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A systematic survey to identify lethal recessive variation in highly managed pig populations
Martijn F L Derks1, Hendrik-Jan Megens2, Mirte Bosse2
1Wageningen University & Research, Animal Breeding and Genomics, Wageningen, The Netherlands. martijn.derks@wur.nl.
BMC Genomics
|November 11, 2017
Summary
Lethal recessive genetic variations in pigs cause embryonic death, impacting reproductive traits. Researchers identified 145 such haplotypes, with one linked to mid-gestation fetal death and the BMPER gene.
Area of Science:
- Animal Genetics
- Reproductive Biology
- Genomics
Background:
- Recessive lethal variations can cause prenatal death in homozygous offspring.
- Detecting embryonic lethal variation was previously indirect, relying on reduced fertility.
- Commercial breeding companies generate extensive genome data suitable for such analyses.
Purpose of the Study:
- To estimate the presence of genetic loci associated with early and late embryonic development termination in pigs.
- To leverage large-scale commercial genome data for genetic variation analysis.
Main Methods:
- Analysis of 80K SNP-chip genotypes in three commercial pig populations (Sus scrofa).
- Examination of 24,000 pigs for missing or depleted homozygous haplotypes.
- Identification and characterization of haplotypes with absence or depletion of homozygous animals.
Main Results:
- 145 haplotypes (0.5-4 Mb) showed absence or depletion of homozygotes.
- Thirty-five haplotypes negatively impacted reproductive traits (total born, stillborn, mummified piglets).
- A specific variant was linked to mid-gestation fetal death (mummies), with BMPER identified as a candidate gene.
Conclusions:
- Lethal recessive variation is present in managed pig populations, though allele frequencies are low.
- Cumulative effects of deleterious variants lead to significant numbers of affected offspring.
- Large-scale commercial genetic data can systematically screen for 'natural knockouts' to understand gene function.
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