A high resolution genome-wide scan for significant selective sweeps: an application to pooled sequence data in laying chickens.

In most studies aimed at localizing footprints of past selection, outliers at tails of the empirical distribution of a given test statistic are assumed to reflect locus-specific selective forces. Significance cutoffs are subjectively determined, rather than being related to a clear set of hypotheses...

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Autores principales:	Saber Qanbari, Tim M Strom, Georg Haberer, Steffen Weigend, Almas A Gheyas, Frances Turner, David W Burt, Rudolf Preisinger, Daniel Gianola, Henner Simianer
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/f9829b2ee68545c5b1858bfb0d58ca58
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spelling	oai:doaj.org-article:f9829b2ee68545c5b1858bfb0d58ca582021-11-18T08:07:09ZA high resolution genome-wide scan for significant selective sweeps: an application to pooled sequence data in laying chickens.1932-620310.1371/journal.pone.0049525https://doaj.org/article/f9829b2ee68545c5b1858bfb0d58ca582012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23209582/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203In most studies aimed at localizing footprints of past selection, outliers at tails of the empirical distribution of a given test statistic are assumed to reflect locus-specific selective forces. Significance cutoffs are subjectively determined, rather than being related to a clear set of hypotheses. Here, we define an empirical p-value for the summary statistic by means of a permutation method that uses the observed SNP structure in the real data. To illustrate the methodology, we applied our approach to a panel of 2.9 million autosomal SNPs identified from re-sequencing a pool of 15 individuals from a brown egg layer line. We scanned the genome for local reductions in heterozygosity, suggestive of selective sweeps. We also employed a modified sliding window approach that accounts for gaps in the sequence and increases scanning resolution by moving the overlapping windows by steps of one SNP only, and suggest to call this a "creeping window" strategy. The approach confirmed selective sweeps in the region of previously described candidate genes, i.e. TSHR, PRL, PRLHR, INSR, LEPR, IGF1, and NRAMP1 when used as positive controls. The genome scan revealed 82 distinct regions with strong evidence of selection (genome-wide p-value<0.001), including genes known to be associated with eggshell structure and immune system such as CALB1 and GAL cluster, respectively. A substantial proportion of signals was found in poor gene content regions including the most extreme signal on chromosome 1. The observation of multiple signals in a highly selected layer line of chicken is consistent with the hypothesis that egg production is a complex trait controlled by many genes.Saber QanbariTim M StromGeorg HabererSteffen WeigendAlmas A GheyasFrances TurnerDavid W BurtRudolf PreisingerDaniel GianolaHenner SimianerPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 11, p e49525 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Saber Qanbari Tim M Strom Georg Haberer Steffen Weigend Almas A Gheyas Frances Turner David W Burt Rudolf Preisinger Daniel Gianola Henner Simianer A high resolution genome-wide scan for significant selective sweeps: an application to pooled sequence data in laying chickens.
description	In most studies aimed at localizing footprints of past selection, outliers at tails of the empirical distribution of a given test statistic are assumed to reflect locus-specific selective forces. Significance cutoffs are subjectively determined, rather than being related to a clear set of hypotheses. Here, we define an empirical p-value for the summary statistic by means of a permutation method that uses the observed SNP structure in the real data. To illustrate the methodology, we applied our approach to a panel of 2.9 million autosomal SNPs identified from re-sequencing a pool of 15 individuals from a brown egg layer line. We scanned the genome for local reductions in heterozygosity, suggestive of selective sweeps. We also employed a modified sliding window approach that accounts for gaps in the sequence and increases scanning resolution by moving the overlapping windows by steps of one SNP only, and suggest to call this a "creeping window" strategy. The approach confirmed selective sweeps in the region of previously described candidate genes, i.e. TSHR, PRL, PRLHR, INSR, LEPR, IGF1, and NRAMP1 when used as positive controls. The genome scan revealed 82 distinct regions with strong evidence of selection (genome-wide p-value<0.001), including genes known to be associated with eggshell structure and immune system such as CALB1 and GAL cluster, respectively. A substantial proportion of signals was found in poor gene content regions including the most extreme signal on chromosome 1. The observation of multiple signals in a highly selected layer line of chicken is consistent with the hypothesis that egg production is a complex trait controlled by many genes.
format	article
author	Saber Qanbari Tim M Strom Georg Haberer Steffen Weigend Almas A Gheyas Frances Turner David W Burt Rudolf Preisinger Daniel Gianola Henner Simianer
author_facet	Saber Qanbari Tim M Strom Georg Haberer Steffen Weigend Almas A Gheyas Frances Turner David W Burt Rudolf Preisinger Daniel Gianola Henner Simianer
author_sort	Saber Qanbari
title	A high resolution genome-wide scan for significant selective sweeps: an application to pooled sequence data in laying chickens.
title_short	A high resolution genome-wide scan for significant selective sweeps: an application to pooled sequence data in laying chickens.
title_full	A high resolution genome-wide scan for significant selective sweeps: an application to pooled sequence data in laying chickens.
title_fullStr	A high resolution genome-wide scan for significant selective sweeps: an application to pooled sequence data in laying chickens.
title_full_unstemmed	A high resolution genome-wide scan for significant selective sweeps: an application to pooled sequence data in laying chickens.
title_sort	high resolution genome-wide scan for significant selective sweeps: an application to pooled sequence data in laying chickens.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/f9829b2ee68545c5b1858bfb0d58ca58
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A high resolution genome-wide scan for significant selective sweeps: an application to pooled sequence data in laying chickens.

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