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Article
Open AccessGenomic prediction using a reference population of multiple pure breeds and admixed individuals
In dairy cattle populations in which crossbreeding has been used, animals show some level of diversity in their origins. In rotational crossbreeding, for instance, crossbred dams are mated with purebred sires ...
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Article
Open AccessNovel approach to incorporate information about recessive lethal genes increases the accuracy of genomic prediction for mortality traits
The genetic underpinnings of calf mortality can be partly polygenic and partly due to deleterious effects of recessive lethal alleles. Prediction of the genetic merits of selection candidates should thus take ...
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Article
Open AccessCorrection: Multi-trait single-step genomic prediction accounting for heterogeneous (co)variances over the genome
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Article
Open AccessMulti-trait single-step genomic prediction accounting for heterogeneous (co)variances over the genome
Widely used genomic prediction models may not properly account for heterogeneous (co)variance structure across the genome. Models such as BayesA and BayesB assume locus-specific variance, which are highly infl...
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Article
Open AccessReliability of genomic prediction for milk fatty acid composition by using a multi-population reference and incorporating GWAS results
Large-scale phenoty** for detailed milk fatty acid (FA) composition is difficult due to expensive and time-consuming analytical techniques. Reliability of genomic prediction is often low for traits that are ...
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Article
Meta-analysis of genome-wide association studies for cattle stature identifies common genes that regulate body size in mammals
Stature is affected by many polymorphisms of small effect in humans 1 . In contrast, variation in dogs, even within breeds, has been suggested to be largely due to variants in a ...
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Article
Open AccessModeling heterogeneous (co)variances from adjacent-SNP groups improves genomic prediction for milk protein composition traits
Accurate genomic prediction requires a large reference population, which is problematic for traits that are expensive to measure. Traits related to milk protein composition are not routinely recorded due to co...
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Article
Open AccessSequence variants selected from a multi-breed GWAS can improve the reliability of genomic predictions in dairy cattle
Sequence data can potentially increase the reliability of genomic predictions, because such data include causative mutations instead of relying on linkage disequilibrium (LD) between causative mutations and pr...
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Article
Open AccessGenetic evaluation for three-way crossbreeding
Commercial pig producers generally use a terminal crossbreeding system with three breeds. Many pig breeding organisations have started to use genomic selection for which genetic evaluation is often done by app...
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Article
Open AccessGenome-wide association study for female fertility in Nordic Red cattle
The Nordic Red Cattle (NRC) consists of animls belonging to the Danish Red, Finnish Ayrshire, and Swedish Red breeds. Compared to the Holstein breed, NRC animals are smaller, have a shorter calving interval, lowe...
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Article
Open AccessSelection of haplotype variables from a high-density marker map for genomic prediction
Using haplotype blocks as predictors rather than individual single nucleotide polymorphisms (SNPs) may improve genomic predictions, since haplotypes are in stronger linkage disequilibrium with the quantitative...
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Article
Open AccessEstimation of inbreeding using pedigree, 50k SNP chip genotypes and full sequence data in three cattle breeds
Levels of inbreeding in cattle populations have increased in the past due to the use of a limited number of bulls for artificial insemination. High levels of inbreeding lead to reduced genetic diversity and in...
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Article
Open AccessRuns of homozygosity and distribution of functional variants in the cattle genome
Recent developments in sequencing technology have facilitated widespread investigations of genomic variants, including continuous stretches of homozygous genomic regions. For cattle, a large proportion of thes...
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Article
Open AccessAssociation analysis for udder health based on SNP-panel and sequence data in Danish Holsteins
The sensitivity of genome-wide association studies for the detection of quantitative trait loci (QTL) depends on the density of markers examined and the statistical models used. This study compares the perform...
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Article
Open AccessIdentification of genomic regions associated with female fertility in Danish Jersey using whole genome sequence data
Female fertility is an important trait in cattle breeding programs. In the Nordic countries selection is based on a fertility index (FTI). The fertility index is a weighted combination of four female fertility...
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Article
Open AccessLoci associated with adult stature also affect calf birth survival in cattle
Understanding the underlying pleiotropic relationships among quantitative traits is necessary in order to predict correlated responses to artificial selection. The availability of large-scale next-generation s...
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Article
Open AccessGenomic prediction of genetic merit using LD-based haplotypes in the Nordic Holstein population
A haplotype approach to genomic prediction using high density data in dairy cattle as an alternative to single-marker methods is presented. With the assumption that haplotypes are in stronger linkage disequili...
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Article
Open AccessFine map** QTL for female fertility on BTA04 and BTA13 in dairy cattle using HD SNP and sequence data
Female fertility is important for the maintenance of the production in a dairy cattle herd. Two QTL regions on BTA04 and on BTA13 previously detected in Nordic Holstein (NH) and validated in the Danish Jersey ...
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Article
Whole-genome sequencing of 234 bulls facilitates map** of monogenic and complex traits in cattle
Ben Hayes and colleagues report the whole-genome sequencing of 234 bulls as phase one of the 1000 bull genomes project. They identify 28.3 million variants in the cattle sequences and also report genome-wide a...
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Article
Open AccessGenomic relationships based on X chromosome markers and accuracy of genomic predictions with and without X chromosome markers
Although the X chromosome is the second largest bovine chromosome, markers on the X chromosome are not used for genomic prediction in some countries and populations. In this study, we presented a method for co...
