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Background  Cattle breeding populations are susceptible to the propagation of recessive diseases. Individual sires generate tens of thousands of progeny  via  artificial insemination. The frequency of deleterious alleles carried by such sires may increase considerably within few generations. Deleterious alleles manifest themselves often by missing homozygosity resulting from embryonic/fetal, perinatal or juvenile lethality of homozygotes.    Results  A scan for homozygous haplotype deficiency in 25,544 Fleckvieh cattle uncovered four haplotypes affecting reproductive and rearing success. Exploiting whole-genome resequencing data from 263 animals facilitated to pinpoint putatively causal mutations in two of these haplotypes. A mutation causing an evolutionarily unlikely substitution in  SUGT1  was perfectly associated with a haplotype compromising insemination success. The mutation was not found in homozygous state in 10,363 animals (P = 1.79 × 10 −5 ) and is thus likely to cause lethality of homozygous embryos. A frameshift mutation in  SLC2A2  encoding glucose transporter 2 (GLUT2) compromises calf survival. The mutation leads to premature termination of translation and activates cryptic splice sites resulting in multiple exon variants also with premature translation termination. The affected calves exhibit stunted growth, resembling the phenotypic appearance of Fanconi-Bickel syndrome in humans (OMIM 227810), which is also caused by mutations in  SLC2A2 .    Conclusions  Exploiting comprehensive genotype and sequence data enabled us to reveal two deleterious alleles in  SLC2A2  and  SUGT1  that compromise pre- and postnatal survival in homozygous state. Our results provide the basis for genome-assisted approaches to avoiding inadvertent carrier matings and to improving reproductive and rearing success in Fleckvieh cattle.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-015-1483-7) contains supplementary material, which is available to authorized users.

Homozygous haplotype deficiency reveals deleterious mutations compromising reproductive and rearing success in cattle