ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2015
Functional classification of 15 million SNPs detected from diverse chicken populations.
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Multiomic data integration unveils molecular mechanisms underlying chestnut and skin tissue differentiation in Dezhou donkeys.BMC genomics · 2026Article
- Whole-Genome Resequencing Reveals Population Structure and Loci Associated with Growth and Meat-Quality Traits in Meigu Yanying Chickens.Animals : an open access journal from MDPI · 2026Article
- Comparative genomics reveals common diversity and adaptation to harsh environments in the Arabian Peninsula indigenous chickens.Animal genetics · 2025Article
- Article
- Genomic analysis of Nigerian indigenous chickens reveals their genetic diversity and adaptation to heat-stress.Scientific reports · 2024Article
- Genetic models of fibrillinopathies.Genetics · 2024Review
- A novel intron variant in the prolactin gene associated with eggshell weight and thickness with putative alternative splicing patterns in chickens.Journal of genetics · 2024Article
- Genetic variation in chicken interferon signalling pathway genes in research lines showing differential viral resistance.Animal genetics · 2022Article
- Rare and population-specific functional variation across pig lines.Genetics, selection, evolution : GSE · 2022Article
- Whole genome sequences of 234 indigenous African chickens from Ethiopia.Scientific data · 2022Article
- Transcriptome Analysis of Bovine Rumen Tissue in Three Developmental Stages.Frontiers in genetics · 2022Article
- Review
- Accumulation of genetic variants associated with immunity in the selective breeding of broilers.BMC genetics · 2020Article
- Analysis of the Progeny of Sibling Matings Reveals Regulatory Variation Impacting the Transcriptome of Immune Cells in Commercial Chickens.Frontiers in genetics · 2019Article
- A survey of functional genomic variation in domesticated chickens.Genetics, selection, evolution : GSE · 2018Article
- Genome-wide characterization of genetic variants and putative regions under selection in meat and egg-type chicken lines.BMC genomics · 2018Article
- Deciphering signature of selection affecting beef quality traits in Angus cattle.Genes & genomics · 2018Article
- Commercial chicken breeds exhibit highly divergent patterns of linkage disequilibrium.Heredity · 2016Article
- Cryopreservation of specialized chicken lines using cultured primordial germ cells.Poultry science · 2016Article
- Gigwa-Genotype investigator for genome-wide analyses.GigaScience · 2016Article
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Authors and funding
7 authors.
Funding
Abstract
Next-generation sequencing has prompted a surge of discovery of millions of genetic variants from vertebrate genomes. Besides applications in genetic association and linkage studies, a fraction of these variants will have functional consequences. This study describes detection and characterization of 15 million SNPs from chicken genome with the goal to predict variants with potential functional implications (pfVars) from both coding and non-coding regions. The study reports: 183K amino acid-altering SNPs of which 48% predicted as evolutionary intolerant, 13K splicing variants, 51K likely to alter RNA secondary structures, 500K within most conserved elements and 3K from non-coding RNAs. Regions of local fixation within commercial broiler and layer lines were investigated as potential selective sweeps using genome-wide SNP data. Relationships with phenotypes, if any, of the pfVars were explored by overlaying the sweep regions with known QTLs. Based on this, the candidate genes and/or causal mutations for a number of important traits are discussed. Although the fixed variants within sweep regions were enriched with non-coding SNPs, some non-synonymous-intolerant mutations reached fixation, suggesting their possible adaptive advantage. The results presented in this study are expected to have important implications for future genomic research to identify candidate causal mutations and in poultry breeding.
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Registered trials
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 Socratic graph.