Location: Warmwater Aquaculture Research UnitTitle: SNP discovery in wild and domesticated populations of blue catfish, Ictalurus furcatus, using genotyping-by-sequencing and subsequent SNP validation Author
Submitted to: Molecular Ecology Resources
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/28/2014
Publication Date: 11/15/2014
Citation: Li, C., Waldbieser, G.C., Bosworth, B.G., Beck, B.H., Thongda, W., Peatman, E. 2014. SNP discovery in wild and domesticated populations of blue catfish, Ictalurus furcatus, using genotyping-by-sequencing and subsequent SNP validation. Molecular Ecology Resources. 14(6):1261-1270. Interpretive Summary: The blue catfish, Ictalurus furcatus, is native to North America and serves as the paternal species of the blue x channel catfish hybrid that is valued for U.S. aquaculture production. Little is known about the extent of genetic diversity in blue catfish as a basis for genetic selection in this species. We used Genotyping-by-Sequencing to obtain DNA sequences from individuals of five wild and domesticated blue catfish populations, then aligned those sequences to identify DNA sequence variation between individuals. The analysis results in 4,907 putative single nucleotide loci across all five populations, and population genetic analyses revealed potential shared ancestry and admixture between populations. This research resulted in an initial assessment of the relatedness of blue catfish populations that can be used for hybrid catfish production, and also resulted in highly informative DNA markers useful for parentage and kinship determination in blue catfish and hybrid catfish families.
Technical Abstract: Blue catfish, Ictalurusfurcatus, are valued in the United States as a trophy fishery for their capacity to reach large sizes, sometimes exceeding 45 kg. Additionally blue catfish x channel catfish (I. punctatus) hybrid food fish production has recently increased the demand for blue catfish broodstock. However, there has been little study of the genetic impacts and interaction of farmed, introduced, and stocked populations of blue catfish. We utilized genotyping-by-sequencing (GBS) to capture and genotype SNP markers on 190 individuals from 5 wild and domesticated populations (Mississippi River, Missouri, D&B, Rio Grande, and Texas). Stringent filtering of SNP-calling parameters resulted in 4,907 SNP loci represented across all five populations. Population genetics and structure analyses revealed potential shared ancestry and admixture between populations. We utilized the SequenomMassARRAY to validate two multiplex panels of SNPs selected from the GBS data. Selection criteria included SNPs shared between populations, SNPs specific to populations, number of reads per individual and number of individuals genotyped by GBS. Putative SNPs were validated in the discovery population and in two additional populations not used in the GBS analysis. A total of 64 SNPs were genotyped successfully in 191 individuals from 7 populations. Our results should guide the development of highly-informative, flexible genotyping multiplexes for blue catfish from the larger GBS SNP set as well as provide an example of a rapid, low-cost approach to generate and genotype informative marker loci in aquatic species with minimal previous genetic information.