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

Dataset type: Genomic
Data released on March 23, 2017

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

DOI10.5524/100291

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.

Additional details

Read the peer-reviewed publication(s):

Li, D., Che, T., Chen, B., Tian, S., Zhou, X., Zhang, G., … Li, M. (2017). Genomic data for 78 chickens from 14 populations. GigaScience, 6(6), 1–5. doi:10.1093/gigascience/gix026

Accessions (data included in GigaDB):

SRA: SRP067615
BioProject: PRJNA241474





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
TCQH59031ChickenGallus gallus Description:Genomic DNA extracted from blood of he...
Experiment type:DNA extraction
Infra specific rank:Breed
...
+
TCQH89031ChickenGallus gallus Description:Genomic DNA extracted from blood of he...
Experiment type:DNA extraction
Infra specific rank:Breed
...
+
TCQH99031ChickenGallus gallus Description:Genomic DNA extracted from blood of he...
Experiment type:DNA extraction
Infra specific rank:Breed
...
+
TCSN19031ChickenGallus gallus Description:Genomic DNA extracted from blood of he...
Experiment type:DNA extraction
Infra specific rank:Breed
...
+
TCSN39031ChickenGallus gallus Description:Genomic DNA extracted from blood of he...
Experiment type:DNA extraction
Infra specific rank:Breed
...
+
TCSN49031ChickenGallus gallus Description:Genomic DNA extracted from blood of he...
Experiment type:DNA extraction
Infra specific rank:Breed
...
+
TCSN59031ChickenGallus gallus Description:Genomic DNA extracted from blood of he...
Experiment type:DNA extraction
Infra specific rank:Breed
...
+
TCSN69031ChickenGallus gallus Description:Genomic DNA extracted from blood of he...
Experiment type:DNA extraction
Infra specific rank:Breed
...
+
TCSN79031ChickenGallus gallus Description:Genomic DNA extracted from blood of he...
Experiment type:DNA extraction
Infra specific rank:Breed
...
+
TCSN89031ChickenGallus gallus Description:Genomic DNA extracted from blood of he...
Experiment type:DNA extraction
Infra specific rank:Breed
...
+
Displaying 81-90 of 91 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
TCLZ5Sequence variantsVCF167.31 MB2017-01-10
TCQH10Sequence variantsVCF190.13 MB2017-01-10
TCQH11Sequence variantsVCF200.75 MB2017-01-10
TCQH1Sequence variantsVCF129.9 MB2017-01-10
TCQH5Sequence variantsVCF118.01 MB2017-01-10
TCQH8Sequence variantsVCF186.27 MB2017-01-10
TCQH9Sequence variantsVCF200.99 MB2017-01-10
TCSN1Sequence variantsVCF197.45 MB2017-01-10
TCSN3Sequence variantsVCF196.82 MB2017-01-10
TCSN4Sequence variantsVCF190.22 MB2017-01-10
Displaying 71-80 of 94 File(s).
Funding body Awardee Award ID Comments
Sichuan Provincial Department of Science & Technology Diyan Li 2015JQO023
National Natural Science Foundation of China Mingzhou Li 31522055
China Agricultural Research System Qing Zhu CARS-41
12th Five Year Plan for breeding program in Sichuan Qing Zhu 2011NZ0099-7
National Natural Science Foundation of China Diyan Li 31402063
Date Action
March 23, 2017 Dataset publish
October 2, 2017 Manuscript Link added : 10.1093/gigascience/gix026