玉米丝黑穗病菌基因组SSR信息分析及其引物设计  

Bioinformatic Analysis of Microsatellites in the Genome of Sporisorium reilianum and the Design of SSR Primers

作　　者：王雪梅[1] 李新凤[1] 路平[1] 王建明[1] 

机构地区：[1]山西农业大学农学院,山西太谷030801

出　　处：《山西农业大学学报（自然科学版）》2015年第5期454-461,共8页Journal of Shanxi Agricultural University(Natural Science Edition)

基　　金：山西省科技攻关项目(20120311019-3)

摘　　要：探讨玉米丝黑穗病菌(Sporisorium reilianum)基因组序列中SSR位点的分布与组成特点,为开发可用于玉米丝黑穗病菌遗传多样性分析的Genomic-SSR标记奠定基础。从NCBI公共数据库下载玉米丝黑穗病菌的23条染色体基因组序列,利用SSRIT在线软件对第4、5、6、7条染色体进行SSR位点的搜索,并且利用Primer 3.0软件设计Genomic-SSR引物。结果表明:在玉米丝黑穗病菌基因组序列的第4、5、6、7条染色体中,共搜索到317个SSR位点,平均每条染色体出现79个SSR位点,其总长度为6.89kb,占这四条染色体基因组总长的0.21%,大约每10.3kb中就有一个大于18bp的SSR序列。其中,主要的重复类型是三核苷酸重复单元,占全部SSR的53.94%(171个),其次为二核苷酸重复单元,占全部SSR的16.09%(51个)。数量最少的是六碱基重复单元,为17个(5.36%)。出现频率最高的的重复基序为(GCA/TGC)n(13.25%),其次是(AGC/GCT)n和(CAG/CTG)n,出现频率分别为8.52%、8.20%。并在此基础上,利用Primer3.0在线软件设计了40对SSR引物。玉米丝黑穗病菌基因组序列中SSR位点丰富,具有发掘玉米丝黑穗病菌SSR标记的潜力。The objective of this study is to investigate the distribution and components of Sporisorium reilianum SSRs derived from Genomics. These researches could lay the foundation for the development of Genomic‐SSR markers that would be useful for the genetic diversity analysis of Sporisorium reilianum. The whole genome sequence of Sporisorium reilianum were obtained from NCBI.SSRIT （simple sequence repeat identification tool） was used to search SSRs in fourth ,fifth ,sixth and seventh chromosome and Primer3.0 was used to design Genomic‐SSR primers. A total of 171 SSRs were observed in fourth ,fifth ,sixth and seventh chromosome ,with an average of 79 SSR loci per chromo‐some. Total length of SSRs was 6.89 kb ,about 0.21% of the size of whole chromosomes. It was about one SSR loci（〈18 bp） from every 10.3 kb on average. The most abundant microsatellites were trinucleotide repeats with the proportion of 53.94 ,the second was dinucleotide repeats with the proportion of 16.09. The least abundant was hexanucleotide re‐peat ,only 17 were found. The main type of motif was （GCA/TGC）n ,about 13.25% of the whole SSRs ,followed by （AGC/GCT ）n and （CAG/CTG）n ,about 8.52% 、8.20% .We designed 40 primers using Primer3.0 based on the whole genome SSR loci. Sporisorium reilianum SSRs was abundant ,which had the potential of SSR markers exploration.

关 键 词：玉米丝黑穗病菌 基因组 SSR 引物设计 

分 类 号：S435.131.42[农业科学—农业昆虫与害虫防治]