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.
Highlights
The common carp (Cyprinus carpio) is one of the most important aquaculture species in the world, accounting for nearly 14 percent of the total global freshwater aquaculture production in 2002, which has increased by an average global rate of 9.5 percent/year [1]
Working toward the construction of a high-density linkage map for the common carp, high throughput microsatellite screening and characterization have been conducted on common carp whole genome shotgun (WGS) and Bacterial Artificial Chromosome (BAC) end sequences
A total of 963 microsatellite markers have been successfully validated as polymorphic markers in the mapping panel (Supplemental Table S1), which are exploited for linkage mapping and physical map/linkage map integration
Summary
The common carp (Cyprinus carpio) is one of the most important aquaculture species in the world, accounting for nearly 14 percent of the total global freshwater aquaculture production in 2002, which has increased by an average global rate of 9.5 percent/year [1]. Rapid progress is being made, some key elements, including high-density linkage mapping and physical mapping, are still unavailable in order to create a comprehensive whole genome assembly for molecular breeding and other usages of the common carp and related species. BAC-anchored microsatellite markers developed from BAC end sequences could serve as important tools for BAC-based physical map and linkage map integration [20,21]. With the common carp whole genome-sequencing project, large-scale whole genome shotgun (WGS) sequences and BAC end sequences (BES) [17] have been collected and analyzed. Working toward the construction of a high-density linkage map for the common carp, high throughput microsatellite screening and characterization have been conducted on common carp WGS and BAC end sequences. A number of microsatellite markers have been validated and genotyped in the mapping population
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