OMIA:002435-9823 : Sperm, short tail, SPEF2-related in Sus scrofa (pig) |
Categories: Reproductive system phene
Possibly relevant human trait(s) and/or gene(s)s (MIM numbers): 610172 (gene) , 618751 (trait)
Links to MONDO diseases: No links.
Mendelian trait/disorder: yes
Mode of inheritance: Autosomal recessive
Considered a defect: yes
Key variant known: yes
Year key variant first reported: 2006
Species-specific name: Immotile short-tail sperm defect; Sterilizing short-tail sperm defect
Species-specific symbol: ISTS
Species-specific description: "The ISTS phenotype is characterized as lowered sperm counts, short sperm tails, and axonemal abnormalities" (Sironen et al., 2006)
Inheritance: Autosomal recessive, sex-limited
Molecular basis: "Sequence analysis of a candidate gene KPL2 revealed the presence of an inserted retrotransposon within an intron. The insertion affects splicing of the KPL2 transcript in two ways; it either causes skipping of the upstream exon, or causes the inclusion of an intronic sequence as well as part of the insertion in the transcript. Both changes alter the reading frame leading to premature termination of translation." (Sironen et al., 2006) The KPL2 gene is now called SPEF2 (sperm flagellar 2).
Sironen et al. (2014) “analyzed the expression of the genomic region adjacent to the L1 insertion on porcine chromosome 16. Based on the RNA-seq data analysis, prolactin receptor (PRLR) was identified as down-regulated in the oviduct of ISTS homozygous sows. Quantitative PCR (qPCR) analysis confirmed the significant down-regulation of PRLR in the ovary, oviduct, and uterus of ISTS homozygous and carrier sows compared with controls. In addition, three unannotated loci between PRLR and SPEF2 showed some transcription activity in the analyzed samples. …. The current data suggest that the presence of the L1 affects by some mechanism the expression patterns upstream of the insertion site.”
Clinical features: Homozygous boars are eliminated from the population due to infertility.
Sironen et al. (2012) “investigated the association of the L1 insertion and PRLR haplotype with reproduction traits in the Finnish Yorkshire population. ….. The L1-insertion within SPEF2 gene was associated with litter size in the first parity.”
Prevalence: "In 2001, the insertion frequency was already 0.23. Even though all homozygous boars are eliminated from the population due to infertility, the amount of affected boars increased rapidly until marker-assisted selection against the defect was established." (Sironen et al., 2014)
Breed:
Large White, Finland (Pig) (VBO_0012408).
Breeds in which the phene has been documented. For breeds in which a likely causal variant has been documented, see the variant table below
Associated gene:
| Symbol | Description | Species | Chr | Location | OMIA gene details page | Other Links |
|---|---|---|---|---|---|---|
| SPEF2 | sperm flagellar 2 | Sus scrofa | 16 | NC_010458.4 (21088463..21264591) | SPEF2 | Homologene, Ensembl , NCBI gene |
Variants
By default, variants are sorted chronologically by year of publication, to provide a historical perspective.
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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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 392 | Sperm, short tail | SPEF2 | splicing | Naturally occurring variant | 16 | an inserted retrotransposon within an intron | 2006 | 16549801 |
Cite this entry
Nicholas, F. W., Tammen, I., & Sydney Informatics Hub. (2021). OMIA:002435-9823: 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.
| 2021 | Derks, M.F.L., Steensma, M. : |
| Review: Balancing selection for deleterious alleles in livestock. Front Genet 12:761728, 2021. Pubmed reference: 34925454 . DOI: 10.3389/fgene.2021.761728. | |
| 2014 | Sironen, A., Fischer, D., Laiho, A., Gyenesei, A., Vilkki, J. : |
| A recent L1 insertion within SPEF2 gene is associated with changes in PRLR expression in sow reproductive organs. Anim Genet 45:500-7, 2014. Pubmed reference: 24712415 . DOI: 10.1111/age.12153. | |
| 2012 | Sironen, A., Uimari, P., Iso-Touru, T., Vilkki, J. : |
| L1 insertion within SPEF2 gene is associated with increased litter size in the Finnish Yorkshire population. J Anim Breed Genet 129:92-7, 2012. Pubmed reference: 22394230 . DOI: 10.1111/j.1439-0388.2011.00977.x. | |
| 2008 | Kopp, C., Ijäs, R., Flyckt, A., Taponen, J., Parvinen, M., Andersson, M. : |
| Morphometric evaluations of testicular tissues from azoospermic boars in Finnish Yorkshire and Landrace breeds. Theriogenology 70:1129-35, 2008. Pubmed reference: 18640712 . DOI: 10.1016/j.theriogenology.2008.06.034. | |
| Kopp, C., Sironen, A., Ijäs, R., Taponen, J., Vilkki, J., Sukura, A., Andersson, M. : | |
| Infertile boars with knobbed and immotile short-tail sperm defects in the Finnish Yorkshire breed. Reprod Domest Anim 43:690-5, 2008. Pubmed reference: 18397189 . DOI: 10.1111/j.1439-0531.2007.00971.x. | |
| 2007 | Sironen, A., Vilkki, J., Bendixen, C., Thomsen, B. : |
| Infertile Finnish Yorkshire boars carry a full-length LINE-1 retrotransposon within the KPL2 gene. Mol Genet Genomics 278:385-91, 2007. Pubmed reference: 17610085 . DOI: 10.1007/s00438-007-0256-7. | |
| 2006 | Mikkola, M., Sironen, A., Kopp, C., Taponen, J., Sukura, A., Vilkki, J., Katila, T., Andersson, M. : |
| Transplantation of normal boar testicular cells resulted in complete focal spermatogenesis in a boar affected by the immotile short-tail sperm defect. Reprod Domest Anim 41:124-8, 2006. Pubmed reference: 16519717 . DOI: 10.1111/j.1439-0531.2006.00651.x. | |
| Sironen, A., Thomsen, B., Andersson, M., Ahola, V., Vilkki, J. : | |
| An intronic insertion in KPL2 results in aberrant splicing and causes the immotile short-tail sperm defect in the pig. Proc Natl Acad Sci U S A 103:5006-11, 2006. Pubmed reference: 16549801 . DOI: 10.1073/pnas.0506318103. | |
| 2002 | Sironen, A.I., Andersson, M., Uimari, P., Vilkki, J. : |
| Mapping of an immotile short tail sperm defect in the Finnish Yorkshire on porcine Chromosome 16 Mammalian Genome 13:45-49, 2002. Pubmed reference: 11773969 . | |
| Sukura, A., Makipaa, R., Vierula, M., Rodriguez-Martinez, H., Sundback, P., Andersson, M. : | |
| Hereditary sterilizing short-tail sperm defect in Finnish Yorkshire boars Journal of Veterinary Diagnostic Investigation 14:382-388, 2002. Pubmed reference: 12296389 . | |
| 2000 | Andersson, M., Peltoniemi, O.A.T., Makinen, A., Sukura, A., Rodriguez-Martinez, H. : |
| The hereditary 'short tail' sperm defect - A new reproductive problem in Yorkshire boars Reproduction in Domestic Animals 35:59-63, 2000. |
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- Created by Imke Tammen2 on 27 Sep 2021