ArticlePLoS genetics2021
A 12 kb multi-allelic copy number variation encompassing a GC gene enhancer is associated with mastitis resistance in dairy cattle.
Article in PLoS genetics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers, 1 of them a synthesis that pooled it.
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28 citing papers in PubMed, 1 synthesis or guideline pooled it, 74 citations in OpenAlex.
- Meta-analysis of six dairy cattle breeds reveals biologically relevant candidate genes for mastitis resistance.Genetics, selection, evolution : GSE · 2024Pooled it
- Molecular QTL are enriched for structural variants in a cattle long-read cohort.Communications biology · 2026Article
- Integrative analysis of GWAS, Bayesian fine-mapping, Mendelian randomization and colocalization reveals genetic determinants underlying milk-related traits in dairy cattle.Genetics, selection, evolution : GSE · 2026Article
- Recessive Effect ofAnimals : an open access journal from MDPI · 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
- Detecting and characterizing copy number variation in a large commercial U.S. Holstein cattle population.BMC genomics · 2025Article
- Sequence-based GWAS in 180,000 German Holstein cattle reveals new candidate variants for milk production traits.Genetics, selection, evolution : GSE · 2025Article
- Genome-wide association analysis of body conformation traits in Chinese Holstein Cattle.BMC genomics · 2024Article
- A large structural variant collection in Holstein cattle and associated database for variant discovery, characterization, and application.BMC genomics · 2024Article
- Genetic and genomic analysis of reproduction traits in holstein cattle using SNP chip data and imputed sequence level genotypes.BMC genomics · 2024Article
- RNA-DNA differences in variant calls from cattle tissues result in erroneous eQTLs.BMC genomics · 2024Article
- Using expression data to fine map QTL associated with fertility in dairy cattle.Genetics, selection, evolution : GSE · 2024Article
- Genome-wide association and functional genomic analyses for body conformation traits in North American Holstein cattle.Frontiers in genetics · 2024Article
- Copy number variant scan in more than four thousand Holstein cows bred in Lombardy, Italy.PloS one · 2024Article
- Structural variations in livestock genomes and their associations with phenotypic traits: a review.Frontiers in veterinary science · 2024Review
- Identification of genetic variants and individual genes associated with postpartum hypocalcemia in Holstein cows.Scientific reports · 2023Article
- Structural variants and short tandem repeats impact gene expression and splicing in bovine testis tissue.Genetics · 2023Article
- An organism-wide ATAC-seq peak catalog for the bovine and its use to identify regulatory variants.Genome research · 2023Article
- Robust identification of regulatory variants (eQTLs) using a differential expression framework developed for RNA-sequencing.Journal of animal science and biotechnology · 2023Article
- High-resolution structural variants catalogue in a large-scale whole genome sequenced bovine family cohort data.BMC genomics · 2023Article
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Authors and funding
15 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Clinical mastitis (CM) is an inflammatory disease occurring in the mammary glands of lactating cows. CM is under genetic control, and a prominent CM resistance QTL located on chromosome 6 was reported in various dairy cattle breeds. Nevertheless, the biological mechanism underpinning this QTL has been lacking. Herein, we mapped, fine-mapped, and discovered the putative causal variant underlying this CM resistance QTL in the Dutch dairy cattle population. We identified a ~12 kb multi-allelic copy number variant (CNV), that is in perfect linkage disequilibrium with a lead SNP, as a promising candidate variant. By implementing a fine-mapping and through expression QTL mapping, we showed that the group-specific component gene (GC), a gene encoding a vitamin D binding protein, is an excellent candidate causal gene for the QTL. The multiplicated alleles are associated with increased GC expression and low CM resistance. Ample evidence from functional genomics data supports the presence of an enhancer within this CNV, which would exert cis-regulatory effect on GC. We observed that strong positive selection swept the region near the CNV, and haplotypes associated with the multiplicated allele were strongly selected for. Moreover, the multiplicated allele showed pleiotropic effects for increased milk yield and reduced fertility, hinting that a shared underlying biology for these effects may revolve around the vitamin D pathway. These findings together suggest a putative causal variant of a CM resistance QTL, where a cis-regulatory element located within a CNV can alter gene expression and affect multiple economically important traits.
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