Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Comparative genomic hybridization of chicken and Japanese quail

ABSTRACT: Since Japanese quail and chicken belong to the same order Galliforms, DNA sequence of both species are highly conserved and proved to be applicable for various analyses each other. Quail are commonly used to address physiological questions for reasons of economy. To test whether chicken microarrays are useful to quail samples, we compared hybridization signals of chicken and quail genomic DNA on Affymetrix chicken genome array. Experiment Overall Design: Genomic DNA of female chicken and quail were extracted individually from liver of three birds and hybridized on Affymetrix microarrays. Samples were analyzed in triplicate set of array (three biological replicates).

ORGANISM(S): Coturnix japonica

SUBMITTER: Takashi Yoshimura

PROVIDER: E-GEOD-8016 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Thyrotrophin in the pars tuberalis triggers photoperiodic response.

Nakao Nobuhiro N Ono Hiroko H Yamamura Takashi T Anraku Tsubasa T Takagi Tsuyoshi T Higashi Kumiko K Yasuo Shinobu S Katou Yasuhiro Y Kageyama Saburo S Uno Yumiko Y Kasukawa Takeya T Iigo Masayuki M Sharp Peter J PJ Iwasawa Atsushi A Suzuki Yutaka Y Sugano Sumio S Niimi Teruyuki T Mizutani Makoto M Namikawa Takao T Ebihara Shizufumi S Ueda Hiroki R HR Yoshimura Takashi T

Nature 20080301 7185

Molecular mechanisms regulating animal seasonal breeding in response to changing photoperiod are not well understood. Rapid induction of gene expression of thyroid-hormone-activating enzyme (type 2 deiodinase, DIO2) in the mediobasal hypothalamus (MBH) of the Japanese quail (Coturnix japonica) is the earliest event yet recorded in the photoperiodic signal transduction pathway. Here we show cascades of gene expression in the quail MBH associated with the initiation of photoinduced secretion of lu ...[more]

PMID: 18354476

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Project description: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. 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).

Dataset Information

Comparative genomic hybridization of chicken and Japanese quail

Publications

Thyrotrophin in the pars tuberalis triggers photoperiodic response.

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