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Background  Dmrt2a is a zinc finger like transcription factor with several roles during zebrafish early development: left-right asymmetry, synchronisation of the somite clock genes and fast muscle differentiation. Despite the described functions, Dmrt2a mechanism of action is unknown. Therefore, with this work, we propose to identify Dmrt2a downstream genes during zebrafish early development.    Results  We generated and validated a heat-shock inducible transgenic line, to timely control  dmrt2a  overexpression, and  dmrt2a  mutant lines.  We characterised  dmrt2a  overexpression phenotype and verified that it was very similar to the one described after knockdown of this gene, with left-right asymmetry defects and desynchronisation of somite clock genes. Additionally, we identified a new phenotype of somite border malformation.  We generated several  dmrt2a  mutant lines, but we only detected a weak to negligible phenotype. As  dmrt2a  has a paralog gene,  dmrt2b , with similar functions and expression pattern, we evaluated the possibility of redundancy. We found that  dmrt2b  does not seem to compensate the lack of  dmrt2a . Furthermore, we took advantage of one of our mutant lines to confirm  dmrt2a  morpholino specificity, which was previously shown to be a robust knockdown tool in two independent studies.  Using the described genetic tools to perform and validate a microarray, we were able to identify six genes downstream of Dmrt2a:  foxj1b ,  pxdc1b, cxcl12b, etv2 ,  foxc1b  and  cyp1a .    Conclusions  In this work, we generated and validated several genetic tools for  dmrt2a  and identified six genes downstream of this transcription factor. The identified genes will be crucial to the future understanding of Dmrt2a mechanism of action in zebrafish.    Electronic supplementary material  The online version of this article (10.1186/s12861-018-0173-5) contains supplementary material, which is available to authorized users.

Identification of Dmrt2a downstream genes during zebrafish early development using a timely controlled approach