Estimating Genomic Variance Explained per Chromosome Using Pedigree and Genomic Data in Sheep

Abstract

We used a half sib data structure for a growth trait in sheep as a potentially powerful design for partitioning the genetic variance across the different chromosomes. Records for post weaning weight were used from 2455 merino sheep. The model of analysis accounted for population structure by fitting genetic group effects as well as the numerator relationship matrix (A) based on pedigree. We then fitted the matrix D representing the difference between the genomic relationship matrix (G) and A. The matrix G was based on 48,599 SNP markers across the entire genome, or on all SNPs of an individual chromosome. There was a relationship between chromosome length (L) and variance explained (Vgi), but we found significant differences in (Vgi/L) between chromosomes.