|Other Abstract||Cyprinids are the most important cultivated fish group in term of production, especially in China. The DNA marker technology has had a revolutionary impact on fish genetics and breeding since 1980s, but its applications in the studies of genetic and breeding in Cyprinids is still in its infancy. As far as DNA marker development and applications in Cyprinids were concerned, the following studies were carried out in this dissertation.
Due to the tetraploid origin and lack of genetic markers, genetic mapping in common carp (Cyprinus carpio) is more difficult than in other fishes. By using AFLP and microsatellite (SSR) marker technology and gynogenetic haploids, a genetic linkage map of common carp was generated. The map reported here contains 699 AFLP and 20 microsatellite markers. It spans 5506.9 cM in 64 linkage groups, for an average marker spacing of 7.66cM. The correlation analysis indicates that markers in this map are randomly distributed among different linkage groups, but the normality test on interval map distances suggests the occurrence of AFLP marker clusters. In order to add gene and/or EST on the map, a large number of SNPs were identified by bioinformatic approach from public EST database of C. carpio. In a pilot study, some randomly selected SNPs were characterized in the common carp samples from China. The results show that carp genome harbors a large number of SNP variations, and allele frequencies of SNPs vary in different common carp populations or strains. Therefore, before these SNPs are added into the map and used in the marker-assisted breeding, their validation and variation should be tested in the given carp population or strain.
Silver carp (Hypophthalmichthys molitrix), together with the closely related bighead carp (H. nobilis), are among the most important freshwater foodfishes in China. However, depression of natural resources of these river-lake migratory fishes has become a severe problem in China. To more efficiently protect and exploit resources, studies on molecular population genetics of bighead carp and silver carp are urgently necessary. In this study, a set of novel polymorphic microsatellite markers of these two species were developed from an enriched genomic library of H. nobilis. Twenty-five polymorphic microsatellite loci (including previously available markers) were applied to investigate the genetic diversity and population structure of silver carp and bighead carp from Dongting Lake, Poyang Lake, and the Shishou section of the Yangtze River in China. Low genetic diversity, moderate population differentiation and genetic bottlenecks within silver carp and bighead carp were observed. Bighead carp was characterized by higher level of population differentiation and lower gene diversity than silver carp. These results suggest that recent demographic declines caused by human activity during last few decades have had tremendous impacts on the genetic structure of Hypophthalmichthys spp., especially to bighead carp. However, it does not appear that extensive hybridization or introgression between bighead and silver carps, which might result from habitat change or escape of hybrids from aquaculture, is occurring in the middle reaches of the Yangtze River. As samples of Hypophthalmichthys spp. in this study were collected before 2003when Three Gorges Dam (TGD) began to impound and alter river flow, the present study might act as a reference for future genetic studies of silver carp and bighead carp in middle reaches of the Yangtze River as well as other regions.
EST-derived microsatellite markers are becoming very important in studies of genomics and molecular breeding, because they represent coding regions of the genome and putative function can often be deduced by homology searches. As byproducts of the EST projects, EST-SSR markers are usually developed from the EST databases by bioinformatics method. However, so far large amount of EST sequences are available only in limited cyprinid species. In a case study in rare minnow (Gobiocyrpis Rarus), an FIASCO-based strategy which could be called as cDNA-FIASCO was proposed. The results demonstrate that this novel method is highly efficient for the fast isolation of EST-SSRs from a fish species in which EST sequences are not abundant.|