ArticleBMC genomics2011
Structural variation in the chicken genome identified by paired-end next-generation DNA sequencing of reduced representation libraries.
Article in BMC genomics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Whole-Genome Sequencing Reveals Genetic Diversity and Structure of Taiwan Commercial Red-Feathered Country Chickens.Animals : an open access journal from MDPI · 2026Article
- Genome Wide Identification of Structure Variations in Five Italian Turkey Populations.Animals : an open access journal from MDPI · 2025Article
- A comprehensive map of copy number variations in dromedary camels based on whole genome sequence data.Scientific reports · 2024Article
- Assessment of linkage disequilibrium patterns between structural variants and single nucleotide polymorphisms in three commercial chicken populations.BMC genomics · 2022Article
- The Chicken Pan-Genome Reveals Gene Content Variation and a Promoter Region Deletion in IGF2BP1 Affecting Body Size.Molecular biology and evolution · 2021Article
- Identification of Copy Number Variation in Domestic Chicken Using Whole-Genome Sequencing Reveals Evidence of Selection in the Genome.Animals : an open access journal from MDPI · 2019Article
- Article
- Structural Variant Detection by Large-scale Sequencing Reveals New Evolutionary Evidence on Breed Divergence between Chinese and European Pigs.Scientific reports · 2016Article
- aCGH Analysis to Estimate Genetic Variations among Domesticated Chickens.BioMed research international · 2016Article
- Genome Wide Sampling Sequencing for SNP Genotyping: Methods, Challenges and Future Development.International journal of biological sciences · 2016Review
- Article
- Generation of SNP datasets for orangutan population genomics using improved reduced-representation sequencing and direct comparisons of SNP calling algorithms.BMC genomics · 2014Article
- The challenges and importance of structural variation detection in livestock.Frontiers in genetics · 2014Review
- Identification of null alleles and deletions from SNP genotypes for an intercross between domestic and wild chickens.G3 (Bethesda, Md.) · 2013Article
- Genome-wide patterns of genetic variation in two domestic chickens.Genome biology and evolution · 2013Article
- A complex genomic rearrangement involving the endothelin 3 locus causes dermal hyperpigmentation in the chicken.PLoS genetics · 2011Article
- Genome-wide genetic marker discovery and genotyping using next-generation sequencing.Nature reviews. Genetics · 2011Review
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6 authors.
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Abstract
backgroundVariation within individual genomes ranges from single nucleotide polymorphisms (SNPs) to kilobase, and even megabase, sized structural variants (SVs), such as deletions, insertions, inversions, and more complex rearrangements. Although much is known about the extent of SVs in humans and mice, species in which they exert significant effects on phenotypes, very little is known about the extent of SVs in the 2.5-times smaller and less repetitive genome of the chicken.
resultsWe identified hundreds of shared and divergent SVs in four commercial chicken lines relative to the reference chicken genome. The majority of SVs were found in intronic and intergenic regions, and we also found SVs in the coding regions. To identify the SVs, we combined high-throughput short read paired-end sequencing of genomic reduced representation libraries (RRLs) of pooled samples from 25 individuals and computational mapping of DNA sequences from a reference genome.
conclusionWe provide a first glimpse of the high abundance of small structural genomic variations in the chicken. Extrapolating our results, we estimate that there are thousands of rearrangements in the chicken genome, the majority of which are located in non-coding regions. We observed that structural variation contributes to genetic differentiation among current domesticated chicken breeds and the Red Jungle Fowl. We expect that, because of their high abundance, SVs might explain phenotypic differences and play a role in the evolution of the chicken genome. Finally, our study exemplifies an efficient and cost-effective approach for identifying structural variation in sequenced genomes.
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