OMIA:002514-9913 : Haplotypes with homozygous deficiency OH2-OH6 in Bos taurus (taurine cattle)
Categories: Mortality / aging (incl. embryonic lethal)
Links to MONDO diseases: No links.
Mendelian trait/disorder: unknown
Considered a defect: yes
Species-specific symbol: OH2, OH3, OH4, OH5, OH6
Species-specific description: Häfliger et al. (2021) investigated “the two Braunvieh populations reared in Switzerland, the dairy Brown Swiss (BS) and the dual-purpose Original Braunvieh (OB). We performed a genome-wide analysis of array data of trios (sire, dam, and offspring) from the routine genomic selection to identify candidate regions showing missing homozygosity and phenotypic associations with five fertility, ten birth, and nine growth-related traits. In addition, genome-wide single SNP regression studies based on 114,890 single nucleotide polymorphisms (SNPs) for each of the two populations were performed. Furthermore, whole-genome sequencing data of 430 cattle including 70 putative haplotype carriers were mined to identify potential candidate variants that were validated by genotyping the current population using a custom array. …Using a trio-based approach, we identified 38 haplotype regions for BS and five for OB … . For the BS population, we confirmed two known haplotypes, BH1 and BH2 [OMIA 001825-9913 and OMIA 001939-9913]. Twenty-four variants that potentially explained the missing homozygosity and associated traits were detected …. We propose a list of six protein-changing variants as potentially causing missing homozygosity. These variants need to be functionally validated and incorporated in the breeding program.”
The mapping information for the haplotypes with homozygous deficiency identified in the Original Braunvieh population are described below. Haplotypes for which a likely causal variant has been proposed (OH2 and OH4) have additional OMIA entries which contain the variant information.
Mapping: Häfliger et al. (2021) “The OB dataset included 10,085 genotyped animals, … [with] 3287 trios (trio: sire, dam, and offspring) … . … we detected “five significant novel haplotypes [with homozygous deficiency (OH2-6)]
Mapping positions for each haplotype are based on the ARS-UCS1.2 reference genome:
Haplotype OH2 Chr2:1005580-1614673 -Proposed associated gene TUBGCP5 – see OMIA 002515-9913
Haplotype OH3 Chr11:10406494-104418358 -Proposed associated gene MYMK
Haplotype OH4 Chr19:14336760-15222429 -Proposed associated gene LIG3 – see OMIA002516-9913
Haplotype OH5 Chr21:5195518-6367707 -Proposed associated gene LYSMD4
Haplotype OH6 Chr25:9596610-10624288 -Proposed associated gene USP7
Brown Swiss (Cattle) (VBO_0000166).
Breeds in which the phene has been documented. For breeds in which a likely causal variant has been documented, see the variant table below
Cite this entry
|2021||Häfliger, I.M., Seefried, F.R., Spengeler, M., Drögemüller, C. :|
|Mining massive genomic data of two Swiss Braunvieh cattle populations reveals six novel candidate variants that impair reproductive success. Genet Sel Evol 53:95, 2021. Pubmed reference: 34915862 . DOI: 10.1186/s12711-021-00686-3.|
- Created by Imke Tammen2 on 14 Jan 2022
- Changed by Imke Tammen2 on 14 Jan 2022