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OMIA:002721-9940 : Tail, length, HOXB13-related in Ovis aries (sheep)

Categories: Skeleton phene (incl. short stature & teeth) , Limbs / fins / digit / tail phene

Mendelian trait/disorder: yes

Disease-related: no

Key variant known: yes

Year key variant first reported: 2023

Mapping: Lagler et al. (2022) analysed "the natural tail length variation in the Merinolandschaf ... to identify causal alleles for the short tail phenotype segregating within long-tailed breeds. We used SNP-based association analysis and haplotype-based mapping in 362 genotyped (Illumina OvineSNP50) and phenotyped Merinolandschaf lambs. Genome-wide significant regions were capture sequenced in 48 lambs and comparatively analyzed in various long and short-tailed sheep breeds and wild sheep subspecies. ... [The authors report] a SNP [rs413316737] located in the first exon of HOXB13 and a SINE element located in the promotor of HOXB13 as promising candidates. ... While we were investigating ... [the SINE elelment] region on ARS-UI_Ramb_v2.0 assembly, we came across a pre-print by Li et al. [2023] who reported an insertion in the same region." Li et al. (2023) "compared [structural variants] SVs in the long (Asian long fat-tailed and European long thin-tailed) with those in short-tailed (Asian short fat-tailed and North European short thin-tailed) breeds within the 649 domestic sheep ... The most significant variation pointed to an ∼168-bp insertion (Chr 11: 37,525,005) adjacent to the annotated 5′ UTR of HOXB13 ... . ... We measured the tail length of 201 individuals from an East Friesian × (Hu sheep × East Friesian) hybrid population and performed a genome-wide association study (GWAS) using a 40K SNP chip (see Methods) and found that the regions surrounding the 168-bp insertion are clearly associated with tail length ... . ... The tails of individuals homozygous for the insertion were found to be significantly longer than tails of the heterozygotes by 2.77 cm on average ... ."

Molecular basis: Li et al. (2023): "A novel 168-bp insertion in the 5' untranslated region (5' UTR) of HOXB13 is found at high frequency in long-tailed sheep. Further genome-wide association study and gene expression analyses suggest that this mutation is causative for the long-tail trait."

Breed: Merinolandschaf (Sheep) (VBO_0001512).
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
HOXB13 homeobox B13 Ovis aries 11 NC_056064.1 (37525009..37530787) HOXB13 Homologene, Ensembl , NCBI gene

Variants

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
1742 Tail length, long HOXB13 insertion, gross (>20) Naturally occurring variant ARS-UI_Ramb_v2.0 11 NC_056064.1:g.37524995_37524996insN[168] 2022 36068271
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Cite this entry

Nicholas, F. W., Tammen, I., & Sydney Informatics Hub. (2024). OMIA:002721-9940: Online Mendelian Inheritance in Animals (OMIA) [dataset]. https://omia.org/. https://doi.org/10.25910/2AMR-PV70

References

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 Zhu, Q., Liu, P., Zhang, M., Kang, Y., Lv, L., Xu, H., Zhang, Q., Li, R., Pan, C., Lan, X. :
The detection of a functional 168 bp deletion of the HOXB13 gene determining short tail and its association with senior growth traits in sheep breeds worldwide. Animals (Basel) 14:1617, 2024. Pubmed reference: 38891664. DOI: 10.3390/ani14111617.
2023 Li, R., Gong, M., Zhang, X., Wang, F., Liu, Z., Zhang, L., Yang, Q., Xu, Y., Xu, M., Zhang, H., Zhang, Y., Dai, X., Gao, Y., Zhang, Z., Fang, W., Yang, Y., Fu, W., Cao, C., Yang, P., Ghanatsaman, Z.A., Negari, N.J., Nanaei, H.A., Yue, X., Song, Y., Lan, X., Deng, W., Wang, X., Pan, C., Xiang, R., Ibeagha-Awemu, E.M., Heslop-Harrison, P.J.S., Rosen, B.D., Lenstra, J.A., Gan, S., Jiang, Y. :
A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypes. Genome Res 33:463-477, 2023. Pubmed reference: 37310928. DOI: 10.1101/gr.277372.122.
2022 Lagler, D.K., Hannemann, E., Eck, K., Klawatsch, J., Seichter, D., Russ, I., Mendel, C., Lühken, G., Krebs, S., Blum, H., Upadhyay, M., Medugorac, I. :
Fine-mapping and identification of candidate causal genes for tail length in the Merinolandschaf breed. Commun Biol 5:918, 2022. Pubmed reference: 36068271. DOI: 10.1038/s42003-022-03854-3.

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  • Created by Imke Tammen2 on 15 Jun 2023
  • Changed by Imke Tammen2 on 15 Jun 2023
  • Changed by Imke Tammen2 on 18 Jun 2024