endangered tropical orchid species

2016 ◽  
Vol 15 (1) ◽  
pp. 93-96 ◽  
Author(s):  
Evandro Vagner Tambarussi ◽  
Lou C. Menezes ◽  
Bruna Ibañes ◽  
Lia Maris Orth Ritter Antiqueira ◽  
Gabriel Dequigiovanni ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Linkage Disequilibrium ◽  
Microsatellite Markers ◽  
Significant Linkage Disequilibrium ◽  
Orchid Species ◽  
Polymorphic Loci ◽  
Tropical Orchid ◽  
First Time ◽  
Significant Linkage ◽  
Different Levels

Cattleya walkeriana, one of the most improved Brazilian Cattleyas, is a popular tropical orchid endemic from Brazil and currently endangered. In the present study, for the first time microsatellite markers were developed for C. walkeriana and their transferability was tested for the species C. loddigesii and C. nobilior. The markers were used for genotyping 26 C. walkeriana specimens from different growers and from different levels of improvement. The transferability was successful, with five polymorphic loci transferred to C. loddigesii and six polymorphic loci to C. nobilior. Eight loci were polymorphic, revealing a maximum of two to ten alleles per locus in C. walkeriana and two to four and two to five in C. loddigesii and C. nobilior, respectively. There was no significant linkage disequilibrium in the studied loci. For C. walkeriana, the observed and expected heterozygosities ranged from 0 to 0.963 and from 0.138 to 0.841, respectively. These markers identified polymorphisms and may be used to study the genetic diversity, gene flow or hybridization of these species.

Protein Variation in ADH and ADH-RELATED in Drosophila pseudoobscura: Linkage Disequilibrium Between Single Nucleotide Polymorphisms and Protein Alleles

Genetics ◽  
2001 ◽  
Vol 159 (2) ◽  
pp. 673-687
Author(s):  
Stephen W Schaeffer ◽  
C Scott Walthour ◽  
Donna M Toleno ◽  
Anna T Olek ◽  
Ellen L Miller
Keyword(s):  
Linkage Disequilibrium ◽  
Single Nucleotide Polymorphisms ◽  
Drosophila Pseudoobscura ◽  
Linkage Disequilibrium Mapping ◽  
Nucleotide Polymorphisms ◽  
Neutral Model ◽  
Significant Linkage Disequilibrium ◽  
Single Nucleotide ◽  
Synonymous Sites ◽  
Significant Linkage

Abstract A 3.5-kb segment of the alcohol dehydrogenase (Adh) region that includes the Adh and Adh-related genes was sequenced in 139 Drosophila pseudoobscura strains collected from 13 populations. The Adh gene encodes four protein alleles and rejects a neutral model of protein evolution with the McDonald-Kreitman test, although the number of segregating synonymous sites is too high to conclude that adaptive selection has operated. The Adh-related gene encodes 18 protein haplotypes and fails to reject an equilibrium neutral model. The populations fail to show significant geographic differentiation of the Adh-related haplotypes. Eight of 404 single nucleotide polymorphisms (SNPs) in the Adh region were in significant linkage disequilibrium with three ADHR protein alleles. Coalescent simulations with and without recombination were used to derive the expected levels of significant linkage disequilibrium between SNPs and 18 protein haplotypes. Maximum levels of linkage disequilibrium are expected for protein alleles at moderate frequencies. In coalescent models without recombination, linkage disequilibrium decays between SNPs and high frequency haplotypes because common alleles mutate to haplotypes that are rare or that reach moderate frequency. The implication of this study is that linkage disequilibrium mapping has the highest probability of success with disease-causing alleles at frequencies of 10%.

Estimates of linkage disequilibrium and the recombination parameter determined from segregating nucleotide sites in the alcohol dehydrogenase region of Drosophila pseudoobscura.

Genetics ◽  
1993 ◽  
Vol 135 (2) ◽  
pp. 541-552 ◽  
Author(s):  
S W Schaeffer ◽  
E L Miller
Keyword(s):  
Linkage Disequilibrium ◽  
Alcohol Dehydrogenase ◽  
Distance Effect ◽  
Theoretical Distribution ◽  
Drosophila Pseudoobscura ◽  
Significant Linkage Disequilibrium ◽  
Effective Population ◽  
Nucleotide Distance ◽  
Significant Linkage ◽  
Recombination Parameter

