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Mining expressed sequences for single nucleotide polymorphisms in Pacific abalone Haliotis discus hannai

文献类型：期刊论文

作者Qi, Haigang1,2; Liu, Xiao1; Zhang, Guofan1; Wu, Fucun1; Liu, X, Chinese Acad Sci, Inst Oceanol, 7 Nanhai Rd, Qingdao 266071, Peoples R China
刊名AQUACULTURE RESEARCH
出版日期2009-09-30
卷号40期号:14页码:1661-1667
关键词Snps Est Pacific Abalone Haliotis Discus Hannai Pcr-ds As-pcr
ISSN号1355-557X
DOI10.1111/j.1365-2109.2009.02269.x
文献子类Article
英文摘要Although single nucleotide polymorphisms (SNPs) are important resources for population genetics, pedigree analysis and genomic mapping, such loci have not been reported in Pacific abalone so far. In this study, a bioinformatics strategy was adopted to discover SNPs within the expressed sequences (ESTs) of Pacific abalone, Haliotis discus hannai, and furthermore, polymerase chain reaction direct sequencing (PCR-DS) and allele-specific PCR (AS-PCR) were used for SNPs detection and genotype scoring respectively. A total of 5893 ESTs were assembled and 302 putative SNPs were identified. The average density of SNPs in ESTs was 1%. Fifty-two sets of sequencing primers were designed from SNPs flanking ESTs to amplify the genomic DNA, and 13 could generate products of expected size. Polymerase chain reaction direct sequencing of the amplification products from pooled DNA samples revealed 40 polymorphic SNP loci. Using a modified tetra-primer AS-PCR, seven mitochondrial and six nuclear SNPs were typed and characterized among 37 wild abalones. In conclusion, it is feasible to discover SNPs from number limited ESTs and the AS-PCR as a simple, robust and reliable assay could be a primary method for small- and medium-scale SNPs detection in abalones as well as other non-model organisms.; Although single nucleotide polymorphisms (SNPs) are important resources for population genetics, pedigree analysis and genomic mapping, such loci have not been reported in Pacific abalone so far. In this study, a bioinformatics strategy was adopted to discover SNPs within the expressed sequences (ESTs) of Pacific abalone, Haliotis discus hannai, and furthermore, polymerase chain reaction direct sequencing (PCR-DS) and allele-specific PCR (AS-PCR) were used for SNPs detection and genotype scoring respectively. A total of 5893 ESTs were assembled and 302 putative SNPs were identified. The average density of SNPs in ESTs was 1%. Fifty-two sets of sequencing primers were designed from SNPs flanking ESTs to amplify the genomic DNA, and 13 could generate products of expected size. Polymerase chain reaction direct sequencing of the amplification products from pooled DNA samples revealed 40 polymorphic SNP loci. Using a modified tetra-primer AS-PCR, seven mitochondrial and six nuclear SNPs were typed and characterized among 37 wild abalones. In conclusion, it is feasible to discover SNPs from number limited ESTs and the AS-PCR as a simple, robust and reliable assay could be a primary method for small- and medium-scale SNPs detection in abalones as well as other non-model organisms.
学科主题Fisheries
URL标识查看原文
语种英语
WOS记录号WOS:000270124500011
公开日期2010-11-18
源URL[http://ir.qdio.ac.cn/handle/337002/1865]  
专题海洋研究所_海洋生物技术研发中心
通讯作者Liu, X, Chinese Acad Sci, Inst Oceanol, 7 Nanhai Rd, Qingdao 266071, Peoples R China
作者单位1.Chinese Acad Sci, Inst Oceanol, Qingdao 266071, Peoples R China
2.Chinese Acad Sci, Grad Sch, Beijing, Peoples R China
推荐引用方式
GB/T 7714		 Qi, Haigang,Liu, Xiao,Zhang, Guofan,et al. Mining expressed sequences for single nucleotide polymorphisms in Pacific abalone Haliotis discus hannai[J]. AQUACULTURE RESEARCH,2009,40(14):1661-1667.
APA Qi, Haigang,Liu, Xiao,Zhang, Guofan,Wu, Fucun,&Liu, X, Chinese Acad Sci, Inst Oceanol, 7 Nanhai Rd, Qingdao 266071, Peoples R China.(2009).Mining expressed sequences for single nucleotide polymorphisms in Pacific abalone Haliotis discus hannai.AQUACULTURE RESEARCH,40(14),1661-1667.
MLA Qi, Haigang,et al."Mining expressed sequences for single nucleotide polymorphisms in Pacific abalone Haliotis discus hannai".AQUACULTURE RESEARCH 40.14(2009):1661-1667.

入库方式： OAI收割

来源：海洋研究所

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