Threespine stickleback fish is an emerging model system for studying the developmental genetic basis of quantitative traits. Researchers within the community agree that tools to leverage and enhance the recently completed genomic sequence are essential. We propose to help investigators understand the underlying genetics of the naturally varing traits seen in stickleback by providing to the community a microarray-based system for efficient and cost effective genotyping. The high-throughput genotyping system that we have developed, RAD mapping, will enable the rapid identification of the genes controlling complex traits ranging from behavior to bone shape. In order to facilitate the use of this tool, simple web-accessible array analysis tools and a hands-on course to train researchers new to genomics will be provided. Stickleback are a complementary model system for many laboratory-based organisms, in that the numerous isolated and divergent natural populations have evolved adult traits that are a difficult or impossible to study by traditional mutagenesis approaches. Importantly, many of these traits are quantitative, influenced by alleles at genetic diseases, and stickleback are a unique vertebrate model for examining these quantitiative traits. The genotyping tools that we propose here will greatly accelerate this important research. Investigators from other research communities such as Drosophila, zebrafish, and mouse have expressed enthusiasm for initiating work in stickleback if these proposed tools were available. Thus, our genomic tools will increase the rate of discoveries of the genetic basis quantitative variation that underlies most common human diseases both by assisting present stickleback researchers;and by drawing additional researchers to work on this emerging model organism. Relevance: Most common human diseases, such as heart disease, high blood pressure, and osteoarthritis, are the result of complex interactions between an individual's genes and her or his environment. Threespine stickleback fish are an excellent model for these kinds of traits, and have numerous traits that are similarly controlled by many genes and the particular environment in which they live. We propose to create research tools to enable the rapid discovery of the genes controlling these complex traits, and help further the emergence of stickleback as an important model for common human traits specifically, and complex traits in general.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Resource-Related Research Projects (R24)
Project #
5R24GM079486-03
Application #
7656793
Study Section
Genomics, Computational Biology and Technology Study Section (GCAT)
Program Officer
Portnoy, Matthew
Project Start
2007-08-01
Project End
2011-07-31
Budget Start
2009-08-01
Budget End
2010-07-31
Support Year
3
Fiscal Year
2009
Total Cost
$133,446
Indirect Cost
Name
University of Oregon
Department
Biology
Type
Organized Research Units
DUNS #
948117312
City
Eugene
State
OR
Country
United States
Zip Code
97403
Leve, Leslie D; Neiderhiser, Jenae M; Harold, Gordon T et al. (2018) Naturalistic Experimental Designs as Tools for Understanding the Role of Genes and the Environment in Prevention Research. Prev Sci 19:68-78
Bassham, Susan; Catchen, Julian; Lescak, Emily et al. (2018) Repeated Selection of Alternatively Adapted Haplotypes Creates Sweeping Genomic Remodeling in Stickleback. Genetics 209:921-939
Lescak, Emily A; Bassham, Susan L; Catchen, Julian et al. (2015) Evolution of stickleback in 50 years on earthquake-uplifted islands. Proc Natl Acad Sci U S A 112:E7204-12
Catchen, Julian; Hohenlohe, Paul A; Bassham, Susan et al. (2013) Stacks: an analysis tool set for population genomics. Mol Ecol 22:3124-40
O'Brien, C; Unruh, L; Zimmerman, C et al. (2013) Geography of the circadian gene clock and photoperiodic response in western North American populations of the three-spined stickleback Gasterosteus aculeatus. J Fish Biol 82:827-39
Merz, Clayton; Catchen, Julian M; Hanson-Smith, Victor et al. (2013) Replicate phylogenies and post-glacial range expansion of the pitcher-plant mosquito, Wyeomyia smithii, in North America. PLoS One 8:e72262
Catchen, Julian; Bassham, Susan; Wilson, Taylor et al. (2013) The population structure and recent colonization history of Oregon threespine stickleback determined using restriction-site associated DNA-sequencing. Mol Ecol 22:2864-83
Hohenlohe, Paul A; Bassham, Susan; Currey, Mark et al. (2012) Extensive linkage disequilibrium and parallel adaptive divergence across threespine stickleback genomes. Philos Trans R Soc Lond B Biol Sci 367:395-408
O'Brien, Conor S; Bourdo, Ryan; Bradshaw, William E et al. (2012) Conservation of the photoperiodic neuroendocrine axis among vertebrates: evidence from the teleost fish, Gasterosteus aculeatus. Gen Comp Endocrinol 178:19-27
Bradshaw, William E; Emerson, Kevin J; Catchen, Julian M et al. (2012) Footprints in time: comparative quantitative trait loci mapping of the pitcher-plant mosquito, Wyeomyia smithii. Proc Biol Sci 279:4551-8

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