ArticleBMC genomics2015
Investigation of regions impacting inbreeding depression and their association with the additive genetic effect for United States and Australia Jersey dairy cattle.
Article in BMC genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 32 citations in OpenAlex.
- Identification of runs of homozygosity associated with male fertility in Italian Brown Swiss cattle.Frontiers in genetics · 2023Article
- Inbreeding Calculated with Runs of Homozygosity Suggests Chromosome-Specific Inbreeding Depression Regions in Line 1 Hereford.Animals : an open access journal from MDPI · 2021Article
- Identification of unique ROH regions with unfavorable effects on production and fertility traits in Canadian Holsteins.Genetics, selection, evolution : GSE · 2021Article
- The value of genomic relationship matrices to estimate levels of inbreeding.Genetics, selection, evolution : GSE · 2021Article
- Effect of recent and ancient inbreeding on production and fertility traits in Canadian Holsteins.BMC genomics · 2020Article
- Population structure and genetic diversity in Colombian Simmental cattle.Tropical animal health and production · 2020Article
- Inbreeding depression due to recent and ancient inbreeding in Dutch Holstein-Friesian dairy cattle.Genetics, selection, evolution : GSE · 2019Article
- Inbreeding depression in line 1 Hereford cattle population using pedigree and genomic information.Journal of animal science · 2019Article
- Non-additive Effects in Genomic Selection.Frontiers in genetics · 2018Review
- Effects of abiotic factors on ecosystem health of Taihu Lake, China based on eco-exergy theory.Scientific reports · 2017Article
- Genomics advances the study of inbreeding depression in the wild.Evolutionary applications · 2016Review
- Characterization and management of long runs of homozygosity in parental nucleus lines and their associated crossbred progeny.Genetics, selection, evolution : GSE · 2016Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundVariation in environment, management practices, nutrition or selection objectives has led to a variety of different choices being made in the use of genetic material between countries. Differences in genome-level homozygosity between countries may give rise to regions that result in inbreeding depression to differ. The objective of this study was to characterize regions that have an impact on a runs of homozygosity (ROH) metric and estimate their association with the additive genetic effect of milk (MY), fat (FY) and protein yield (PY) and calving interval (CI) using Australia (AU) and United States (US) Jersey cows.
methodsGenotyped cows with phenotypes on MY, FY and PY (n = 6751 US; n = 3974 AU) and CI (n = 5816 US; n = 3905 AU) were used in a two-stage analysis. A ROH statistic (ROH4Mb), which counts the frequency of a SNP being in a ROH of at least 4 Mb was calculated across the genome. In the first stage, residuals were obtained from a model that accounted for the portion explained by the estimated breeding value. In the second stage, these residuals were regressed on ROH4Mb using a single marker regression model and a gradient boosted machine (GBM) algorithm. The relationship between the additive and ROH4Mb of a region was characterized based on the (co)variance of 500 kb estimated genomic breeding values derived from a Bayesian LASSO analysis. Phenotypes to determine ROH4Mb and additive effects were residuals from the two-stage approach and yield deviations, respectively.
resultsAssociations between yield traits and ROH4Mb were found for regions on BTA13, BTA23 and BTA25 for the US population and BTA3, BTA7, BTA17 for the AU population. Only one association (BTA7) was found for CI and ROH4Mb for the US population. Multiple potential epistatic interactions were characterized based on the GBM analysis. Lastly, the covariance sign between ROH4Mb and additive SNP effect of a region was heterogeneous across the genome.
conclusionWe identified multiple genomic regions associated with ROH4Mb in US and AU Jersey females. The covariance of regions impacting ROH4Mb and the additive genetic effect were positive and negative, which provides evidence that the homozygosity effect is location dependent.
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