Identification of sex-specific SNPS in burbot Lota lota using RAD sequencing: conservation and management applications

Ninh V Vu,Daniel L Eardley,Thomas A Delomas,Matthew R Campbell

doi:10.1186/s41240-019-0133-4

Abstract

The development of sex-specific genetic assays in a species provides both a method for identifying the system of sex determination and a valuable tool to address questions of conservation and management importance. In this study, we focused on the identification of single nucleotide polymorphisms (SNPs) that differentiate genetic sex in burbot Lota lota. Burbot are the only true freshwater representative of the cod family and a species of conservation and management importance throughout Eurasia and North America. To identify sex-specific SNPs, we utilized restriction site-associated DNA sequencing (RADseq) to interrogate thousands of SNPs in burbot samples of known phenotypic sex. We discovered 170,569 biallelic SNPs, none of which fit the pattern expected under female heterogamety. However, we identified 22 SNPs that fit the pattern expected under male heterogamety (males heterozygous XY, females fixed XX) and, from these, developed two genetic assays that robustly (~ 97% genotyping success) and accurately (> 99% correct) sexed burbot samples. These sex-specific genetic assays will benefit growing conservation aquaculture programs for this species and allow future assessments of sex-specific migration, growth, and mortality.

Highlights

Burbot Lota lota are a holoarctic species adapted to coldwater rivers and lakes throughout Eurasia and North America
Twenty-two single nucleotide polymorphisms (SNPs) were found that fit the pattern expected under male heterogamety
The identification of a SNP with genotypes that are predictive of phenotypic sex demonstrates genetic sex determination in burbot

Summary

Introduction

Burbot Lota lota are a holoarctic species adapted to coldwater rivers and lakes throughout Eurasia and North America. Many burbot populations have been extirpated or are in severe decline, attributed to habitat alterations or loss from dam development, invasive species, over-exploitation, and climate change (Stapanian et al 2010). In response to these declines, several breeding and reintroduction programs have been initiated in both Europe and North America (Paragamian and Hansen 2011; Vught et al 2007). Moyie Lake was chosen as a donor population because it is in the Kootenai River Basin and large enough to avoid impacting the spawning

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Results

Discussion

Conclusion