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 c ommercial animals, which have not been genotyped for genetic markers, to ca lculate marker assisted estimates of breeding value (MA-EBV) for nucleus an imals, where the commercial animals are descendants of the marker genotyped nucleus animals. The first method reduced the number of mixed model equati ons per commercial animal to one, instead of one plus twice the number of m arked quantitative trait loci in conventional MA-EBV equations. Without thi s reduction, the time taken to solve the mixed model equations including ma rkers could be very large especially if the number of commercial animals an d the number of markers is large. The solutions of the reduced set of equat ions were exact and did not require more iterations than the conventional s et of equations. A second method was developed for the situation where the records of the commercial animals were not directly available to the nucleu s 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 thes e non-MA-EBV, the MA-EBV of the nucleus animals were approximated. In an ex ample, the approximated MA-EBV were very close to the exact MA-EBV. (C) Inr a/Elsevier, Paris.