Methods for screening for gene specific hybridization polymorphisms (GSHPs) and their use in genetic mapping ane marker development
AssigneeSyngenta Participations AG
InventorsJohn Salmeron, Tong Zhu
Life of this patent
Estimating the term…
Abstract
A method for identification of gene specific hybridization polymorphisms (GSHPs) and their use is presented. The method involves the steps of a) global screening for hybridization polymorphisms using microarray; b) enzyme mediated genome complexity reduction; c) enzyme mediated differential signal amplification and noise reduction; d) data extraction and GSHP identification; and e) use of GSHPs in high throughput screening. The method is useful in a particular application for the fingerprinting of maize exotic germplasm and the identification of new and commercially useful loci therein.
Claims17
A method for detection of gene specific hybridization polymorphisms in polynucleotide sequences of genomic DNA from exotic species, the method comprising:
- a. selecting short oligonucleotide sequences complementary to the genomic polynucleotide sequences, said short oligonucleotide sequences to be synthesized directly onto or synthesized and placed onto a microarray surface;
- b. preparing genomic DNA from two genetic sources and subjecting said genomic DNA to site-specific restriction using one or more restriction enzymes to produce restriction fragment length polymorphisms (RFLPs);
- c. selectively amplifying RFLPs of a selected size range to create amplified polymorphism targets;
- d. fragmenting the amplified targets randomly into fragments of from about 50 to about 200 bases and end-labeling the fragments unselectively;
- e. hybridizing the end-labeled fragments to the short oligonucleotide sequences on the microarray surface;
- and
- f. quantifying the signals from the hybridization and detecting polymorphisms.
Dependencies are inferred from the claim text.