摘要：

为了研究谷子基因组中SSR的分布偏好,采用生物信息学方法搜索和分析了谷子基因组中SSR在基因座5'侧翼区、3'侧翼区、外显子区和内含子区的分布规律。结果发现,随着5'侧翼区与起始密码子间距离的增加,SSR在5'侧翼区的频率与其基因组频率的比值(相对频率)逐渐下降,在1~700 bp区域内相对频率远大于1.50,而在3'侧翼区、外显子区和内含子区中SSR的相对频率均接近1.00。进一步分析发现,随着5'侧翼区与起始密码子间距离的增加,不同单一SSR类型的相对频率的变化趋势各不相同,总体上,包括CCG、AG、AGG、AGGG、ACC和AGC在内的这6个SSR类型在5'侧翼区的频率和相对频率均较高,其中,AG在5'侧翼区相对频率大于1.5的区域最大(1~1 800 bp),而在CCG的区域最小(1~200 bp)。在外显子区,CCG、AGG、AGC、ACG和ACC这5个高C/G含量的三碱基SSR类型具有较高的频率和相对频率。综上,SSR在基因座5'侧翼区1~700 bp内特异性出现,其中,包括CCG、AG、AGG、AGGG、ACC和AGC在内的6个SSR类型为主要的特异性分布类型;而在基因座3'侧翼区、外显子区和内含子区中,SSR的分布与整个基因组无明显差别,但在外显子区,CCG、AGG、AGC、ACG和ACC这5个SSR类型具有明显的分布特异性。

关键词: 谷子, SSR, 分布偏好, 5'侧翼区, 外显子区

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