葡萄EST-SNP位点的信息与特征  

Information and characteristics of EST-SNP loci in grape(Vitis vinifera L.)

作　　者：李猛[1] 郭大龙[1] 刘崇怀[2] 张国海[1] 侯小改[3] 

机构地区：[1]河南科技大学林学院,河南洛阳471003 [2]中国农业科学院郑州果树研究所,河南郑州450009 [3]河南科技大学农学院,河南洛阳471003

出　　处：《浙江大学学报（农业与生命科学版）》2012年第3期263-270,共8页Journal of Zhejiang University:Agriculture and Life Sciences

基　　金：国家自然科学基金资助项目(30800742);河南省高等学校青年骨干教师资助计划资助项目(2010GGJS-072);现代农业产业技术体系建设专项资金资助项目(CARS-30-yz-1)

摘　　要：为了从不同基因型葡萄组织的表达序列标签(EST)中得到候选单核苷酸多态性(SNP)位点,从NCBI的dbEST数据库中下载来源于9个不同葡萄基因型的不同组织EST序列42 493条,利用CAP3软件拼接得到6 126个重叠群(contig),将拼接结果导入QualitySNP进行SNP筛选;同时,为提高候选SNP位点的可靠度,降低小规格contig开发SNP的假阳性率和大规格contig开发SNP的假阴性率,设置候选SNP位点的次要等位基因频率至少为30%,SNP侧翼序列保守度至少为5bp。结果表明:仅在1 195个contig中存在候选SNP位点,共5 032个,其中包括1 800个颠换类型,2 896个转换类型,336个单碱基的插入与缺失(indel),SNP的平均出现频率为4.2SNP.contig-1。利用CAPS(酶切扩增多态序列)分子标记和重测序方法对其中几个候选SNP位点进行验证表明,符合人工筛选原则且来自于小规格contig的候选SNP位点检测结果较好,可靠度最高。Aiming to mine candidate single nucleotide polymorphism （SNP） loci by aligning homologous expressed sequence tags （EST） using bioinformatics software, 42 493 EST sequences were retrieved from different tissues of nine different grape genotypes in NCBI dbEST database and assembled into 6 126 contigs by CAP3 software, then candidate SNP loci of the contigs were screened by QualitySNP software. Meanwhile, in order to improve the reliability of mined candidate SNP and reduce false positive in small contig sizes and false negative in large contig sizes, the minor allele frequency was set at least 30% in a candidate SNP locus, and the SNP flanking sequences were perfect matching at least in 5 bp. The results showed that only 1 195 eontigs contained candidate SNP loci. A total of 5 032 candidate SNPs were identified, and the amount of transversions, transitions and one base indel were 1 800, 2 896 and 336 respectively, and the average frequency of SNP occurrence was at 4.2 SNP. contig -1 . CAPS （cleaved amplified polymorphic sequences） molecular markers and re-sequencing methods were used to validate the selected candidate SNP loci. The validation results indicated that they were corresponded with the manual filtration principle, and those from small contig sizes showed better validation results with highest reliability.

关 键 词：葡萄 表达序列标签 单核苷酸多态性 筛选原则 

分 类 号：Q344[生物学—遗传学] S663.1[农业科学—果树学]