Patent ID: 6484105
Filing Date: 2002-11-19
Classification: C12Q,G16B

Abstract:
A method of identifying a plant containing a deletion in a gene sequence, the method comprising:(a) providing a collection of nucleic acids derived from a plurality of source plants, wherein the nucleic acids comprise the gene sequence, or the gene sequence with a deletion, and at least one of the nucleic acids comprises the gene sequence with a deletion, and wherein the gene sequence or gene sequence with the deletion is flanked by a 5â€² flanking polynucleotide sequence and 3â€² flanking polynucleotide sequence; (b) providing a database that associates each nucleic acid in the collection with the source plant from which the nucleic acid was derived; (c) amplifying the gene sequence with the deletion from the collection of nucleic acids using a first primer that specifically hybridizes to the 5â€² flanking polynucleotide sequence, or its complement, and a second primer that specifically hybridizes to the 3â€² flanking polynucleotide sequence, or its complement, wherein the amplification includes a shortened extension step, the length of which is chosen so that proper amplification only occurs if the distance between the primers is less than is the case when the gene sequence lacks a deletion, whereby the gene sequence with the deletion is preferentially amplified compared to the gene sequence lacking a deletion; (d) detecting the preferential amplification of the gene sequence with the deletion compared to the amplification of the gene sequence lacking a deletion, thereby identifying a nucleic acid comprising the gene sequence with a deletion; and (e) identifying the source plant from which the nucleic acid identified in step (d) was derived by referring to the database provided in step (b), thereby identifying a plant containing a deletion in the gene sequence.