OMIA 001694-9940 : Resistance/susceptibility to lentivirus in Ovis aries
In a separate GWAS of "964 sheep from Rambouillet, Polypay, and Columbia breeds with serological status and proviral concentration phenotypes", White et al. (2012) confirmed the TMEM154 results of Heaton et al. (2012) and reported "12 additional genomic regions associated with odds of infection, and provided 13 regions associated with control of infection (all nominal P<1 × 10(-5))".Markers: In a global survey of sheep breeds, Heaton et al. (2013) observed "The average frequency of TMEM154 E35 among 74 breeds was 0.51 [which] indicated that highly-susceptible alleles were present in most breeds around the world." They concluded that "The widespread distribution of highly-susceptible TMEM154 alleles suggests that genetic testing and selection may improve the health and productivity of infected flocks." Molecular basis: Following up the results of their GWAS described above, Heaton et al. (2012) showed that the two OAR17 SNPs are located in "an ovine gene homologous to the human TMEM154 gene". Subsequent sequencing and association analysis showed that "Two TMEM154 haplotypes encoding glutamate (E) at position 35 were associated with infection. . . . The odds of infection for ewes with one copy of a full-length TMEM154 E35 allele were 28 times greater than the odds for those without (p-value<0.0001, 95% CI 5–1,100). In a combined analysis of nine cohorts with 2,705 sheep from Nebraska, Idaho, and Iowa, the relative risk of infection was 2.85 times greater for sheep with a full-length TMEM154 E35 allele (p-value<0.0001, 95% CI 2.36–3.43). Although rare, some sheep were homozygous for TMEM154 deletion mutations and remained uninfected despite a lifetime of significant exposure." Taken together, these results led to Heaton et al. (2012) concluding that "TMEM154 may play a central role in ovine lentivirus infection and removing sheep with the most susceptible genotypes may help eradicate OPP and protect flocks from reinfection". While the actual function of the membrane protein encoded by TMEM154 is still to be worked out, the apparent resistance of sheep homozygous for a mutant that results in no functional peptide strongly suggests a mechanism for resistance/susceptibility, namely that the lentivirus needs this peptide in order to infect cells.
Following up one of the most promising regions for control of infection from the GWAS of White et al. (2012), White et al. (2013) "identified a small insertion/deletion variant near [5' of] ZNF389 [LOC105603932; OAR20; g.29500068_29500069delAT; GenBank NC_019477.1] that showed consistent association with proviral concentration in three animal sets . . . The best estimate of proviral concentration by genotype, obtained from all 1310 OvLV-positive animals tested, showed insertion homozygotes had less than half the proviral concentration of other genotypes (P < 0.0001). . . . To our knowledge, this is the first genetic variant consistently associated with host control of OvLV post-infection in multiple sheep flocks."Clinical features: As reported by Heaton et al. (2013), "The first signs of disease typically appear after age two and often include the loss of body condition and indurative mastitis (hard udder). Disease progression is associated with severe clinical signs that include difficulty breathing, chronic wasting, loss of motor control, and arthritis." Breeds: Columbia, Polypay, Rambouillet. Associated genes:
|Symbol||Description||Species||Chr||Location||OMIA gene details page||Other Links|
|TMEM154||transmembrane protein 154||Ovis aries||17||NC_056070.1 (5175905..5228028)||TMEM154||Homologene, Ensembl, NCBI gene|
|LOC105603932||zinc finger protein 397-like||Ovis aries||20||NC_056073.1 (29567154..29536488)||LOC105603932||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||Inferred EVA rsID||Year Published||PubMed ID(s)||Acknowledgements|
|915||Polypay||Resistance to lentivirus||LOC105603932||regulatory||Naturally occurring variant||Oar_rambouillet_v1.0||20||g.32931861_32931862del||Published as ZNF389 deletion(NC_019477.1:g.29500068_29500069delAT ovine chromosome 20, NCBI dbSNP ss748775100).||rs397514112||2013||24303974||The genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager, EMAI, NSW Department of Primary Industries.|
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.
