通过比较EST分析在鲶鱼种间杂种中发现推定的单核苷酸多态性

Putative SNP discovery in interspecific hybrids of catfish by comparative EST analysis.

作者信息

He C, Chen L, Simmons M, Li P, Kim S, Liu Z J

机构信息

Department of Fisheries and Allied Aquacultures and Program of Cell and Molecular Biosciences, The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, Auburn University, Auburn, AL 36849, USA.

出版信息

Anim Genet. 2003 Dec;34(6):445-8. doi: 10.1046/j.0268-9146.2003.01054.x.

DOI:10.1046/j.0268-9146.2003.01054.x

PMID:14687075

Abstract

In this study, we identified putative SNP markers within genes by comparative analysis of expressed sequence tags (ESTs). Comparison of 849 ESTs from blue catfish (Ictalurus furcatus) with >11,000 ESTs from channel catfish (I. punctatus) deposited in GenBank resulted in the identification of 1020 putative SNPs within 161 genes, of which 145 were nuclear genes of known function. The observed frequency of SNPs within ESTs of the two closely related catfish species was 1.32 SNP per 100 bp. The majority of identified SNPs differed between the two species and, therefore, these SNPs are useful for mapping genes in channel catfish x blue catfish interspecific resource families. The SNPs that differed within species were also observed; these can be applied to genome scans in channel catfish resource families.

摘要

在本研究中，我们通过对表达序列标签（EST）进行比较分析，在基因内鉴定出了推定的单核苷酸多态性（SNP）标记。将蓝鲶（Ictalurus furcatus）的849个EST与GenBank中存放的斑点叉尾鮰（I. punctatus）的11,000多个EST进行比较，结果在161个基因内鉴定出1020个推定的SNP，其中145个是已知功能的核基因。在这两种亲缘关系密切的鲶鱼物种的EST中，观察到的SNP频率为每100 bp有1.32个SNP。大多数鉴定出的SNP在这两个物种之间存在差异，因此，这些SNP可用于斑点叉尾鮰×蓝鲶种间资源家系的基因定位。在物种内也观察到了存在差异的SNP；这些SNP可应用于斑点叉尾鮰资源家系的基因组扫描。