OMIA:002377-8845 : Knob, basal in Anser cygnoides (swan goose) |
Categories: Craniofacial phene
Possibly relevant human trait(s) and/or gene(s) (MIM number): 601413 (gene)
Links to MONDO diseases: No links.
Mendelian trait/disorder: yes
Mode of inheritance: Autosomal
Considered a defect: no
Key variant known: yes
Year key variant first reported: 2021
Cross-species summary: The basal knob is a prominent bump, swelling, bulge, or projection at the base of a bird's upper bill.
Molecular basis: Deng et al. (2021): "integrated radiographic, histological, transcriptomic and genomic analyses revealed the histomorphological characteristics and genetic mechanism of goose knob. ... integrated transcriptomic and genomic analysis contributed to the identification of 17 and 21 candidate genes associated with the knob formation in the skin and bone, respectively. Of them, DIO2 gene could play a pivotal role in determining the knob phenotype in geese. .... a non-synonymous mutation (c.642,923 G > A, P265L) changed DIO2 protein secondary structure in knob geese, and Sanger sequencing further showed that the AA genotype was identified in the population of knob geese ..." Chen et al. (2023): "To identify candidate genes responsible for this trait [protuberant knob], we inspected 397 genes selected in Chinese domestic breeds ... . ... CACNA1I is an important paralog of CACNA1H, which was previously reported to relate to protuberant knob in geese [Ji et al. 2021]. ... In the genomic region of CACNA1I, we identified four SNPs, three intronic and one exonic, that exhibit genotype differentiation between Chinese domestic breeds and their wild counterpart, the swan goose ... . However, all four SNPs were excluded as candidate sites because their genotypes did not segregate with the phenotype when examined in another 62 individuals ... . The other candidate gene was an osteochondroma-related gene, Exostosin glycosyltransferase 1 (EXT1), which also showed a relatively high level of population differentiation ... . ... Genotype screening ... identified four intronic SNPs in EXT1 to present genotype differentiation between populations ... . Linkage analysis of the four SNPs revealed that two SNPs (NW_013185721.1: 4,792,818 and 4,793,508) were in complete linkage disequilibrium (LD, r2 = 1.0; ...). Genotype analysis of the four SNPs in another 62 individuals revealed the two linked SNPs to have perfect genotype segregation with protuberant knob ... , suggesting that these two SNPs may be associated with the trait.
Genetic engineering:
Unknown
Have human generated variants been created, e.g. through genetic engineering and gene editing
Breeds:
Lion Head (Goose (domestic)) (VBO_0000867),
Sichuan White, China (Goose (domestic)) (VBO_0009996).
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 genes:
| Symbol | Description | Species | Chr | Location | OMIA gene details page | Other Links |
|---|---|---|---|---|---|---|
| EXT1 | exostosin glycosyltransferase 1 | Anser cygnoides domesticus | NW_025927717.1 (4960907..4791291) | EXT1 | Homologene, Ensembl , NCBI gene | |
| DIO2 | deiodinase, iodothyronine, type II | Anser cygnoides domesticus | NW_025927676.1 (4002261..4019571) | DIO2 | 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 | Inferred EVA rsID | Year Published | PubMed ID(s) | Acknowledgements |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1335 | Lion Head (Goose (domestic)) Sichuan White, China (Goose (domestic)) | Knob, basal | DIO2 | missense | Naturally occurring variant | AnsCyg_PRJNA183603_v1.0 | NW_013185827.1 | g.642923G>A | p.(P265L) | 2021 | 34193033 |
Cite this entry
Nicholas, F. W., Tammen, I., & Sydney Informatics Hub. (2023). OMIA:002377-8845: 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.
| 2023 | Chen, L., Cao, Y., Li, G., Tian, Y., Zeng, T., Gu, T., Xu, W., Konoval, O., Lu, L. : |
| Population structure and selection signatures of domestication in geese. Biology (Basel) 12:532, 2023. Pubmed reference: 37106733. DOI: 10.3390/biology12040532. | |
| 2021 | Deng, Y., Hu, S., Luo, C., Ouyang, Q., Li, L., Ma, J., Lin, Z., Chen, J., Liu, H., Hu, J., Chen, G., Shu, D., Pan, Y., Hu, B., He, H., Qu, H., Wang, J. : |
| Integrative analysis of histomorphology, transcriptome and whole genome resequencing identified DIO2 gene as a crucial gene for the protuberant knob located on forehead in geese. BMC Genomics 22:487, 2021. Pubmed reference: 34193033. DOI: 10.1186/s12864-021-07822-9. | |
| Ji, W., Hou, L.E., Yuan, X., Gu, T., Chen, Z., Zhang, Y., Zhang, Y., Chen, G., Xu, Q., Zhao, W. : | |
| Identifying molecular pathways and candidate genes associated with knob traits by transcriptome analysis in the goose (Anser cygnoides). Sci Rep 11:11978, 2021. Pubmed reference: 34099774. DOI: 10.1038/s41598-021-91269-1. |
Edit History
- Created by Imke Tammen2 on 11 Aug 2021
- Changed by Imke Tammen2 on 21 Sep 2021
- Changed by Imke Tammen2 on 29 Apr 2023