Construction Of The Genetic-physical Integrated Map For Common Carp And Comparative Mapping With Zebrafish Genome

Common carp (Cyprinus carpio) is one of the most important aquaculture species with an annualglobal production of3.4million metric tons that accounts for nearly14%of all freshwateraquaculture production in the world. In China, common carp has quite a long history ofcultivation and certain cultural meanings. Besides, common carp becomes an importantornamental species. Nowadays, researchers from home and abroad have carried out extensivestudies on common carp, such as the development of new molecular markers, construction ofseveral low or medium density genetic linkage maps, location of important economicquantitative trait locis, construction of a bacterial artificial chromosome library, BAC endsequences and a physical map. However, higher density genetic linkage map andgenetic-physical integrated map are not available for common carp. The objective of this studywas to construct a higher density genetic linkage map and genetic-physical integrated map forcommon carp. In addition, through comparative mapping between common carp and zebrafishgenomes, the three maps (common carp genetic linkage map, common carp physical map andzebrafish whole genome map) are finally successfully connected to each other. The study willhelp us enrich the field in genomics and comparative analysis of common carp and verify thecommon carp whole genome sequencing and assembly. The results as follows:1. A total of629BAC-anchored microsatellite loci from the common carp230largest physicalmap contigs were developed. Of these contig-anchored microsatellites,550markers had PCRproduct and a total of226showed the presence of polymorphism and genotyped them in themapping family.2. The flank sequences of664microsatellite and5000SNP markers randomly developed byHeilongjiang Fisheries Research Institute were aligned to the BES database and a total of40microsatellite and137SNP markers were mapped to physical map contigs or single BAC clones.3. A total of1359polymorphic genetic markers, including newly developed226microsatellitemarkers, previously developed332microsatellite markers,664microsatellite markers and137SNP markers developed by Heilongjiang Fisheries Research Institute were used for linkageanalysis. After using software JoinMap4.0, a total of1209genetic markers were finally mappedto50linkage groups. Spanning3565.9cM of the common carp genome and the genetic length ofeach linkage group ranged from17.3cM to126.7cM, and the average interval between markersis3.077cM.4. A total of620BAC-anchored or BAC-associated markers serve as anchor points that connect genetic linkage map and physical map together. The genetic-physical integrated map composedof463physical map contigs and88single BACs, of which166contigs are newly developed.Combined lengths of the contigs and single BACs covered a physical length of498.75Mb(among them258.28Mb are from newly developed markers), or around30%of the commoncarp genome.5. The flank sequences of1209markers from common carp genetic linkage map were aligned tothe zebrafish reference genome (zv9) using BLASTn and successfully mapped597markers on25chromosomes of zebrafish. The results showed that two linkage groups of common carp werehomologs with one particular chromosome of zebrafish, which confirmed the two-to-onehomologous relationship of common carp and zebrafish chromosomes, which means commoncarp have experienced an additional round of whole genome duplication that doubled thechromosome number.6. A total of442physical map contigs (from the463integrated contigs) that formed synteniesbetween the common carp and zebrafish genomes, of which13449BAC end sequences hadsignificant hits to zebrafish chromosomes.