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Background  Conception is a fundamental trait for successful cattle reproduction. However, conception rates in Japanese Black cattle have been gradually declining over the last two decades. Although conception failures are mainly caused by embryonic mortality, the role of maternal genetic factors in the process remains unknown. Copy number variation (CNV), defined as large-scale genomic structural variants, contributes to several genetic disorders. To identify CNV associated with embryonic mortality in Japanese Black cattle, we evaluated embryonic mortality as a categorical trait with a threshold model and conducted a genome-wide CNV association study for embryonic mortality using 791 animals.    Results  We identified a deleted-type CNV ranging from 378,127 to 412,061 bp on bovine chromosome 8, which was associated with embryonic mortality at 30–60 days after artificial insemination (AI). The CNV harbors exon 2 to 6 of ANNEXIN A10  (ANXA10) . Analysis of sequence traces from the CNV identified that 63 bp reads bridging the breakpoint were present on both sides of the CNV, indicating that the CNV was generated by non-allelic homologous recombination using the 63 bp homologous sequences. Western blot analysis showed that the CNV results in a null allele of  ANXA10 . This association was replicated using a sample population size of 2552 animals. To elucidate the function of ANXA10 in vivo, we generated  Anxa10  null mice using the CRISPR/Cas9 system. Crossbreeding experiments showed that litter size from crosses of both  Anxa10   -/-  and  Anxa10   +/-  females had fewer pups than did  Anxa10   +/+  females, and embryos of  Anxa10   -/-  females died between implantation stages E4.5 and E12.5. These results indicate that loss of maternal  Anxa10  causes embryonic mortality.    Conclusions  This study identified a deleted-type CNV encompassing  ANXA10  in cows that was associated with embryonic mortality at 30–60 days after AI. Using a mouse model, we confirmed that litter sizes were smaller in crosses of both  Anxa10   -/-  and  Anxa10   +/-  females relative to those of wild females. These results indicate that  ANXA10  is a maternal factor that is critical for embryo development.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-016-3312-z) contains supplementary material, which is available to authorized users.

Loss of maternal ANNEXIN A10 via a 34-kb deleted-type copy number variation is associated with embryonic mortality in Japanese Black cattle