Identification and use of conserved noncoding sequences

Abstract

The invention is directed to the identification of conserved noncoding sequences in various organisms and the use of those sequences as primers for use in amplifying, mapping and analysis of DNA among different species.

1 . A method of identifying a polymorphism between two or more DNA sequences; comprising: 
 a) selecting a first and a second primer for use in an amplification reaction for each DNA sequence wherein said first or second primer is a CNS in said two or more DNA sequences;    b) hybridizing said first and second primers to each DNA sequence to form primer-DNA hybrids;    c) amplifying said primer-DNA hybrids to form amplified DNA products; and    d) separating said DNA products by size to identify a polymorphism between said two or more DNA sequences.    
     
     
         2 . The method of  claim 1  wherein said DNA sequences are plant DNA sequences.  
     
     
         3 . The method of  claim 1  wherein said polymorphism is utilized for mapping.  
     
     
         4 . The method of  claim 1  wherein said first primer is a CNS and said second primer is an exon sequence.  
     
     
         5 . The method of  claim 1  wherein both the first and second primers are CNSS.  
     
     
         6 . The method of  claim 1  wherein said DNA products are digested with a restriction endonuclease prior to separation in step d).  
     
     
         7 . The method of  claim 1  wherein said DNA products are separated by electrophoresis.  
     
     
         8 . The method of  claim 1  wherein said primers are PCR primers.  
     
     
         9 . The method of  claim 1  wherein the primer-DNA hybrids are amplified using an amplification technique selected from the group consisting of cloning, PCR, LCR, TAS, 3SR, NASBA and QP amplification.  
     
     
         10 . The method of  claim 9  wherein said technique is PCR.  
     
     
         11 . A method of mapping a polymorphism between two or more species; comprising: 
 a) selecting a first and a second primer for use in an amplification reaction wherein said first or second primer is a CNS in the genomes of said two or more species wherein said genomes include genomic DNA;    b) hybridizing said first and second primers to said genomic DNA sequences to form primer-genomic DNA hybrids;    c) amplifying said primer-genomic DNA hybrids to form amplified DNA products; and    d) separating said DNA products by size to map a polymorphism between said two or more DNA sequences.    
     
     
         12 . The method of  claim 11  wherein said DNA sequences are plant DNA sequences.  
     
     
         13 . The method of  claim 11  wherein said plant DNA is grass DNA.  
     
     
         14 . The method of  claim 11  wherein said first primer is a CNS and said second primer is an exon sequence.  
     
     
         15 . The method of  claim 11  wherein both the first and second primers are CNSs.  
     
     
         16 . The method of  claim 11  wherein said DNA products are digested with a restriction endonuclease prior to separation in step d).  
     
     
         17 . The method of  claim 11  wherein said DNA products are separated by electrophoresis.  
     
     
         18 . The method of  claim 11  wherein said primers are PCR primers.  
     
     
         19 . The method of  claim 1  wherein the primer-DNA hybrids are amplified using an amplification technique selected from the group consisting of cloning, PCR, LCR, TAS, 3SR, NASBA and Qβ amplification.  
     
     
         20 . The method of  claim 19  wherein said technique is PCR.