ArticleBMC genomics2021
Characterization of a haplotype-reference panel for genotyping by low-pass sequencing in Swiss Large White pigs.
Article in BMC genomics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers, 1 of them a synthesis that pooled it.
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19 citing papers in PubMed, 1 synthesis or guideline pooled it, 39 citations in OpenAlex.
- Comparison of two multi-trait association testing methods and sequence-based fine mapping of six additive QTL in Swiss Large White pigs.BMC genomics · 2023Pooled it
- Low-pass whole-genome sequencing reveals genomic diversity and ecotype-specific adaptation in indigenous Tigrayan chickens.Scientific reports · 2026Article
- The influence of structural variants from 2445 pigs on gene expression and complex traits.Nature communications · 2026Article
- Genetic analysis of iris pigmentation in Swiss pig breeds identifies a missense KITLG variant as a potential causal factor for pale and heterochromatic irises.Genetics, selection, evolution : GSE · 2026Article
- Runs of homozygosity reveal candidate genes for economic traits in Danish Large White pigs.Archives animal breeding · 2026Article
- Genomic insights into the demographic history and local adaptation of wild boars across Eurasia.Cell genomics · 2025Article
- Single-variant genome-wide association study and regional heritability mapping of protein efficiency and performance traits in Large White pigs.Genetics, selection, evolution : GSE · 2025Article
- The 1000 Chinese Indigenous Pig Genomes Project provides insights into the genomic architecture of pigs.Nature communications · 2024Article
- Optimization of Whole-Genome Resequencing Depth for High-Throughput SNP Genotyping inInternational journal of molecular sciences · 2024Article
- Deciphering the population structure and genetic basis of growth traits from whole-genome resequencing of the leopard coral grouper (Zoological research · 2024Article
- Low-pass sequencing plus imputation using avidity sequencing displays comparable imputation accuracy to sequencing by synthesis while reducing duplicates.G3 (Bethesda, Md.) · 2024Article
- Detection of Runs of Homozygosity and Identification of Candidate Genes in the Whole Genome of Tunchang Pigs.Animals : an open access journal from MDPI · 2024Article
- Exploiting public databases of genomic variation to quantify evolutionary constraint on the branch point sequence in 30 plant and animal species.Nucleic acids research · 2023Article
- Recent advances in the genomic resources for sheep.Mammalian genome : official journal of the International Mammalian Genome Society · 2023Review
- Accurate haplotype construction and detection of selection signatures enabled by high quality pig genome sequences.Nature communications · 2023Article
- The size and composition of haplotype reference panels impact the accuracy of imputation from low-pass sequencing in cattle.Genetics, selection, evolution : GSE · 2023Article
- Animal-SNPAtlas: a comprehensive SNP database for multiple animals.Nucleic acids research · 2023Article
- Best practices for analyzing imputed genotypes from low-pass sequencing in dogs.Mammalian genome : official journal of the International Mammalian Genome Society · 2022Article
- Mining massive genomic data of two Swiss Braunvieh cattle populations reveals six novel candidate variants that impair reproductive success.Genetics, selection, evolution : GSE · 2021Article
Corrections and comments
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe key-ancestor approach has been frequently applied to prioritize individuals for whole-genome sequencing based on their marginal genetic contribution to current populations. Using this approach, we selected 70 key ancestors from two lines of the Swiss Large White breed that have been selected divergently for fertility and fattening traits and sequenced their genomes with short paired-end reads.
resultsUsing pedigree records, we estimated the effective population size of the dam and sire line to 72 and 44, respectively. In order to assess sequence variation in both lines, we sequenced the genomes of 70 boars at an average coverage of 16.69-fold. The boars explained 87.95 and 95.35% of the genetic diversity of the breeding populations of the dam and sire line, respectively. Reference-guided variant discovery using the GATK revealed 26,862,369 polymorphic sites. Principal component, admixture and fixation index (F
conclusionsWe assessed genetic diversity within and between two lines of the Swiss Large White pig breed. Our analyses revealed considerable differentiation, even though the split into two populations occurred only few generations ago. The sequenced haplotypes of the key ancestor animals enabled us to implement genotyping by low-pass sequencing which offers an intriguing cost-effective approach to increase the variant density over current array-based genotyping by more than 350-fold.
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