Ph.D. 2006, Washington State University
Genomics and quantitative genetics, domestication of fish
My research integrates genomic and quantitative genetic approaches to investigate adaptations in fish, primarily adaptations to captive environments. Domesticated populations often undergo physiological changes that enhance growth and reproduction, and reduce fear-related behavior and sensitivity to stress. These phenotypic changes have been observed in a variety of taxa including fish, birds, and mammals, suggesting that this is an example of parallel phenotypic evolution. Fish species are particularly suited to the study of domestication because they have been recently domesticated and wild populations are still available for comparison.
Studies of the physiological and genetic changes underlying domestication have a number of potential broader impacts, including genetic improvement of aquaculture stocks and rapid integration of desirable traits (e.g. disease resistance) from wild populations. Conversely, understanding the genetics of domestication will help manage genetic impacts of aquaculture escapements on wild populations and minimize domestication of captive-reared populations of endangered species.
My laboratory combines quantitative genetics, linkage analysis, and microarray analysis of gene expression to investigate morphological, physiological, and behavioral adaptations underlying fish domestication. In the near term, our overall approach will use a systematic strategy to identify and evaluate changes in gene regulation as causative factors underlying variation in complex traits including growth rate, stress physiology, and behavior.
Over the long term, I am particularly interested in the following questions:
- Are physiological adaptations to captivity the result of changes in gene regulation or gene function?
- Are the same genes or gene pathways responsible for parallel patterns of physiological adaptation observed across populations and species?
- Are the suites of traits that evolve during domestication genetically correlated?
Behavioral Genetics in Zebrafish: One of our current projects is examining the genetic basis of behavioral variation among strains of zebrafish with different histories of captive rearing. Like other fish species, domesticated zebrafish show reductions in fear-related behaviors and increases in feeding behavior compared to zebrafish from wild populations, even when reared under identical conditions. The availability of a whole genome sequence and well developed genomics tools make the zebrafish an ideal model for examining genetic variation underlying domestication. We are using quantitative genetics and genomics tools to determine if behavior variation among zebrafish strains is the result of differences in gene expression in the brain. This project is funded by the National Science Foundation and is in collaboration with Dr. Barrie Robison at the University of Idaho.
Alfaqih MA, Brunelli JP, Drew RE & Thorgaard GH. (2009). Mapping of five candidate sex-determining loci in rainbow trout (Oncorhynchus mykiss). BMC Genetics 10, 2.
Chapalamadugu KC, Robison BD, Drew RE, Powell MS, Hill RA, Amberg JJ, Rodnick KJ, Hardy RW, Hill ML, Murdoch GK. (2009). Dietary carbohydrate level affects transcription factor expression that regulates skeletal muscle myogenesis in rainbow trout. Comp Biochem Physiol Part B Biochem Mol Biol 153:66-72.
Phillips RB, DeKoning JJ, Ventura AB, Nichols KM, Drew RE, Chaves LD, Reed KM, Felip A, Thorgaard GH. Accepted. Recombination is suppressed over a large region of the rainbow trout Y Chromosome. Animal Genetics.
Barroso RM, Wheeler PA, LaPatra SE, Drew RE & Thorgaard GH. (2008). QTL for IHNV resistance and growth identified in a rainbow (Oncorhynchus mykiss) X Yellowstone cutthroat (Oncorhynchus clarki bouvieri) trout cross. Aquaculture 277, 156-163.
Drew RE, Rodnick KJ, Settles M, Wacyk J, Churchill E, Powell MS, Hardy RW, Murdoch GK, Hill RA & Robison BD. (2008). Effect of starvation on transcriptomes of brain and liver in adult female zebrafish (Danio rerio). Physiol Genomics 35, 283–295.
Heredia-Middleton P, Brunelli J, Drew RE & Thorgaard GH. (2008). Heat shock protein (HSP70) RNA expression differs among rainbow trout (Oncorhynchus mykiss) clonal lines. Comp Biochem Physiol Part B Biochem Mol Biol 149, 552–556.
Robison BD, Drew RE, Murdoch GK, Powell M, Rodnick KJ, Settles M, Stone D, Churchill E, Hill RA, Papasani MR, Lewis SS & Hardy RW. (2008). Sexual dimorphism in hepatic gene expression and the response to dietary carbohydrate manipulation in the zebrafish (Danio rerio). Comp Biochem Physiol Part D Genomics and Proteomics 3, 141-154.
Drew RE, Schwabl H, Wheeler PA & Thorgaard GH. (2007). Detection of QTL influencing cortisol levels in rainbow trout (Oncorhynchus mykiss). Aquaculture 272, S183–S194.
Brown KH, Drew RE, Weber LA & Thorgaard GH. (2006). Intraspecific variation in the rainbow trout mitochondrial DNA genome. Comp Biochem Physiol Part D Genomics and Proteomics 1, 219-226.
Landis ED, Palti Y, Dekoning J, Drew R, Phillips RB & Hansen JD. (2006). Identification and regulatory analysis of rainbow trout tapasin and tapasin-related genes. Immunogenetics 58, 56-69.
Phillips RB, Nichols KM, DeKoning JJ, Morasch MR, Keatley KA, Rexroad III C, Gahr SA, Danzmann RG, Drew RE & Thorgaard GH. (2006). Assignment of rainbow trout linkage groups to specific chromosomes. Genetics 174, 1661–1670.
Sundin K, Brown KH, Drew RE, Nichols KM, Wheeler PA & Thorgaard GH. (2005). Genetic analysis of a development rate QTL in backcrosses of clonal rainbow trout, Oncorhynchus mykiss. Aquaculture 247, 75-83.
Lucas MD, Drew RE, Wheeler PA, Verrell PA & Thorgaard GH. (2004). Behavioral differences among rainbow trout clonal lines. Behav Genet 34, 355-365.
Drew RE, Hallett JG, Aubry KB, Cullings KW, Koepf SM & Zielinksi WJ. (2003). Conservation genetics of the fisher (Martes pennanti) based on mitochondrial DNA sequencing. Mol Ecol 12, 51-62.
Nichols KM, Young WP, Danzmann RG, Robison BD, Rexroad C, Noakes M, Phillips RB, Bentzen P, Spies I, Knudsen K, Allendorf FW, Cunningham BM, Brunelli J, Zhang H, Ristow S, Drew R, Brown KH, Wheeler PA & Thorgaard GH. (2003). A consolidated linkage map for rainbow trout (Oncorhynchus mykiss). Anim Genet 34, 102-115.