Characterization of sixteen polymorphic microsatellite DNA loci in the chum salmon ( Oncorhynchus keta ) isolated by nex
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MICROSATELLITE LETTERS
Characterization of sixteen polymorphic microsatellite DNA loci in the chum salmon (Oncorhynchus keta) isolated by next-generation sequencing H. Tsukagoshi • S. Terui • S. Abe
Received: 18 August 2014 / Accepted: 23 August 2014 / Published online: 3 September 2014 Ó Springer Science+Business Media Dordrecht 2014
Abstract Chum salmon (Oncorhynchus keta) is an important fisheries resource around the North Pacific region. However, the genetic characteristics of this species mostly remain to be elucidated with competent molecular genetic markers for their effective resource management and sustainable use. A total of sixteen novel microsatellite markers in chum salmon were isolated using a next-generation sequencing approach. All loci were polymorphic with 6–21 alleles, with the observed and expected heterozygosities of 0.41667–0.97917 and 0.66184–0.92434, respectively. These new loci will provide a tool for examining the genetic diversity and population structure of chum salmon, which are an important information for the adaptive management of this species. Keywords Chum salmon Oncorhynchus keta Fisheries resources Microsatellite DNA Next-generation sequencing Chum salmon, Oncorhynchus keta, widely ranging from the Far East to North America, have high commercial importance in North Pacific fisheries. They are semelparous and anadromous with homing to spawn in natal rivers or tributaries within major river systems. Such homing behavior will lead regional populations to partial genetic isolation as seen in other Pacific salmon species. Understanding of the genetic characteristics in chum salmon is Electronic supplementary material The online version of this article (doi:10.1007/s12686-014-0322-5) contains supplementary material, which is available to authorized users. H. Tsukagoshi (&) S. Terui S. Abe Sanriku Fisheries Research Center, Iwate University, Kamaishishi Heita 3-75-1, kamaishi 026-0001, Japan e-mail: [email protected]
therefore important for planning their conservation and resource management for sustainable use. Although genetic variation among chum salmon populations has been demonstrated with a variety of genetic markers, these findings are still insufficient to define genetically distinct population groups and to address the population history, the ocean migration patterns, and the consequence of hatchery-wild interactions (e.g. Seeb et al. 2011). Development of single locus biparental markers, such as polymorphic microsatellites, and use of multiple markers may be equally important for an increased resolution of genetic features in chum salmon. Here, we developed sixteen novel microsatellite markers in chum salmon using next-generation sequencing approach. Total DNA was extracted from the fin clips of O. Keta collected from the Yana River, Iwate Prefecture, Japan, using a DNeasy Blood and Tissue Kit (QIAGEN). An Illumina paired-end shotgun library was prepared by shearing 2 lg of DNA using a Covaris S220 and following the standard protocol of the Illumina TruSeq DNA P
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