Comparing genomic relationship matrices with relationship estimated from pedigree data.

In this study, we tested 3 methods of building variations of genomic relationship matrix and compared these with the classic A matrix (pedigree based). Brahman bulls (n = 1,695) genotyped for or imputed to more than 700,000 single nucleotide polymorphisms were used. The allele frequencies used to obtain the 3 variations of G were: 0.5 for all SNPs (G50), the average minor allele frequency (GMF), and the observed allele frequency of each SNP (GOF). Our results indicate that, it is relevant to evaluate the allele frequency in the population and select the method of building matrices to increase the importance of rare alleles, which can help with estimating more precise relationships.