OMIA:000151-9913 : Brachyspina in Bos taurus (taurine cattle)

Categories: Mortality / aging (incl. embryonic lethal)

Links to possible relevant human trait(s) and/or gene(s) in OMIM: 609053 (trait) , 611360 (gene)

Mendelian trait/disorder: yes

Mode of inheritance: Autosomal recessive

Considered a defect: yes

Key variant known: yes

Year key variant first reported: 2012

Species-specific name: Haplotype HH0

Species-specific symbol: HH0

Mapping: In the course of their large-scale study of BovineSNP50 BeadChip haplotypes that are common but never homozygous, VanRaden et al. (2011) mapped this disorder to BTA21 at 20-25Mb (UMD 3.0 genome assembly). Genotyping six affected Holstein-Friesian calves and 15 normal H-F controls with a custom-made 50K bovine SNP chip, followed by autozygosity mapping, enabled Charlier et al. (2012) to map this disorder to a 2.46Mb region of chromosome BTA21, which contains 56 annotated genes. Fritz et al. (2013) confirmed the existence and location of this deleterious haplotype. By genotyping each of 7,937 Nordic Holstein bulls with the BovineSNP50 BeadChip, yielding 36,387 informative autosomal SNPs, and then searching for 25-marker haplotypes that never occur as a homozygote where the minimum expectation is 6 occurrences, Sahana et al. (2013) "identified 17 homozygote deficient haplotypes which could be loosely clustered into eight genomic regions harboring possible recessive lethal alleles". One of the eight regions (marked by haplotypes 21-276, 21-301 and 21-326) seems to coincide with Brachyspina.

Molecular basis: Using mate-pair libraries from one affected and three controls, Charlier et al. (2012) obtained around 3.4Gb of sequence from each animal. Comparison of sequence in the candidate BTA21 region "revealed a 3.3 Kb deletion removing exons 25–27 of the 37 composing the FANCI (Fanconi anemia complementation-group I) gene". Noting that the carrier frequency is far too high (up to 7.4%) to be consistent with a relatively rare autosomal recessive disorder, Charlier et al. (2012) also showed that a large proportion of affected calves die in utero. Thus this causal mutation also contributes to natural abortions and hence to reduced fertility.

Clinical features: As summarised by Charlier et al. (2012), "Affected animals are characterized by severely reduced body weight, growth retardation, extensive vertebral malformations causing a significant shortening of the spine (brachyspina) and long and slender limbs. In addition, affected calves exhibit inferior brachygnatism (i.e. uneven alignment of the upper and lower teeth), as well as malformation of the inner organs, in particular the heart, kidneys and gonads."

Breed: Holstein (black and white) (Cattle) (VBO_0000237).
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).

Associated gene:

Symbol Description Species Chr Location OMIA gene details page Other Links
FANCI Fanconi anemia complementation group I Bos taurus 21 NC_037348.1 (20723039..20787646) FANCI Homologene, Ensembl , NCBI gene


By default, variants are sorted chronologically by year of publication, to provide a historical perspective. Readers can re-sort on any column by clicking on the column header. Click it again to sort in a descending order. To create a multiple-field sort, hold down Shift while clicking on the second, third etc relevant column headers.

WARNING! Inclusion of a variant in this table does not automatically mean that it should be used for DNA testing. Anyone contemplating the use of any of these variants for DNA testing should examine critically the relevant evidence (especially in breeds other than the breed in which the variant was first described). If it is decided to proceed, the location and orientation of the variant sequence should be checked very carefully.

Since October 2021, OMIA includes a semiautomated lift-over pipeline to facilitate updates of genomic positions to a recent reference genome position. These changes to genomic positions are not always reflected in the ‘acknowledgements’ or ‘verbal description’ fields in this table.

OMIA Variant ID Breed(s) Variant Phenotype Gene Allele Type of Variant Source of Genetic Variant Reference Sequence Chr. g. or m. c. or n. p. Verbal Description EVA ID Year Published PubMed ID(s) Acknowledgements
646 Holstein (black and white) (Cattle) Brachyspina FANCI deletion, gross (>20) Naturally occurring variant ARS-UCD1.2 21 g.20773899_20777226del p.(V877Lfs*27) 2012 22952632 Breed and variant information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (

Cite this entry

Nicholas, F. W., Tammen, I., & Sydney Informatics Hub. (2015). OMIA:000151-9913: Online Mendelian Inheritance in Animals (OMIA) [dataset].


Note: the references are listed in reverse chronological order (from the most recent year to the earliest year), and alphabetically by first author within a year.

