Marker assisted estimation of breeding values when marker information is missing on many animals

Two methods are presented that use information from a large population of commercial animals, which have not been genotyped for genetic markers, to calculate marker assisted estimates of breeding value (MA-EBV) for nucleus animals, where the commercial animals are descendants of the marker genotyped nucleus animals. The first method reduced the number of mixed model equations per commercial animal to one, instead of one plus twice the number of marked quantitative trait loci in conventional MA-EBV equations. Without this reduction, the time taken to solve the mixed model equations including markers could be very large especially if the number of commercial animals and the number of markers is large. The solutions of the reduced set of equations were exact and did not require more iterations than the conventional set of equations. A second method was developed for the situation where the records of the commercial animals were not directly available to the nucleus breeding programme but conventional non-MA-EBVs and their accuracies were available for nucleus animals from a large scale (e.g. national) breeding value evaluation, which uses nucleus and commercial information. Using these non-MA-EBV, the MA-EBV of the nucleus animals were approximated. In an example, the approximated MA-EBV were very close to the exact MA-EBV. (C) Inra/Elsevier, Paris.