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Background  Genomic BLUP (GBLUP) can predict breeding values for non-phenotyped individuals based on the identity-by-state genomic relationship matrix ( G ). The  G  matrix can be constructed from thousands of markers spread across the genome. The strongest assumption of  G  and consequently of GBLUP is that all markers contribute equally to the genetic variance of a trait. This assumption is violated for traits that are controlled by a small number of quantitative trait loci (QTL) or individual QTL with large effects. In this paper, we investigate the performance of using a weighted genomic relationship matrix ( wG ) that takes into consideration the genetic architecture of the trait in order to improve predictive ability for a wide range of traits. Multiple methods were used to calculate weights for several economically relevant traits in US Holstein dairy cattle. Predictive performance was tested by k-means cross-validation.    Results  Relaxing the GBLUP assumption of equal marker contribution by increasing the weight that is given to a specific marker in the construction of the trait-specific  G  resulted in increased predictive performance. The increase was strongest for traits that are controlled by a small number of QTL (e.g. fat and protein percentage). Furthermore, bias in prediction estimates was reduced compared to that resulting from the use of regular  G . Even for traits with low heritability and lower general predictive performance (e.g. calving ease traits), weighted  G  still yielded a gain in accuracy.    Conclusions  Genomic relationship matrices weighted by marker realized variance yielded more accurate and less biased predictions for traits regulated by few QTL. Genome-wide association analyses were used to derive marker weights for creating weighted genomic relationship matrices. However, this can be cumbersome and prone to low stability over generations because of erosion of linkage disequilibrium between markers and QTL. Future studies may include other sources of information, such as functional annotation and gene networks, to better exploit the genetic architecture of traits and produce more stable predictions.    Electronic supplementary material  The online version of this article (doi:10.1186/s12711-015-0100-1) contains supplementary material, which is available to authorized users.

Accounting for trait architecture in genomic predictions of US Holstein cattle using a weighted realized relationship matrix