Development of the Catfish 690K SNP Arrays for Analysis of Quantitative Traits

Availability of genome-wide molecular markers is crucial for the analysis of quantitative traits. Single nucleotide polymorphisms (SNPs) are one of the most widely used molecular markers due to their ubiquitous distribution and analytical simplicity. In this work, we developed a high-density SNP genotyping array for channel catfish (Ictalurus punctatus) and blue catfish (I. furcatus). Whole genome sequencing, RNA-seq, and GBS data over 700 channel catfish and 200 blue catfish from previous experiments were used for SNP mining. Criteria-based quality filtration and Affymetrix in-silico probe converting test were used to select the final set of 690,662 high quality SNPs, comprising 581,002 channel catfish specific, 44,694 blue catfish specific, 19,124 inter-species, and 45,842 ubiquitous SNPs. A total of 48,434 strain-specific markers for 5 domestic and wild strains were also included on the array, which should be useful in study channel catfish domestication events. The selected SNPs were relatively evenly distributed on the genome reference, with 0.5-1.3 kb interquartile range of intervals. They cover 98.6% of the genome scaffolds and 93.9% of the BAC-based physical map contigs. The high coverage benefits the detection of linkage disequilibrium in further genome-wide association studies and fine-scale linkage mapping. To represent gene-associated regions well, 24,878 of 26,661 genes on the reference genome sequence were covered with at least one marker. 2,000 additional probes generated from non-polymorphic genomic regions were also included as negative controls. This is the highest density SNP array developed in aquaculture species, which should serve as valuable resources for further construction of genetic map, genome-wide association studies, and QTL analysis.