Mapping and analysis of simple sequence repeats in the Arabidopsis thaliana genome

Simple sequence repeats (SSRs) are becoming standard DNA markers for plant genome analysis and are being used as markers in marker assisted breeding. And hence because of its great significance we have initiated this study to analyze complete genome of Arabidopsis thaliana for the prevalence of mono-, di-, tri-, tetra-, penta- and hexa- mer repeats in the coding and non-coding regions of the chromosome and to map their exact position on the sequence. We have developed a program that can search a repeat of any length, its exact position on the chromosome and also its frequency of occurrence in the genome. Analysis of the results reveal that maximum number of repeats were found in chromosome 1 followed by chromosome 2 and 4 whereas, chromosome 3 and 5 contain relatively less number of these repeats. Among the SSRs, hexamers and dimers were more predominant in the chromosomes. Overall data showed that Chromosome 5 has minimum number of repeats. The abundance or rarity of various simple repeats in different chromosomes is not explained by nucleotide composition of sequence or potential repeated motifs to form alternative DNA structures. This suggests that in addition to nucleotide composition of repeat motifs, characteristic DNA replication / repair / recombination machinery might play an important role in genesis of repeats. The positional information is given at www.geocities.com/amubioinfo/ARD. This positional information can help Arabidopsis researchers to identify new polymorphisms in chromosomal regions of interest based on the SSRs that map in the area.