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| Status |
Public on Dec 10, 2015 |
| Title |
Comprehensive identification of sexual dimorphism-associated differentially expressed genes in two-factorial designed RNA-seq data on Japanese Quail (Coturnix coturnix japonica) |
| Organism |
Coturnix japonica |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Japanese quail (Coturnix coturnix japonica) reach sexual maturity early, breed rapidly and successfully, and cost less and require less space than other birds raised for their meat and eggs. Given the value of this species for commercial production and experimental use as well as recent increasing demand, more studies are necessary to determine chromosomal regions and genes associated with gender and breed-differentiation in the species. Identification of sex-related genes can help target chromosomal regions for molecular sexing purposes. This study employed Trinity and edgeR for transcriptome analysis of next-generation RNA-seq data, which included 4 tissues obtained from 3 different breeds of Japanese quail (wild, miniature, and jumbo). The initial goal was to identify genes related to sexual dimorphism, as well as potential novel candidate genes for molecular sexing. Analysis and interpretation of differentially expressed genes shared between female and male tissue contrast groups provided insight into sex-related differences. Several of the genes identified in the present study as significant sex-related genes have been previously found in avian gene expression analyses (e.g. NIPBL, UBAP2), and other genes found differentially expressed in this study and not previously associated with sex-related differences may be considered potential candidates for molecular sexing (e.g. TERA, MYP0, PPR17, CASQ2). Additionally, other genes likely associated with neuronal and brain development (e.g. CHKA, NYAP), as well as body development and size differentiation (e.g. ANKRD26, GRP87) in quail were identified. Expression of homeobox protein regulating genes in the sex-related contrast group revealed two genes (HXC4, ISL1) that may regulate sex-specific anatomical development. Results of these analyses expand the currently limited pool of knowledge on the genetic features of the quail breed and could allow for more effective molecular sexing as well as selective breeding for traits important in commercial production.
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| Overall design |
This study employed Trinity and edgeR for transcriptome analysis of next-generation RNA-seq data, which included 4 tissues obtained from 3 different breeds of Japanese quail (wild, miniature, and jumbo).
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| Contributor(s) |
Lee H, Song K |
| Citation(s) |
26418419 |
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| Submission date |
Jan 14, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Minseok Seo |
| E-mail(s) |
[email protected]
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| Phone |
82-10-3410-5302
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| Organization name |
Seoul National University
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| Department |
Interdisciplinary program of bioinformatics
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| Street address |
Kwan-ak ro 1
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| City |
Seoul |
| ZIP/Postal code |
151-742 |
| Country |
South Korea |
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| Platforms (1) |
| GPL19652 |
Illumina HiSeq 2000 (Coturnix japonica) |
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| Samples (12)
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| Relations |
| BioProject |
PRJNA272589 |
| SRA |
SRP052227 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE64961_Processed_data.csv.gz |
85.6 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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