Simple SummaryThe embryos from Japanese Black cows are used for embryo transfer in Japan, which could contribute to obtaining a greater number of fattened progenies from dams with superior genetic abilities for the sustainable supply of high-quality Wagyu beef. We previously reported the possibility of genetically improving the in vivo embryo production performance of Japanese Black donor cows. We performed single-step genomic prediction of breeding values for superovulatory response traits in Japanese Black donor cows using genome-wide single-nucleotide polymorphism markers. The results indicate that introducing the single-step genomic prediction scheme could allow more effective selection for superovulatory response traits at a younger age of donor cows, and it might achieve more efficient genetic improvements than breeding value prediction based on only pedigree information. To the best of our knowledge, this is the first study performing single-step genomic prediction of female reproductive traits in Japanese Black cattle. In future work, an approach suitable for managing genetic diversity while continuing sound selection should be developed.AbstractWe assessed the performance of single-step genomic prediction of breeding values for superovulatory response traits in Japanese Black donor cows. A total of 25,332 records of the total number of embryos and oocytes (TNE) and the number of good embryos (NGE) per flush for 1874 Japanese Black donor cows were collected during 2008 and 2022. Genotype information on 36,426 autosomal single-nucleotide polymorphisms (SNPs) for 575 out of the 1,874 cows was used. Breeding values were predicted exploiting a two-trait repeatability animal model. Two genetic relationship matrices were used, one based on pedigree information (Amatrix) and the other considering both pedigree and SNP marker genotype information (Hmatrix). Estimated heritabilities of TNE and NGE were 0.18 and 0.11, respectively, when using theHmatrix, which were both slightly lower than when using theAmatrix (0.26 for TNE and 0.16 for NGE). Estimated genetic correlations between the traits were 0.61 and 0.66 when usingHandAmatrices, respectively. When the variance components were the same in breeding value prediction, the mean reliability was greater when using theHmatrix than when using theAmatrix. This advantage seems more prominent for cows with low reliability when using theAmatrix. The results imply that introducing single-step genomic prediction could boost the rate of genetic improvement of superovulatory response traits, but efforts should be made to maintain genetic diversity when performing selection.