ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2018
Genome-wide mapping of large deletions and their population-genetic properties in dairy cattle.
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 34 citations in OpenAlex.
- Genetic advancements and future directions in ruminant livestock breeding: from reference genomes to multiomics innovations.Science China. Life sciences · 2025Review
- A large structural variant collection in Holstein cattle and associated database for variant discovery, characterization, and application.BMC genomics · 2024Article
- Genome-Wide Analysis of Genetic Diversity and Selection Signatures in Zaobei Beef Cattle.Animals : an open access journal from MDPI · 2024Article
- Article
- Structural variants and short tandem repeats impact gene expression and splicing in bovine testis tissue.Genetics · 2023Article
- High-resolution structural variants catalogue in a large-scale whole genome sequenced bovine family cohort data.BMC genomics · 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
- Article
- High confidence copy number variants identified in Holstein dairy cattle from whole genome sequence and genotype array data.Scientific reports · 2020Article
- Functional and population genetic features of copy number variations in two dairy cattle populations.BMC genomics · 2020Article
- Review: Genomics of bull fertility.Animal : an international journal of animal bioscience · 2018Review
Corrections and comments
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Authors and funding
8 authors at 4 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Large genomic deletions are potential candidate for loss-of-function, which could be lethal as homozygote. Analysing whole genome data of 175 cattle, we report 8,480 large deletions (199 bp-773 KB) with an overall false discovery rate of 8.8%; 82% of which are novel compared with deletions in the dbVar database. Breakpoint sequence analyses revealed that majority (24 of 29 tested) of the deletions contain microhomology/homology at breakpoint, and therefore, most likely generated by microhomology-mediated end joining. We observed higher differentiation among breeds for deletions in some genic-regions, such as ABCA12, TTC1, VWA3B, TSHR, DST/BPAG1, and CD1D. The genes overlapping deletions are on average evolutionarily less conserved compared with known mouse lethal genes (P-value = 2.3 × 10-6). We report 167 natural gene knockouts in cattle that are apparently nonessential as live homozygote individuals are observed. These genes are functionally enriched for immunoglobulin domains, olfactory receptors, and MHC classes (FDR = 2.06 × 10-22, 2.06 × 10-22, 7.01 × 10-6, respectively). We also demonstrate that deletions are enriched for health and fertility related quantitative trait loci (2-and 1.5-fold enrichment, Fisher's P-value = 8.91 × 10-10 and 7.4 × 10-11, respectively). Finally, we identified and confirmed the breakpoint of a ∼525 KB deletion on Chr23:12,291,761-12,817,087 (overlapping BTBD9, GLO1 and DNAH8), causing stillbirth in Nordic Red Cattle.
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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 OpenQuestion graph.