Maize genomic marker set

Abstract

Maize markers useful for genotyping and association studies, e.g. association with oil content QTLs in populations derived from the Illinois High Oil and Illinois Low Oil maize lines. Primers and hybridization probes for Taqman™ assays are provided for 488 SNP markers in 484 loci.

1 . A method of identifying oil-associated QTLs in maize comprising
 (a) establishing a random mated population of maize plants derived from crossing the Illinois high oil line with the Illinois low oil line,   (b) selecting a set of allelic polymorphic markers from the polymorphic genomic amplicon DNA sequences listed in Table 1,   (c) identify in said set of allelic polymorphic makers a subset of oil informative markers having an allelic frequency difference of at least 0.6 between the Illinois high oil line and the Illinois low oil line,   (d) identify kernel oil levels in individual plants of said random-mated population,   (e) genotyping plants in said random-mated population using said subset of oil informative markers,   (f) analyzing the association between said oil informative markers and said kernel oil levels to establish a statistical significance level,   (g) select as oil QTLs genes those oil informative markers having a statistical significance of greater than 0.05.   
     
     
         2 . A method of  claim 1  wherein said SNP markers are linked to markers mapped in Table 2. 
     
     
         3 . A method of  claim 2  wherein the SNP markers are the markers listed in Table 2. 
     
     
         4 . A method of genotyping populations of maize plants comprising determining the presence in said plants of polymorphic allelic DNA for a marker listed in Table 2. 
     
     
         5 . A collection of sets of four oligonucleotides comprising a forward primer, a reverse primer, a FAM-labeled hybridization probe and a VIC-labeled hybridization probe for assaying a single SNP polymorphism identified in Table 2, wherein all of the oligonucleotides in said collection comprise nucleic acid molecules having DNA sequences of SEQ ID NO:485 through SEQ ID NO:2436. 
     
     
         6 . One set of four oligonucleotides from the collection of  claim 5 . 
     
     
         7 . A method of breeding maize comprising selecting a maize line having a polymorphism identified in Table 2 by SNP detection assay using a set of four oligonucleotides of  claim 6 .