Development of a microhaplotype panel for steelhead/rainbow trout (Oncorhynchus mykiss) and application for phylogenetic analysis in California

Abstract Advances in high-throughput sequencing and bioinformatic data processing have prompted a transition in wildlife and fisheries genetics from the use of allozymes, mtDNA, or microsatellites towards markers that are more amenable to genotyping by sequencing, increasing the amount of data obtained for a lower cost with less time-consuming techniques. Microhaplotypes are novel multi-allelic genetic markers that utilize a high-throughput genomic amplicon sequencing approach to genotype large numbers of individuals for parentage and kinship analysis and population genetic studies, including applications in monitoring and fisheries management. We describe the development of a panel of microhaplotypes for Oncorhynchus mykiss , a species of high cultural and economic importance throughout its native range and globally through introductions for aquaculture and due to its reputation as a prized sport fish among recreational fishers. The panel includes 124 loci presumed to be neutral, a marker for the sex determination locus ( SdY) , and 10 loci targeting previously identified adaptive genomic variants associated with important life-history traits in this species. We demonstrate that this panel provides high resolution for phylogeographic and other genetic analysis and on initial standardized reference population genetic baseline of California O. mykiss .