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

Abstract

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.

Large-scale SNP discovery and construction of a high-density genetic map of Colossoma macropomum through genotyping-by-sequencing

“…The use of zebrafish to perform synteny and collinearity analyses may provide a framework for mapping candidate genes responsible for the traits related to phenotypic divergence in tambaqui. Zebrafish genome also enables the transfer of genomic information between zebrafish and others species, such as Mexican tetra11, gudgeons42, common carp43, rainbow trout44, and channel catfish45.…”

Fine mapping QTL for resistance to VNN disease using a high-density linkage map in Asian seabass

“…Riding the wave of GBS, genetic studies, high-density maps and/or QTL mapping for economically important traits have been conducted in several aquatic species. For example, GBS has been used in Atlantic salmon ( Salmo salar ) for disease resistance7 and genetic map8, blue catfish ( Ictalurus furcatus ) for genetic structure9, sea cucumber ( Apostichopus japonicas ) for body weight10, and Pacific white shrimp ( Litopenaeus vannamei )11, Asian seabass ( Lates calcarifer )12 and large yellow croaker ( Larimichthys crocea )13 for growth traits. Besides these commercial fish species, GBS was also applied in several species of ecological importance, such as Chinook salmon ( Oncorhynchus tshawytscha ) for population structure14, sticklebacks ( Gasterosteus aculeatus ) for skeletal traits15 and Mexican tetra ( Astyanax mexicanus ) for genetic map16.…”

Construction of a High-Density Genetic Map and Quantitative Trait Locus Mapping in the Manila clam Ruditapes philippinarum

“…Aquatic organisms are well-represented among studies using GBS and other restriction site-associated DNA sequencing (RAD-seq)–based methodologies 23 . The majority of GBS studies in aquatic animals have focused on fish species of commercial 24,25 or conservational concern 26–28 . In this study, we adapted this technology to construct a high-density linkage map for genomic and genetic studies in the marine bivalve R. philippinarum .…”