A Microsatellite Genome Screen Identifies Chromosomal Regions under Differential Selection in Steelhead and Rainbow Trout

Abstract

AbstractNovel genetic resources now make it possible to directly assess the effects of natural selection on specific regions of the salmonid genome. Natural selection on specific genetic loci will also affect the variation in linked flanking regions through “hitchhiking” effects, causing greater differentiation between populations than would be expected from purely neutral processes. Here we identify candidate genomic regions for the effects of differential natural selection in two closely related populations of steelhead–rainbow trout Oncorhynchus mykiss separated for the last century following anthropogenic introduction above a barrier waterfall in a coastal California stream. A set of 110 expressed sequence tag (EST)‐linked and 188 anonymous microsatellite loci, most of which are mapped, were chosen to provide distributed coverage of all linkage groups in the O. mykiss genome. A genome screen was then performed to identify genomic regions under divergent selection. Multiple complementary statistical methods were used to detect outlier loci, and loci identified by more than one method were considered strong candidates for genomic regions affected by recent natural selection and genomic adaptation to the environment above the waterfall. We identified six strongly supported outlier loci, including one linked to an EST and two located in a genomic region that contains quantitative trait loci associated with egg development, spawning time, and other life history variation. Identification of regions in the genome that are potentially under selection provides valuable information about the genetic basis of selection in novel habitats and the genetic architecture of salmonid life history variation.