ArticleGenome biology2020
Bovine breed-specific augmented reference graphs facilitate accurate sequence read mapping and unbiased variant discovery.
Article in Genome biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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37 citing papers in PubMed, 64 citations in OpenAlex.
- European ash pangenome reveals widespread structural variation and genetic basis of low ash dieback susceptibility.Nature communications · 2026Article
- Pan-genomics and multi-omics for deciphering genetic variation and accelerating genetic improvement in ruminant livestock.Functional & integrative genomics · 2026Review
- Pangenome-based structural variant imputation enables large-scale genotype-phenotype studies in dairy cattle.Nature communications · 2026Article
- Phylogeny-driven pangenome analysis uncovers the genomic landscape of domesticated and wild Armeniaca species.Horticulture research · 2026Article
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- Phased-assembly-driven pangenome graphs for structural variant genotyping and complex trait mapping in dairy cattle.Nature communications · 2026Article
- The chromosome-level genome of Chinese indicine cattle breed provides insights into bovine adaptation and immunity.DNA research : an international journal for rapid publication of reports on genes and genomes · 2026Article
- Long read and preliminary pangenome analyses reveal breed-specific structural variations and novel sequences in Holstein and Jersey cattle.Journal of advanced research · 2026Article
- Exploring cattle structural variation in the era of long reads, pangenome graphs, and near-complete assemblies.Journal of animal science and biotechnology · 2025Review
- Global Pangenome Analysis Highlights the Critical Role of Structural Variants in Cattle Improvement and Identifies a Unique Event as a Novel Enhancer in IGFBP7+ Cells.Molecular biology and evolution · 2025Article
- Pangenome graph mitigates heterozygosity overestimation from mapping bias: a case study in Chinese indigenous pigs.BMC biology · 2025Article
- A gentle introduction to pangenomics.Briefings in bioinformatics · 2024Review
- An overview of recent technological developments in bovine genomics.Veterinary and animal science · 2024Review
- Beef Cattle Genome Project: Advances in Genome Sequencing, Assembly, and Functional Genes Discovery.International journal of molecular sciences · 2024Review
- Measuring, visualizing, and diagnosing reference bias with biastools.Genome biology · 2024Article
- When Livestock Genomes Meet Third-Generation Sequencing Technology: From Opportunities to Applications.Genes · 2024Review
- Measuring, visualizing and diagnosing reference bias with biastools.bioRxiv : the preprint server for biology · 2024Article
- DNA methylation analysis to differentiate reference, breed, and parent-of-origin effects in the bovine pangenome era.GigaScience · 2024Article
- Article
- Recent advances in the genomic resources for sheep.Mammalian genome : official journal of the International Mammalian Genome Society · 2023Review
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe current bovine genomic reference sequence was assembled from a Hereford cow. The resulting linear assembly lacks diversity because it does not contain allelic variation, a drawback of linear references that causes reference allele bias. High nucleotide diversity and the separation of individuals by hundreds of breeds make cattle ideally suited to investigate the optimal composition of variation-aware references.
resultsWe augment the bovine linear reference sequence (ARS-UCD1.2) with variants filtered for allele frequency in dairy (Brown Swiss, Holstein) and dual-purpose (Fleckvieh, Original Braunvieh) cattle breeds to construct either breed-specific or pan-genome reference graphs using the vg toolkit. We find that read mapping is more accurate to variation-aware than linear references if pre-selected variants are used to construct the genome graphs. Graphs that contain random variants do not improve read mapping over the linear reference sequence. Breed-specific augmented and pan-genome graphs enable almost similar mapping accuracy improvements over the linear reference. We construct a whole-genome graph that contains the Hereford-based reference sequence and 14 million alleles that have alternate allele frequency greater than 0.03 in the Brown Swiss cattle breed. Our novel variation-aware reference facilitates accurate read mapping and unbiased sequence variant genotyping for SNPs and Indels.
conclusionsWe develop the first variation-aware reference graph for an agricultural animal ( https://doi.org/10.5281/zenodo.3759712 ). Our novel reference structure improves sequence read mapping and variant genotyping over the linear reference. Our work is a first step towards the transition from linear to variation-aware reference structures in species with high genetic diversity and many sub-populations.
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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 OpenQuestion graph.