OMIA 001569-9031 : Feather colour, dark brown in Gallus gallus
Aided by improved sequencing techniques and a better reference genome assembly (GRCg6a, compared with Galgal3), Zhu et al. (2022) showed that light yellow plumage segregating in the F1 of a cross between Rhode Island Red and White Leghorn is due to the same deletion (now characterised as 7638 bp) as reported by Gunnarsson et al. (2011).Associated gene:
|Symbol||Description||Species||Chr||Location||OMIA gene details page||Other Links|
|SOX10||SRY (sex determining region Y)-box 10||Gallus gallus||1||NC_052532.1 (51095091..51104261)||SOX10||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|
|661||Dark brown/yellow plumage||SOX10||deletion, gross (>20)||Naturally occurring variant||GRCg6a||1||g.51035106_51042744delinsGGTGCGGTGA||Gunnarsson et al. (2011): "an 8.3-kb deletion upstream of SOX10" Zhu et al. (2022): "the genome region from 51,035,106 bp to 51,042,744 bp is missing in LY [yellow] chickens, with this region showing a novel 10 bp insertion (GGTGCGGTGA)"||2011||21210960|
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||Zhu, T., Liu, M., Peng, S., Zhang, X., Chen, Y., Lv, X., Yang, W., Li, K., Zhang, J., Wang, H., Li, H., Ning, Z., Wang, L., Qu, L. :|
|A Deletion Upstream of SOX10 Causes Light Yellow Plumage Colour in Chicken. Genes (Basel) 13:, 2022. Pubmed reference: 35205371. DOI: 10.3390/genes13020327.|
|2020||Andersson, L., Bed’hom, B., Chuong, CM., Inaba, M.Inaba, M., Okimoto, R.Okimoto, R., Tixier-Boichard, M. :|
|The genetic basis for pigmentation phenotypes in poultry In S. E. Aggrey, H. Zhou, M. Tixier-Boichard, & D. D. Rhoads (Eds.), Advances in Poultry Genetics and Genomics. Cambridge, UK: Burleigh Dodds Science Publishing. :, 2020.|
|2019||Nie, C., Ban, L., Ning, Z., Qu, L. :|
|Feather colour affects the aggressive behaviour of chickens with the same genotype on the dominant white (I) locus. PLoS One 14:e0215921, 2019. Pubmed reference: 31048862. DOI: 10.1371/journal.pone.0215921.|
|2011||Gunnarsson, U., Kerje, S., Bed'hom, B., Sahlqvist, A.S., Ekwall, O., Tixier-Boichard, M., Kämpe, O., Andersson, L. :|
|The Dark brown plumage color in chickens is caused by an 8.3-kb deletion upstream of SOX10. Pigment Cell Melanoma Res 24:268-74, 2011. Pubmed reference: 21210960. DOI: 10.1111/j.1755-148X.2011.00825.x.|
|1993||Carefoot, WC. :|
|Further studies of linkage and mappings of the loci of genes in group 3 on chromosome 1 of the domestic fowl. Br Poult Sci 34:205-9, 1993. Pubmed reference: 8467400. DOI: 10.1080/00071669308417576.|
|1972||Moore, JW., Smyth, JR. :|
|Genetic factors associated with the plumage pattern of the barred Fayoumi. Poult Sci 51:1149-56, 1972. Pubmed reference: 4647577.|
- Created by Frank Nicholas on 28 May 2011
- Changed by Frank Nicholas on 09 Dec 2011
- Changed by Frank Nicholas on 10 Mar 2022