CONSTRUCTION OF A HIGH-RESOLUTION GENETIC MAP FOR RAINBOW TROUT USING GYNOGENETICALLY PRODUCED RECOMBINANT PROGENY AND RESTRICTION-SITE ASSOCIATED DNA (RAD) SEQUENCING
Lucydalila Cedillo, Sean O'Rourke, Ismail Saglam, Michael Miller.
University of California, Davis, Davis, CA.
The rainbow trout (Oncorhynchus mykiss) is an important species in aquaculture, sport fishing, and biomedical research. Despite widespread interest in studying rainbow trout, the current genome assembly is mostly composed of contiguous sequences and scaffolds with no definitive order. Genetic maps have been produced to infer the order of the genome. However, they are currently limited due to the presence of low recombination rates in progeny derived from male meiosis or a low density of genetic markers used for mapping. We hypothesized that a combination of gynogenetically produced recombinant progeny, which represent recombination events derived from female meiosis, and high-density genotyping methods will produce an improved genetic map that will greatly enhance the current state of the reference genome. To this end, we produced 635 recombinant progeny via gynogenesis, and used next generation sequencing of restriction-site associated DNA tags to discover and genotype approximately 40,000 single nucleotide polymorphisms, and constructed a high-resolution genetic map for rainbow trout. Furthermore, we mapped quantitative trait loci (QTL) to investigate chromosomal regions of the genome that are associated with phenotypes such as length, weight, and number of parr marks. The linkage and QTL maps constructed here provide critical genetic resources that can be applied to future conservation, aquaculture, and biomedical research.