ArticleAnimals : an open access journal from MDPI2021
Investigating the Effect of Imputed Structural Variants from Whole-Genome Sequence on Genome-Wide Association and Genomic Prediction in Dairy Cattle.
Article in Animals : an open access journal from MDPI, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 26 citations in OpenAlex.
- Pan-genomics and multi-omics for deciphering genetic variation and accelerating genetic improvement in ruminant livestock.Functional & integrative genomics · 2026Review
- Accurate imputation of inversions in human genomes using different algorithms and data sources.NAR genomics and bioinformatics · 2026Article
- Integrated Analysis of SNPs and Structural Variations via High-depth Whole-genome Sequencing Reveals the Genetic Architecture and Optimizes Genomic Prediction in Chickens.Poultry science · 2026Article
- Whole genome copy number variation analysis to detect genomic regions for resistance to Haemonchus contortus in Sheep.BMC genomics · 2026Article
- Large deletions in the DNA primase large subunit PRIM2 are associated with NADP-malate dehydrogenase activity in a porcine FAnimal genetics · 2026Article
- Detection and evaluation of copy number variation using both linked-read and short-read sequencing in New Zealand dairy cattle.Frontiers in genetics · 2026Article
- Detection and functional assessment of structural variants using whole-genome re-sequencing data in Nellore cattle.Scientific reports · 2025Article
- Candidate Genes, Markers, Signatures of Selection, and Quantitative Trait Loci (QTLs) and Their Association with Economic Traits in Livestock: Genomic Insights and Selection.International journal of molecular sciences · 2025Review
- DPImpute: A Genotype Imputation Framework for Ultra-Low Coverage Whole-Genome Sequencing and its Application in Genomic Selection.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Systematic benchmarking of tools for structural variation detection using short- and long-read sequencing data in pigs.iScience · 2025Article
- Integrating Gene Expression Data into Single-Step Method (ssBLUP) Improves Genomic Prediction Accuracy for Complex Traits of Duroc × Erhualian FCurrent issues in molecular biology · 2024Article
- A large structural variant collection in Holstein cattle and associated database for variant discovery, characterization, and application.BMC genomics · 2024Article
- Structural variations in livestock genomes and their associations with phenotypic traits: a review.Frontiers in veterinary science · 2024Review
- Importance of genetic architecture in marker selection decisions for genomic prediction.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2023Article
- HIBLUP: an integration of statistical models on the BLUP framework for efficient genetic evaluation using big genomic data.Nucleic acids research · 2023Article
- In it for the long run: perspectives on exploiting long-read sequencing in livestock for population scale studies of structural variants.Genetics, selection, evolution : GSE · 2023Review
- Accurate prediction of quantitative traits with failed SNP calls in canola and maize.Frontiers in plant science · 2023Article
- Structural variants and tandem repeats in the founder individuals of four FBMC genomics · 2022Article
- Article
- A 104-bp Structural Variation of theFrontiers in genetics · 2021Article
Corrections and comments
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Authors and funding
4 authors at 4 institutions in 1 country.
Funding
Abstract
Structural variations (SVs) are large DNA segments of deletions, duplications, copy number variations, inversions and translocations in a re-sequenced genome compared to a reference genome. They have been found to be associated with several complex traits in dairy cattle and could potentially help to improve genomic prediction accuracy of dairy traits. Imputation of SVs was performed in individuals genotyped with single-nucleotide polymorphism (SNP) panels without the expense of sequencing them. In this study, we generated 24,908 high-quality SVs in a total of 478 whole-genome sequenced Holstein and Jersey cattle. We imputed 4489 SVs with R2 > 0.5 into 35,568 Holstein and Jersey dairy cattle with 578,999 SNPs with two pipelines, FImpute and Eagle2.3-Minimac3. Genome-wide association studies for production, fertility and overall type with these 4489 SVs revealed four significant SVs, of which two were highly linked to significant SNP. We also estimated the variance components for SNP and SV models for these traits using genomic best linear unbiased prediction (GBLUP). Furthermore, we assessed the effect on genomic prediction accuracy of adding SVs to GBLUP models. The estimated percentage of genetic variance captured by SVs for production traits was up to 4.57% for milk yield in bulls and 3.53% for protein yield in cows. Finally, no consistent increase in genomic prediction accuracy was observed when including SVs in GBLUP.
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