OMIA:002513-9913 : Haplotypes with homozygous deficiency BH1-BH38 in Bos taurus (taurine cattle)

Categories: Mortality / aging (incl. embryonic lethal)

Mendelian trait/disorder: unknown

Considered a defect: yes

Species-specific name: BH1 BH2 BH3 BH4 BH5 BH6 BH7 BH8 BH9 BH10 BH11 BH12 BH13 BH14 BH15 BH16 BH17 BH18 BH19 BH20 BH21 BH22 BH23 BH24 BH25 BH26 BH27 BH28 BH29 BH30 BH31 BH32 BH33 BH34 BH35 BH36 BH37 BH38

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 Brown Swiss population are described below. Haplotypes for which a likely causal variant has been proposed (BH2, BH6, BH14, BH24 and BH34) have additional OMIA entries which contain the variant information.

Mapping: Häfliger et al. (2021) “The BS dataset included 48,807 genotyped animals, with 14,450 trios [trio: sire, dam, and offspring] … . …we detected 38 haplotypes [with homozygous deficiency (BH1-BH38)] …. Two of the identified haplotypes, BH1 on chromosome 7 and BH2 on chromosome 19 had already been detected … [OMIA 001825-9913 and OMIA 001939-9913].” Mapping positions for each haplotype are based on the ARS-UCS1.2 reference genome: Haplotype BH1 Chr7:41371808-42545291 -Proposed associated gene:TCF3 - see OMIA 001825-9913 Haplotype BH2 Chr19:9726237-10819756 -Proposed associated gene:TUBD1 - see OMIA 001939-9913 Haplotype BH3 Chr1:34908448-36034631 Haplotype BH4 Chr1:76587512-77861430 -Proposed associated gene:GMNC Haplotype BH5 Chr2:57787148-58768161 -Proposed associated gene:LRP1B Haplotype BH6 Chr2:86065338-87460373 -Proposed associated gene:MARS2 – see OMIA002517-9913 Haplotype BH7 Chr2:120284002-121473182 -Proposed associated gene:SPATA3 Haplotype BH8 Chr2:127933873-129004898 Haplotype BH9 Chr3:52432936-52689742 -Proposed associated gene:HFM1 Haplotype BH10 Chr3:101636810-102827915 Haplotype BH11 Chr4:108811998-109953666 Haplotype BH12 Chr5:57653479-59777422 -Proposed associated gene:RNF41 and LRP1 Haplotype BH13 Chr5:110617654-111664596 Haplotype BH14 Chr7:2588873-3357718 -Proposed associated gene:MRPL55 – see OMIA 002518-9913 Haplotype BH15 Chr7:33954389-34956540 Haplotype BH16 Chr7:79845977-80708046 Haplotype BH17 Chr11:82034654-82881173 -Proposed associated gene:PGGHG Haplotype BH18 Chr11:91766016-92804942 Haplotype BH19 Chr11:103891372-105003404 Haplotype BH20 Chr12:10254014-10967287 Haplotype BH21 Chr12:74954939-75817277 Haplotype BH22 Chr14:12290759-13350202 Haplotype BH23 Chr17:69786512-70645226 Haplotype BH24 Chr18:52977041-54113281 -Proposed associated gene:CPT1C – see OMIA002519-9913 Haplotype BH25 Chr19:35808547-36844178 -Proposed associated gene:SNF8 Haplotype BH26 Chr19:47874708-48724082 Haplotype BH27 Chr20:50058036-51370414 Haplotype BH28 Chr21:19368258-20362870 Haplotype BH29 Chr22:311724-1277064 Haplotype BH30 Chr23:39600366-40609442 Haplotype BH31 Chr25:27713801-29132187 -Proposed associated gene:ITGAD and SPN Haplotype BH32 Chr26:9215188-10180467 Haplotype BH33 Chr26:26659976-27689471 Haplotype BH34 Chr26:31353340-32429589 -Proposed associated gene:ACSL5 – see 002226-9913 Haplotype BH35 Chr27:28524504-29550764 Haplotype BH36 Chr28:26661955-27743768 Haplotype BH37 Chr28:45215132-45913154 Haplotype BH38 Chr29:14497752-15554643

Breed: Brown Swiss (Cattle) (VBO_0000166).
Breeds in which the phene has been documented. (If a likely causal variant has been documented for the phene, see the variant table breeds in which the variant has been reported).

Cite this entry

Nicholas, F. W., Tammen, I., & Sydney Informatics Hub. (2022). OMIA:002513-9913: Online Mendelian Inheritance in Animals (OMIA) [dataset].


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.

Edit History

  • Created by Imke Tammen2 on 14 Jan 2022
  • Changed by Imke Tammen2 on 14 Jan 2022
  • Changed by Imke Tammen2 on 17 Nov 2022