# 14 26 14 12 1 33 13.3 1 0 1 1 0 2 0 1 0 0įirst you need to extract the M matrix (marker genotype matrix). # animal sire dam mean EDC fat_DYD SNP1 SNP2 SNP3 SNP4 SNP5 SNP6 SNP7 SNP8 SNP9 SNP10 The following example is from Chapter 11 from Mrode’s Linear Models book. This book is very excellent because it has examples that you can follow along and program yourself if you don’t understand. We will be using an example from Mrode’s 3rd Edition of Linear Models for the Prediction of Animal Breeding Values. These two full-sibs would be less related based on genomic information, but equally related without known genotypes. Comparing two full-sib piglets, the \(\phi\) term would be negative if the pig received the bad recessive stress gene (a) from the sire while the \(\phi\) term would be positive (creating a better EBV) for the other full-sib that received the A allele. Genotyping allows us to observe this characteristic directly.Įxample: For instance, let us say that a boar (male pig) is heterozygous at a large QTL for meat quality (Aa). Prior to genotyping the offspring, there would be no way to separate offspring due to this major QTL. If you cross Aa x Aa parents, the offspring will be aa, Aa, and AA. Think of two parents both being Aa for a major QTL. People often forget however, that phenotyping can exploit at least part of the Mendelian sampling term. This can separate full-sibs prior to having any phenotypes.
Genomic relationships allow us to exploit the Mendelian sampling portion ( \(\phi\))of the breeding value equation from parents. The expected relationship for full-sibs is 0.5 (non-inbred). 2015) showing observed vs expected relationships among full-sibs.
\Īn example can be seen in the following histogram from (Lourenco et al.
This is because the A matrix cannot exploit the Mendelian sampling term when offspring inherit chromosome segments from the parents. Some call this matrix the ‘realized’ relationship matrix ( G) in place of the ‘expected’ relationship matrix ( A). Genomic BLUP (GBLUP) is a simple way to utilize genotypes to create a new relationship among animals.
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