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浙江大学学报（农业与生命科学版）
Journal of Zhejiang University: Agric. & Life Sci.  2011, Vol. 37 Issue (3): 280-288    DOI: 10.3785/j.issn.1008-9209.2011.03.007
Biological sciences & biotechnology     
Development and characterization of EST-cSNP markers in Miichthys miiuy
XU Tian-jun,SUN Yue-na,SHI Ge,WANG Ri-xin
Laboratory for M arine Living Resources and Molecular Engineering ,College of Marine Science , Zhejiang Ocean University , Zhoushan ,Zhejiang 316000 , China
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Abstract  To promote molecular-assisted breeding in M iichthys miiuy , a normalized full-length cDNA library was established to develop the EST-cSNP markers using the double-specific nuclease normalization method combined with switching mechanism at 5'end of RNA transcript technique . The results showed that a total of 5053 expressed sequence tags (EST) were obtained , 4609 high quality EST sequences in which were generated . For mining single nucleotide polymorphism (SNP) from EST sequences ,707 contig sequences were assembled by Vector NTI 11.0 software . A total of 209 putative and reliable SNPs were detected in all contigs . The appearance frequency of SNPs was 0.743 SNP per 100 bp in the obtained SNP sequences . Among these SNPs , 114 of which were transition , 74 were transversion and the other 21 were indels . The overall ratio of transition to transversion was 1.54. Gene annotation indicated that some SNP-containing genes belonged to immune-related genes that encoded major histocompatibility complex , immunoglobulin , T-cell receptor and other protease , respectively ,showing that the identified SNPs were useful for studying molecular genetics and molecular-assisted breeding in M . miiuy .

Published: 20 May 2011
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XU Tian-jun
SUN Yue-na
SHI Ge
WANG Ri-xin
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XU Tian-jun,SUN Yue-na,SHI Ge,WANG Ri-xin. Development and characterization of EST-cSNP markers in Miichthys miiuy. Journal of Zhejiang University: Agric. & Life Sci., 2011, 37(3): 280-288.

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http://www.zjujournals.com/agr/10.3785/j.issn.1008-9209.2011.03.007     OR     http://www.zjujournals.com/agr/Y2011/V37/I3/280


鮸鱼EST-cSNP位点发掘及其特征分析

为发掘鮸鱼的EST-cSNP 位点,以测序获得的鮸鱼脾脏4609条高质量表达序列标签(expressed sequence tags ,EST) 序列为源序列,利用Vector NTI 11.0 软件拼接出707 条重叠群(contig)序列,检测到209个可信度高的编码区单核苷酸多态性(coding-region single nucleotide polymorphism ,cSNP)位点;SNP 位点数在包含SNP 序列中的发生概率为0.743%,在209个SNP 位点中包含114个碱基转换位点、74个碱基颠换位点和21个插入缺失位点,转换与颠换比为1.54;对所鉴定的SNP 位点的相关序列进行基因注释表明,这些序列包括一批与免疫抗逆相关的基因,例如主要组织相容性复合体、免疫球蛋白、T 细胞受体以及各类蛋白酶等.说明所发掘的SNP 将有助于促进鮸鱼的分子遗传学及分子辅助育种研究.
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