Population genomic structure and linkage disequilibrium analysis of South African goat breeds using genome-wide SNP data

2016 ◽  
Vol 47 (4) ◽  
pp. 471-482 ◽  
Author(s):  
K. Mdladla ◽  
E. F. Dzomba ◽  
H. J. Huson ◽  
F. C. Muchadeyi
Keyword(s):  
Linkage Disequilibrium ◽  
South African ◽  
Genomic Structure ◽  
Linkage Disequilibrium Analysis ◽  
Population Genomic ◽  
Snp Data ◽  
Genome Wide

scholarly journals Genetic Diversity and Population Structure in South African, French and Argentinian Angora Goats from Genome-Wide SNP Data

PLoS ONE ◽  
2016 ◽  
Vol 11 (5) ◽  
pp. e0154353 ◽  
Author(s):  
Carina Visser ◽  
Simon F. Lashmar ◽  
Este Van Marle-Köster ◽  
Mario A. Poli ◽  
Daniel Allain
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
South African ◽  
Snp Data ◽  
Genome Wide ◽  
Angora Goats

scholarly journals Mapping and linkage disequilibrium analysis with a genome-wide collection of SNPs that detect polymorphism in cultivated tomato

2010 ◽  
Vol 62 (6) ◽  
pp. 1831-1845 ◽  
Author(s):  
Matthew D. Robbins ◽  
Sung-Chur Sim ◽  
Wencai Yang ◽  
Allen Van Deynze ◽  
Esther van der Knaap ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Linkage Disequilibrium Analysis ◽  
Genome Wide ◽  
A Genome

scholarly journals Genome wide analysis reveals genetic divergence between Goldsinny wrasse populations 

2020 ◽  
Author(s):  
Eeva Jansson ◽  
Francois Besnier ◽  
Ketil Malde ◽  
Carl André ◽  
Geir Dahle ◽  
...  
Keyword(s):  
Genetic Divergence ◽  
De Novo ◽  
Genomic Structure ◽  
Snp Markers ◽  
Genomic Diversity ◽  
Full Genome Sequencing ◽  
Population Genomic ◽  
Genome Wide ◽  
Ctenolabrus Rupestris ◽  
Goldsinny Wrasse

Abstract Background Marine fish populations are often characterized by high levels of gene flow and correspondingly low genetic divergence. This presents a challenge to define management units. Goldsinny wrasse ( Ctenolabrus rupestris ) is a heavily exploited species due to its importance as a cleaner-fish in commercial salmonid aquaculture. However, at the present, the population genetic structure of this species is still largely unresolved. Here, full-genome sequencing was used to produce the first genomic reference for this species, to study population-genomic divergence among four geographically distinct populations, and, to identify informative SNP markers for future studies. Results After construction of a de novo assembly, the genome was estimated to be highly polymorphic and of ~600Mbp in size. 33 235 genome wide SNPs were thereafter selected to assess genomic diversity and differentiation among four populations collected from Scandinavia, Scotland, and Spain. Global F ST among these populations was 0.015–0.092. Approximately 4% of the investigated loci were identified as putative global outliers, and ~1% within Scandinavia. SNPs showing large divergence ( F ST >0.15) were picked as candidate diagnostic markers for population assignment. 173 of the most diagnostic SNPs between the two Scandinavian populations were validated by genotyping 47 individuals from each end of the species’ Scandinavian distribution range. 69 of these SNPs were significantly ( p <0.05) differentiated (mean F ST_173_loci = 0.065, F ST_69_loci = 0.140). Using these validated SNPs, individuals were assigned with high probability (≥ 94%) to their populations of origin. Conclusions Goldsinny wrasse displays a highly polymorphic genome, and substantial population genomic structure. Diversifying selection likely affects population structuring globally and within Scandinavia. The diagnostic loci identified now provide a promising and cost-efficient tool to investigate goldsinny wrasse populations further.

scholarly journals A fast linkage disequilibrium-based statistical test for Genome-Wide Epistatic Selection Scans in structured populations

