Retro-transposon based genetic similarity within the genus Citrus and its relatives

Retro-transposons are common components of plant genomes, functional at transcription, translation and integration levels. Their abundance and ability to transpose render them good potential markers. Present study was undertaken with the view of IRAP (inter-retrotransposon amplified polymorphism) and REMAP (retrotransposon-microsatellite amplified polymorphism) based DNA marker analysis for genus Citrus and related taxa. Both the IRAP and REMAP exhibited a remarkable variation among the tested genotypes. As a whole, ISSR, IRAP and REMAP analysis generated 113 score able bands ranging from 250 to 2,000 bps. There were 94 polymorphic bands, with an average of eight polymorphic bands per primer combination. The level of polymorphism was found to be 84%. No bands were shared with the ISSR pattern in REMAP analysis. Genetic similarity analysis was performed based on the Dice coefficient, and dendrogram was constructed by using the average linkage methods from combined analysis of IRAP and REMAP. A cophenetic correlation coefficient was also calculated. The clustering approach revealed a good adjustment between matrixes, with correlation coefficient of 0.77. Average similarity for all the genotype pairs was used as a cutoff value for defining the clusters. UPGMA demonstrated eight different clusters. Citrus genus showed wide range of heterogeneity, specially the mandarin group. Genera Fortunella and Poncirus were placed in relatively divergent cluster.