NATIONAL ANIMAL GENOME RESEARCH PROGRAM

• Sponsoring Institution: National Institute of Food and Agriculture
• Project Status: TERMINATED
• Funding Source: HATCH
• Reporting Frequency: Annual
• Accession No.: 1002116
• Project No.: CA-D-ASC-2193-RR
• Multistate No.: NRSP-8
• Project Start Date: Jan 3, 2014
• Project End Date: Sep 30, 2018

Project Director
Miller, M.

Recipient Organization
UNIVERSITY OF CALIFORNIA, DAVIS
410 MRAK HALL
DAVIS,CA 95616-8671

Performing Department
Animal Science

Non Technical Summary
Rainbow trout are the most widely cultivated cold freshwater fish in the world and an important model species for many research areas. Despite this importance, the complex nature of the rainbow trout genome (pseudotetraploid and high repeat content) has hindered the production of a high-quality reference genome assembly. We are generating and improving a reference genome sequence assembly for rainbow trout which helps address all three project objectives.

Animal Health Component

0%

Research Effort Categories

Basic

33%

Applied

33%

Developmental

34%

Classification

Knowledge Area (KA)	Subject of Investigation (SOI)	Field of Science (FOS)	Percent
304	3711	1080	50%
304	0899	1080	50%

Knowledge Area
304 - Animal Genome;

Subject Of Investigation
3711 - Trout; 0899 - Wildlife and natural fisheries, general/other;

Field Of Science
1080 - Genetics;

Keywords

trout

salmonids

fish

aquaculture

genome

genomics

reference

assembly

sequence

Goals / Objectives
Advance the status of reference genomes for all species, including basic annotation of worldwide genetic variation, by broad sequencing among different lines and breeds of animals. Develop strategies to identify and exploit genes and allelic variation that contribute to economically relevant phenotypes and traits, in part through improving functional annotation of the genomes of our species. Facilitate analysis, curation, storage, distribution and application of the enormous datasets now being generated by next-generation sequencing and related "omics" technologies with regard to animal species of agricultural interest.

Project Methods
We are generating and improving a reference genome sequence assembly for rainbow trout. This is a difficult task due to the complex nature of the rainbow trout genome which is pseudotetraploid and has high repetitive element content. We are using/testing a variety of genomics and bioinformatics methods such as a bacterial artificial chromosome (BAC) clone based physical map minimal tiling path to reduce sequence and assembly complexity. Currently, most of our sequence data has been generated using the Illumina platform and includes indexed BAC paired-end, whole genome shotgun (WGS) paired-end, and WGS mate-pair sequencing libraries. We plan to generate longer read sequence data using new technologies from Moleculo Incorporated and Pacific Biosciences. We have developed and tested a variety of preexisting and custom bioinformatics pipelines to assembly this data. We will continue to improve the sequence data and bioinformatics pipelines to generate and improve the reference genome sequence assembly for rainbow trout.

Progress 01/03/14 to 09/30/18

Outputs
Target Audience:The rainbow trout and other salmonid aquaculture, natural resource management, and research communities as well as members of the general public that are interested in salmonid-related issues. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?This project has provided significant training and professional development for undergraduate, graduate, and postdoctoral researchers in my group. How have the results been disseminated to communities of interest?Project results have been disseminated through the publication of articles in journals read by the target audiences. In addition, project results have been disseminated through oral presentations to groups that do not engage in research but are interested in various salmonid-related issues. For example, project results were presented to groups including but not limited to the The North Umpqua Foundation, Salmon River Restoration Council, California Trout, Nature Fish Society, Pacific Gas and Electric Company, Salmonid Restoration Federation, Winnemem Wintu Tribe, Karuk Tribe, Yurok Tribe, and Hoopa Valley Tribe. These presentations are designed to enhance public understanding of research by explaining how the results can improve strategies for salmonid conservation, management, production and restoration. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? Broadly speaking, we have 1) generated sequence data that has been used to improve the rainbow trout genome assembly, and 2) advanced the basic annotation of worldwide genetic variation in rainbow trout and other salmonids by broad sequencing among different lines. More specific examples include 1) generating high resolution genetic maps for rainbow trout that were used to scaffold the most recent genome assembly and revealed striking differences in the spatial distribution of recombination between sexes, 2) developing a new genotyping method called Rapture to improve the characterization of genetic variation that contributes to economically relevant phenotypes and traits in rainbow trout and other salmonids, and 3) generating PacBio sequence data that was incorporated into the most recent rainbow trout genome assembly.

