Use of genotyping by sequencing data to develop a high-throughput and multifunctional SNP panel for conservation applications in Pacific lamprey

• Published in: Molecular ecology resources Vol. 15; no. 1; pp. 187 - 202
• Main Authors: Hess, Jon E., Campbell, Nathan R., Docker, Margaret F., Baker, Cyndi, Jackson, Aaron, Lampman, Ralph, McIlraith, Brian, Moser, Mary L., Statler, David P., Young, William P., Wildbill, Andrew J., Narum, Shawn R.
• Format: Journal Article
• Language: English
• Published: England Blackwell Publishing Ltd 01.01.2015; Wiley Subscription Services, Inc
• Subjects: animal mating/breeding systems; Animals; conservation genetics; ecological genetics; Entosphenus tridentatus; fisheries management; Genes; Genetic Markers; Genotype; Genotyping Techniques - methods; High-Throughput Screening Assays; Lampreys - classification; Lampreys - genetics; life history evolution; Molecular Sequence Data; Petromyzontidae; Polymorphism; Polymorphism, Single Nucleotide; population genetics - empirical; Sequence Analysis, DNA; I, Pacific; population genetics - empirical; life history evolution; ecological genetics; fisheries management; animal mating/breeding systems; conservation genetics
• ISSN: 1755-098X; 1755-0998
• DOI: 10.1111/1755-0998.12283

Next‐generation sequencing data can be mined for highly informative single nucleotide polymorphisms (SNPs) to develop high‐throughput genomic assays for nonmodel organisms. However, choosing a set of SNPs to address a variety of objectives can be difficult because SNPs are often not equally informative. We developed an optimal combination of 96 high‐throughput SNP assays from a total of 4439 SNPs identified in a previous study of Pacific lamprey (Entosphenus tridentatus) and used them to address four disparate objectives: parentage analysis, species identification and characterization of neutral and adaptive variation. Nine of these SNPs are FST outliers, and five of these outliers are localized within genes and significantly associated with geography, run‐timing and dwarf life history. Two of the 96 SNPs were diagnostic for two other lamprey species that were morphologically indistinguishable at early larval stages and were sympatric in the Pacific Northwest. The majority (85) of SNPs in the panel were highly informative for parentage analysis, that is, putatively neutral with high minor allele frequency across the species’ range. Results from three case studies are presented to demonstrate the broad utility of this panel of SNP markers in this species. As Pacific lamprey populations are undergoing rapid decline, these SNPs provide an important resource to address critical uncertainties associated with the conservation and recovery of this imperiled species.