NPTII is not a good marker for selecting transformants in our plant system. Can we use BIBAC2 and select for HYG?
You could, but you probably don’t want to. The marker that is used to initially select for transformants should be located adjacent to the left T-DNA border (LB) since the T-DNA is transferred right border (RB) to left border. If you use BIBAC2 and select for hygromycin resistant transformed plant tissue it is likely (although this may vary depending on the plant system) that the T-DNAs transferred will not be complete/intact.
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