OMIA 002513-9913 : Haplotypes with homozygous deficiency BH1-BH38 in Bos taurus

Mendelian trait/disorder: unknown

Considered a defect: yes

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.

Reference


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