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Data released on March 23, 2017

Supporting data for "Genomic data for 78 chickens from 14 populations"

Che, T; Chen, B; Gaur, U; Jin, L; Li, D; Li, M; Li, Y; Luo, M; Tang, Q; Tian, S; Wang, Y; Xu, Z; Yin, H; Zhang, G; Zhang, L; Zhao, X; Zhou, X; Xu, H; Yang, M; Zhou, R; Li, R; Li, M; Zhu, Q (2017): Supporting data for "Genomic data for 78 chickens from 14 populations" GigaScience Database. http://dx.doi.org/10.5524/100291 RIS BibTeX Text

Since the domestication of the red jungle fowls (Gallus gallus) (dating back to ~10,000 B.P.) in Asia, domestic chickens (Gallus gallus domesticus) have been subjected to the combined effects of natural selection and human-driven artificial selection; this has resulted in marked phenotypic diversity in a number of traits, including behavior, body composition, egg production and skin color. Population genomic variations through diversifying selection have not been fully investigated.
The whole genomes of 78 domestic chickens were sequenced to an average of 18-fold coverage for each bird. By combining this data with publicly available genomes of 5 wild red jungle fowls and 8 Xishuangbanna game fowls, we conducted a comprehensive comparative genomics analysis of 91 chickens from 17 populations. After aligning ~21.30 gigabases (Gb) of high quality data from each individual to the reference chicken genome, we identified ~6.44 million (M) SNPs for each population. These SNPs included 1.10 M novel SNPs in 17 populations that were absent in the current chicken dbSNP (Build 145) entries.
The current data is important for population genetics and further studies in chicken, and will serve as a valuable resource for investigating diversifying selection and candidate genes for selective breeding in chicken.

Contact Submitter

Related manuscripts:

doi:10.1093/gigascience/gix026

Accessions (data included in GigaDB):

SRA: SRP067615
BioProject: PRJNA241474

Keywords:

Chicken Genetic diversity Population genomics Whole-genome resequencing 

Genomic

http://gigadb.org/images/data/cropped/100291.jpg

Funding:

  • Funding body - Sichuan Provincial Department of Science & Technology
  • Award ID - 2015JQO023
  • Awardee - Diyan Li
  • Funding body - National Natural Science Foundation of China
  • Award ID - 31522055
  • Awardee - Mingzhou Li
  • Funding body - China Agricultural Research System
  • Award ID - CARS-41
  • Awardee - Qing Zhu
  • Funding body - 12th Five Year Plan for breeding program in Sichuan
  • Award ID - 2011NZ0099-7
  • Awardee - Qing Zhu
  • Funding body - National Natural Science Foundation of China
  • Award ID - 31402063
  • Awardee - Diyan Li

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
LCEM19031ChickenGallus gallus Description:Genomic DNA extracted from blood of he...
Experiment type:DNA extraction
Infra_specific_rank:Breed
...
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LCEM29031ChickenGallus gallus Description:Genomic DNA extracted from blood of he...
Experiment type:DNA extraction
Infra_specific_rank:Breed
...
+
LCEM39031ChickenGallus gallus Description:Genomic DNA extracted from blood of he...
Experiment type:DNA extraction
Infra_specific_rank:Breed
...
+
LCEM49031ChickenGallus gallus Description:Genomic DNA extracted from blood of he...
Experiment type:DNA extraction
Infra_specific_rank:Breed
...
+
LCEM59031ChickenGallus gallus Description:Genomic DNA extracted from blood of he...
Experiment type:DNA extraction
Infra_specific_rank:Breed
...
+
LCEM69031ChickenGallus gallus Description:Genomic DNA extracted from blood of he...
Experiment type:DNA extraction
Infra_specific_rank:Breed
...
+
LCJY19031ChickenGallus gallus Description:Genomic DNA extracted from blood of he...
Experiment type:DNA extraction
Infra_specific_rank:Breed
...
+
LCJY39031ChickenGallus gallus Description:Genomic DNA extracted from blood of he...
Experiment type:DNA extraction
Infra_specific_rank:Breed
...
+
LCJY59031ChickenGallus gallus Description:Genomic DNA extracted from blood of he...
Experiment type:DNA extraction
Infra_specific_rank:Breed
...
+
LCJY79031ChickenGallus gallus Description:Genomic DNA extracted from blood of he...
Experiment type:DNA extraction
Infra_specific_rank:Breed
...
+
Displaying 1-10 of 91 Sample(s).

Files: (FTP site) Table Settings

Columns:

File Description
Sample ID
File Type
File Format
Size
Release Date
Download Link
File Attributes

File NameSample IDFile TypeFile FormatSizeRelease Date 
txtTEXT202.36 MB2017-01-10
LCEM1Sequence variantsVCF110.03 MB2017-01-10
LCEM2Sequence variantsVCF188.19 MB2017-01-10
LCEM3Sequence variantsVCF116.6 MB2017-01-10
LCEM4Sequence variantsVCF220.58 MB2017-01-10
LCEM5Sequence variantsVCF116.72 MB2017-01-10
LCEM6Sequence variantsVCF116.26 MB2017-01-10
LCJY1Sequence variantsVCF124.68 MB2017-01-10
LCJY3Sequence variantsVCF214.31 MB2017-01-10
LCJY5Sequence variantsVCF229.48 MB2017-01-10
Displaying 1-10 of 94 File(s).

History:

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