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With the hardware technology advancing, the cost of storing is decreasing. Thus there is an urgent need for new techniques and tools that can intelligently and automatically assist us in transferring this data into useful knowledge. Different techniques of data mining are developed which are helpful for handling these large size databases [7]. Data mining is also finding its role in the field of biotechnology. Pedigree means the associated ancestry of a crop variety. Genetic diversity is the variation in the genetic composition of individuals within or among species. Genetic diversity depends upon the pedigree information of the varieties. Parents at lower hierarchic levels have more weightage for predicting genetic diversity as compared to the upper hierarchic levels. The weightage decreases as the level increases. For crossbreeding, the two varieties should be more and more genetically diverse so as to incorporate the useful characters of the two varieties in the newly developed variety. This paper discusses the searching and analyzing of different possible pairs of varieties selected on the basis of morphological characters, Climatic conditions and Nutrients so as to obtain the most optimal pair that can produce the required crossbreed variety. An algorithm was developed to determine the genetic diversity between the selected wheat varieties. Cluster analysis technique is used for retrieving the results.