Genetic architecture of complex traits and accuracy of genomic Prediction: Coat colour, Milk-fat percentage, and type in holstein cattle as contrasting model traits

Hayes, Ben J., Pryce, Jennie, Chamberlain, Amanda J., Bowman, Phil J. and Goddard, Mike E. (2010) Genetic architecture of complex traits and accuracy of genomic Prediction: Coat colour, Milk-fat percentage, and type in holstein cattle as contrasting model traits. PLoS Genetics, 6 9: . doi:10.1371/journal.pgen.1001139


Author Hayes, Ben J.
Pryce, Jennie
Chamberlain, Amanda J.
Bowman, Phil J.
Goddard, Mike E.
Title Genetic architecture of complex traits and accuracy of genomic Prediction: Coat colour, Milk-fat percentage, and type in holstein cattle as contrasting model traits
Journal name PLoS Genetics   Check publisher's open access policy
ISSN 1553-7390
Publication date 2010
Sub-type Article (original research)
DOI 10.1371/journal.pgen.1001139
Open Access Status DOI
Volume 6
Issue 9
Total pages 1
Language eng
Subject 1311 Genetics
1312 Molecular Biology
1105 Dentistry
1306 Cancer Research
2716 Genetics (clinical)
Abstract Prediction of genetic merit using dense SNP genotypes can be used for estimation of breeding values for selection of livestock, crops, and forage species; for prediction of disease risk; and for forensics. The accuracy of these genomic predictions depends in part on the genetic architecture of the trait, in particular number of loci affecting the trait and distribution of their effects. Here we investigate the difference among three traits in distribution of effects and the consequences for the accuracy of genomic predictions. Proportion of black coat colour in Holstein cattle was used as one model complex trait. Three loci, KIT, MITF, and a locus on chromosome 8, together explain 24% of the variation of proportion of black. However, a surprisingly large number of loci of small effect are necessary to capture the remaining variation. A second trait, fat concentration in milk, had one locus of large effect and a host of loci with very small effects. Both these distributions of effects were in contrast to that for a third trait, an index of scores for a number of aspects of cow confirmation ("overall type"), which had only loci of small effect. The differences in distribution of effects among the three traits were quantified by estimating the distribution of variance explained by chromosome segments containing 50 SNPs. This approach was taken to account for the imperfect linkage disequilibrium between the SNPs and the QTL affecting the traits. We also show that the accuracy of predicting genetic values is higher for traits with a proportion of large effects (proportion black and fat percentage) than for a trait with no loci of large effect (overall type), provided the method of analysis takes advantage of the distribution of loci effects.
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Unknown

Document type: Journal Article
Sub-type: Article (original research)
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