粳稻基因组SSR偏好性分布研究  

Preference distribution of simple sequence repeats in Oryza sativa ssp.japonica genome

作　　者：高建明 桂枝 施利利 赵飞 CAO Jian-ming;CUI Zi;SHI Li-li;ZHAO Fei(College of Agronomy,Resources and Environmental Science,Tianjin Agricultural University,Tianjin 300384,China;Research Office,Hetian Vocational and Technical College,Hetian,Xinjiang 848000,China)

机构地区：[1]天津农学院农学与资源环境学院,天津300384 [2]和田职业技术学院科研处,新疆和田848000

出　　处：《西南农业学报》2024年第5期936-943,共8页Southwest China Journal of Agricultural Sciences

基　　金：天津市农业产学研用“揭榜挂帅”项目(JBGG202210)。

摘　　要：【目的】旨在分析简单重复序列(Simple sequence repeat, SSR)在粳稻(Oryza sativa ssp japonica)基因组中的分布偏好性。【方法】采用生物信息学的方法搜索和分析粳稻全基因组中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】随着5′侧翼区距起始密码子距离的增加,SSR的相对频率(某一区域的频率与基因组频率的比值)逐渐下降,且在1~500 bp区域内大于1.50;在外显子区和3′侧翼区,SSR的相对频率略大于1.00,而内含子区SSR的相对频率明显小于1.00。进一步分析发现,在5′侧翼区,CCG、AGG和AG 3类SSR的频率最高,其相对频率分别在1~200、1~400、1~600 bp区间内大于1.50;在3′侧翼区,A、ATCG、AAG和AATT 4类SSR表现出较高的频率和较高的相对频率,但它们的相对频率大于1.50的区域并不相同;外显子区的SSR大多数为三碱基类型,其中,CCG、AGG、ACG、AGC和ACC 5种高C/G含量的SSR类型在外显子区的频率和相对频率均较高;在内含子区,A具有较高的频率和相对频率。【结论】SSR在基因座5′侧翼区大约1~500 bp范围内特异性出现,CCG、AGG和AG为主要的3个特异性分布SSR类型;外显子区和3′侧翼区的SSR频率与基因组频率接近,前者的SSR类型以C/G含量较高的三碱基类型,即CCG、AGG、ACG、AGC和ACC为主,后者以A、ATCG、AAG和AATT为主;而内含子区较少出现SSR,但A为主要的特异性分布类型。本研究可为更好地理解SSR的功能和开发水稻SSR分子标记提供参考。[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,AAG 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 specif

关 键 词：微卫星 水稻 分布偏好 5′侧翼区 外显子区 

分 类 号：S522[农业科学—作物学]