Publications

• Type: Journal Articles Status: Published Year Published: 2018 Citation: Pearse DE, Barson NJ, Nome R, Gao G, Campbell MA, Abadía-Cardoso A, Anderson EC, Rundio DE, Williams TH, Naish KA, Moen T, Liu S, Kent M, Minkley DR, Rondeau EB, Brieuc MSO, Sandve SR, Miller MR, Cedillo L, Baruch K, Hernandez AG, Ben-Zvi G, Shem-Tov D, Barad O, Kuzishchin K, Garza JC, Lindley ST, Koop BF, Thorgaard GH, Palti Y, Lien S. (2018) Sex-dependent dominance maintains migration supergene in rainbow trout. bioRxiv.
• Type: Journal Articles Status: Published Year Published: 2018 Citation: Thompson TQ, Bellinger RM, ORourke SM, Prince DJ, Stevenson AE, Rodrigues AT, Sloat MR, Speller CF, Yang DY, Butler VL, Banks MA, Miller MR. (2019) Anthropogenic habitat alteration leads to rapid loss of adaptive variation and restoration potential in wild salmon populations. Proceedings of the National Academy of Sciences. 116(1):177-186.

Progress 10/01/16 to 09/30/17

Outputs
Target Audience:The rainbow trout and other salmonid aquaculture, natural resource management, and research communities as well as members of the general public that are interested in salmonid-related issues. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?This project has provided significant training and professional development for undergraduate, graduate, and postdoctoral researchers in my group. How have the results been disseminated to communities of interest?Project results have and will continue to be disseminated through the publication of articles in journals read by the target audiences. In addition, project results are disseminated through oral presentations to groups that do not engage in research but are interested in various salmonid-related issues. For example, during this reporting period, project results were presented to the Salmon River Restoration Council and California Trout as well as multiple other groups. These presentations are designed to enhance public understanding of research by explaining how the results can improve strategies for salmonid conservation, management, production and restoration. What do you plan to do during the next reporting period to accomplish the goals?We will continue to work on improving the status of the rainbow trout and other salmonid reference genome assemblies as well as characterizing genetic variation that contributes to economically relevant phenotypes and traits.

Impacts
What was accomplished under these goals? 1) We have generated sequence data that has been used to improve the rainbow trout genome assembly. 2) We have advanced the basic annotation of worldwide genetic variation in rainbow trout and other salmonids by broad sequencing among different lines.

Publications

• Type: Journal Articles Status: Published Year Published: 2017 Citation: Prince DJ, O'Rourke SM, Thompson TQ, Ali OA, Lyman HS, Saglam IK, Hotaling TJ, Spidle AP, Miller MR. (2017) The evolutionary basis of premature migration in Pacific salmon highlights the utility of genomics for informing conservation. Science Advances. 3(8):e1603198.
• Type: Journal Articles Status: Published Year Published: 2017 Citation: Saglam IK, Prince DJ, Meek M, Ali OA, Miller MR, Peacock M, Neville H, Mellison C, Somer W, May B, Finger AJ. (2017) Genomic analysis reveals genetic distinctiveness of the Paiute cutthroat trout (Oncorhynchus clarkii seleniris). Transactions of the American Fisheries Society. 146(6):1291-1302.

Progress 10/01/15 to 09/30/16

Outputs
Target Audience:The rainbow trout and other salmonid aquaculture, natural resource management, and research communities as well as members of the general public that are interested in salmonid-related issues. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?This project has provided significant training and professional development for undergraduate, graduate, and postdoctoral researchers in my group. How have the results been disseminated to communities of interest?Project results have and will continue to be disseminated through the publication of articles in journals read by the target audiences. In addition, project results are disseminated through oral presentations to groups that do not engage in research but are interested in various salmonid-related issues. For example, during this reporting period, project results were presented to the Nature Fish Society, Pacific Gas and Electric Company, Salmonid Restoration Federation, Salmon River Restoration Council and Winnemem Wintu Tribe as well as multiple other groups. These presentations are designed to enhance public understanding of research by explaining how the results can improve strategies for salmonid conservation, management, production and restoration. What do you plan to do during the next reporting period to accomplish the goals?We will continue to work on improving the status of the rainbow trout and other salmonid reference genome assemblies as well as characterizing genetic variation that contributes to economically relevant phenotypes and traits.

Impacts
What was accomplished under these goals? 1) We have generated PacBio sequence data that has been incorporated into an improved rainbow trout genome assembly. 2) We have advanced the basic annotation of worldwide genetic variation in rainbow trout and other salmonids by broad sequencing among different lines. 3) We have developed a new genotyping method called Rapture to improve the characterization of genetic variation that contributes to economically relevant phenotypes and traits in rainbow trout and other salmonids.

Publications

• Type: Journal Articles Status: Published Year Published: 2016 Citation: Ali OA, O'Rourke SM, Amish SJ, Meek MH, Luikart G, Jeffres C, Miller MR. (2016) RAD Capture (Rapture): Flexible and efficient sequence-based genotyping. Genetics. 202(2):389-400.
• Type: Journal Articles Status: Published Year Published: 2016 Citation: Meek MH, Baerwald MR, Stephens MR, Goodbla A, Miller MR, Tomalty KMH, May B. (2016) Sequencing improves our ability to study threatened migratory species: genetic population assignment in California's Central Valley Chinook salmon. Ecology and Evolution. 6:77067716.