Abstract The alcohol dehydrogenase (Adh) region of Drosophila pseudoobscura, which includes the two genes Adh and Adh-Dup, was used to examine the pattern and organization of linkage disequilibrium among pairs of segregating nucleotide sites. A collection of 99 strains from the geographic range of D. pseudoobscura were nucleotide-sequenced with polymerase chain reaction-mediated techniques. All pairs of the 359 polymorphic sites in the 3.5-kb Adh region were tested for significant linkage disequilibrium with Fisher's exact test. Of the 74,278 pairwise comparisons of segregating sites, 127 were in significant linkage disequilibrium at the 5% level. The distribution of five linkage disequilibrium estimators D(ij), D2, r(ij), r2 and D(ij) were compared to theoretical distributions. The observed distributions of D(ij), D2, r(ij) and r2 were consistent with the theoretical distribution given an infinite sites model. The observed distribution of D(ij) differed from the theoretical distribution because of an excess of values at -1 and 1. No spatial pattern was observed in the linkage disequilibrium pattern in the Adh region except for two clusters of sites nonrandomly associated in the adult intron and intron 2 of Adh. The magnitude of linkage disequilibrium decreases significantly as nucleotide distance increases, or a distance effect. Adh-Dup had a larger estimate of the recombination parameter, 4Nc, than Adh, where N is the effective population size and c is the recombination rate. A comparison of the mutation and recombination parameters shows that 7-17 recombination events occur for each mutation event. The heterogeneous estimates of the recombination parameter and the inverse relationship between linkage disequilibrium and nucleotide distance are no longer significant when the two clusters of Adh intron sites are excluded from analyses. The most likely explanation for the two clusters of linkage disequilibria is epistatic selection between sites in the cluster to maintain pre-mRNA secondary structure.

scholarly journals Linkage disequilibrium in growing and stable populations.

Genetics ◽  
1994 ◽  
Vol 137 (1) ◽  
pp. 331-336 ◽  
Author(s):  
M Slatkin
Keyword(s):  
Linkage Disequilibrium ◽  
Sequence Data ◽  
Significant Linkage Disequilibrium ◽  
Rapid Population Growth ◽  
Exact Test ◽  
Dna Sequence Data ◽  
Constant Size ◽  
Significant Linkage ◽  
Stable Populations ◽  
Growing Population

Abstract Nonrandom associations between alleles at different loci can be tested for using Fisher's exact test. Extensive simulations show that there is a substantial probability of obtaining significant nonrandom associations between closely or completely linked polymorphic neutral loci in a population of constant size at equilibrium under mutation and genetic drift. In a rapidly growing population, however, there will be little chance of finding significant nonrandom associations even between completely linked loci if the growth has been sufficiently rapid. This result is illustrated by the analysis of mitochondrial DNA sequence data from humans. In comparing all pairs of informative sites, fewer than 5% of the pairs show significant disequilibrium in Sardinians, which have apparently undergone rapid population growth, while 20% to 30% in !Kung and Pygmies, which apparently have not undergone rapid growth, show significance. The extent of linkage disequilibrium in a population is closely related to the gene genealogies of the loci examined, with "star-like" genealogies making significant linkage disequilibrium unlikely.

scholarly journals A new set of microsatellite loci for Cattleya walkeriana Gardner, an endangered tropical orchid species and its transferability to Cattleya loddigesii Lindl. and Cattleya nobilior Reichenbach

2017 ◽  
Vol 16 (3) ◽  
pp. 284-287
Author(s):  
Bruno C. Rossini ◽  
Mariá B. Kampa ◽  
Celso L. Marino ◽  
Fernanda Bortolanza Pereira ◽  
Fábio M. Alves ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Microsatellite Loci ◽  
Null Alleles ◽  
Germplasm Resources ◽  
Significant Linkage Disequilibrium ◽  
Orchid Species ◽  
Expected Heterozygosity ◽  
Tropical Orchid ◽  
Significant Linkage

AbstractIn this study, we isolate and analyse a new set of microsatellite loci for Cattleya walkeriana. Twenty-two primer pairs were screened for C. walkeriana (n = 32) and assessed for their transferability to Cattleya loddigesii (n = 12) and Cattleya nobilior (n = 06). All loci amplified for C. walkeriana; however, for C. loddigesii and C. nobilior, four and five primers, respectively, did not present amplification. The polymorphic loci presented between 2 and 13 alleles per locus for both C. walkeriana and C. loddigesii, with respective averages of 5.1 and 4.2. For C. nobilior, we found between two and five alleles per locus, with an average of 2.6. For C. walkeriana, observed heterozygosity varied from 0.100 to 0.966, whereas expected heterozygosity ranged from 0.097 to 0.900. The observed and expected heterozygosity for C. loddigesii and C. nobilior were also estimated. We found no significant linkage disequilibrium between any pair of loci, and evidence of null alleles at four loci (Cw16, Cw24, Cw30 and Cw31) for C. walkeriana. The combined power to exclude the first parent and combined non-exclusion probability of identity were 0.999 and 2.3 × 10−20, respectively. These new loci can be used in studies of germplasm resources, and assessments of genotypic and genetic diversity and population structure, thus improving the accuracy of such analyses and their applicability in the conservation and protection of these endangered species.

