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