scholarly journals Extent of linkage disequilibrium, consistency of gametic phase, and imputation accuracy within and across Canadian dairy breeds

2014 ◽  
Vol 97 (5) ◽  
pp. 3128-3141 ◽  
Author(s):  
S.G. Larmer ◽  
M. Sargolzaei ◽  
F.S. Schenkel
Keyword(s):  
Linkage Disequilibrium ◽  
Imputation Accuracy ◽  
Consistency Of Gametic Phase ◽  
Gametic Phase

scholarly journals Characterization of linkage disequilibrium, consistency of gametic phase and admixture in Australian and Canadian goats

BMC Genetics ◽  
2015 ◽  
Vol 16 (1) ◽  
Author(s):  
Luiz F. Brito ◽  
Mohsen Jafarikia ◽  
Daniela A. Grossi ◽  
James W. Kijas ◽  
Laercio R. Porto-Neto ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Consistency Of Gametic Phase ◽  
Gametic Phase

scholarly journals Homozygosity and Linkage Disequilibrium

Genetics ◽  
2002 ◽  
Vol 160 (4) ◽  
pp. 1707-1719
Author(s):  
Chiara Sabatti ◽  
Neil Risch
Keyword(s):  
Phase Equilibrium ◽  
Linkage Disequilibrium ◽  
Specific Form ◽  
Polymorphic Markers ◽  
Biological Interpretation ◽  
Gametic Phase

Abstract We illustrate how homozygosity of haplotypes can be used to measure the level of disequilibrium between two or more markers. An excess of either homozygosity or heterozygosity signals a departure from the gametic phase equilibrium: We describe the specific form of dependence that is associated with high (low) homozygosity and derive various linkage disequilibrium measures. They feature a clear biological interpretation, can be used to construct tests, and are standardized to allow comparison across loci and populations. They are particularly advantageous to measure linkage disequilibrium between highly polymorphic markers.

scholarly journals Genetic diversity, extent of linkage disequilibrium and persistence of gametic phase in Canadian pigs

BMC Genetics ◽  
2017 ◽  
Vol 18 (1) ◽  
Author(s):  
Daniela A. Grossi ◽  
Mohsen Jafarikia ◽  
Luiz F. Brito ◽  
Marcos E. Buzanskas ◽  
Mehdi Sargolzaei ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Linkage Disequilibrium ◽  
Gametic Phase

scholarly journals Evaluation of imputation accuracy using the combination of two high-density panels in Nelore beef cattle

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Priscila Arrigucci Bernardes ◽  
Guilherme Batista do Nascimento ◽  
Rodrigo Pelicioni Savegnago ◽  
Marcos Eli Buzanskas ◽  
Rafael Nakamura Watanabe ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Beef Cattle ◽  
Haplotype Block ◽  
Imputation Accuracy ◽  
High Density ◽  
Low Density ◽  
Common Snps ◽  
Haplotype Blocks ◽  
Genome Wide ◽  
Trait Locus

AbstractThis study compared imputation from lower-density commercial and customized panels to high-density panels and a combined panel (Illumina and Affymetrix) in Nelore beef cattle. Additionally, linkage disequilibrium and haplotype block conformation were estimated in individual high-density panels and compared with corresponding values in the combined panel after imputation. Overall, 814 animals were genotyped using BovineHD BeadChip (IllumHD), and 93 of these animals were also genotyped using the Axion Genome-Wide BOS 1 Array Plate (AffyHD). In general, customization considering linkage disequilibrium and minor allele frequency had the highest accuracies. The IllumHD panel had higher values of linkage disequilibrium for short distances between SNPs than AffyHD and the combined panel. The combined panel had an increased number of small haplotype blocks. The use of a combined panel is recommended due to its increased density and number of haplotype blocks, which in turn increase the probability of a marker being close to a quantitative trait locus of interest. Considering common SNPs between IllumHD and AffyHD for the customization of a low-density panel increases the imputation accuracy for IllumHD, AffyHD and the combined panel.

scholarly journals Linkage Disequilibrium-Based Inference of Genome Homology and Chromosomal Rearrangements Between Species

2020 ◽  
Vol 10 (7) ◽  
pp. 2327-2343 ◽  
Author(s):  
Daniel Jordan de Abreu Santos ◽  
Gregório Miguel Ferreira de Camargo ◽  
Diercles Francisco Cardoso ◽  
Marcos Eli Buzanskas ◽  
Rusbel Raul Aspilcueta-Borquis ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Genome Assembly ◽  
Chromosomal Rearrangement ◽  
Bos Taurus ◽  
Bovine Genome ◽  
Imputation Accuracy ◽  
Haplotype Diversity ◽  
Evolutionary Relationship ◽  
Snp Markers ◽  
Nucleotide Polymorphisms

