Method for identifying polymorphic markers in a population

Abstract

A method is provided for the identification of polymorphic markers in a population. The method includes genotypically characterizing a first sample of a population, selecting one or more individuals of the first sample based upon the genotypic characterization, fabricating a microarray with genomic DNA from each individual selected, and genotyping a second sample of the population using each fabricated microarray as a reference, thereby identifying the polymorphic markers in the population. Also provided is a method for the identification of polymorphic markers in a bacterial population. The method includes phenotypically characterizing a first sample of a population, selecting one or more individuals of the first sample based upon the phenotypic characterization, fabricating a microarray with genomic DNA from each individual selected, and genotyping a second sample of the population using each fabricated microarray as a reference, thereby identifying the polymorphic markers in the population. Also provided is a method for identifying unique bits among a plurality of bit strings including providing a plurality of bit strings, wherein each string has the same number and position of bits, and each bit has a value of 0 or 1, generating a graphical representation—including selectable elements—representing the relatedness of the bit strings, making a selection of a first selectable element, making a selection of a second selectable element, and identifying bits that are present in each bit string represented by the first selectable element and absent in each bit string represented by the second selectable element, or vice-versa.

1 - 15 . (canceled).  
     
     
         16 . A method for identifying polymorphic markers in a population, comprising the steps of: 
 selecting a first and second individual from a plurality of individuals of the population;    providing a reference genomic DNA microarray;    hybridizing genomic DNA of each of the first and second individuals to the reference microarray;    determining segments of hybridization between the genomic DNA of each of the first and second individuals and the reference microarray;    calculating a hybridization intensity ratio for each hybridized and non-hybridized segment;    converting each intensity ratio into a binary digit consisting of a 0 or 1 bit such that each segment of the reference microarray is represented by a 0 or 1 bit;    compiling data consisting of the numerical elements to produce a bit string for each individual, each bit string having the same total number of bits and each bit having a unique position common to both strings; and    analyzing the data to identify patterns of hybridization present in the population, wherein the relatedness of the bit strings is determined by comparing the value of each bit within the bit string of the first individual to the value of each bit within the bit string of the second individual.    
     
     
         17 . The method of  claim 16 , wherein the reference microarray is fabricated from genomic DNA from an individual in the population.  
     
     
         18 . The method of  claim 16 , wherein the step of selecting a first individual involves selecting an individual that shares the most characteristics among other individuals of the same population.  
     
     
         19 . The method of  claim 16 , further comprising the step of hybridizing genomic DNA from each of the individuals in the population to the reference microarray to determine genetic relatedness of all of the individuals from the population.  
     
     
         20 . The method of  claim 16 , wherein at least one of the first and second individuals is characterized by genotype, and at least one of the individuals is selected based upon the genotypic characterization.  
     
     
         21 . The method of  claim 16 , wherein at least one of the first and second individuals is characterized by phenotype, and at least one of the individuals is selected based upon the phenotypic characterization.  
     
     
         22 . The method of  claim 18 , further comprising the step of labeling the genomic DNA of each selected individual with a fluorescent dye.  
     
     
         23 . The method of  claim 22 , wherein the genomic DNA of each selected individual is labeled with a different fluorescent dye.  
     
     
         24 . The method of  claim 22 , wherein the step of determining each segment's hybridization intensity includes determining the fluorescent intensities of the hybridized segments.  
     
     
         25 . The method of  claim 16 , further including the step of collecting the bit string for each individual into a composite file.  
     
     
         26 . The method of  claim 25 , wherein the step of analyzing further includes normalizing the data through mean and median centering of each of the hybridization intensity ratios.  
     
     
         27 . The method of  claim 25 , further including the step of preparing a graphical representation for each bit string.  
     
     
         28 . The method of  claim 16 , wherein the population is a bacterial population.  
     
     
         29 . The method of  claim 28 , wherein the bacterial population is selected from the group consisting of  Listeria monocytogenes, Escherichia coli, Lactobacillus casei, Lactobacillus lactus, Salmonella typhimurium, Salmonella entereditis , and  Salmonella typhi.    
     
     
         30 . A method for identifying polymorphic markers in a bacterial population comprising a plurality of individuals, involving the steps of: 
 providing a plurality of bit strings, each string representing an individual within the population and having the same number and position of bits, each bit having a value of 0 or 1;    generating a graphical representation of the relatedness of the bit strings, the graphical representation including selectable elements;    selecting a first selectable element;    selecting a second selectable element; and    identifying bits that are present in each bit string representing the first selectable element and absent in each bit string representing the second selectable element, or bits that are absent in each bit string representing the first selectable element and present in each bit string representing the second selectable element.    
     
     
         31 . The method of  claim 30 , wherein the relatedness of the bit strings is determined by the commonality of bit values at corresponding positions in the bit strings.  
     
     
         32 . The method of  claim 30 , wherein the graphical representation is a dendrogram and the selectable elements are leaves and nodes, each leaf representing a single bit string, and each node representing two or more bit strings.