Progress 10/01/14 to 09/30/15

Outputs
Target Audience:The rainbow trout and other salmonid aquaculture, natural resource management, and research communities. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?This project has provided significant training and professional development for undergraduate, graduate, and postdoctoral researchers in my group. How have the results been disseminated to communities of interest?Project results have and will continue to be disseminated through the publication of articles in journals read by the target audiences. What do you plan to do during the next reporting period to accomplish the goals?We will continue to work on assembly pipelines to improve the status of the rainbow trout reference genome assembly and post improved assembly versions to the National Genome Research Program website (http://www.animalgenome.org/).

Impacts
What was accomplished under these goals? 1) We have generated high resolution genetic maps for rainbow trout that improve genome assembly and reveal striking differences in the spatial distribution of recombination between sexes. Rainbow trout (Oncorhynchus mykiss) is an important species in aquaculture, sport fishing, and biomedical research. Despite widespread interest, the current genome assembly primarily contains unordered contiguous sequences and scaffolds. The utility of current genetic maps for improving genome assembly is limited by recombination suppression in male meiosis and/or relatively low genetic marker density. Since females exhibit far less recombination suppression, we generated gynogenetic recombinant progeny that represent recombination events derived from female meiosis. We hypothesized that a combination of gynogenetically produced recombinant progeny and high-density genotyping would produce an improved genetic map to enhance the current reference genome assembly. To this end, we produced 550 recombinant progeny via gynogenesis and 85 progeny produced through androgenesis. We then used restriction-site associated DNA (RAD) sequencing to discover and genotype approximately 30,000 single nucleotide polymorphisms (SNPs) and constructed both female and male-derived genetic maps. The linkage maps we constructed provide a critical genetic resource that can be applied to future aquaculture, conservation, and biomedical research. In addition, a comparison of corresponding linkage groups from both genetic maps reveals striking differences in the spatial distribution of recombination between sexes. 2) We have advanced the basic annotation of worldwide genetic variation in rainbow trout by broad sequencing among different lines. 3) We have developed strategies to identify genes and allelic variation that contribute to economically relevant phenotypes and traits have be developed for rainbow trout.

Publications

• Type: Journal Articles Status: Published Year Published: 2015 Citation: Palti Y, Gao G, Liu S, Kent MP, Lien S, Miller MR, Rexroad CE 3rd, Moen T. (2015) The development and characterization of a 57K single nucleotide polymorphism array for rainbow trout. Molecular Ecology Resources. 15(3):662672.
• Type: Journal Articles Status: Published Year Published: 2015 Citation: Hand BK, Hether TD, Kovach RP, Muhlfeld CC, Amish SJ, Boyer MC, ORourke SM, Miller MR, Lowe WH, Hohenlohe PA, Luikart G. (2015) Genomics and introgression: discovery and mapping of thousands of species-diagnostic SNPs using RAD sequencing. Current Zoology. 61(1):146-154.
• Type: Journal Articles Status: Published Year Published: 2015 Citation: Arciniega M, Clemento AJ, Miller MR, Peterson M, Garza JC, Pearse DE. (2015) Parallel evolution of the summer steelhead ecotype in multiple populations from Oregon and Northern California. Conservation Genetics. 1-11.

Progress 01/03/14 to 09/30/14

Outputs
Target Audience: The rainbow trout and other salmonid aquaculture, natural resource management, and research communities. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? This project has provided significant training and professional development for undergraduate, graduate, and postdoctoral researchers in my group. How have the results been disseminated to communities of interest? The projects results have been disseminated through the publication of articles in journals read by the target audiences. What do you plan to do during the next reporting period to accomplish the goals? We will continue to work on assembly pipelines to improve the status of the rainbow trout reference genome assembly and post improved assembly versions to the National Genome Research Program website (http://www.animalgenome.org/).

Impacts
What was accomplished under these goals? 1) The project has advanced the basic annotation of worldwide genetic variation in rainbow trout by broad sequencing among different lines. 2) Strategies to identify genes and allelic variation that contribute to economically relevant phenotypes and traits have be developed for rainbow trout.

Publications

• Type: Journal Articles Status: Published Year Published: 2014 Citation: Palti Y, Gao G, Miller MR, Vallejo RL, Wheeler PA, Quillet E, Yao J, Thorgaard GH, Salem M, Rexroad CE 3rd. (2014) A resource of single-nucleotide polymorphisms for rainbow trout generated by RAD sequencing of doubled haploids. Molecular Ecology Resources. 14(3):588596.
• Type: Journal Articles Status: Published Year Published: 2014 Citation: Pearse DE, Miller MR, Abad�a-Cardoso A, Garza JC. (2014) Rapid parallel evolution of standing variation in a single, complex, genomic region is associated with life history in steelhead/rainbow trout. Proceedings of the Royal Society B: Biological Sciences. 281(1783):20140012.