A method for detecting a gene deletion in a host species comprises: (a) amplifying a first DNA region surrounding the gene deletion with at least a pair of pre-PCR primers to form a pre-PCR product, wherein one of the pair of prePCR primers carries an adaptor sequence at 5'-end, wherein the adaptor sequence is not found in the host species' genome; (b) hybridizing the pre-PCR product to at least one circularizing probe, wherein the circularizing probe is designed to have a ligation arm and an extension arm targeting a strand complementary to the adapter sequence.