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浙江大学学报（农业与生命科学版）
浙江大学学报(农业与生命科学版)  2012, Vol. 38 Issue (3): 263-270    DOI: 10.3785/j.issn.1008-9209.2012.03.005
生物科学与技术     
葡萄EST-SNP位点的信息与特征
李猛1， 郭大龙1， 刘崇怀2， 张国海1， 侯小改3
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
Information and characteristics of ESTSNP loci in grape (Vitis vinifera L.).
LI Meng1, GUO Dalong1, LIU Chonghuai2, ZHANG Guohai1, HOU Xiaogai3
1. College of Forestry, Henan University of Science & Technology, Luoyang, Henan 471003, China; 2. Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China； 3. College of Agriculture, Henan University of Science & Technology, Luoyang, Henan 471003, China
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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42493条，利用CAP3软件拼接得到6126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5 bp。结果表明：仅在1195个contig中存在候选SNP位点，共5032个，其中包括1800个颠换类型，2896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4.2 SNP·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。
Abstract: Aiming to mine candidate single nucleotide polymorphism (SNP) loci by aligning homologous expressed sequence tags (EST) using bioinformatics software, 42493 EST sequences were retrieved from different tissues of nine different grape genotypes in NCBI dbEST database and assembled into 6126 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 1195 contigs contained candidate SNP loci. A total of 5032 candidate SNPs were identified, and the amount of transversions, transitions and one base indel were 1800, 2896 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.
出版日期: 2012-05-24
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李猛
郭大龙
刘崇怀
张国海
侯小改

引用本文:

李猛， 郭大龙， 刘崇怀， 张国海， 侯小改. 葡萄EST-SNP位点的信息与特征[J]. 浙江大学学报(农业与生命科学版), 2012, 38(3): 263-270.

LI Meng, GUO Dalong, LIU Chonghuai, ZHANG Guohai, HOU Xiaogai. Information and characteristics of ESTSNP loci in grape (Vitis vinifera L.).. , 2012, 38(3): 263-270.

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http://www.zjujournals.com/agr/CN/10.3785/j.issn.1008-9209.2012.03.005    或    http://www.zjujournals.com/agr/CN/Y2012/V38/I3/263

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