摘要
SNP标记是一类应用广泛的第三代分子标记。从GenBank下载普通烟草EST序列共计317 175条,用CAP3软件对序列进行拼接。设定SNP位点的冗余度大于2,采用AutoSNP软件检测cSNP。结合位点所在序列的文库和品种信息以及多个SNP位点的共分离分值来评价其可信度。结果表明,317 175条普通烟草EST拼接成重叠群中15 429个重叠群至少包含4个读长,鉴定出53 477个冗余度大于2的候选SNP,烟草中出现SNP的频率为0.34%。其中SNP的转换率大于颠换,插入/删除表现出A/T偏好。这些高质量SNP标记的发掘为开展烟草基因功能研究和分子育种奠定了良好的基础。
Single nucleotide polymorphisms （SNPs）, which belong to the third-generation molecular markers, were widely used. Derived from different tobacco cDNA libraries in Genbank, 317 175 expressed sequence tags （ESTs） were used to identify high-quality candidate SNPs. Using a redundancy-based approach, valid SNPs were detected by their representation multiple times in an alignment of sequence reads. A second measure of validity was also calculated based on the cosegregation of the SNP pattern between multiple SNP loci in an alignment. By CAP3 assembling, 15 429 contigs assembled at least four reads, and 53 477 candidate SNPs or insertions/deletions were identified. Also, the ratio of transition/transversion was 1.67：1 and indel sequences indicated a bias toward A and T nucleotides. The single nucleotide polymorphic density of tobacco was estimated to be 0.34% by sequence diversity. These markers can contribute to gene functional research and molecular breeding in tobacco.
出处
《中国烟草科学》
CSCD
2012年第6期61-65,共5页
Chinese Tobacco Science
基金
国家烟草专卖局项目(110200701021
110200701022)
关键词
单核苷酸多态性
序列表达标签
单体型
烟草
single nucleotide polymorphisms
expressed sequence tag
haplotype
tobacco
