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Enhanced localization of genetic samples through linkage-disequilibrium correction.

ABSTRACT: Characterizing the spatial patterns of genetic diversity in human populations has a wide range of applications, from detecting genetic mutations associated with disease to inferring human history. Current approaches, including the widely used principal-component analysis, are not suited for the analysis of linked markers, and local and long-range linkage disequilibrium (LD) can dramatically reduce the accuracy of spatial localization when unaccounted for. To overcome this, we have introduced an approach that performs spatial localization of individuals on the basis of their genetic data and explicitly models LD among markers by using a multivariate normal distribution. By leveraging external reference panels, we derive closed-form solutions to the optimization procedure to achieve a computationally efficient method that can handle large data sets. We validate the method on empirical data from a large sample of European individuals from the POPRES data set, as well as on a large sample of individuals of Spanish ancestry. First, we show that by modeling LD, we achieve accuracy superior to that of existing methods. Importantly, whereas other methods show decreased performance when dense marker panels are used in the inference, our approach improves in accuracy as more markers become available. Second, we show that accurate localization of genetic data can be achieved with only a part of the genome, and this could potentially enable the spatial localization of admixed samples that have a fraction of their genome originating from a given continent. Finally, we demonstrate that our approach is resistant to distortions resulting from long-range LD regions; such distortions can dramatically bias the results when unaccounted for.

SUBMITTER: Baran Y

PROVIDER: S-EPMC3675263 | biostudies-literature | 2013 Jun

REPOSITORIES: biostudies-literature

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Enhanced localization of genetic samples through linkage-disequilibrium correction.

Baran Yael Y Quintela Inés I Carracedo Angel A Pasaniuc Bogdan B Halperin Eran E

American journal of human genetics 20130530 6

Characterizing the spatial patterns of genetic diversity in human populations has a wide range of applications, from detecting genetic mutations associated with disease to inferring human history. Current approaches, including the widely used principal-component analysis, are not suited for the analysis of linked markers, and local and long-range linkage disequilibrium (LD) can dramatically reduce the accuracy of spatial localization when unaccounted for. To overcome this, we have introduced an ...[more]

PMID: 23726367

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Project description:BackgroundPeach (Prunus persica (L.) Batsch) is one of the most important model fruits in the Rosaceae family. Native to the west of China, where peach has been domesticated for more than 4,000 years, its cultivation spread from China to Persia, Mediterranean countries and to America. Chinese peach has had a major impact on international peach breeding programs due to its high genetic diversity. In this research, we used 48 highly polymorphic SSRs, distributed over the peach genome, to investigate the difference in genetic diversity, and linkage disequilibrium (LD) among Chinese cultivars, and North American and European cultivars, and the evolution of current peach cultivars.ResultsIn total, 588 alleles were obtained with 48 SSRs on 653 peach accessions, giving an average of 12.25 alleles per locus. In general, the average value of observed heterozygosity (0.47) was lower than the expected heterozygosity (0.60). The separate analysis of groups of accessions according to their origin or reproductive strategies showed greater variability in Oriental cultivars, mainly due to the high level of heterozygosity in Chinese landraces. Genetic distance analysis clustered the cultivars into two main groups: one included four wild related Prunus, and the other included most of the Oriental and Occidental landraces and breeding cultivars. STRUCTURE analysis assigned 469 accessions to three subpopulations: Oriental (234), Occidental (174), and Landraces (61). Nested STRUCTURE analysis divided the Oriental subpopulation into two different subpopulations: 'Yu Lu' and 'Hakuho'. The Occidental breeding subpopulation was also subdivided into nectarine and peach subpopulations. Linkage disequilibrium (LD) analysis in each of these subpopulations showed that the percentage of linked (r2 > 0.1) intra-chromosome comparisons ranged between 14% and 47%. LD decayed faster in Oriental (1,196 Kbp) than in Occidental (2,687 Kbp) samples. In the 'Yu Lu' subpopulation there was considerable LD extension while no variation of LD with physical distance was observed in the landraces. From the first STRUCTURE result, LG1 had the greatest proportion of alleles in LD within all three subpopulations.ConclusionsOur study demonstrates a high level of genetic diversity and relatively fast decay of LD in the Oriental peach breeding program. Inclusion of Chinese landraces will have a greater effect on increasing genetic diversity in Occidental breeding programs. Fingerprinting with genotype data for all 658 cultivars will be used for accession management in different germplasms. A higher density of markers are needed for association mapping in Oriental germplasm due to the low extension of LD. Population structure and evaluation of LD provides valuable information for GWAS experiment design in peach.

Dataset Information

Enhanced localization of genetic samples through linkage-disequilibrium correction.

Publications

Enhanced localization of genetic samples through linkage-disequilibrium correction.

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