Development of a High Density 250K SNP Genotyping Array for Common Carp

Single nucleotide polymorphisms (SNPs) have been widely used as universal marker for genetic and genome studies in many species. Genome-wide SNPs could offer sufficient markers for trait related research and further more could themselves be causative SNPs for traits. Common carp (Cyprinus carpio) is one of the most important aquaculture species with high degree of genetic diversity in the world. There are numerous strains and populations with distinct phenotypes and specific economic traits. The genetic mechanism underlying the different traits, however, has been rarely elucidated yet. To facilitate the study in the whole genome scale, we developed a high density common carp 250K SNP genotyping array based on the Affymetrix Axiom technology. Common carp SNPs were obtained from multiple sources including RNA-seq and whole genome re-sequencing data from representative accessions. A set of 380,000 high-quality SNPs was initially picked as candidates from 35 million SNP loci. The panel of 250,000 SNPs was finally acquired after further quality analysis based on minor allele frequencies, distributions in the genome, and analysis of the flanking sequences. The average of SNP intervals in the common carp reference genome is 6.6 kb and most of SNP intervals range from 3 kb to 8 kb. The common carp 250K SNP array is being evaluated by genotyping individuals from various domesticated strains and wild populations of the common carp, as well as relative Cyprinidae species. The common carp 250K SNP array should provide valuable resources on genome-wide association studies (GWAS), linkage disequilibrium (LD) analysis, haplotype construction, high-density linkage mapping and genome selection in the common carp, as well as in those closely related species.