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United States Department of Agriculture

Agricultural Research Service

Research Project: UTILIZATION OF GENOMICS FOR IMPROVING PRODUCTION TRAITS IN COOL AND COLD WATER AQUACULTURE

Location: Cool and Cold Water Aquaculture Research

Title: Next-generation sequencing reveals a conserved haplotype controlling parallel adaptation in geographically distant rainbow trout (Oncorhynchus mykiss) populations

Authors
item Miller, Michael -
item Brunelli, Joesph -
item Wheeler, Paul -
item Liu, Sixin
item Rexroad, Caird
item Palti, Yniv
item Doe, Chris -
item Thorgaard, Gary -

Submitted to: Molecular Ecology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: September 1, 2011
Publication Date: January 4, 2012
Citation: Miller, M.R., Brunelli, J.P., Wheeler, P.A., Liu, S., Rexroad III, C.E., Palti, Y., Doe, C.Q., Thorgaard, G.H. 2012. Next-generation sequencing reveals a conserved haplotype controlling parallel adaptation in geographically distant rainbow trout (Oncorhynchus mykiss) populations. Molecular Ecology. 21(2):237-249.

Interpretive Summary: Rainbow trout is one of the most important aquaculture species in the United States and around the world, but little is known about its genetic makeup. The genome is the sum of all the genetic material in a cell. A genome map shows the specific locations of a species' genes and/or markers on each chromosome. These types of maps are important for finding variation in genes that impact aquaculture production traits and can be exploited for increasing the efficiency of producing this important source of nutritious protein and healthy unsaturated oils for consumers. We report the generation of a high density genetic map of rainbow trout genome with close to 5,000 single nucleotide polymorphism markers, an improvement over previous medium density maps which contained ~1000 microsatellite markers. As proof for the utility of the new genetic map, we used it to map a region of the genome harboring genes that affect the rate of embryonic development. This mapping approach is now available for identifying genes affecting production traits such as disease resistance and stress tolerance.

Technical Abstract: Local adaptation is the process by which different individuals of the same species are exposed to distinct forces of natural selection and populations adapt or acquire traits that provide an advantage in their local environment. Salmonid fishes exhibit extensive local adaptations due to an abundant environmental variation and precise natal homing. This extensive local adaptation makes conservation and restoration of salmonids a challenge. For example, defining unambiguous units of conservation is difficult and restoration attempts often fail due to inadequate adaptive matching of translocated populations. Here we used a combination of laboratory crosses and next-generation sequencing of Restriction-site Associated DNA (RAD) tags to investigate the genetic architecture of the parallel adaptation of rapid development rate in two geographically distant populations of the salmonid Oncorhynchus mykiss. Strikingly, we found that a conserved haplotype is responsible for this intriguing parallel adaptation. This further strengthen the evidence from our previous quantitative trait loci (QTL) mapping studies and implies that indeed a parallel genetic mechanism is affecting rapid development rate in these doubled haploid laboratory lines. The repeated use of adaptive genetic variation across distant geographical areas could be a general theme in salmonids and could be exploited for developing better tools for the design of management and restoration programs.

Last Modified: 8/22/2014