Genetical genomics of inbreeding depression

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Goals, objectives and outcomes:******Inbreeding lowers fitness-related characters in many species of plants and animals, but can also be a source of novel variation. To understand the nature of genetic changes caused by inbreeding, we need models for the mode of action and the pathways of gene interaction. These models can be then used to retrospectively infer such actions and interactions using powerful genomic tools. ******“Genetical genomics” combines gene expression studies with genetic linkage analysis, and opens up an entirely new class of inferences about gene expression: the amount and direction of interaction between the component expressed genes underlying inbreeding depression. Conducting genetical genomics involves controlled crosses, growing up plant material for RNA extraction, barcoding and Illumina HiSeq sequencing or the like, and then statistical data analysis of gene expression either with established software or our own programs. ******To study the genetic architecture of inbreeding depression, we will use monkeyflower (Mimulus species). This genus has much variation of life history and mating system, and is emerging as a model system in plant evolutionary biology. We focus on four yellow monkeyflower species: outbreeding M. guttutus (representing the ancestral outbreeding archeotype), and the largely independently derived inbreeders M. micranthus, M. platycalyx and M. lacinatus. These species are intercrossible, yet conspicuously differ for mating system and floral traits related to inbreeding, making them ideal for quantitative genetic studies. ******In our proposed research, we will cross each of six pairings among the four taxa, then self-fertilize hybrid individuals to produce the generation for genetical genomic analysis (using activity 3 below). We will also (1) employ “QTL lineage mapping” to infer changes of gene expression are inferred along each branch of a phylogenetic lineage, (2) examine expression QTL evolution in extended comparisons involving species within the yellow monkeyflower species complex, and possibly comparisons with plant species, and (3) develop, evaluate, and use a new statistical genetic approach to infer causation in expression networks. The expected outcomes will the discovery of genomic mechanisms responsible for the expression and evolution of inbreeding depression.******Importance and benefits:******Inbreeding is not just a feature of monkeyflowers, but of most plant and animal species. Inbreeding has even been invoked to shape human evolution, with small populations fostering not only unique adaptations, but also the evolution of culture and technology. With regard to training of HQP, there is currently a shortage of scientists who can work across the boundary of evolution, genomics and bioinformatics. With my continued tutorage, a new generation of scientists will learn to apply genomics and bioinformatic data to questions in ecology and evolution.