Using strutural variation to analyze genomic differences for the prediction of heterosis

Abstract

A novel method for prediction of the degree of heterotic phenotypes in plants is disclosed. Structural variation analyses of the genome are used to predict the degree of a heterotic phenotype in plants. In some examples, copy number variation is used to predict the degree of heterotic phenotype. In some methods copy number variation is detected using competitive genomic hybridization arrays. Further, methods for optimizing the arrays are disclosed, together with kits for producing such arrays, as well as hybrid plants selected for development based on the predicted results.

1 - 5 . (canceled) 
     
     
         6 . A method comprising:
 a) contacting genomic DNA from a first inbred plant with a first plurality of oligonucleotide probe molecules;   b) detecting the hybridization intensities for at least a subset of oligonucleotide probe molecules in the first plurality of oligonucleotide probe molecules;   c) contacting genomic DNA from a second inbred plant with a second plurality of oligonucleotide probe molecules, wherein said first and second plurality of oligonucleotide probe molecules have at least one subset of oligonucleotide probe molecules in common;   d) detecting the hybridization intensities for at least a subset of oligonucleotide probe molecules in the second plurality of oligonucleotide probe molecules;   e) determining relative measures of hybridization intensity for a plurality of the individual oligonucleotide probe molecules in said common subset of oligonucleotide probe molecules; and   f) using said relative hybridization intensities to predict the degree of a heterosis-related phenotype for a hybrid progeny plant derived from said first and second inbred plant.   
     
     
         7 . The method of  claim 6 , wherein at least one of said first and second plants comprises prepared genomic DNA. 
     
     
         8 . The method of  claim 6 , wherein the plant is maize. 
     
     
         9 . The method of  claim 6 , wherein the genomic DNA from the first and second inbred plants comprises prepared genomic DNA. 
     
     
         10 . The method of  claim 6 , wherein said first or said second plurality of oligonucleotide probe molecules comprise at least 50% oligonucleotide probe molecules which hybridize to coding regions or other non-repetitive genomic DNA sequences. 
     
     
         11 . The method of  claim 6 , wherein said subset of oligonucleotide probe molecules contains at least 100 oligonucleotide probe molecules. 
     
     
         12 . The method of  claim 6 , wherein said subset of oligonucleotide probe molecules contains no more than 150 oligonucleotide probe molecules. 
     
     
         13 . The method of  claim 6 , wherein the heterosis-related phenotype is plant yield. 
     
     
         14 . The method of  claim 6 , wherein the plurality of oligonucleotide probe molecules comprise an oligonucleotide array. 
     
     
         15 . The method of  claim 6 , wherein said oligonucleotide probe molecules are at least 20 but are not more than 100 nucleotides in length. 
     
     
         16 . The method of  claim 6 , wherein said relative hybridization intensity comprises a ratio of hybridization intensity. 
     
     
         17 . The method of  claim 16 , wherein oligonucleotide probe molecules exhibiting at least a three fold difference, but less than a ten fold difference in hybridization intensity are included in said comparison. 
     
     
         18 . The method of  claim 6 , further comprising selecting said first and second inbred plants for development of a F1 hybrid plant variety based at least in part on said prediction of a heterosis-related phenotype. 
     
     
         19 . The method of  claim 6 , wherein the relative hybridization intensities comprise a measurement of copy number variations between said first plant and said second inbred plant. 
     
     
         20 - 32 . (canceled)