Preference distribution of simple sequence repeats in Oryza sativa ssp.japonica genome
[Objective]The study aimed to reveal the distribution preference pattern of simple sequence repeats(SSR)in Oryza sativa ssp.ja-ponica genome.[Method]Using bioinformatics methods,a genome-wide analysis was performed to analyze the distribution regularities of SSRs among the 5'-flanking regions,the 3'-flanking regions,the extron regions and the intron regions in gene locus.[Result]The relative frequency(a ratio of the frequency of a type of SSR in a certain genomic region by the frequency of this SSR in whole genome)of SSRs de-creased with increasing of the distance of 5'-flanking regions from start codon,and was more than 1.50 obviously in a range from about 1 bp to 500 bp.However,the relative frequency of SSRs was slightly larger than 1.00 in both extron regions and 3'-flanking regions while the rel-ative frequency of SSRs was less than 1.00 obviously in intron regions.Furthermore,in 5'-flanking regions,3 SSR types,including CCG,AGG and AG,showed the highest frequency and the relative frequency of each of them was more than 1.50 in a distance ranges of 1-200,1-400 and 1-600 bp,respectively;In 3'-flanking regions,4 SSR types,including A,ATCG,A AG and AATT,possessed both a high frequency and a high relative frequency in a near range from coding regions,and showed various ranges with a relative frequency greater than 1.50;In the extron regions,most of SSRs belonged to triplet SSR type and among them,5 types with a high C/G contents,including CCG,AGG,ACG,AGC and ACC,showed both a high frequency and a high relative frequency;In intron regions,it was found that A had both a high frequency and a relative frequency.[Conclusion]SSRs distribute preferentially in a distance range from about 1 bp to 500 bp of the 5'-flanking regions with 3 major specific types,including CCG,AGG and AG;Both in the extron regions and in the 3'-flanking regions,the mount of SSRs is slightly more than that in genome and the major specific SSRs types of the former possess a high C/G content,including CCG,AGG,ACG,AGC and ACC,while the major specific SSRs types of the latter include A,ATCG,AAG and AATT;However,the in-tron region contains a small amount of SSRs with a major specific type of A.The study can provide a reference for better understanding the function of SSR and developing SSR molecular markers in rice.
MicrosatelliteRiceDistribution preference5'-flanking regionsExtron regions
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