| Mining expressed sequences for single nucleotide polymorphisms in Pacific abalone Haliotis discus hannai | |
| Qi, Haigang1,2; Liu, Xiao1; Zhang, Guofan1; Wu, Fucun1; Liu, X, Chinese Acad Sci, Inst Oceanol, 7 Nanhai Rd, Qingdao 266071, Peoples R China | |
| 2009-09-30 | |
| 发表期刊 | AQUACULTURE RESEARCH
 |
| ISSN | 1355-557X |
| 卷号 | 40期号:14页码:1661-1667 |
| 文章类型 | Article |
| 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. |
| 关键词 | Snps Est Pacific Abalone Haliotis Discus Hannai Pcr-ds As-pcr |
| 学科领域 | Fisheries |
| DOI | 10.1111/j.1365-2109.2009.02269.x |
| URL | 查看原文 |
| 收录类别 | SCI |
| 语种 | 英语 |
| WOS记录号 | WOS:000270124500011 |
| 引用统计 | |
| 文献类型 | 期刊论文 |
| 条目标识符 | http://ir.qdio.ac.cn/handle/337002/1864 |
| 专题 | 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 |
| 第一作者单位 | 中国科学院海洋研究所 |
| 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. |
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