Linkage disequilibrium between two chromosomally distinct loci associated with increased resistance to chloroquine in Plasmodium falciparum

Parasitology ◽  
2000 ◽  
Vol 121 (1) ◽  
pp. 1-7 ◽  
Author(s):  
M. T. DURAISINGH ◽  
L. VON SEIDLEIN ◽  
A. JEPSON ◽  
P. JONES ◽  
I. SAMBOU ◽  
...  
Keyword(s):  
Plasmodium Falciparum ◽  
Linkage Disequilibrium ◽  
Sequence Polymorphism ◽  
Chloroquine Resistance ◽  
Strong Linkage Disequilibrium ◽  
Base Pairs ◽  
Size Polymorphism ◽  
Sensitivity Tests ◽  
Significant Linkage

Chloroquine-resistance in Plasmodium falciparum is associated with polymorphisms in a locus on or near the cg2 gene on chromosome 7, and in the pfmdr1 gene on chromosome 5. In this study we typed P. falciparum DNA from uncomplicated malaria cases in The Gambia in 1990, 1995 and 1996 for size polymorphism in the omega repeat of cg2, for sequence polymorphisms in pfmdr1 at codons 86 and 184, in dhfr at codon 108 and in the msp2 gene. Chloroquine sensitivity tests were conducted in vitro. A significant but incomplete association was found between the presence of the cg2 Dd2-like omega repeat size polymorphism and in vitro resistance, and between the tyr-86 allele of pfmdr1 and in vitro resistance. Furthermore there was strong linkage disequilibrium between the pfmdr1 asn-86 allele and the cg2 not Dd2-like omega repeat allele located on different chromosomes. In contrast, no linkage disequilibrium was found between these alleles and either the dhfr ser-108 allele or the msp2 IC sequence polymorphism. No significant linkage was measured between pfmdr1 asn-86 and phe-184 although these loci are separated only by 296 base pairs. Our results suggest that genetic elements linked to the cg2 and the pfmdr1 genes are important determinants of chloroquine resistance. It can be concluded that the observed linkage disequilibrium is maintained epistatically through selection by chloroquine.

scholarly journals Linkage disequilibrium and within-breed genetic diversity in Iranian Zandi sheep

2019 ◽  
Vol 62 (1) ◽  
pp. 143-151 ◽  
Author(s):  
Seyed Mohammad Ghoreishifar ◽  
Hossein Moradi-Shahrbabak ◽  
Nahid Parna ◽  
Pourya Davoudi ◽  
Majid Khansefid
Keyword(s):  
Genetic Diversity ◽  
Linkage Disequilibrium ◽  
Association Studies ◽  
Genome Wide Association Studies ◽  
Effective Population ◽  
High Genetic Diversity ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Snp Panel ◽  
Zandi Sheep

Abstract. This research aimed to measure the extent of linkage disequilibrium (LD), effective population size (Ne), and runs of homozygosity (ROHs) in one of the major Iranian sheep breeds (Zandi) using 96 samples genotyped with Illumina Ovine SNP50 BeadChip. The amount of LD (r2) for single-nucleotide polymorphism (SNP) pairs in short distances (10–20 kb) was 0.21±0.25 but rapidly decreased to 0.10±0.16 by increasing the distance between SNP pairs (40–60 kb). The Ne of Zandi sheep in past (approximately 3500 generations ago) and recent (five generations ago) populations was estimated to be 6475 and 122, respectively. The ROH-based inbreeding was 0.023. We found 558 ROH regions, of which 37 % were relatively long (> 10 Mb). Compared with the rate of LD reduction in other species (e.g., cattle and pigs), in Zandi, it was reduced more rapidly by increasing the distance between SNP pairs. According to the LD pattern and high genetic diversity of Zandi sheep, we need to use an SNP panel with a higher density than Illumina Ovine SNP50 BeadChip for genomic selection and genome-wide association studies in this breed.

scholarly journals Broad-scale puma connectivity could restore genomic diversity to fine-scale coastal populations

2021 ◽  
Author(s):  
Kyle D Gustafson ◽  
Roderick B Gagne ◽  
Michael R Buchalski ◽  
T Winston Vickers ◽  
Seth PD Riley ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Linkage Disequilibrium ◽  
Puma Concolor ◽  
Genomic Diversity ◽  
Strong Linkage Disequilibrium ◽  
Fine Scale ◽  
High Genetic Diversity ◽  
Population Genomic ◽  
Genome Wide ◽  
Genetic Clusters

