摘要
利用长牡蛎已有的EST序列数据库,筛选得到候选SNP位点共计1140个。根据候选SNP位点共设计引物82组,通过片段长度差异等位基因特异性PCR(fragment length discrepant allele specific PCR,FLDAS-PCR)的分型方法,在一野生群体中进行检测和验证,结果共有17个SNP候选位点显示多态性。研究结果表明,通过基于EST数据库的SNP开发,可以有效弥补某些海洋生物因基因组学滞后影响SNP标记开发的现状。
Some 29000 EST sequences of Crassostrea gigas from the GenBank were clustered into 4548 groups, of which 1079 contained 4 or more ESTs. After manual quality filtering, 313 clusters could be used for the SNP development. 82 candidate SNPs were amplified with fragment length discrepant allele specific PCR （FLDAS-PCR）, of which 17 were polymorphic in a wild population. The function of the ESTs was predicted, and ORF was deduced based on BlastX analysis The expected and observed heterozygosities of the SNPs ranged from 0.088 to 0.506 and 0.091 to 0.667, respectively. No significant linkage disequilibria were observed in most of the loci. Only three loci did not conform to Hardy-Weinberg equilibrium at the level of P〈0.05. The results show that EST database is an important source to develop SNPs for the species whose genome research is on the primary stage.
出处
《海洋与湖沼》
CAS
CSCD
北大核心
2010年第2期274-281,共8页
Oceanologia Et Limnologia Sinica
基金
国家重点基础研究发展计划(973)项目
2010CB126402号
国家自然科学基金项目
40730845号
国家公益性行业(农业)科研专项资助
nyhyzx07-047号
中国科学院知识创新工程领域前沿项目资助
2008-2010
关键词
长牡蛎
单核苷酸多态性
表达序列标签
片段长度差异等位基因特异性PCR
Crassostrea gigas, Single nucleotide polymorphism （SNP）, Expressed sequence tag （EST）, Fragment length discrepant allele specific PCR （FLDAS-PCR）
