title: Identification of candidate gonadal sex differentiation genes in the chicken embryo using RNA-seq.
abstract: BACKGROUND
  Despite some advances in recent years, the genetic control of gonadal sex differentiation during embryogenesis is still not completely understood. To identify new candidate genes involved in ovary and testis development, RNA-seq was used to define the transcriptome of embryonic chicken gonads at the onset of sexual differentiation (day 6.0/stage 29).
  
  
  RESULTS
  RNA-seq revealed more than 1000 genes that were transcribed in a sex-biased manner at this early stage of gonadal differentiation. Comparison with undifferentiated gonads revealed that sex biased expression was derived primarily from autosomal rather than sex-linked genes. Gene ontology and pathway analysis indicated that many of these genes encoded proteins involved in extracellular matrix function and cytoskeletal remodelling, as well as tubulogenesis. Several of these genes are novel candidate regulators of gonadal sex differentiation, based on sex-biased expression profiles that are altered following experimental sex reversal. We further characterised three female-biased (ovarian) genes; calpain-5 (CAPN5), G-protein coupled receptor 56 (GPR56), and FGFR3 (fibroblast growth factor receptor 3). Protein expression of these candidates in the developing ovaries suggests that they play an important role in this tissue.
  
  
  CONCLUSIONS
  This study provides insight into the earliest steps of vertebrate gonad sex differentiation, and identifies novel candidate genes for ovarian and testicular development.
authors.affiliation: Murdoch Childrens Research Institute, Royal Children's Hospital, Flemington Road, 3052, Parkville, VIC, Australia. katie.ayers@mcri.edu.au.|Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia. katie.ayers@mcri.edu.au.
authors.forename: Katie L
authors.initials: KL
authors.lastname: Ayers
authors.affiliation: Murdoch Childrens Research Institute, Royal Children's Hospital, Flemington Road, 3052, Parkville, VIC, Australia. luke.lambeth@mcri.edu.au.
authors.forename: Luke S
authors.initials: LS
authors.lastname: Lambeth
authors.affiliation: Murdoch Childrens Research Institute, Royal Children's Hospital, Flemington Road, 3052, Parkville, VIC, Australia. nadia.davidson@mcri.edu.au.
authors.forename: Nadia M
authors.initials: NM
authors.lastname: Davidson
authors.affiliation: Murdoch Childrens Research Institute, Royal Children's Hospital, Flemington Road, 3052, Parkville, VIC, Australia. andrew.sinclair@mcri.edu.au.|Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia. andrew.sinclair@mcri.edu.au.
authors.forename: Andrew H
authors.initials: AH
authors.lastname: Sinclair
authors.affiliation: Murdoch Childrens Research Institute, Royal Children's Hospital, Flemington Road, 3052, Parkville, VIC, Australia. alicia.oshlack@mcri.edu.au.
authors.forename: Alicia
authors.initials: A
authors.lastname: Oshlack
authors.affiliation: Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, 3168, Australia. craig.smith@monash.edu.
authors.forename: Craig A
authors.initials: CA
authors.lastname: Smith
mesh_terms: D000818:Animals; D002642:Chick Embryo; D016000:Cluster Analysis; D047108:Embryonic Development / Q000235:genetics; D005260:Female; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D056726:Genetic Association Studies; D006066:Gonads / Q000378:metabolism*; D008297:Male; D017423:Sequence Analysis, RNA; D012733:Sex Differentiation / Q000235:genetics*; D059467:Transcriptome