2020 ◽  
Author(s):  
Léa Boyrie ◽  
Corentin Moreau ◽  
Florian Frugier ◽  
Christophe Jacquet ◽  
Maxime Bonhomme
Keyword(s):  
Population Structure ◽  
Linkage Disequilibrium ◽  
Experimental Evidence ◽  
Medicago Truncatula ◽  
Genetic Interaction ◽  
Correlation Coefficients ◽  
Statistical Test ◽  
Structured Populations ◽  
Snp Data ◽  
Genome Wide

AbstractThe quest for genome-wide signatures of selection in populations using SNP data has proven efficient to uncover genes involved in conserved or adaptive molecular functions, but none of the statistical methods were designed to identify interacting genes as targets of selective processes. Here, we propose a straightforward statistical test aimed at detecting epistatic selection, based on a linkage disequilibrium (LD) measure accounting for population structure and heterogeneous relatedness between individuals. SNP-based (Trv) and window-based (TcorPC1v) statistics fit a Student distribution, allowing to easily and quickly test the significance of correlation coefficients in the frame of Genome-Wide Epistatic Selection Scans (GWESS) using candidate genes as baits. As a proof of concept, use of SNP data from the Medicago truncatula symbiotic legume plant uncovered a previously unknown gene coadaptation between the MtSUNN (Super Numeric Nodule) receptor and the MtCLE02 (CLAVATA3-Like) signalling peptide, and experimental evidence accordingly supported a MtSUNN-dependent negative role of MtCLE02 in symbiotic root nodulation. Using human HGDP-CEPH SNP data, our new statistical test uncovered strong LD between SLC24A5 and EDAR worldwide, which persists after correction for population structure and relatedness in Central South Asian populations. This result suggests adaptive genetic interaction or coselection between skin pigmentation and the ectodysplasin pathway involved in the development of ectodermal organs (hairs, teeth, sweat glands), in some human populations. Applying this approach to genome-wide SNP data will foster the identification of evolutionary coadapted gene networks.Author summaryPopulation genomic methods have allowed to identify many genes associated with adaptive processes in populations with complex histories. However, they are not designed to identify gene coadaptation between genes through epistatic selection, in structured populations. To tackle this problem, we developed a straightforward LD-based statistical test accounting for population structure and heterogeneous relatedness between individuals, using SNP-based (Trv) or windows-based (TcorPC1v) statistics. This allows easily and quickly testing for significance of correlation coefficients between polymorphic loci in the frame of Genome Wide Epistatic Selection Scans (GWESS). Following detection of gene coadaptation using SNP data from human and the model plant Medicago truncatula, we report experimental evidence of genetic interaction between two receptors involved in the regulation of root nodule symbiosis in Medicago truncatula. This test opens new avenues for exploring the evolution of genes as interacting units and thus paves the way to infer new networks based on evolutionary coadaptation between genes.

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.

A STUDY OF THE POPULATION GENOMIC STRUCTURE AND THE CHARACTER OF THE GENETIC DIVERGENCE OF EQUINE BREEDS (EQUUS CABALLUS L.)

2021 ◽  
Vol 1 (19) ◽  
pp. 335-338
Author(s):  
V.V. Kalashnikov ◽  
L.A. Khrabrova ◽  
N.V. Blokhina ◽  
T.V. Kalashnikova
Keyword(s):  
High Efficiency ◽  
Genomic Structure ◽  
Genome Wide Analysis ◽  
Horse Breeding ◽  
Population Genomic ◽  
Genome Wide ◽  
A Genome ◽  
Selected Traits ◽  
First Time ◽  
Genome Wide Study

For the first time, a genome-wide study was conducted for 6 native breeds (Kabardian, Vyatka, zabaikalian, Yakut) with unique adaptive qualities and 2 cultural breeds that are strictly selected for multidirectional characteristics. Data on the state of the genetic structure of breeds were obtained. The phylogenetic relationships between breeds were studied, the ancestral groups that participated in the formation of the breed structure were determined, and the influence of factory improver breeds on the microevolution of local breeds was estimated. the results of the research are correlated with the freely available results of the genome-wide analysis of foreign horse populations and breeds. The ways of identifying complexes that characterize the severity of selected traits in breeds with different directions of use are outlined. The high efficiency of using the obtained results to determine belonging to a particular breed is determined. A database of mitochondrial DNA and Y-chromosome haplotypes was created to conduct a retrospective analysis of the origin and refinement of breeding records in the system of centralized breeding records in horse breeding. As additional markers, we used targeted SNPs that characterize the severity of selected traits

