OMIA 002184-9823 : Haplotype with homozygous deficiency LA4 in Sus scrofa

Mendelian trait/disorder: yes

Mode of inheritance: Autosomal Recessive, Semi-Lethal

Considered a defect: yes

Key variant known: no

Species-specific description: Derks et al. (2019) identified five relatively frequent haplotypes for which there was either a deficit or a complete lack of homozygotes in large populations of Landrace (28,085) and Duroc (11,255). One of the four Landrace haplotypes (LA4) is the subject of this entry. LA4 is the only one of the five haplotypes for which a likely causal variant has yet to be identified.

History: This haplotype was first identified in two commercial pig populations in Norway (Derks et al., 2019). (Edited by Emmi Payten 24/8/2021)

Mapping: Derks et al. (2019): "To identify lethal alleles segregating in the pig populations we examined genotype data from 28,085 (Landrace), and 11,255 (Duroc) animals. All animals were genotyped or imputed to a medium-density 50K SNPchip ... . The genotypes were phased to build haplotypes, and then we applied an overlapping sliding window approach to identify haplotypes that show a deficit in homozygosity ... . The analysis yielded one strong candidate haplotype (DU1) harbouring a lethal recessive allele in the Duroc population, and four candidates in the Landrace population (LA1-4), respectively." (Edited by Emmi Payten 24/8/2021)

Clinical features: Derks et al. (2019): "analysed the effect of the haplotypes on fertility phenotypes including total number born (TNB), number born alive (NBA), number of stillborn (NSB), and number of mummified piglets (MUM)." The reduction in litter size (total number born) in carrier x carrier matings, compared with carrier x non-carrier matings, was 18.3%. "No significant increase in number of stillborn (NSB) or mummified piglets (MUM) was found, suggesting that homozygotes die very early in pregnancy." (Edited by Emmi Payten 24/8/2021)

Prevalence: Derks et al. (2019) reported the carrier frequency of haplotype LA4 as 4.6%, with 3 observed homozygotes (compared with 14.4 expected).

Breed: Landrace.

Reference


2019 Derks, M.F.L., Gjuvsland, A.B., Bosse, M., Lopes, M.S., van Son, M., Harlizius, B., Tan, B.F., Hamland, H., Grindflek, E., Groenen, M.A.M., Megens, H.J., Derks, M.F.L., Gjuvsland, A.B., Bosse, M., Lopes, M.S., van Son, M., Harlizius, B., Tan, B.F., Hamland, H., Grindflek, E., Groenen, M.A.M., Megens, H.J. :
Loss of function mutations in essential genes cause embryonic lethality in pigs. PLoS Genet 15:e1008055, 2019. Pubmed reference: 30875370. DOI: 10.1371/journal.pgen.1008055.

Edit History


  • Created by Frank Nicholas on 26 Mar 2019
  • Changed by Frank Nicholas on 26 Mar 2019
  • Changed by Imke Tammen2 on 27 May 2021
  • Changed by Imke Tammen2 on 24 Aug 2021