The aim of this study was to analyze the genomic homology between cattle (Bos taurus) and buffaloes (Bubalus bubalis) and to propose a rearrangement of the buffalo genome through linkage disequilibrium analyses of buffalo SNP markers referenced in the cattle genome assembly and also compare it to the buffalo genome assembly. A panel of bovine SNPs (single nucleotide polymorphisms) was used for hierarchical, non-hierarchical and admixture cluster analyses. Thus, the linkage disequilibrium information between markers of a specific panel of buffalo was used to infer chromosomal rearrangement. Haplotype diversity and imputation accuracy of the submetacentric chromosomes were also analyzed. The genomic homology between the species enabled us to use the bovine genome assembly to recreate a buffalo genomic reference by rearranging the submetacentric chromosomes. The centromere of the submetacentric chromosomes exhibited high linkage disequilibrium and low haplotype diversity. It allowed hypothesizing about chromosome evolution. It indicated that buffalo submetacentric chromosomes are a centric fusion of ancestral acrocentric chromosomes. The chronology of fusions was also suggested. Moreover, a linear regression between buffalo and cattle rearranged assembly and the imputation accuracy indicated that the rearrangement of the chromosomes was adequate. When using the bovine reference genome assembly, the rearrangement of the buffalo submetacentric chromosomes could be done by SNP BTA (chromosome of Bos taurus) calculations: shorter BTA (shorter arm of buffalo chromosome) was given as [(shorter BTA length – SNP position in shorter BTA)] and larger BTA length as [shorter BTA length + (larger BTA length – SNP position in larger BTA)]. Finally, the proposed linkage disequilibrium-based method can be applied to elucidate other chromosomal rearrangement events in other species with the possibility of better understanding the evolutionary relationship between their genomes.

Genomic data reveals large similarities among Canadian and French maternal pig lines

2018 ◽  
Vol 98 (4) ◽  
pp. 809-817 ◽  
Author(s):  
Raphael Boré ◽  
Luiz F. Brito ◽  
Mohsen Jafarikia ◽  
Alban Bouquet ◽  
Laurence Maignel ◽  
...  
Keyword(s):  
Principal Component ◽  
Reference Population ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Genomic Breeding ◽  
Breeding Values ◽  
Very High ◽  
Genomic Relatedness ◽  
Consistency Of Gametic Phase ◽  
Gametic Phase

Combining reference populations from different countries and breeds could be an affordable way to enlarge the size of the reference populations for genomic prediction of breeding values. Therefore, the main objectives of this study were to assess the genetic diversity within and between two Canadian and French pig breeds (Landrace and Yorkshire) and the genomic relatedness among populations to evaluate the feasibility of an across-country reference population for pig genomic selection. A total of 14 756 pigs were genotyped on two single nucleotide polymorphism (SNP) chip panels (∼65K SNPs). A principal component analysis clearly discriminated Landrace and Yorkshire breeds, and also, but to a lesser extent, the Canadian and French purebred pigs of each breed. Linkage disequilibrium (LD) between adjacent SNPs was similar within Yorkshire populations. However, levels of LD were slightly different for Landrace populations. The consistency of gametic phase was very high between Yorkshire populations (0.96 at 0.05 Mb) and high for Landrace (0.88 at 0.05 Mb). Based on consistency of gametic phase, Canadian and French pig maternal lines are genetically close to each other. These results are promising, as they indicate that the accuracy of estimated genomic breeding values may increase by combining reference populations from the two countries.

Association of multiple nucleotide variations in the pituitary glutaminyl cyclase gene QPC with low radial BMD in adult women.

2020 ◽  
Author(s):  
Lungwani Muungo
Keyword(s):  
Linkage Disequilibrium ◽  
Multiple Regression ◽  
Genetic Variations ◽  
Strong Linkage Disequilibrium ◽  
Adult Women ◽  
Nucleotide Polymorphisms ◽  
Haplotype Estimation ◽  
Factors Affecting ◽  
Glutaminyl Cyclase ◽  
Strong Linkage

Correlation between 13 genetic variations of the glutaminyl-peptide cyclotransferase gene andadjusted aBMD was tested among 384 adult women. Among 13 variations with strong linkage disequilibrium,R54W showed a prominent association (p ? 0.0003), which was more striking when examined among 309 eldersubjects (>50 years; p ? 0.0001). Contribution for postmenopausal bone loss was suggested.Introduction: Alterations in homeostatic regulation of estrogen through the hypothalamus-pituitary-gonadal axis(HPG axis) importantly affect the pathogenesis of osteoporosis. Osteoporosis-susceptibility genes have beenproposed in this hormonal axis, such as estrogen receptor genes and the gonadotropin-releasing hormone gene(GnRH). Here we report another example of genes: glutaminyl-peptide cyclotransferase gene (QPCT), an essentialmodifier of pituitary peptide hormones, including GnRH.Materials and Methods: Analyses of association of 13 single nucleotide polymorphisms (SNPs) at the QPCT locuswith adjusted areal BMD (adj-aBMD) were carried out among 384 adult women. Linkage disequilibrium (LD) wasanalyzed by haplotype estimation and calculation of D? and r2. Multiple regression analysis was applied forevaluating the combined effects of the variations.Results and Conclusions: LD analysis indicated strong linkage disequilibrium within the entire 30-kb region of theQPCT gene. Significant correlations were observed between the genotypes of the six SNPs and the radial adj-aBMD,among which R54W (nt ? 160C?T) presented the most prominent association (p ? 0.0003). Striking associationwas observed for these SNPs among the 309 subjects ?50 years of age (R54W, p ? 0.0001; ?1095T?C, p ?0.0002; ?1844C?T, p ? 0.0002). Multiple regression analyses indicated that multiple SNPs in the gene might actin combination to determine the radial adj-aBMD. These results indicate that genetic variations in QPCT are theimportant factors affecting the BMD of adult women that contribute to susceptibility for osteoporosis. The datashould provide new insight into the etiology of the disease and may suggest a new target to be considered duringtreatment.J Bone Miner

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