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| Status |
Public on Oct 07, 2019 |
| Title |
Affymetrix SNP array data for chicken samples |
| Organism |
Gallus gallus |
| Experiment type |
SNP genotyping by SNP array
Genome variation profiling by SNP array
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| Summary |
The conservation and development of chicken has considerably affected human activities, but the admixture history of chicken breeds has so far been poorly demonstrated especially for Chinese indigenous breeds. Using genotypes from 580961 single nucleotide polymorphism markers scored in 1201 animals, we evaluate the genetic diversity (heterozygosity and proportion of polymorphic markers), Linkage disequilibrium (LD) decay, population structure (principal component analysis and neighbor-joining tree), genetic differentiation (FST and genetic distance) and migration events (Treemix and f-statistics) of eight domesticated chicken breeds. All population analytical methods reveal patterns of hybridization which occurred after divergence in Tibetan chicken. We argue that chicken migration and admixture followed by trade have been important forces in shaping modern Chinese chicken genomic variation. Moreover, isolation by distance may play critical role in the shaping genomic variation within Eurasia continent chicken breeds.
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| Overall design |
Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from blood samples.
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| Contributor(s) |
Nie C, Almeida P, Jia Y, Bao H, Ning Z, Qu L |
| Citation(s) |
31263886 |
| |
| Submission date |
Mar 06, 2019 |
| Last update date |
Oct 07, 2019 |
| Contact name |
Changsheng Nie |
| E-mail(s) |
changshengnie@gmail.com
|
| Organization name |
China Agricultural University
|
| Department |
Animal Genetics and Breeding
|
| Street address |
Yuanmingyuan road 2#
|
| City |
Beijing |
| ZIP/Postal code |
100193 |
| Country |
China |
| |
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| Platforms (1) |
| GPL23815 |
[Axiom_GW_GT_Chicken] 600K Affymetrix Axiom® HD Genotyping Array |
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| Samples (1193)
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| Relations |
| BioProject |
PRJNA525994 |
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