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. 2015 Sep 29;10(9):e0139324. doi: 10.1371/journal.pone.0139324. eCollection 2015.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Avian Proteins / genetics
  • Body Weight / genetics
  • Brain / metabolism
  • Breeding
  • Cluster Analysis
  • Coturnix / classification
  • Coturnix / genetics*
  • Female
  • Gene Expression Profiling / methods*
  • Gene Expression Profiling / statistics & numerical data
  • Male
  • Oligonucleotide Array Sequence Analysis
  • Ovary / metabolism
  • Reverse Transcriptase Polymerase Chain Reaction
  • Sequence Analysis, RNA / methods*
  • Sequence Analysis, RNA / statistics & numerical data
  • Sex Factors
  • Species Specificity
  • Testis / metabolism
  • Transcriptome / genetics*


  • Avian Proteins

Associated data

  • GEO/GSE64961

Grant support

This work was supported by a grant from the Next-Generation BioGreen 21 Program (No. PJ01104401), Rural Development Administration, Republic of Korea, the Achievement Rewards for College Scientists (ARCS) Foundation to KC, and the National Science Foundation (NSF) under Grant No IIA-1415113 to KC.