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High Throughput Mining and Characterization of Microsatellites from Common Carp Genome
The Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 100141, China
Heilongjiang Fishery Research Institute, Chinese Academy of Fishery Sciences, Harbin 150070, China
* Authors to whom correspondence should be addressed.
Received: 6 June 2012; in revised form: 8 July 2012 / Accepted: 24 July 2012 / Published: 6 August 2012
Abstract: 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.
Keywords: microsatellites; common carp; genome; linkage map; BAC end sequences
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Ji, P.; Zhang, Y.; Li, C.; Zhao, Z.; Wang, J.; Li, J.; Xu, P.; Sun, X. High Throughput Mining and Characterization of Microsatellites from Common Carp Genome. Int. J. Mol. Sci. 2012, 13, 9798-9807.
Ji P, Zhang Y, Li C, Zhao Z, Wang J, Li J, Xu P, Sun X. High Throughput Mining and Characterization of Microsatellites from Common Carp Genome. International Journal of Molecular Sciences. 2012; 13(8):9798-9807.
Ji, Peifeng; Zhang, Yan; Li, Chao; Zhao, Zixia; Wang, Jian; Li, Jiongtang; Xu, Peng; Sun, Xiaowen. 2012. "High Throughput Mining and Characterization of Microsatellites from Common Carp Genome." Int. J. Mol. Sci. 13, no. 8: 9798-9807.