1	Methods to explain genomic estimates of breeding value
2	Genomic Goals Predict young bulls and cows more accurately Compare actual DNA inherited Use exact relationship matrix G instead of expected values in A Trace chromosome segments Locate genes with large effects
3	How Related are Relatives? Example: Full sibs are expected to share 50% of their DNA on average may actually share 45% or 55% of their DNA because each inherits a different mixture of chromosome segments from the two parents. Combine genotype and pedigree data to determine exact fractions
4	Genomic Relationships Measures of genetic similarity A = Expected % genes identical by descent from pedigree (Wright, 1922) G = Actual % of DNA shared (using genotype data) T = % genes shared that affect a given trait (using genotype and phenotype) Best measure depends on use
5	Markers vs QTLs Models contain markers, not QTLs M is markers inherited minus freq M M’ / ∑ p(1-p) = G List all QTL affecting a trait Q is alleles inherited minus freq q contains effects of alleles u = Q q , var(q) = V_q var(u) = E(u u’) = Q V_q Q’ = T
6	QTL Relationship Matrix (T) Three bulls have +50 PTA protein. Do they have the same genes? Extremely unlikely. Bull A could have 10 positive genes. Bull B could have 10 positive genes, but on different chromosomes. Bull C could have 20 positive and 10 negative genes.
7	Genes in Common at One Locus
8	Alleles Shared by Sibs
9	Unrelated Individuals? No known common ancestors Many unknown common ancestors born before the known pedigree Relationships in base 0 ± x.x% due to earlier ancestors Called linkage disequilibrium (LD) Poor terminology, genes may not be physically linked
10	Traditional Pedigree
11	Genomic Pedigree
12	Example of a SNP haplotype
13	SNP Pedigree
14	Haplotype Pedigree
15	Translate Haplotype to Genotype
16	Genotype Pedigree Count number of second allele
17	Reliability from Full Sibs 50,000 markers, 1000 QTLs, sib REL = 99%
18	Conclusions Relationships can be defined as: A = expected genes in common G = actual DNA in common T = QTL alleles in common for a trait Full sibs share 50% ± 3.5% of DNA. “Unrelated” animals share more or fewer unknown ancestors than average. Reliability can increase if genomic (G) replace traditional (A) relationships