High Throughput Mining and Characterization of Microsatellites from Common Carp Genome

International Journal of Molecular Sciences

Peifeng Ji²  Yan Zhang²  Chao Li¹  Zixia Zhao²  Jian Wang²  Jiongtang Li²  Peng Xu² 

[1] Heilongjiang Fishery Research Institute, Chinese Academy of Fishery Sciences, Harbin 150070, China; E-Mail:;The Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 100141, China; E-Mails:

关键词: microsatellites;    common carp;    genome;    linkage map;    BAC end sequences;   

DOI  :  10.3390/ijms13089798

来源: mdpi

【 摘 要 】

In order to supply sufficient microsatellite loci for high-density linkage mapping, whole genome shotgun (WGS) sequences of the common carp (Cyprinus carpio) were assembled and surveyed for microsatellite identification. A total of 79,014 microsatellites were collected which were harbored in 68,827 distinct contig sequences. These microsatellites were characterized in the common carp genome. Information of all microsatellites, including previously published BAC-based microsatellites, was then stored in a MySQL database, and a web-based database interface (http://genomics.cafs.ac.cn/ssrdb) was built for public access and download. A total of 3,110 microsatellites, including 1,845 from WGS and 1,265 from BAC end sequences (BES), were tested and genotyped on a mapping family with 192 individuals. A total of 963 microsatellites markers were validated with polymorphism in the mapping family. They will soon be used for high-density linkage mapping with a vast number of polymorphic SNP markers.

【 授权许可】

CC BY   
© 2012 by the authors; licensee Molecular Diversity Preservation International, Basel, Switzerland.