SNP discovery in wild and domesticated populations of blue catfish, I ctalurus furcatus , using genotyping‐by‐sequencing and subsequent SNP validation

• Published in: Molecular ecology resources 2014-11, Vol.14 (6), p.1261-1270
• Main Authors: Li, Chao, Waldbieser, Geoff, Bosworth, Brian, Beck, Benjamin H., Thongda, Wilawan, Peatman, Eric
• Format: Article
• Language: English
• ISSN: 1755-098X; 1755-0998
• DOI: 10.1111/1755-0998.12272

Blue catfish, I ctalurus furcatus , are valued in the U nited S tates 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 ( M ississippi R iver, M issouri, D & B , R io G rande and T exas). 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 S equenom M ass ARRAY to validate two multiplex panels of SNP s selected from the GBS data. Selection criteria included SNP s shared between populations, SNP s specific to populations, number of reads per individual and number of individuals genotyped by GBS . Putative SNP s were validated in the discovery population and in two additional populations not used in the GBS analysis. A total of 64 SNP s 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.