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Research Project: Integrated Research Approaches for Improving Production Efficiency in Rainbow Trout

Location: Cool and Cold Water Aquaculture Research

Title: De-novo genome assemblies of four rainbow trout genetic lines towards a pan-genome reference

item Gao, Guangtu
item Waldbieser, Geoffrey - Geoff
item YOUNGBLOOD, RAMEY - Mississippi State University
item WHEELER, PAUL - Washington State University
item Scheffler, Brian
item NARUM, SHAWN - Columbia River Intertribal Fish Commission
item THORGAARD, GARY - Washington State University
item Palti, Yniv

Submitted to: International Conference on Integrative Salmonid Biology
Publication Type: Abstract Only
Publication Acceptance Date: 1/2/2024
Publication Date: 2/1/2024
Citation: Gao, G., Waldbieser, G.C., Youngblood, R., Wheeler, P., Scheffler, B.E., Narum, S., Thorgaard, G., Palti, Y. 2024. De-novo genome assemblies of four rainbow trout genetic lines towards a pan-genome reference. International Conference on Integrative Salmonid Biology. 0311:0314.

Interpretive Summary:

Technical Abstract: Currently, we are working towards generating a rainbow trout pan-genome reference that will better represent the genetic diversity in this species using de-novo chromosome level assemblies. To that end we have previously generated the reference genome from the Arlee line (USDA_OmykA_1.1; GCA_013265735.3), an improved assembly for the Swanson line (Omyk_2.0; GCA_025558465.1), and a genome assembly from the Whale Rock Male line (USDA_OmyWR_1.0; GCA_029834435.1). The Swanson YY male line was originated from a semi-domesticated resident fish from the Kenai Peninsula in Alaska with a haploid number of 29 chromosomes. The Arlee doubled haploid YY male line has a different genetic background from the Swanson line. It has a haploid number of 32 chromosomes and was originated from a well-known domesticated hatchery strain that was originally collected from the northern California coast. The karyotype difference between the Swanson and Arlee lines is due to three fission or fusion events. The three Swanson metacentric chromosomes that are being divided into two acrocentric chromosomes in the Arlee karyotype are Omy04, 14 and 25. The Whale Rock line is also a YY male. Like the Arlee line, it has 2N=64 chromosomes and it was originated from the Central California Coast. The one known major difference from the Arlee line is that it was originated from a wild fish from a landlocked steelhead population. The fourth de-novo genome assembly (USDA_OmykKC_1.0) is from a Keithley Creek (KC) male rainbow trout. The KC is from the inland lineage of rainbow trout (O. m. gairdneri) in contrast to the three previous assemblies that were done using fish from the coastal lineage (O. m. irideus). The geographic distribution of the resident KC population is from the Snake River Drainage of the Interior Columbia Basin. The individual XY male that was sampled for DNA sequencing is an offspring of fish collected from the wild, thus representing a wild population. The KC population of Redband trout is from the Montane ecosystem in contrast with the desert Redband trout. The exact Karyotype of the KC population is unknown. However, our de-novo chromosome level genome assembly provides strong support for 2N=60 number of chromosomes. The sex determination gene (sdY) is located on Chromosome 29 in all four assemblies.