Brassica polymorphisms

• US 20050208570A1
• Filed: 05/09/2005
• Published: 09/22/2005
• Est. Priority Date: 12/02/1996
• Status: Abandoned Application

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Murigneux, Alain, Lemieux, Bertrand, Landry, Benoit S., Sapolsky, Ronald J.
• Application Number:
  US11/125,588
• Publication Number:
  US 20050208570A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: C07H 21/02 with ribosyl as saccharide radical
• CPC Class Codes: C07H 21/04 with deoxyribosyl as saccharide radical
• CPC Class Codes: C12Q 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 1/6895 for plants, fungi or algae
• CPC Class Codes: C12Q 2600/158 Expression markers

Abstract

The invention provides oligonucleotides and their complements that can be used as allele-specific probes or primers for sequencing, oligonucleotide probe hybridization, and allele-specific amplification. Such oligonucleotides can be used, for example, to facilitate genetic distinction between individual plants in plant populations.

Claims

1. A nucleic acid segment comprising at least 10 contiguous nucleotides from a sequence shown in Table 1 including a polymorphic site;

or the complement of the segment.

2. The nucleic acid segment of claim 1, wherein the segment is less than 100 bases.

3. The nucleic acid segment of claim 1 that is DNA.

4. The nucleic acid segment of claim 1 that is RNA.

5. The segment of claim 1 that is less than 50 bases.

6. The segment of claim 1 that is less than 20 bases.

7. The segment of claim 1, wherein the polymorphic site is diallelic.

8. An allele-specific oligonucleotide that hybridizes to a sequence shown in Table 1 or its complement.

9. The allele-specific oligonucleotide of claim 8 that is a probe.

10. The allele-specific oligonucleotide of claim 9, wherein the a central position of the probe aligns with the polymorphic site in the sequence.

11. The allele-specific oligonucleotide of claim 8 that is a primer.

12. The allele-specific oligonucleotides of claim 11, wherein the 3′

end of the primer aligns with the polymorphic site of the segment.

13. The method of analyzing a nucleic acid, comprising:

obtaining the nucleic acid from a subject; and

determining a base occupying any one of the polymorphic sites shown in Table 1.

14. The method of claim 13, wherein the determining comprises determining a set of bases occupying a set of the polymorphic sites shown in Table 1.

15. The method of claim 13, wherein the nucleic acid is obtained from a plurality of subjects, and a base occupying one of the polymorphic positions is determined in each of the subjects, and the method further comprises testing each subject for the presence of a phenotype, and correlating the presence of the phenotype with the base.