Utilisation of genetic variation by marker assisted selection in commercial dairy cattle populations

Potential genetic benefits of marker assisted selection (MAS) were evaluated by calculating selection response resulting from four pathways of selection. Genetic variation was partitioned into polygenic and loci that were in linkage disequilibrium with marker loci or haplotypes. The percentage of genetic variation that was marked was varied from 0 to 100%. These assumptions describe the degree of genetic knowledge that may be available in 10 years. Three breeding strategies with markers were evaluated: progeny test scheme (BMARK); progeny test scheme but unproven bulls allowed on the bull to bull selection path (YBULL); and a breeding programme where cows without lactation information and bulls without progeny information were eligible for selection (OPEN). Rates of genetic gain (per year) with no marked genetic variance were 0.26 σ(G) for the BMARK and YBULL schemes and 0.28 σ(G) for the OPEN scheme. On average, an increase of 1% marked genetic variance resulted in an increase in genetic gain of ~0.25% for the BMARK scheme, 0.5% for the YBULL scheme and 1% for the OPEN scheme. Maximum genetic response (100% marked genetic variance) for the BMARK scheme was 1.24 times that achieved with no marked genetic variance, 1.52 times for the YBULL scheme, and 2.05 times for the OPEN scheme. Changes in the structure of the breeding scheme are needed to fully gain the benefits of identified loci especially for medium to large proportions of marked genetic variance.