Genome-wide linkage disequilibrium analysis in bread wheat and durum wheat

Genome ◽  
2007 ◽  
Vol 50 (6) ◽  
pp. 557-567 ◽  
Author(s):  
Daryl J. Somers ◽  
Travis Banks ◽  
Ron DePauw ◽  
Stephen Fox ◽  
John Clarke ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Durum Wheat ◽  
Bread Wheat ◽  
Simple Sequence Repeats ◽  
Linkage Disequilibrium Analysis ◽  
Microsatellite Data ◽  
Significance Level ◽  
Genome Wide ◽  
Simple Sequence ◽  
Genome Wide Linkage Disequilibrium

Bread wheat and durum wheat were examined for linkage disequilibrium (LD) using microsatellite markers distributed across the genome. The allele database consisted of 189 bread wheat accessions genotyped at 370 loci and 93 durum wheat accessions genotyped at 245 loci. A significance level of p < 0.001 was set for all comparisons. The bread and durum wheat collections showed that 47.9% and 14.0% of all locus pairs were in LD, respectively. LD was more prevalent between loci on the same chromosome compared with loci on independent chromosomes and was highest between adjacent loci. Only a small fraction (bread wheat, 0.9%; durum wheat, 3.2%) of the locus pairs in LD showed R2 values > 0.2. The LD between adjacent locus pairs extended (R2 > 0.2) approximately 2–3 cM, on average, but some regions of the bread and durum wheat genomes showed high levels of LD (R2 = 0.7 and 1.0, respectively) extending 41.2 and 25.5 cM, respectively. The wheat collections were clustered by similarity into subpopulations using unlinked microsatellite data and the software Structure. Analysis within subpopulations showed 14- to 16-fold fewer locus pairs in LD, higher R2 values for those pairs in LD, and LD extending further along the chromosome. The data suggest that LD mapping of wheat can be performed with simple sequence repeats to a resolution of <5 cM.

scholarly journals Haplotype heterogeneity and low linkage disequilibrium reduce reliable prediction of genotypes for the ‑α3.7I form of α-thalassaemia using genome-wide microarray data

2021 ◽  
Vol 5 ◽  
pp. 287
Author(s):  
Carolyne M. Ndila ◽  
Vysaul Nyirongo ◽  
Alexander W. Macharia ◽  
Anna E. Jeffreys ◽  
Kate Rowlands ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Snp Markers ◽  
Gwas Data ◽  
Reliable Prediction ◽  
Broad Agreement ◽  
Snp Data ◽  
Genome Wide ◽  
Typing Methods ◽  
Potential Use ◽  
Rule Out

Background: The -α3.7I-thalassaemia deletion is very common throughout Africa because it protects against malaria. When undertaking studies to investigate human genetic adaptations to malaria or other diseases, it is important to account for any confounding effects of α-thalassaemia to rule out spurious associations. Methods: In this study, we have used direct α-thalassaemia genotyping to understand why GWAS data from a large malaria association study in Kilifi Kenya did not identify the α-thalassaemia signal. We then explored the potential use of a number of new approaches to using GWAS data for imputing α-thalassaemia as an alternative to direct genotyping by PCR. Results: We found very low linkage-disequilibrium of the directly typed data with the GWAS SNP markers around α-thalassaemia and across the haemoglobin-alpha (HBA) gene region, which along with a complex haplotype structure, could explain the lack of an association signal from the GWAS SNP data. Some indirect typing methods gave results that were in broad agreement with those derived from direct genotyping and could identify an association signal, but none were sufficiently accurate to allow correct interpretation compared with direct typing, leading to confusing or erroneous results. Conclusions: We conclude that going forwards, direct typing methods such as PCR will still be required to account for α-thalassaemia in GWAS studies.

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