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A genome-wide analysis of population structure in the Finnish Saami with implications for genetic association studies.

ABSTRACT: The understanding of patterns of genetic variation within and among human populations is a prerequisite for successful genetic association mapping studies of complex diseases and traits. Some populations are more favorable for association mapping studies than others. The Saami from northern Scandinavia and the Kola Peninsula represent a population isolate that, among European populations, has been less extensively sampled, despite some early interest for association mapping studies. In this paper, we report the results of a first genome-wide SNP-based study of genetic population structure in the Finnish Saami. Using data from the HapMap and the human genome diversity project (HGDP-CEPH) and recently developed statistical methods, we studied individual genetic ancestry. We quantified genetic differentiation between the Saami population and the HGDP-CEPH populations by calculating pair-wise F(ST) statistics and by characterizing identity-by-state sharing for pair-wise population comparisons. This study affirms an east Asian contribution to the predominantly European-derived Saami gene pool. Using model-based individual ancestry analysis, the median estimated percentage of the genome with east Asian ancestry was 6% (first and third quartiles: 5 and 8%, respectively). We found that genetic similarity between population pairs roughly correlated with geographic distance. Among the European HGDP-CEPH populations, F(ST) was smallest for the comparison with the Russians (F(ST)=0.0098), and estimates for the other population comparisons ranged from 0.0129 to 0.0263. Our analysis also revealed fine-scale substructure within the Finnish Saami and warns against the confounding effects of both hidden population structure and undocumented relatedness in genetic association studies of isolated populations.

SUBMITTER: Huyghe JR

PROVIDER: S-EPMC3062008 | biostudies-other | 2011 Mar

REPOSITORIES: biostudies-other

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A genome-wide analysis of population structure in the Finnish Saami with implications for genetic association studies.

Huyghe Jeroen R JR Fransen Erik E Hannula Samuli S Van Laer Lut L Van Eyken Els E Mäki-Torkko Elina E Aikio Pekka P Sorri Martti M Huentelman Matthew J MJ Van Camp Guy G

European journal of human genetics : EJHG 20101208 3

The understanding of patterns of genetic variation within and among human populations is a prerequisite for successful genetic association mapping studies of complex diseases and traits. Some populations are more favorable for association mapping studies than others. The Saami from northern Scandinavia and the Kola Peninsula represent a population isolate that, among European populations, has been less extensively sampled, despite some early interest for association mapping studies. In this pape ...[more]

PMID: 21150888

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Project description:IntroductionThis study focuses on cowpea, a vital crop for smallholder farmers in sub-Saharan Africa, particularly in Malawi. The research aimed to understand the genetic diversity and population structure of cowpea and to perform genome-wide association studies (GWAS) to identify marker-trait associations (MTAs) for yield and related traits. These insights are intended to support varietal development and address agricultural challenges in Malawi.MethodsA total of 306 cowpea genotypes were characterized using single nucleotide polymorphism (SNP) markers and morphological traits. The study assessed the effects of genotype, location, and their interactions on morphological traits. The Fixed and Random Model Circulating Probability Unification (FarmCPU) algorithm was used to identify significant MTAs.ResultsThe morphological traits showed significant genotype, location, and interaction effects. Genotypes MWcp24, MWcp47, MWcp2232, and TVu-3524 yielded the highest values. Grain yield was positively correlated with peduncle length, seeds per pod, and pods per plant. Three distinct clusters were identified based on morphological traits. Genetic diversity analysis revealed an average minor allele frequency of 0.31, observed heterozygosity of 0.06, and gene diversity of 0.33. The average inbreeding coefficient was 0.82, indicating a high level of inbreeding. Most of the genetic variation (73.1%) was found among genotypes within populations. Nine groups and ancestral populations were identified, which did not entirely overlap with geographic origins. Sixteen significant MTAs were linked to six morphological traits.DiscussionThe validation of these identified MTAs, along with the observed genetic diversity, offers valuable opportunities for cowpea improvement through marker-assisted selection, to addresses the challenges faced by Malawian farmers. The identification of thirty cowpea lines as key founder lines for breeding programs in Malawi, Mozambique, and Tanzania is a significant outcome. These efforts aim to develop more productive cowpea lines for the region, enhancing food security and agricultural sustainability.

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A genome-wide analysis of population structure in the Finnish Saami with implications for genetic association studies.

Publications

A genome-wide analysis of population structure in the Finnish Saami with implications for genetic association studies.

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