2024 Khan, M.Y.A., Dai, D., Su, X., Tian, J., Zhou, J., Ma, L., Wang, Y., Wen, W., Zhang, Y. :
Multiplex fluorescent amplification-refractory mutation system PCR method for the detection of 10 genetic defects in Holstein cattle and its comparison with the KASP genotyping assay. Anim Genet , 2024. Pubmed reference: 38622758. DOI: 10.1111/age.13432.
Shormanova, M., Makhmutov, A., Shormanova, A., Muslimova, Z., Ussenbekov, Y. :
Development of alternative diagnosis of HH1, HH3, HH5 and HCD fertility haplotypes and subfertility syndrome in cattle. Reprod Domest Anim 59:e14533, 2024. Pubmed reference: 38268216. DOI: 10.1111/rda.14533.
2023 Kamiński, S. :
Eradication of carriers of complex vertebral malformation (CVM) and brachyspina in Polish Holstein-Friesian bulls. Pol J Vet Sci 26:315-317, 2023. Pubmed reference: 37389451. DOI: 10.24425/pjvs.2023.145031.
Sudhakar, A., Nayee, N., Saha, S., Donthula, S.K., Poojara, H.V., Gohil, T., Patel, A.C., Maurya, B.K. :
Role of genetic introgression in introducing mutant alleles in Bos indicus cattle and prevalence of lethal genetic disorders in Bos taurus × Bos indicus and Bos indicus cattle in India. Trop Anim Health Prod 55:399, 2023. Pubmed reference: 37940810. DOI: 10.1007/s11250-023-03798-8.
2016 Cole, J.B., Null, D.J., VanRaden, P.M. :
Phenotypic and genetic effects of recessive haplotypes on yield, longevity, and fertility. J Dairy Sci 99:7274-88, 2016. Pubmed reference: 27394947. DOI: 10.3168/jds.2015-10777.
2015 Ruść, A., Kamiński, S. :
Detection of Brachyspina carriers within Polish Holstein-Friesian bulls. Pol J Vet Sci 18:453-4, 2015. Pubmed reference: 26172199. DOI: 10.1515/pjvs-2015-0059.
2013 Fang, L., Li, Y., Zhang, Y., Sun, D., Liu, L., Zhang, Y., Zhang, S. :
Identification of brachyspina syndrome carriers in Chinese Holstein cattle. J Vet Diagn Invest 25:508-10, 2013. Pubmed reference: 23674463. DOI: 10.1177/1040638713488387.
Fritz, S., Capitan, A., Djari, A., Rodriguez, S.C., Barbat, A., Baur, A., Grohs, C., Weiss, B., Boussaha, M., Esquerré, D., Klopp, C., Rocha, D., Boichard, D. :
Detection of haplotypes associated with prenatal death in dairy cattle and identification of deleterious mutations in GART, SHBG and SLC37A2. PLoS One 8:e65550, 2013. Pubmed reference: 23762392. DOI: 10.1371/journal.pone.0065550.
Sahana, G., Nielsen, U.S., Aamand, G.P., Lund, M.S., Guldbrandtsen, B. :
Novel harmful recessive haplotypes identified for fertility traits in nordic holstein cattle. PLoS One 8:e82909, 2013. Pubmed reference: 24376603. DOI: 10.1371/journal.pone.0082909.
2012 Charlier, C., Agerholm, J.S., Coppieters, W., Karlskov-Mortensen, P., Li, W., de Jong, G., Fasquelle, C., Karim, L., Cirera, S., Cambisano, N., Ahariz, N., Mullaart, E., Georges, M., Fredholm, M. :
A Deletion in the Bovine FANCI Gene Compromises Fertility by Causing Fetal Death and Brachyspina. PLoS One 7(8):e43085, 2012. Pubmed reference: 22952632. DOI: 10.1371/journal.pone.0043085.
Norman, H.D., Miller, R.H., Wright, J.R., Hutchison, J.L., Olson, K.M. :
Factors associated with frequency of abortions recorded through Dairy Herd Improvement test plans. J Dairy Sci 95:4074-84, 2012. Pubmed reference: 22720964. DOI: 10.3168/jds.2011-4998.
2011 VanRaden, P.M., Olson, K.M., Null, D.J., Hutchison, J.L. :
Harmful recessive effects on fertility detected by absence of homozygous haplotypes. J Dairy Sci 94:6153-61, 2011. Pubmed reference: 22118103. DOI: 10.3168/jds.2011-4624.
2010 Agerholm, J.S., DeLay, J., Hicks, B., Fredholm, M. :
First confirmed case of the bovine brachyspina syndrome in Canada. Can Vet J 51:1349-50, 2010. Pubmed reference: 21358926.
Buck, B.C., Ulrich, R., Wöhlke, A., Kuiper, H., Baumgärtner, W., Distl, O. :
[Vertebral and multiple organ malformations in a black and white German Holstein calf]. Berl Munch Tierarztl Wochenschr 123:251-5, 2010. Pubmed reference: 20496833.
2008 Testoni, S., Diana, A., Olzi, E., Gentile, A. :
Brachyspina syndrome in two Holstein calves. Vet J 177:144-6, 2008. Pubmed reference: 17502161. DOI: 10.1016/j.tvjl.2007.03.011.
2007 Agerholm, JS., Peperkamp, K. :
Familial occurrence of Danish and Dutch cases of the bovine brachyspina syndrome. BMC Vet Res 3:8, 2007. Pubmed reference: 17488494. DOI: 10.1186/1746-6148-3-8.
2006 Agerholm, JS., McEvoy, F., Arnbjerg, J. :
Brachyspina syndrome in a Holstein calf. J Vet Diagn Invest 18:418-22, 2006. Pubmed reference: 16921889.

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  • Created by Frank Nicholas on 06 Sep 2005
  • Changed by Frank Nicholas on 19 Jan 2012
  • Changed by Frank Nicholas on 30 Aug 2012
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