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Abstract

With advances in genotyping and cost-effective sequencing technologies, Genome-wide association studies (GWAS) have emerged as approaches to study the genetics of natural variation. GWAS are particularly useful when inbred lines are available (as once they are genotyped, these lines can be phenotyped multiple times) and also with the availability of automated image acquisition and analysis systems for rapid phenotyping. The objective of this thesis is to identify a variety of phenotypic traits from the inbred lines of the teleost fish Medaka (Oryzias latipes) which will then assist in the investigation of the genetic basis for such a variety. Medaka is chosen as the model organism because of the presence of still free living wild populations in Japan and East Asia and for the ability to generate new inbred strains from these wild fish. Moreover, Quantitative Trait Loci (QTL) analysis done so far on craniofacial traits in adult Medaka shows that a substantial genetic component underlies the variance seen between two inbred strains. In this study different southern and northern Japanese Medaka hatchlings at 10 days post fertilization (dpf) and 20 dpf were characterized. The focus is on the two elements that essentially define an organism: morphology and behavior. Gross morphological features were extracted and quantified using custom developed algorithms. In addition, behavioral patterns of the different inbred lines are studied since behavior provides a link and a perspective of how an organism relates to its environment. Specifically, locomotion, feeding, and prey capture behavior were analyzed and quantified. To our knowledge, this is the first characterization of prey capture behavior in Medaka. This behavior reveals interesting prey capture strategies and a comparison with a related teleost fish, the zebrafish, suggests that prey capture is not necessarily conserved. This combination of morphometric and behavioral features provides a large phenotype parameter set that will be used as a basis for genotyping to study the degree of polymorphism and to eventually establish a phenotype-genotype map for the inbred lines.