EAGER: Developing epigenetic genotyping-by-sequencing in the non-model invasive Japanese knotweed

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Biologists have long been interested in understanding the mechanistic basis of adaptation. Epigenetic effects (e.g., methylation) can contribute to variation in the traits of organisms even in the complete absence of differences in DNA sequence information. Epigenetic changes in DNA can be induced by environmental stress and lead to a more rapid response to natural selection but there is little information on how epigenetic mechanisms function in natural populations. This project will develop a novel next generation sequencing technique allowing for the measurement of both genetic and epigenetic variation under different environmental conditions in non-model organisms with no reference genome. The technique will combine Genotyping-By-Sequencing and bisulfite sequencing to simultaneously measure DNA sequence and methylation polymorphisms at tens to hundreds of thousands of fragments across the genome. As a proof of principle, the technique will be developed in Fallopia japonica, a highly invasive polyploid plant with a large and complex genome.The techniques developed in this EAGER will be used in workshops with Hillsborough County Public School teachers and students to allow for effective outreach of the latest in innovative genomics approaches that will be applicable to a wide variety of biological research as well as understanding of social issues like personalized medicine, and genetically modified crops. At the University of South Florida the project will include summer research for undergraduates, and graduate student training.