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

生物学家长期以来一直对了解适应的机制基础感兴趣。表观遗传效应(如甲基化)可导致生物体特征的变异，即使在DNA序列信息完全没有差异的情况下也是如此。DNA的表观遗传变化可以由环境压力引起，并导致对自然选择的更快反应，但关于表观遗传机制如何在自然种群中发挥作用的信息很少。该项目将开发一种新的下一代测序技术，允许在没有参考基因组的非模式生物中测量不同环境条件下的遗传和表观遗传变异。这项技术将结合测序和亚硫酸氢盐测序来同时测量基因组中数万到数十万个片段的DNA序列和甲基化多态。作为原则的证明，这项技术将在费洛佩身上开发，这是一种高度入侵的多倍体植物，具有巨大而复杂的基因组。在这种渴望中开发的技术将在希尔斯伯勒县公立学校的教师和学生的研讨会上使用，以便有效地推广最新的创新基因组学方法，这些方法将适用于各种生物学研究，以及对个性化医学和转基因作物等社会问题的理解。在南佛罗里达大学，该项目将包括本科生的暑期研究和研究生培训。

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.