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

Dataset type: Genomic, Transcriptomic
Data released on April 27, 2018

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 DW; 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

DOI10.5524/100441

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.

Additional details

Read the peer-reviewed publication(s):

Wu, Y., Zhang, Y., Hou, Z., Fan, G., Pi, J., Sun, S., … Du, J. (2018). Population genomic data reveal genes related to important traits of quail. GigaScience, 7(5). doi:10.1093/gigascience/giy049

Accessions (data included in GigaDB):

BioProject: PRJNA339911





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




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).
Funding body Awardee Award ID Comments
Agricultural Science and Technology Innovation Center of Hubei Jinping Du 2012tsxk09 The specialty of poultry breeding
Agricultural Science and Technology Innovation Center of Hubei Jinping Du 2014jzxjh02 Research and application of functional genes in early maturity traits of quail based on genome wide analysis
Key Laboratory of Animal Embryo and Molecular Breeding of Hubei Yan Wu 2014-2017 ZD146 Molecular breeding of poultry
Date Action
April 27, 2018 Dataset publish
July 9, 2018 Manuscript Link added : 10.1093/gigascience/giy049