Comparisons of Identical by State and Identical by Descent Relationship Matrices Derived from SNP Markers in Genomic Evaluation

In animal populations, family members inherit alleles through common ancestors and these shared regions are referred to as identical by descent (IBD). Furthermore, animals may also share alleles due to a random association with no known common inheritance pattern. This identity by state (IBS) also covers known relationships, such that regions that are IBD are also IBS, however regions that are IBS may not always be IBD. In the genetic evaluation of livestock, IBD and IBS information can be used to build the genomic relationship matrix (GRM) and breeding values can be predicted using genomic best linear unbiased prediction (gBLUP). This study compares a number of different methods to construct the GRM, using IBD and IBS information. Each method was evaluated using a reference dataset of 1781 Merino sheep and validated using 164 progeny tested sires that had accurate breeding values. Estimates of variance components were also compared. There was no significant difference between the accuracy achieved by the IBS and IBD methods. However the accuracy of the EBVs decreased as a greater restriction was applied to whether a region was IBD or not IBD. Furthermore, estimates of variance components were substantially different for IBD and IBS methods.