No, there is no such difference. But the researchers should use the pure variety of Danio rerio as several manipulated varieties are now a days available. Danio rerio is one of the most studied organism for research purposes. Due to several advantages of using the organisms for experiments and available databases, it is considered as model organism.
You can use but not transgenic one. You can go through fishbase website for identifying character. Generally different zebrafish species differ in colouration.