Reporter lines to study site-specific genome editing by CRISPR-Cas9 or similar methods inA. thaliana were generated. Gateway-compatible binary BAC (BIBAC) vectors for plant transformation were described (BIBAC-GW). BIBAC-GW was shown to predominantly result in intact single copy T-DNA integrations inA. thaliana. Individual single-copy integrations lines were shown to have minimal differences in expression level of the transgenes.