A systematic survey to identify lethal recessive variation in highly managed pig populations

Martijn F.L. Derks*, Hendrik Jan Megens, Mirte Bosse, Marcos S. Lopes, Barbara Harlizius, Martien A.M. Groenen

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

12 Citations (Scopus)


Background: Lethal recessive variation can cause prenatal death of homozygous offspring. Although usually present at low-frequency in populations, the impact on individual fitness can be substantial. Until recently, the presence of recessive embryonic lethal variation could only be measured indirectly through reduced fertility. In this study, we estimate the presence of genetic loci associated with both early and late termination of development during gestation in pigs from the wealth of genome data routinely generated by a commercial breeding company. Results: We examined three commercial pig (Sus scrofa) populations for potentially deleterious genetic variation based on 80 K SNP-chip genotypes, and estimate the effects on reproductive traits. 24,000 pigs from three populations were analyzed for missing or depletion of homozygous haplotypes. We identified 145 haplotypes (ranging from 0.5-4 Mb in size) in the genome with complete absence or depletion of homozygous animals. Thirty-five haplotypes show a negative effect on at least one of the analysed reproductive traits (total number born, number of stillborn, and number of mummified piglets). One variant in particular appeared to result in relative late termination of development of fetuses, responsible for a significant fraction of observed stillborn piglets ('mummies'), as they die mid-gestation. Moreover, we identified the BMPER gene as a likely candidate underlying this phenomenon. Conclusions: Our study shows that although lethal recessive variation is present, the frequency of these alleles is invariably low in these highly managed populations. Nevertheless, due to cumulative effects of deleterious variants, large numbers of affected offspring are produced. Furthermore, our study demonstrates the use of a large-scale commercial genetic experiment to systematically screen for 'natural knockouts' that can increase understanding of gene function.
Original languageEnglish
Article number858
JournalBMC Genomics
Issue number1
Publication statusPublished - 9 Nov 2017


  • Deleterious variation
  • Embryonic lethality
  • Genetics
  • Mummified piglets
  • Population genomics

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