ArticleGenome research2024
Pangenome-genotyped structural variation improves molecular phenotype mapping in cattle.
Article in Genome research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
27 citing papers in PubMed.
- Pan-genomics and multi-omics for deciphering genetic variation and accelerating genetic improvement in ruminant livestock.Functional & integrative genomics · 2026Review
- Resolving Cattle GWAS Loci: Current Progress, Persistent Challenges and Future Directions.Current issues in molecular biology · 2026Review
- Pangenome-based structural variant imputation enables large-scale genotype-phenotype studies in dairy cattle.Nature communications · 2026Article
- Building and applying pangenome references to capture genetic diversity.Nature reviews. Genetics · 2026Review
- Haplotype-Resolved Genome Assemblies for Norwegian Red Cattle.Animal genetics · 2026Article
- Phased-assembly-driven pangenome graphs for structural variant genotyping and complex trait mapping in dairy cattle.Nature communications · 2026Article
- Molecular QTL are enriched for structural variants in a cattle long-read cohort.Communications biology · 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
- Advancements in Animal Breeding: From Mendelian Genetics to Machine Learning.International journal of molecular sciences · 2025Review
- High-quality phased genome assemblies of line-bred Korean Hanwoo cattle.Scientific data · 2025Article
- Application of a French cattle pangenome, from structural variant discovery to association studies on key phenotypes.Genetics, selection, evolution : GSE · 2025Article
- 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
- Haplotype-resolved genome and pan-genome graphs reveal the impacts of structural variation on functional genome and feather colors in chickens.iMetaOmics · 2025Article
- Genetic regulation of sperm DNA methylation in cattle through meQTL mapping.BMC genomics · 2025Article
- Structural Variations Associated with Adaptation and Coat Color in Qinghai-Tibetan Plateau Cattle.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Overcoming limitations to customize DeepVariant for domesticated animals with TrioTrain.Genome research · 2025Article
- Integrating parental genomes to reduce reference bias and identify intramuscular fat genes in Qinchuan Black pigs.Journal of animal science and biotechnology · 2025Article
- Taurine pangenome uncovers a segmental duplication upstream ofGenome research · 2025Article
- Graphical pangenomics-enabled characterization of structural variant impact on gene expression in Brassica napus.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Expression and splicing quantitative trait loci (e/sQTL) are large contributors to phenotypic variability. Achieving sufficient statistical power for e/sQTL mapping requires large cohorts with both genotypes and molecular phenotypes, and so, the genomic variation is often called from short-read alignments, which are unable to comprehensively resolve structural variation. Here we build a pangenome from 16 HiFi haplotype-resolved cattle assemblies to identify small and structural variation and genotype them with PanGenie in 307 short-read samples. We find high (>90%) concordance of PanGenie-genotyped and DeepVariant-called small variation and confidently genotype close to 21 million small and 43,000 structural variants in the larger population. We validate 85% of these structural variants (with MAF > 0.1) directly with a subset of 25 short-read samples that also have medium coverage HiFi reads. We then conduct e/sQTL mapping with this comprehensive variant set in a subset of 117 cattle that have testis transcriptome data, and find 92 structural variants as causal candidates for eQTL and 73 for sQTL. We find that roughly half of the top associated structural variants affecting expression or splicing are transposable elements, such as SV-eQTL for
Indexed as
Identifiers
What Socratic holds
Registered trials
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 Socratic graph.