Comprehensive identification of sexual dimorphism-associated differentially expressed genes in two-way factorial designed RNA-seq data on Japanese quail (Coturnix coturnix japonica)

Kelsey Caetano-Anolles, Minseok Seo, Sandra Rodriguez-Zas, Jae Don Oh, Jae Yong Han, Kichoon Lee, Tae Sub Park, Sangsu Shin, Zhang Jiao Jiao, Mrinmoy Ghosh, Dong Kee Jeong, Seoae Cho, Heebal Kim, Ki Duk Song, Hak Kyo Lee

Research output: Contribution to journalArticle

Abstract

Japanese quail (Coturnix coturnix japonica) reach sexual maturity earlier, breed rapidly and successfully, and cost less and require less space than other birds raised commercially. Given the value of this species for food production and experimental use, more studies are necessary to determine chromosomal regions and genes associated with gender and breed-differentiation. This study employed Trinity and edgeR for transcriptome analysis of next-generation RNA-seq data, which included 4 tissues obtained from 3 different breeding lines of Japanese quail (random bred control, heavy weight, low weight). Differentially expressed genes shared between female and male tissue contrast groups were analyzed to identify genes related to sexual dimorphism as well as potential novel candidate genes for molecular sexing. Several of the genes identified in the present study as significant sex-related genes have been previously found in avian gene expression analyses (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 (TERA, MYP0, PPR17, CASQ2). Additionally, other genes likely associated with neuronal and brain development (CHKA, NYAP), as well as body development and size differentiation (ANKRD26, GRP87) in quail were identified. Expression of homeobox protein regulating genes (HXC4, ISL1) shared between our two sex-related contrast groups (Female Brain vs. Male Brain and Ovary vs. Testis) indicates that these genes may regulate sex-specific anatomical development. Results reveal 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.

Original languageEnglish (US)
Article numbere0139324
JournalPloS one
Volume10
Issue number9
DOIs
StatePublished - Sep 29 2015

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • General

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    Caetano-Anolles, K., Seo, M., Rodriguez-Zas, S., Oh, J. D., Han, J. Y., Lee, K., Park, T. S., Shin, S., Jiao, Z. J., Ghosh, M., Jeong, D. K., Cho, S., Kim, H., Song, K. D., & Lee, H. K. (2015). Comprehensive identification of sexual dimorphism-associated differentially expressed genes in two-way factorial designed RNA-seq data on Japanese quail (Coturnix coturnix japonica). PloS one, 10(9), [e0139324]. https://doi.org/10.1371/journal.pone.0139324