|2022||Lv, F.H., Cao, Y.H., Liu, G.J., Luo, L.Y., Lu, R., Liu, M.J., Li, W.R., Zhou, P., Wang, X.H., Shen, M., Gao, L., Yang, J.Q., Yang, H., Yang, Y.L., Liu, C.B., Wan, P.C., Zhang, Y.S., Pi, W.H., Ren, Y.L., Shen, Z.Q., Wang, F., Wang, Y.T., Li, J.Q., Salehian-Dehkordi, H., Hehua, E., Liu, Y.G., Chen, J.F., Wang, J.K., Deng, X.M., Esmailizadeh, A., Dehghani-Qanatqestani, M., Charati, H., Nosrati, M., Štěpánek, O., Rushdi, H.E., Olsaker, I., Curik, I., Gorkhali, N.A., Paiva, S.R., Caetano, A.R., Ciani, E., Amills, M., Weimann, C., Erhardt, G., Amane, A., Mwacharo, J.M., Han, J.L., Hanotte, O., Periasamy, K., Johansson, A.M., Hallsson, J.H., Kantanen, J., Coltman, D.W., Bruford, M.W., Lenstra, J.A., Li, M.H. :|
|Whole-genome resequencing of worldwide wild and domestic sheep elucidates genetic diversity, introgression, and agronomically important loci. Mol Biol Evol 39:msab353, 2022. Pubmed reference: 34893856. DOI: 10.1093/molbev/msab353.|
|2021||Cao, Y.H., Xu, S.S., Shen, M., Chen, Z.H., Gao, L., Lv, F.H., Xie, X.L., Wang, X.H., Yang, H., Liu, C.B., Zhou, P., Wan, P.C., Zhang, Y.S., Yang, J.Q., Pi, W.H., Hehua, E., Berry, D.P., Barbato, M., Esmailizadeh, A., Nosrati, M., Salehian-Dehkordi, H., Dehghani-Qanatqestani, M., Dotsev, A.V., Deniskova, T.E., Zinovieva, N.A., Brem, G., Štěpánek, O., Ciani, E., Weimann, C., Erhardt, G., Mwacharo, J.M., Ahbara, A., Han, J.L., Hanotte, O., Miller, J.M., Sim, Z., Coltman, D., Kantanen, J., Bruford, M.W., Lenstra, J.A., Kijas, J., Li, M.H. :|
|Historical introgression from wild relatives enhanced climatic adaptation and resistance to pneumonia in sheep. Mol Biol Evol 38:838-855, 2021. Pubmed reference: 32941615. DOI: 10.1093/molbev/msaa236.|
|Yaman, Y., Bay, V., Aymaz, R., Keleş, M., Öner, Y., Teferedegn, E.Y., Ün, C. :|
|A novel 2 bp deletion variant in Ovine-DRB1 gene is associated with increased Visna/maedi susceptibility in Turkish sheep. Sci Rep 11:14435, 2021. Pubmed reference: 34262107. DOI: 10.1038/s41598-021-93864-8.|
|2015||Bishop, S.C. :|
|Genetic resistance to infections in sheep. Vet Microbiol 181:2-7, 2015. Pubmed reference: 26260859. DOI: 10.1016/j.vetmic.2015.07.013.|
|Clawson, M.L., Redden, R., Schuller, G., Heaton, M.P., Workman, A., Chitko-McKown, C.G., Smith, T.P., Leymaster, K.A. :|
|Genetic subgroup of small ruminant lentiviruses that infects sheep homozygous for TMEM154 frameshift deletion mutation A4Δ53. Vet Res 46:22, 2015. Pubmed reference: 25756342. DOI: 10.1186/s13567-015-0162-7.|
|2013||Heaton, M.P., Kalbfleisch, T.S., Petrik, D.T., Simpson, B., Kijas, J.W., Clawson, M.L., Chitko-McKown, C.G., Harhay, G.P., Leymaster, K.A. :|
|Genetic testing for TMEM154 mutations associated with lentivirus susceptibility in sheep. PLoS One 8:e55490, 2013. Pubmed reference: 23408992. DOI: 10.1371/journal.pone.0055490.|
|White, S.N., Mousel, M.R., Reynolds, J.O., Herrmann-Hoesing, L.M., Knowles, D.P. :|
|Deletion variant near ZNF389 is associated with control of ovine lentivirus in multiple sheep flocks. Anim Genet :, 2013. Pubmed reference: 24303974. DOI: 10.1111/age.12107.|
|2012||Heaton, M.P., Clawson, M.L., Chitko-Mckown, C.G., Leymaster, K.A., Smith, T.P., Harhay, G.P., White, S.N., Herrmann-Hoesing, L.M., Mousel, M.R., Lewis, G.S., Kalbfleisch, T.S., Keen, J.E., Laegreid, W.W. :|
|Reduced lentivirus susceptibility in sheep with TMEM154 mutations. PLoS Genet 8:e1002467, 2012. Pubmed reference: 22291605. DOI: 10.1371/journal.pgen.1002467.|
|White, S.N., Mousel, M.R., Herrmann-Hoesing, L.M., Reynolds, J.O., Leymaster, K.A., Neibergs, H.L., Lewis, G.S., Knowles, D.P. :|
|Genome-wide association identifies multiple genomic regions associated with susceptibility to and control of ovine lentivirus. PLoS One 7:e47829, 2012. Pubmed reference: 23082221. DOI: 10.1371/journal.pone.0047829.|
- Created by Frank Nicholas on 29 Jun 2012
- Changed by Frank Nicholas on 29 Jun 2012
- Changed by Frank Nicholas on 25 Apr 2013
- Changed by Frank Nicholas on 08 Dec 2013
- Changed by Frank Nicholas on 16 Apr 2020
- Changed by Frank Nicholas on 15 May 2020
- Changed by Frank Nicholas on 20 Apr 2021
- Changed by Imke Tammen2 on 20 Jun 2021
- Changed by Imke Tammen2 on 17 Sep 2022