Development Of The Catfish 250K SNP Array

Quantitative traits, such as disease resistance and growth rate, are most often controlled by a set of genes involving a complex array of regulation. The dissection of genetic basis of these traits requires large numbers of genetic markers. In recent years, next-generation sequencing technologies have enabled discovery of genome-wide SNPs. In catfish, we have identified over eight million SNPs, but the challenge is how to efficiently and economically use such SNP resources for genetic analysis. One of the most efficient ways to genotype large numbers of SNPs is to design a high-density array that includes hundreds of thousands of SNPs distributed throughout the genome. In this work, we are developing a high-density catfish SNP genotyping array based on the Affymetrix Axiom genotyping technology. Catfish SNPs were obtained from multiple sources including gene-associated SNPs, anonymous genomic SNPs, and interspecific SNPs. A set of 640K high-quality SNPs were initially picked for the design, and the panel of 250K SNP was finalized after further quality analysis based on minor allele frequencies, distribution in the genome, and analysis of the flanking sequences. The predicted conversion values for the 250K SNPs were 0.54-0.89 with the average of 0.68. The catfish 250K SNP array is being evaluated by genotyping individuals from various industry strains and wild populations. The catfish 250K SNP array should provide a valuable addition to the repertoire of resources for catfish research community, which will enable genome-wide association studies (GWAS), fine mapping of QTLs, high-density linkage mapping, linkage disequilibrium (LD) analysis and genomic selection in catfish.