基于EST序列的鲤鱼生长相关SNP发掘

Exploitation of SNPs Related to Growth Traits of Common Carp (Cyprinus carpio L.)Based on EST Sequences

以本研究室454测序获得的EST序列和公共数据库中下载的共255,768条鲤鱼EST序列为源序列,鉴定出与生长相关的EST序列5,375条;采用QualitySNP软件,在31个EST重叠群中检测到69个可信度高的与生长相关的SNP,SNP发生频率为0.29/100个碱基。其中包括转换型35个,颠换型30个和缺失型4个。非同义SNP为46个,同义SNP为23个,二者比值为2.0。对所鉴定的SNP进行注释表明,这些包含SNP的生长相关基因归为20类,数量最多的为血纤维蛋白溶酶原基因4个、其次是载脂蛋白基因和磷酸甘油醛脱氢酶基因分别为3个。本研究所开发的SNP将促进鲤鱼生长性状的分子基础研究,为鲤鱼分子育种服务。

In this study, we collected 255,768 EST sequences of common carp （Cyprinus carpio） from 454 sequencing and GenBank database. We identified 5,375 ESTs that related to growth trait. A total of 69 putative and reliable SNPs were detected within 31 genes by comparative analysis of QualitySNP software. The observed frequency of SNPs was 0.29 SNP per 100 bp. Among these SNPs, 35 of which are transition, 30 are tranversion and leaving other 4 as indels. The overall ratio of non-synonymous to synonymous SNPs was 2.0. Annotation indicates that all the SNP-containing genes belong to 20 gene families, the most abundant is plasminogen gene family, flowered by apolipo protein and gapdh protein gene families, respectively. Identified SNPs are useful for study molecular basis of growth traits and will be of benefit to the molecular breeding of common carp.