scholarly journals Caucasian Families Exhibit Significant Linkage of Myopia to Chromosome 11p

2017 ◽  
Vol 58 (9) ◽  
pp. 3547 ◽  
Author(s):  
Anthony M. Musolf ◽  
Claire L. Simpson ◽  
Bilal A. Moiz ◽  
Kyle A. Long ◽  
Laura Portas ◽  
...  
Keyword(s):  
Chromosome 11P ◽  
Significant Linkage

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 Evidence for Selection at thefusedLocus ofDrosophila virilis

Genetics ◽  
2000 ◽  
Vol 155 (4) ◽  
pp. 1701-1709 ◽  
Author(s):  
Jorge Vieira ◽  
Brian Charlesworth
Keyword(s):  
Amino Acid ◽  
Aspartic Acid ◽  
Kinase Domain ◽  
Drosophila Virilis ◽  
Serine Threonine Kinase ◽  
Threonine Kinase ◽  
Usual Equilibrium ◽  
Replacement Site ◽  
Fused Gene ◽  
Significant Linkage

AbstractThe genomic DNA sequence of a 2.4-kb region of the X-linked developmental gene fused was determined in 15 Drosophila virilis strains. One common replacement polymorphism is observed, where a negatively charged aspartic amino acid is replaced by the noncharged amino acid alanine. This replacement variant is located within the serine/threonine kinase domain of the fused gene and is present in ~50% of the sequences in our sample. Significant linkage disequilibrium is detected around this replacement site, although the fused gene is located in a region of the D. virilis X chromosome that seems to experience normal levels of recombination. In a 600-bp region around the replacement site, all eight alanine sequences are identical; of the six aspartic acid sequences, three are also identical. The occurrence of little or no variation within the aspartic acid and alanine haplotypes, coupled with the presence of several differences between them, is very unlikely under the usual equilibrium neutral model. Our results suggest that the fused alanine haplotypes have recently increased in frequency in the D. virilis population.

scholarly journals Genome-wide Scan of IQ Finds Significant Linkage to a Quantitative Trait Locus on 2q

2005 ◽  
Vol 36 (1) ◽  
pp. 45-55 ◽  
Author(s):  
M. Luciano ◽  
M. J. Wright ◽  
D. L. Duffy ◽  
M. A. Wainwright ◽  
G. Zhu ◽  
...  
Keyword(s):  
Quantitative Trait Locus ◽  
Quantitative Trait ◽  
Genome Wide ◽  
Trait Locus ◽  
Significant Linkage ◽  
Genome Wide Scan

Identifying a genomic region at Chromosome 11p.14.1 that is associated to FSH serum level in men with unexplained male infertility

2021 ◽  
Vol 79 ◽  
pp. S391
Author(s):  
M. Schubert ◽  
L. Pérez Lanuza ◽  
M. Wöste ◽  
M. Dugas ◽  
Y. Rassam ◽  
...  
Keyword(s):  
Serum Level ◽  
Male Infertility ◽  
Genomic Region ◽  
Chromosome 11P

Significant linkage to airway responsiveness on chromosome 12q24 in families of children with asthma in Costa Rica

2006 ◽  
Vol 120 (5) ◽  
pp. 691-699 ◽  
Author(s):  
Juan C. Celedón ◽  
Manuel E. Soto-Quiros ◽  
Lydiana Avila ◽  
Stephen L. Lake ◽  
Catherine Liang ◽  
...  
Keyword(s):  
Costa Rica ◽  
Airway Responsiveness ◽  
Children With Asthma ◽  
Significant Linkage ◽  
Chromosome 12Q24

scholarly journals GWAS revealed effect of genotype × environment interactions for grain yield of Nebraska winter wheat

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Shamseldeen Eltaher ◽  
P. Stephen Baenziger ◽  
Vikas Belamkar ◽  
Hamdy A. Emara ◽  
Ahmed A. Nower ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Winter Wheat ◽  
Grain Yield ◽  
Genome Wide Association Study ◽  
Phenotypic Selection ◽  
Wheat Breeding ◽  
Wheat Genotypes ◽  
Genome Wide ◽  
Genomic Regions ◽  
Significant Linkage

Abstract Background Improving grain yield in cereals especially in wheat is a main objective for plant breeders. One of the main constrains for improving this trait is the G × E interaction (GEI) which affects the performance of wheat genotypes in different environments. Selecting high yielding genotypes that can be used for a target set of environments is needed. Phenotypic selection can be misleading due to the environmental conditions. Incorporating information from phenotypic and genomic analyses can be useful in selecting the higher yielding genotypes for a group of environments. Results A set of 270 F3:6 wheat genotypes in the Nebraska winter wheat breeding program was tested for grain yield in nine environments. High genetic variation for grain yield was found among the genotypes. G × E interaction was also highly significant. The highest yielding genotype differed in each environment. The correlation for grain yield among the nine environments was low (0 to 0.43). Genome-wide association study revealed 70 marker traits association (MTAs) associated with increased grain yield. The analysis of linkage disequilibrium revealed 16 genomic regions with a highly significant linkage disequilibrium (LD). The candidate parents’ genotypes for improving grain yield in a group of environments were selected based on three criteria; number of alleles associated with increased grain yield in each selected genotype, genetic distance among the selected genotypes, and number of different alleles between each two selected parents. Conclusion Although G × E interaction was present, the advances in DNA technology provided very useful tools and analyzes. Such features helped to genetically select the highest yielding genotypes that can be used to cross grain production in a group of environments.

scholarly journals Integrated Genomic Profiling Identifies Loss of Chromosome 11p Impacting Transcriptomic Activity in Aggressive Pituitary PRL Tumors

2011 ◽  
pp. no-no ◽  
Author(s):  
Anne Wierinckx ◽  
Magali Roche ◽  
Gérald Raverot ◽  
Catherine Legras-Lachuer ◽  
Séverine Croze ◽  
...  
Keyword(s):  
Genomic Profiling ◽  
Chromosome 11P

scholarly journals Polymorphic Inversion and Esterase Loci Complex on Chromosome 2 of Drosophila buzzatii. I. Linkage Disequilibria

1987 ◽  
Vol 40 (3) ◽  
pp. 257 ◽  
Author(s):  
WR Knibb ◽  
PD East ◽  
JSF Barker
Keyword(s):  
New World ◽  
Genetic Change ◽  
Chromosome 2 ◽  
Population Bottlenecks ◽  
Linkage Disequilibria ◽  
Drosophila Buzzatii ◽  
Conditional Allele ◽  
Esterase Loci ◽  
Almost All ◽  
Significant Linkage

Chromosome 2 inversion, Est-l and Est-2 haplotype frequencies were determined for 19 wild D. buzzatii collections from the known range of this species in Australia. Three different chromosome 2 sequences (ST, j, j z3) were polymorphic across the collections. They occurred at overall frequencies which approximated those in the ancestral New World and colonized Old World populations, which indicated that no radical genetic change was associated with the colonization of Australia by D. buzzatii. Linkage disequilibria of Est-l and Est-2 alleles with the inversions tended to be strong, and consistent in direction, in almost all collections. The distributions of conditional allele frequencies within the different inversions were consistent with stochastic historical explanations for the linkage disequilibria. Significant linkage disequilibria between Est-l and Est-2 were evident after correcting for the inversions, but these disequilibria largely were restricted to southern (higher latitude) populations, and were inconsistent in direction among the collections. Hence, population bottlenecks may underlie these genic disequilibria.

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.

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