Urbanization is decreasing wildlife habitat and connectivity worldwide, including for apex predators, such as the puma (Puma concolor). Puma populations along California's central and southern coastal habitats have experienced rapid fragmentation from development, leading to calls for demographic and genetic management. To address urgent conservation genomic concerns, we used double-digest restriction-site associated DNA (ddRAD) sequencing to analyze 16,285 genome-wide single-nucleotide polymorphisms (SNPs) from 401 broadly sampled pumas. Our analyses indicated support for 4–10 geographically nested, broad- to fine-scale genetic clusters. At the broadest scale, the 4 genetic clusters had high genetic diversity and exhibited low linkage disequilibrium, indicating pumas have retained statewide genomic diversity. However, multiple lines of evidence indicated substructure, including 10 fine-scale genetic clusters, some of which exhibited allelic fixation and linkage disequilibrium. Fragmented populations along the Southern Coast and Central Coast had particularly low genetic diversity and strong linkage disequilibrium, indicating genetic drift and close inbreeding. Our results demonstrate that genetically at-risk populations are typically nested within a broader-scale group of interconnected populations that collectively retains high genetic diversity and heterogeneous fixations. Thus, extant variation at the broader scale has potential to restore diversity to local populations if management actions can enhance vital gene flow and recombine locally sequestered genetic diversity. These state- and genome-wide results are critically important for science-based conservation and management practices. Our broad- and fine-scale population genomic analysis highlights the information that can be gained from population genomic studies aiming to provide guidance for fragmented population conservation management.

scholarly journals Genomic miscellany and allelic frequencies of Plasmodium falciparum msp-1, msp-2 and glurp in parasite isolates

2021 ◽  
Author(s):  
Muzafar Shah ◽  
Ibrar Ullah ◽  
Sahib Gul Afridi ◽  
Muhammad Israr ◽  
Asifullah Khan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Plasmodium Falciparum ◽  
Local Health ◽  
Multiplicity Of Infection ◽  
High Genetic Diversity ◽  
Khyber Pakhtunkhwa ◽  
Chain Reactions ◽  
Allelic Family ◽  
Allelic Frequencies ◽  
The Impact

Plasmodium falciparum, the main causative agent of malaria is an important public health vector in Khyber Pakhtunkhwa, Pakistan. Identification of the genetic diversity of malaria parasites can inform the intensity of transmission and identify potential deficiencies in malaria control programs. The aim of this study was to investigate the genetic diversity, allele frequencies and multiplicity of infection (MOI) of P. falciparum in Khyber Pakhtunkhwa, Pakistan. Methods: A total of 85 isolates from patients presenting to the local health centers with P. falciparum species were collected from 2017 to 2019. Parasite DNA was extracted from a total of 200 micro litter whole blood per patient using the Qiagen DNA extraction kit according to manufactures instructions. The polymorphic region of msp-1, msp-2 and glurp loci were genotyped by using nested polymerase chain reactions followed by gel electrophoresis for fragment analysis. Results: Genetic diversity and allelic frequencies of msp-1, msp-2 and glurp were identified in 85 blood samples. A total of 62 msp alleles were detected in which 30 for msp-1 and 32 for msp-2. For msp-1 the successful amplification occurred in (75/85) 88.23% isolates for msp-1, 78.9% (67/85) for msp-2 and 70% (60/85) for glurp. For msp-1, the K1 allelic family was predominant at 66.66% (50/75), followed by RO33 and MAD20. The frequency of samples having only K1, MAD20 and RO33 were 21.34% (16/75), 8% (6/75) and 10.67% (8/75) respectively. In msp-2, the FC27 allelic family was the most abundant with 70.14% (47/67) compared to 3D7 with 67.16% (45/67). Nine glurp RII region genotypes were identified. The overall mean multiplicity of infection was 2.6 with1.8 and 1.4 for msp-1 and msp-2 respectively while for glurp RII genes (MOI=1.03). There was no significant association between multiplicity of infection and age group (Spearman rank coefficient = 0.050; P = 0.6). There was significant correlation between MOI and parasite density for msp-2 allelic family. Conclusion: Our study showed high genetic diversity and allelic frequency with multiple clones of msp-1, msp-2 and glurp in P. falciparum isolates from malaria patients in Khyber Pakhtunkhwa Pakistan. In the present study the genotype data provided the valuable information which is essential for monitoring the impact of malaria eradication efforts in this region.

Sign in / Sign up

Export Citation Format

Share Document