Sea lamprey RAPTURE baits enable efficient genotyping for population genomic and parentage studies

Session: Application of Genomic Tools to Inform Management of the Great Lakes (1)

Nicholas Sard, Nicholas Sard, [email protected]
Seth Smith, Department of Fisheries & Wildlife, Michigan State University, [email protected]
Jared Homola, Michigan State University, [email protected]
Gale Brevener, Fisheries and Oceans Canada, [email protected]
Jean Adams, US Geological Survey - Great Lakes Science Center, [email protected]
Chris Holbrook, USGS Great Lakes Science Center, [email protected]
Pete Hrodey, USFWS, [email protected]
Kim Scribner, Dept. Fisheries and Wildlife, Michigan State, [email protected]

Abstract

Sea lamprey abundance and wounding in several Great Lakes areas have been higher than target levels over the past decade.  Annual assessments of adult spawner abundance and stock-recruitment relationships are difficult to obtain, particularly in large tributaries. We developed restriction-site associated DNA capture (RAPTURE) baits to genotype 11,970 single nucleotide polymorphisms (SNPs) located within 3446 RAD loci with resolved coordinates on the sea lamprey genome. Estimates of genetic diversity within and among analyzed populations based on our RAPTURE loci were concordant with previous microsatellite-based estimates.  Using simulations, we show that accuracy in pedigree assignment is high when 200 or 500 loci are used, even in situations of high spawner abundance (e.g., 1000s of adults). We genotyped larval lamprey (n = 214) from Duffins Creek, Ontario collected in 2018 to infer pedigree relationships when no parents were sampled. We estimated the number of spawners that contributed offspring to three consecutive cohort samples and identified stream reaches with high numbers of related larvae. Rapid assessment genotyping using this suite of SNP loci will allow biologists to investigate aspects of sea lamprey reproductive ecology, to estimate the number and effective number of adults contributing to annual recruitment, and determine natal origin. 

Twitter handle of presenter
@FisherOfGenes