ArticlePloS one2012
A high resolution genome-wide scan for significant selective sweeps: an application to pooled sequence data in laying chickens.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
45 citing papers in PubMed, 70 citations in OpenAlex.
- Identification of Genomic Differences Resulting from Selection in Iranian Kurdish and Turkmen Horse Breeds Using Single Nucleotide Polymorphisms.Iranian journal of biotechnology · 2026Article
- Genetic Differentiation and Selection Signatures Revealed by Two Successive Genomic Selection of Large Yellow Croaker Against ParasiteEvolutionary applications · 2025Article
- Exploring the genetics of social behaviour in C. calcarata.Scientific reports · 2025Article
- Genome-wide scan for signatures of selection in Hanwoo and Angus cattle using whole-genome sequence data.PloS one · 2025Article
- Genome-Wide Scan for Selective Sweeps Reveals Novel Loci Associated with Prolificacy in Iranian Sheep Breeds in Comparison with Highly Prolific Exotic Breed.Animals : an open access journal from MDPI · 2024Article
- Article
- Detection of selective sweep in European wild sheep breeds.3 Biotech · 2024Article
- Environmental and Socio-Cultural Factors Impacting the Unique Gene Pool Pattern of Mae Hong-Son Chicken.Animals : an open access journal from MDPI · 2023Article
- Selective footprints and genes relevant to cold adaptation and other phenotypic traits are unscrambled in the genomes of divergently selected chicken breeds.Journal of animal science and biotechnology · 2023Article
- Genome variation in tick infestation and cryptic divergence in Tunisian indigenous sheep.BMC genomics · 2022Article
- Whole Exome-Sequencing of Pooled Genomic DNA Samples to Detect Quantitative Trait Loci in Esotropia and Exotropia of Strabismus in Japanese.Life (Basel, Switzerland) · 2021Article
- Article
- Comparison of anadromous and landlocked Atlantic salmon genomes reveals signatures of parallel and relaxed selection across the Northern Hemisphere.Evolutionary applications · 2021Article
- Genomic Signatures After Five Generations of Intensive Selective Breeding: Runs of Homozygosity and Genetic Diversity in Representative Domestic and Wild Populations of Turbot (Frontiers in genetics · 2020Article
- Comprehensive genome and transcriptome analyses reveal genetic relationship, selection signature, and transcriptome landscape of small-sized Korean native Jeju horse.Scientific reports · 2019Article
- Integrative Genomics Reveals the Genetics and Evolution of the Honey Bee's Social Immune System.Genome biology and evolution · 2019Article
- Discovery of genomic variations by whole-genome resequencing of the North American Araucana chicken.PloS one · 2019Article
- Red fox genome assembly identifies genomic regions associated with tame and aggressive behaviours.Nature ecology & evolution · 2018Article
- A genome-wide scan for signatures of selection in Azeri and Khuzestani buffalo breeds.BMC genomics · 2018Article
- Genome-wide characterization of genetic variants and putative regions under selection in meat and egg-type chicken lines.BMC genomics · 2018Article
Corrections and comments
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Authors and funding
10 authors at 7 institutions in 3 countries.
Funding
Abstract
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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.