title: High throughput mining and characterization of microsatellites from common carp genome.
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.
authors.affiliation: The Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 100141, China.
authors.forename: Peifeng
authors.initials: P
authors.lastname: Ji
authors.affiliation: The Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 100141, China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Heilongjiang Fishery Research Institute, Chinese Academy of Fishery Sciences, Harbin 150070, China.
authors.forename: Chao
authors.initials: C
authors.lastname: Li
authors.affiliation: The Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 100141, China.
authors.forename: Zixia
authors.initials: Z
authors.lastname: Zhao
authors.affiliation: The Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 100141, China.
authors.forename: Jian
authors.initials: J
authors.lastname: Wang
authors.affiliation: The Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 100141, China.
authors.forename: Jiongtang
authors.initials: J
authors.lastname: Li
authors.affiliation: The Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 100141, China.
authors.forename: Peng
authors.initials: P
authors.lastname: Xu
authors.affiliation: 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.forename: Xiaowen
authors.initials: X
authors.lastname: Sun
mesh_terms: D000818:Animals; D002347:Carps / Q000235:genetics*; D002874:Chromosome Mapping; D022202:Chromosomes, Artificial, Bacterial; D019295:Computational Biology; D016678:Genome / Q000235:genetics*; D057166:High-Throughput Screening Assays; D018895:Microsatellite Repeats / Q000235:genetics*; D011110:Polymorphism, Genetic / Q000235:genetics*; D017422:Sequence Analysis, DNA