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Data released on April 27, 2018

Supporting data for “Population genomic data reveal genes related to important traits of quail”

Wu, Y; Zhang, Y; Hou, Z; Fan, G; Pi, J; Sun, S; Chen, J; Liu, H; Du, X; Shen, J; Hu, G; Chen, W; Pan, A; Yin, P; Chen, X; Pu, Y; Zhang, H; Liang, Z; Jian, J; Zhang, H; Wu, B; Sun, J; Chen, J; Tao, H; Yang, T; Xiao, H; Yang, H; Zheng, C; Bai, M; Fang, X; Burt, D, W; Wang, W; Li, Q; Xu, X; Li, C; Yang, H; Wang, J; Yang, N; Liu, X; Du, J (2018): Supporting data for “Population genomic data reveal genes related to important traits of quail” GigaScience Database. http://dx.doi.org/10.5524/100441 RIS BibTeX Text

Japanese quail (Coturnix japonica), a recently domesticated poultry species, is important not only as an agricultural product, but also as a model bird species for genetic research. However, most of the biological questions concerning genomics, phylogenetics and genetics of some important economic traits have not been answered. It is thus necessary to complete a high-quality genome sequence as well as a series of comparative genomics, evolution and functional studies. Here, we present a quail genome assembly spanning 1.04Gb with 86.63% of sequences anchored to 30 chromosomes (28 autosomes and two sex chromosomes Z/W). Our genomic data has resolved the long-term debate of phylogeny among Perdicinae (Japanese quail), Meleagridinae (turkey) and Phasianinae (chicken). Comparative genomics and functional genomic data found that four candidate genes involved in early maturation had experienced positive selection, and one of them encodes follicle stimulating hormone beta (FSHβ), which is correlated with different FSHβ levels in quail and chicken. We re-sequenced 31 quails (10 wild, 11 egg-type and 10 meat-type) and identified 18 and 26 candidate selective sweep regions in the egg-type and meat-type lines, respectively. That only one of them is shared between egg-type and meat-type lines suggests that they were subject to an independent selection. We also detected a haplotype on chromosome Z which was closely linked with maroon/yellow plumage in quail using population resequencing and a genome-wide association study. This haplotype block will be useful for quail breeding programs. This study provided a high-quality quail reference genome, identified quail-specific genes and resolved quail phylogeny. We have identified genes related to quail early maturation and a marker for plumage color which is significant for quail breeding. These results will facilitate biological discovery in quails and help us elucidate the evolutionary process within the Phasianidae family.

Contact Submitter

JBrowse:

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Accessions (data included in GigaDB):

BioProject: PRJNA339911

Keywords:

japanese quail genome assembly early maturation phylogeny resequencing plumage color quail breeding 

Genomic, Transcriptomic

http://gigadb.org/images/data/cropped/100441.jpg

Funding:

  • Funding body - Agricultural Science and Technology Innovation Center of Hubei
  • Award ID - 2012tsxk09
  • Comment - The specialty of poultry breeding
  • Awardee - Jinping Du
  • Funding body - Agricultural Science and Technology Innovation Center of Hubei
  • Award ID - 2014jzxjh02
  • Comment - Research and application of functional genes in early maturity traits of quail based on genome wide analysis
  • Awardee - Jinping Du
  • Funding body - Key Laboratory of Animal Embryo and Molecular Breeding of Hubei
  • Award ID - 2014-2017 ZD146
  • Comment - Molecular breeding of poultry
  • Awardee - Yan Wu

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
BL-F93934 Japanese quailCoturnix japonica Description:RNA extracted from hypothalamus and ov...
Alternative_name:Japanese quail
Alternative accession-BioSample:SAMN08893028
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BL-M93934 Japanese quailCoturnix japonica Description:RNA extracted from hypothalamus and te...
Alternative_name:Japanese quail
Alternative accession-BioSample:SAMN08893031
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CAF-193934 Japanese quailCoturnix japonica Description:Genomic DNA extracted from a domestic ...
Alternative_name:Japanese quail
Alternative accession-BioSample:SAMN06756392
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CAF-1093934 Japanese quailCoturnix japonica Description:Genomic DNA extracted from a domestic ...
Alternative_name:Japanese quail
Alternative accession-BioSample:SAMN06756416
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CAF-293934 Japanese quailCoturnix japonica Description:Genomic DNA extracted from a domestic ...
Alternative_name:Japanese quail
Alternative accession-BioSample:SAMN06756393
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CAF-393934 Japanese quailCoturnix japonica Description:Genomic DNA extracted from a domestic ...
Alternative_name:Japanese quail
Alternative accession-BioSample:SAMN06756394
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CAF-493934 Japanese quailCoturnix japonica Description:Genomic DNA extracted from a domestic ...
Alternative_name:Japanese quail
Alternative accession-BioSample:SAMN06756395
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CAF-593934 Japanese quailCoturnix japonica Description:Genomic DNA extracted from a domestic ...
Alternative_name:Japanese quail
Alternative accession-BioSample:SAMN06756396
...
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CAF-693934 Japanese quailCoturnix japonica Description:Genomic DNA extracted from a domestic ...
Alternative_name:Japanese quail
Alternative accession-BioSample:SAMN06756412
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CAF-793934 Japanese quailCoturnix japonica Description:Genomic DNA extracted from a domestic ...
Alternative_name:Japanese quail
Alternative accession-BioSample:SAMN06756413
...
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Displaying 1-10 of 78 Sample(s).

Files: (FTP site) Table Settings

Columns:

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

File NameSample IDData TypeFile FormatSizeRelease Date 
Sequence variantsTAR7.7 GB2018-04-26
Sequence variantsTAR4.71 GB2018-04-26
scriptUNKNOWN0.2 KB2018-04-26
Coding sequenceFASTA8.5 MB2018-04-26
protein sequenceFASTA5.55 MB2018-04-26
otherTSV102.66 KB2018-04-26
otherTSV0.86 KB2018-04-26
Sequence assemblyAGP28.47 KB2018-04-26
Sequence assemblyFASTA257.67 MB2018-04-26
Sequence assemblyFASTA287.65 MB2018-04-26
Displaying 1-10 of 22 File(s).

History:

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