ArticleGenetics, selection, evolution : GSE2020
Inbreeding depression across the genome of Dutch Holstein Friesian dairy cattle.
Article in Genetics, selection, evolution : GSE, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers, 1 of them a synthesis that pooled it.
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Who cites it
16 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Pooled it
- Genetic Diversity and Selection Signatures of Two North American Corriente Cattle Herds in Northeastern New Mexico, United States.International journal of molecular sciences · 2026Article
- Genomic partitioning and functional dissection of inbreeding depression for stature in Brown Swiss cattle.Genetics, selection, evolution : GSE · 2026Article
- Probabilities of two alleles being identity by state at unobserved loci predicted by observed loci in cattle populations.Scientific reports · 2026Article
- A comparative study of runs of homozygosity islands common among 12 Australian beef cattle breeds.Journal of animal science · 2026Article
- Unravelling Heterozygosity-Rich Regions in the Holstein Genome.Animals : an open access journal from MDPI · 2025Article
- Inbreeding patterns and genetic diversity under selection in Teha sheep.Frontiers in genetics · 2025Article
- Exploring inbreeding depression in Brazilian Angus cattle population using pedigree and genomic data.Frontiers in genetics · 2025Article
- Assessment of inbreeding coefficients and inbreeding depression on complex traits from genomic and pedigree data in Nelore cattle.BMC genomics · 2024Article
- Effect of Individual Rate of Inbreeding, Recent and Ancestral Inbreeding on Wool Quality, Muscling Conformation and Exterior in German Sheep Breeds.Animals : an open access journal from MDPI · 2023Article
- Dominance is common in mammals and is associated with trans-acting gene expression and alternative splicing.Genome biology · 2023Article
- Pedigree and genome-based patterns of homozygosity in the South African Ayrshire, Holstein, and Jersey breeds.Frontiers in genetics · 2023Article
- Genomic Prediction Methods Accounting for Nonadditive Genetic Effects.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Inbreeding Calculated with Runs of Homozygosity Suggests Chromosome-Specific Inbreeding Depression Regions in Line 1 Hereford.Animals : an open access journal from MDPI · 2021Article
- Runs of homozygosity analysis reveals consensus homozygous regions affecting production traits in Chinese Simmental beef cattle.BMC genomics · 2021Article
- Grid search approach to discriminate between old and recent inbreeding using phenotypic, pedigree and genomic information.BMC genomics · 2021Article
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6 authors.
Funding
Abstract
backgroundInbreeding depression refers to the decrease in mean performance due to inbreeding. Inbreeding depression is caused by an increase in homozygosity and reduced expression of (on average) favourable dominance effects. Dominance effects and allele frequencies differ across loci, and consequently inbreeding depression is expected to differ along the genome. In this study, we investigated differences in inbreeding depression across the genome of Dutch Holstein Friesian cattle, by estimating dominance effects and effects of regions of homozygosity (ROH).
methodsGenotype (75 k) and phenotype data of 38,792 cows were used. For nine yield, fertility and udder health traits, GREML models were run to estimate genome-wide inbreeding depression and estimate additive, dominance and ROH variance components. For this purpose, we introduced a ROH-based relationship matrix. Additive, dominance and ROH effects per SNP were obtained through back-solving. In addition, a single SNP GWAS was performed to identify significant additive, dominance or ROH associations.
resultsGenome-wide inbreeding depression was observed for all yield, fertility and udder health traits. For example, a 1% increase in genome-wide homozygosity was associated with a decrease in 305-d milk yield of approximately 99 kg. For yield traits only, including dominance and ROH effects in the GREML model resulted in a better fit (P < 0.05) than a model with only additive effects. After correcting for the effect of genome-wide homozygosity, dominance and ROH variance explained less than 1% of the phenotypic variance for all traits. Furthermore, dominance and ROH effects were distributed evenly along the genome. The most notable region with a favourable dominance effect for yield traits was on chromosome 5, but overall few regions with large favourable dominance effects and significant dominance associations were detected. No significant ROH-associations were found.
conclusionsInbreeding depression was distributed quite equally along the genome and was well captured by genome-wide homozygosity. These findings suggest that, based on 75 k SNP data, there is little benefit of accounting for region-specific inbreeding depression in selection schemes.
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