Using Next-Generation Sequencing to Assist a Conservation Hatchery: a Single-Nucleotide Polymorphism Panel for the Genetic Management of Endangered Delta Smelt

Abstract

The Delta Smelt Hypomesus transpacificus, listed as threatened under the California Endangered Species Act, has been cultured at a conservation hatchery since 2008 in response to significant declines in the wild. The conservation hatchery relies on accurate, efficacious, and reproducible molecular techniques to help maintain the captive population's overall genetic diversity and to minimize inbreeding. We created a panel of single-nucleotide polymorphisms (SNPs) to support broodstock pedigree reconstruction and improve upon current genetic management. For the SNP discovery, we sequenced 27 broodstock samples from the 2012 spawn by using restriction site-associated DNA sequencing (RAD-seq). We then created a linkage map by genotyping three single-pair crosses at 2,317 newly discovered loci with RAD-seq. We successfully mapped 1,123 loci and identified 26 linkage groups. Fluidigm SNP Type genotyping assays were developed for 104 mapped loci that were selected for minor allele frequencies (MAFs) greater than 0.20, neutrality (Hardy–Weinberg equilibrium), and marker location. Candidates for the genotyping panel were evaluated on a Fluidigm Integrated Fluidic Circuit 96.96 and were tested for marker accuracy and the ability to correctly assign parentage. When applied in conjunction with mating records, we found that a panel of 24 independent SNPs (mean MAF = 0.47) successfully assigned 100% of tested offspring if all of the samples were genotyped at a minimum of 18 loci. Given its capacity to streamline the screening of broodstock candidates, we foresee that the new SNP parentage panel will assume an integral role in genetic management of the Delta Smelt conservation hatchery. Furthermore, genomic resources created for this study have the potential to propel further advances in studying this imperiled species.

Received November 29, 2014; accepted March 30, 2015

ACKNOWLEDGMENTS

We thank Joan Lindberg, Meredith Nagel, Luke Ellison, Galen Tigan, and the staff at the FCCL for managing the Delta Smelt captive breeding population and raising the Delta Smelt families used for linkage mapping; we also thank Antonia Wong and Melania La Cava for laboratory support. We are grateful to Michael R. Miller, Andrew Whitehead, Nicholas Buckmaster, and Megan Mayo for providing comments in the writing of this manuscript. This work was supported by the U.S. Bureau of Reclamation under Cooperative Agreement Number R10AC20089, CESU Number 3FC810873, to B. May.