Whole Genome SNP Discovery and Analysis of Catfish Genetic Diversity

Single-nucleotide polymorphism (SNP) is the most powerful and widely used genetic markers. Although large scale SNP discovery was conducted in catfish by transcriptome sequencing, whole genome scale SNP discovery has not been conducted. In this project, we conducted genomic sequencing using next-gen technologies with pooled DNA samples from multiple individuals from four channel catfish strains and one wild population.  A total of 8.8 million putative SNPs were identified.  Large numbers of SNPs, 5.15 million, 4.32 million, 3.86 million, 5.75 million and 5.70 million, were identified from each of the 5 channel catfish strains/populations of Marion, Thompson, USDA103, Hatchery strain, and wild population, respectively. A large number of putative strain-specific SNPs were also identified from Marion (38.2K), Thompson (43.7K), USDA103 (41.0K), Hatchery strain (47.2K), and wild population (67.7K), respectively. The range of heterozygosity of all populations is 3.40-5.26 SNPs/Kb. On average, there are one SNP every 219 bp in the catfish genome. Non-reference allelic state analysis shows that wild population has much more non-reference homozygous SNPs than domesticated populations. Analysis is ongoing to identify selective sweeps in domestic strains as compared with the wild population. These SNPs are being used for the construction of the 250K catfish SNP array. The putative strain-specific SNPs, upon validation, will be useful for strain identification.