Abstract:

To reveal the distribution preferences of SSR in foxtail millet genome,the study analyzed distribution regularities of SSRs among the 5'-flanking regions,the 3'-flanking regions,the extron regions and the intron regions in gene locus from foxtail millet genome using bioinformatics methods.The results showed that 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 decreased with increasing of the distance of 5'-flanking regions from start codon,and was more than 1.50 obviously in a range from 1 bp to 700 bp.However,the relative frequency of SSRs was close to 1.00 in each of other three regions.Furthermore,with increasing of the distance of 5'-flanking regions from start codon,the relative frequency of various SSR types revealed the various changing trends,and as a whole,6 SSR types,including CCG,AG,AGG,AGGG,ACC and AGC,showed both the high frequency and the high relative frequency,and of these 6 types,the distance range(1—1 800 bp)of AG,in which its relative frequency was more than 1.50,is the maximum while that of CCG is minimal(1—200 bp).Meanwhile,in the extron regions,5 SSR types with high C/G contents,including CCG,AGG,AGC,ACG and ACC,showed both a high frequency and a high relative frequency.It was concluded that SSRs distributed preferentially in a length range from about 1—700 bp of 5'-flanking regions with 6 main specific SSR types,including CCG,AG,AGG,AGGG,ACC and AGC;on the other hand,in 3'-flanking regions,the intron regions and the extron region,distribution of SSR is close to that in genome,and however,in the extron region,a total of 5 SSR types,including CCG,AGG,AGC,ACG and ACC,are obviously specifically distributed.

Key words: Foxtail millet, SSR, Distribution preference, 5'-flanking regions, Extron regions