title: Best linear unbiased prediction of genomic breeding values using a trait-specific marker-derived relationship matrix.
abstract: BACKGROUND
  With the availability of high density whole-genome single nucleotide polymorphism chips, genomic selection has become a promising method to estimate genetic merit with potentially high accuracy for animal, plant and aquaculture species of economic importance. With markers covering the entire genome, genetic merit of genotyped individuals can be predicted directly within the framework of mixed model equations, by using a matrix of relationships among individuals that is derived from the markers. Here we extend that approach by deriving a marker-based relationship matrix specifically for the trait of interest.
  
  
  RESULTS
  In the framework of mixed model equations, a new best linear unbiased prediction (BLUP) method including a trait-specific relationship matrix (TA) was presented and termed TABLUP. The TA matrix was constructed on the basis of marker genotypes and their weights in relation to the trait of interest. A simulation study with 1,000 individuals as the training population and five successive generations as candidate population was carried out to validate the proposed method. The proposed TABLUP method outperformed the ridge regression BLUP (RRBLUP) and BLUP with realized relationship matrix (GBLUP). It performed slightly worse than BayesB with an accuracy of 0.79 in the standard scenario.
  
  
  CONCLUSIONS
  The proposed TABLUP method is an improvement of the RRBLUP and GBLUP method. It might be equivalent to the BayesB method but it has additional benefits like the calculation of accuracies for individual breeding values. The results also showed that the TA-matrix performs better in predicting ability than the classical numerator relationship matrix and the realized relationship matrix which are derived solely from pedigree or markers without regard to the trait. This is because the TA-matrix not only accounts for the Mendelian sampling term, but also puts the greater emphasis on those markers that explain more of the genetic variance in the trait.
authors.affiliation: Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China.
authors.forename: Zhe
authors.initials: Z
authors.lastname: Zhang
authors.forename: Jianfeng
authors.initials: J
authors.lastname: Liu
authors.forename: Xiangdong
authors.initials: X
authors.lastname: Ding
authors.forename: Piter
authors.initials: P
authors.lastname: Bijma
authors.forename: Dirk-Jan
authors.initials: DJ
authors.lastname: de Koning
authors.forename: Qin
authors.initials: Q
authors.lastname: Zhang
mesh_terms: D000818:Animals; D001947:Breeding; D003198:Computer Simulation; D005260:Female; D005819:Genetic Markers; D005828:Genetics, Population; D023281:Genomics; D005838:Genotype; D006801:Humans; D016014:Linear Models; D008297:Male; D008957:Models, Genetic; D010375:Pedigree; D020641:Polymorphism, Single Nucleotide; D019655:Quantitative Trait, Heritable
chemical_list: D005819:Genetic Markers