ArticleBMC genomics2018
Genome-wide characterization of genetic variants and putative regions under selection in meat and egg-type chicken lines.
Article in BMC genomics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed, 56 citations in OpenAlex.
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- Selection signature analysis in chickens divergently selected for growth rate reveals novel candidate genes regulating fat deposition.BMC genomics · 2025Article
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- Advances in Genomics and Postgenomics in Poultry Science: Current Achievements and Future Directions.International journal of molecular sciences · 2025Review
- Whole-Genome Resequencing Analysis of Athletic Traits in Grassland-Thoroughbred.Animals : an open access journal from MDPI · 2025Article
- Whole genome sequencing of three native chicken varieties (Common Deshi, Hilly and Naked Neck) of Bangladesh.Scientific data · 2024Article
- Runs of homozygosity and selection signature analyses reveal putative genomic regions for artificial selection in layer breeding.BMC genomics · 2024Article
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- RNA-Seq-based discovery of genetic variants and allele-specific expression of two layer lines and broiler chicken.Evolutionary applications · 2023Article
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- Assessing Genomic Diversity and Signatures of Selection in Chinese Red Steppe Cattle Using High-Density SNP Array.Animals : an open access journal from MDPI · 2023Article
- Parent-offspring genotyped trios unravelling genomic regions with gametic and genotypic epistatic transmission bias on the cattle genome.Frontiers in genetics · 2023Article
- Fourth Report on Chicken Genes and Chromosomes 2022.Cytogenetic and genome research · 2022Review
- Mutations in Growth-Related Genes Induced by EMS Treatment in Scallops.Frontiers in genetics · 2022Article
- Assessing the Genetic Background and Selection Signatures of Huaxi Cattle Using High-Density SNP Array.Animals : an open access journal from MDPI · 2021Article
- A genome-wide scan to identify signatures of selection in two Iranian indigenous chicken ecotypes.Genetics, selection, evolution : GSE · 2021Article
- Analysis of selection signatures on the Z chromosome of bidirectional selection broiler lines for the assessment of abdominal fat content.BMC genomic data · 2021Article
- Whole-genome resequencing reveals loci with allelic transmission ratio distortion in FMolecular genetics and genomics : MGG · 2021Article
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Authors and funding
10 authors at 4 institutions in 4 countries.
Funding
Abstract
backgroundMeat and egg-type chickens have been selected for several generations for different traits. Artificial and natural selection for different phenotypes can change frequency of genetic variants, leaving particular genomic footprints throghtout the genome. Thus, the aims of this study were to sequence 28 chickens from two Brazilian lines (meat and white egg-type) and use this information to characterize genome-wide genetic variations, identify putative regions under selection using Fst method, and find putative pathways under selection.
resultsA total of 13.93 million SNPs and 1.36 million INDELs were identified, with more variants detected from the broiler (meat-type) line. Although most were located in non-coding regions, we identified 7255 intolerant non-synonymous SNPs, 512 stopgain/loss SNPs, 1381 frameshift and 1094 non-frameshift INDELs that may alter protein functions. Genes harboring intolerant non-synonymous SNPs affected metabolic pathways related mainly to reproduction and endocrine systems in the white-egg layer line, and lipid metabolism and metabolic diseases in the broiler line. Fst analysis in sliding windows, using SNPs and INDELs separately, identified over 300 putative regions of selection overlapping with more than 250 genes. For the first time in chicken, INDEL variants were considered for selection signature analysis, showing high level of correlation in results between SNP and INDEL data. The putative regions of selection signatures revealed interesting candidate genes and pathways related to important phenotypic traits in chicken, such as lipid metabolism, growth, reproduction, and cardiac development.
conclusionsIn this study, Fst method was applied to identify high confidence putative regions under selection, providing novel insights into selection footprints that can help elucidate the functional mechanisms underlying different phenotypic traits relevant to meat and egg-type chicken lines. In addition, we generated a large catalog of line-specific and common genetic variants from a Brazilian broiler and a white egg layer line that can be used for genomic studies involving association analysis with phenotypes of economic interest to the poultry industry.
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