Molecular genetics and their place in breeding systems

Current estimation of breeding value is based on phenotypic information only. The advent of molecular markers allows determination of actual genotype at specific gene loci, without error due to random and non-random environmental effects. In the ideal situation we can directly identify genotypes at loci containing genes with substantial effects on quantitative traits (QTLs).(2) However, a more likely scenario is where we use genetic markers linked to QTLs to increase the probability of selecting the animals with the desired QTL genotype. With such indirect markers there is no guarantee of QTL genotype. Furthermore, the marker alleles linked to the preferred QTL allele can be different in different families, and information about linkage phase needs to be accumulated based on phenotypic and pedigree information (e.g. a progeny test). Marker-assisted selection is most useful for traits that are hard to measure and have low heritability. Selection of animals based on (most probable) QTL genotype will allow earlier and more accurate selection, increasing short- and medium-term selection response by up to 40%, and may aid in targeting genotypes for specific production environments or markets.