Data from: SNP discovery in wild and domesticated populations of blue catfish, Ictalurus furcatus, using genotyping-by-sequencing and subsequent SNP validation

Blue catfish, Ictalurus furcatus, are valued in the United States as a
trophy fishery for their capacity to reach large sizes, sometimes
exceeding 45 kg. Additionally, blue catfish × 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 five wild and
domesticated populations (Mississippi River, Missouri, D&B, Rio
Grande and Texas). Stringent filtering of SNP-calling parameters resulted
in 4275 SNP loci represented across all five populations. Population
genetics and structure analyses revealed potential shared ancestry and
admixture between populations. We utilized the Sequenom MassARRAY 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 nine
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.