The basis of genetic relationships in the era of genomic selection

In the literature an abundance of genomic relationship matrices have been described which mainly differ in the age of the relationships that they trace. Marker based relationship matrices (G) generally trace very old relationships, since the marker mutations occurred. Pedigree (A) and linkage analysis relationship matrices (GLA) trace relationships since pedigree recording started, i.e. since the founder population. Genomic selection (GS) is based on three sources of information: a) pedigree relationships (A); b) linkage analysis (LA) information and c)linkage disequilibrium (LD) information, where LD is defined between alleles in the founder population. LD due to cosegregation of alleles in the known pedigree is denoted LA information. The described relationship matrices follow the same pattern, i.e. A, GLA and G, respectively. An ideal model for GS is proposed that fits all three sources simultaneously, i.e. the A and GLA matrix and a Bayesian SNP selection model for the LD information.