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Impact of QTL properties on the accuracy of multi-breed genomic prediction

Overview of attention for article published in Genetics Selection Evolution, May 2015
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  • Above-average Attention Score compared to outputs of the same age (52nd percentile)

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Title
Impact of QTL properties on the accuracy of multi-breed genomic prediction
Published in
Genetics Selection Evolution, May 2015
DOI 10.1186/s12711-015-0124-6
Pubmed ID
Authors

Yvonne CJ Wientjes, Mario PL Calus, Michael E Goddard, Ben J Hayes

Abstract

Although simulation studies show that combining multiple breeds in one reference population increases accuracy of genomic prediction, this is not always confirmed in empirical studies. This discrepancy might be due to the assumptions on quantitative trait loci (QTL) properties applied in simulation studies, including number of QTL, spectrum of QTL allele frequencies across breeds, and distribution of allele substitution effects. We investigated the effects of QTL properties and of including a random across- and within-breed animal effect in a genomic best linear unbiased prediction (GBLUP) model on accuracy of multi-breed genomic prediction using genotypes of Holstein-Friesian and Jersey cows. Genotypes of three classes of variants obtained from whole-genome sequence data, with moderately low, very low or extremely low average minor allele frequencies (MAF), were imputed in 3000 Holstein-Friesian and 3000 Jersey cows that had real high-density genotypes. Phenotypes of traits controlled by QTL with different properties were simulated by sampling 100 or 1000 QTL from one class of variants and their allele substitution effects either randomly from a gamma distribution, or computed such that each QTL explained the same variance, i.e. rare alleles had a large effect. Genomic breeding values for 1000 selection candidates per breed were estimated using GBLUP modelsincluding a random across- and a within-breed animal effect. For all three classes of QTL allele frequency spectra, accuracies of genomic prediction were not affected by the addition of 2000 individuals of the other breed to a reference population of the same breed as the selection candidates. Accuracies of both single- and multi-breed genomic prediction decreased as MAF of QTL decreased, especially when rare alleles had a large effect. Accuracies of genomic prediction were similar for the models with and without a random within-breed animal effect, probably because of insufficient power to separate across- and within-breed animal effects. Accuracy of both single- and multi-breed genomic prediction depends on the properties of the QTL that underlie the trait. As QTL MAF decreased, accuracy decreased, especially when rare alleles had a large effect. This demonstrates that QTL properties are key parameters that determine the accuracy of genomic prediction.

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Mendeley readers

The data shown below were compiled from readership statistics for 54 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 2 4%
Colombia 1 2%
Germany 1 2%
Unknown 50 93%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 16 30%
Student > Master 12 22%
Researcher 9 17%
Student > Doctoral Student 3 6%
Other 2 4%
Other 8 15%
Unknown 4 7%
Readers by discipline Count As %
Agricultural and Biological Sciences 40 74%
Biochemistry, Genetics and Molecular Biology 3 6%
Veterinary Science and Veterinary Medicine 1 2%
Mathematics 1 2%
Environmental Science 1 2%
Other 1 2%
Unknown 7 13%

Attention Score in Context

This research output has an Altmetric Attention Score of 2. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 14 July 2015.
All research outputs
#11,512,503
of 19,486,994 outputs
Outputs from Genetics Selection Evolution
#371
of 666 outputs
Outputs of similar age
#111,708
of 241,142 outputs
Outputs of similar age from Genetics Selection Evolution
#2
of 2 outputs
Altmetric has tracked 19,486,994 research outputs across all sources so far. This one is in the 40th percentile – i.e., 40% of other outputs scored the same or lower than it.
So far Altmetric has tracked 666 research outputs from this source. They receive a mean Attention Score of 4.1. This one is in the 43rd percentile – i.e., 43% of its peers scored the same or lower than it.
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We're also able to compare this research output to 2 others from the same source and published within six weeks on either side of this one.