Development of SNP markers for analysis of population structure in white perch ( Morone americana ) using double digest
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TECHNICAL NOTE
Development of SNP markers for analysis of population structure in white perch (Morone americana) using double digest restriction site-associated DNA sequencing Li Bian1 • Yong-quan Su1 • Patrick M. Gaffney2
Received: 26 May 2016 / Accepted: 4 July 2016 Ó Springer Science+Business Media Dordrecht 2016
Abstract The white perch Morone americana is a commercially and recreationally important species found in coastal waters of eastern United States. Despite its wide geographic distribution and economic importance, genomic resources for understanding population structure are limited. In this study, we applied double digest restriction siteassociated DNA sequencing technique to develop SNP markers and investigate the population structure of M. americana sampled from four geographical regions in Delaware Bay and Chesapeake Bay, USA. We identified 621 putatively neutral SNPs by applying a stringent filtering procedure. Based on these SNP markers, population structure inferences were conducted for the four populations. This study provides a valuable resource for further research on genetic structure and demographic history of M. americana. Keywords Morone americana SNP Double digest restriction site-associated DNA sequencing Population genetics White perch, Morone americana, are one of the most common fish found in coastal waters of eastern United States. They are distributed from Nova Scotia to South Electronic supplementary material The online version of this article (doi:10.1007/s12686-016-0571-6) contains supplementary material, which is available to authorized users. & Patrick M. Gaffney [email protected] 1
College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, Fujian, China
2
College of Earth, Ocean, and Environment, University of Delaware, Lewes, DE 19958, USA
Carolina and are typically found in coastal bays and estuaries, as well as in freshwater and brackish lakes and ponds (Jenkins and Burkhead 1994). M. americana supports a robust recreational fishery and in areas where commercial fishing for the species is legal, it was subject to intensive netting (Mansueti 1961). M. americana has been intentionally and unintentionally transplanted from its native range into many inland lakes and reservoirs of United States (Irons et al. 2002), often with detrimental impacts on native species (Madenjian et al. 2000; Parrish and Margraf 1990). The species is considered to exhibit ‘‘partial migration’’, where some individuals in a population remain in their natal freshwater habitat, while others migrate down-estuary into higher salinity waters (Kerr et al. 2009). This dimorphism in life history features is interpreted as a response to environmental factors rather than indicating the existence of genetically distinct subpopulations, although genetic data bearing on this question are limited (Kerr and Secor 2009). Given its abundance and widespread distribution, M. americana may serve as a good model for investigating the population genomics of a partially migrating estuarine species. To
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