ArticleBMC genomics2016
Revealing misassembled segments in the bovine reference genome by high resolution linkage disequilibrium scan.
Article in BMC genomics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Implementation of Metafounders in the Genomic Prediction for the Polled Trait in Brahman Cattle Using a Multi-Breed Population.Animal genetics · 2026Article
- Detection of breeding signatures in wheat using a linkage disequilibrium-corrected mapping approach.Scientific reports · 2021Article
- Investigating the accuracy of imputing autosomal variants in Nellore cattle using the ARS-UCD1.2 assembly of the bovine genome.BMC genomics · 2020Article
- Linkage Disequilibrium-Based Inference of Genome Homology and Chromosomal Rearrangements Between Species.G3 (Bethesda, Md.) · 2020Article
- An improved pig reference genome sequence to enable pig genetics and genomics research.GigaScience · 2020Article
- Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks.Genome research · 2019Article
- Genome Sequence Analysis Reveals Selection Signatures in Endangered Trypanotolerant West African Muturu Cattle.Frontiers in genetics · 2019Article
- SNPrune: an efficient algorithm to prune large SNP array and sequence datasets based on high linkage disequilibrium.Genetics, selection, evolution : GSE · 2018Article
- Genome-wide association study provides insights into genes related with horn development in Nelore beef cattle.PloS one · 2018Article
- Estimation of Recombination Rate and Maternal Linkage Disequilibrium in Half-Sibs.Frontiers in genetics · 2018Article
- Age-based partitioning of individual genomic inbreeding levels in Belgian Blue cattle.Genetics, selection, evolution : GSE · 2017Article
- A PLAG1 mutation contributed to stature recovery in modern cattle.Scientific reports · 2017Article
- Evaluation of the accuracy of imputed sequence variant genotypes and their utility for causal variant detection in cattle.Genetics, selection, evolution : GSE · 2017Article
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Authors and funding
11 authors.
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Abstract
backgroundMisassembly signatures, created by shuffling the order of sequences while assembling a genome, can be detected by the unexpected behavior of marker linkage disequilibrium (LD) decay. We developed a heuristic process to identify misassembly signatures, applied it to the bovine reference genome assembly (UMDv3.1) and presented the consequences of misassemblies in two case studies.
resultsWe identified 2,906 single nucleotide polymorphism (SNP) markers presenting unexpected LD decay behavior in 626 putative misassembled contigs, which comprised less than 1 % of the whole genome. Although this represents a small fraction of the reference sequence, these poorly assembled segments can lead to severe implications to local genome context. For instance, we showed that one of the misassembled regions mapped to the POLL locus, which affected the annotation of positional candidate genes in a GWAS case study for polledness in Nellore (Bos indicus beef cattle). Additionally, we found that poorly performing markers in imputation mapped to putative misassembled regions, and that correction of marker positions based on LD was capable to recover imputation accuracy.
conclusionsThis heuristic approach can be useful to cross validate reference assemblies and to filter out markers located at low confidence genomic regions before conducting downstream analyses.
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