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Background  The probable influence of genes and the environment on sex determination in Nile tilapia suggests that it should be regarded as a complex trait. Detection of sex determination genes in tilapia has both scientific and commercial importance. The main objective was to detect genes and microRNAs that were differentially expressed by gender in early embryonic development.    Results  Artificial fertilization of  Oreochromis niloticus  XX females with either sex-reversed ΔXX males or genetically-modified YY ‘supermales’ resulted in all-female and all-male embryos, respectively. RNA of pools of all-female and all-male embryos at 2, 5 and 9 dpf were used as template for a custom Agilent eArray hybridization and next generation sequencing. Fifty-nine genes differentially expressed between genders were identified by a false discovery rate of p < 0.05. The most overexpressed genes were  amh  and  tspan8  in males, and  cr/20β-hsd ,  gpa33 ,  rtn4ipl  and  zp3  in females (p < 1 × 10 −9 ). Validation of gene expression using qPCR in embryos and gonads indicated copy number variation in  tspan8 ,  gpa33 ,  cr/20β-hsd  and  amh . Sequencing of  amh  identified a male-specific duplication of this gene, denoted  amhy , differing from the sequence of  amh  by a 233 bp deletion on exonVII, hence lacking the capability to encode the protein motif that binds to the transforming growth factor beta receptor (TGF-β domain).  amh  and  amhy  segregated in the mapping family in full concordance with SD-linked marker on LG23 signifying the QTL for SD. We discovered 831 microRNAs in tilapia embryos of which nine had sexually dimorphic expression patterns by a false discovery rate of p < 0.05. An up-regulated microRNA in males, pma-mir-4585, was characterized with all six predicted target genes including  cr/20β-hsd , down-regulated in males.    Conclusions  This study reports the first discovery of sexually differentially expressed genes and microRNAs at a very early stage of tilapia embryonic development, i.e. from 2 dpf. Genes with sexually differential expression patterns are enriched for copy number variation. A novel male-specific duplication of  amh , denoted  amhy , lacking the TGF-β domain was identified and mapped to the QTL region on LG23 for SD, thus indicating its potential role in SD.    Electronic supplementary material  The online version of this article (doi:10.1186/1471-2164-15-774) contains supplementary material, which is available to authorized users.

bmc genomics

Identification of male-specific amh duplication, sexually differentially expressed genes and microRNAs at early embryonic development of Nile tilapia (Oreochromis niloticus)