Abstract
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.
Highlights
Simple sequence repeats (SSRs) are becoming standard DNA markers for plant genome analysis and are being used as markers in marker assisted breeding
[6] These loci mutate by insertions or deletions of one or a few repeat units, and the mutation rates generally increase with an increase in the length of repeat tracks
[7] SSRs are a ubiquitous class of repetitive DNA that is widely used in genetic analyses, there is accumulating evidence that SSRs serve a functional role, affecting gene expression, and that polymorphism of SSR tracts may be important in the evolution of gene regulation [8,9] such repetitive tracts has been described in all eukaryotes analyzed and is thought to result from the mutational effects of replication slippage
Summary
Simple sequence repeats (SSRs) are becoming standard DNA markers for plant genome analysis and are being used as markers in marker assisted breeding. 2004 [13] did same type of work but in our study we have performed detailed analysis of each repeat and given the exact location of each repeat in the genome that is very useful information for Arabidopsis researchers. The SSRs from 1 - 6, that is, from monomer to hexamer repeats were analyzed in the complete chromosome sequence and in the coding region
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
