Ecogenomics

Description

The field of ecological genomics strives to uncover the genetic and molecular mechanisms influencing responses and adaptations of organisms to their environment. Achieving this aim requires insight in evolution and selection pressure and how that results in natural variation. Using this natural variation to study mechanisms requires a good understanding of both ecologically important phenotypes and species with a well-developed genomic tool-kit. Molecular biological and genomic tools have primarily been developed for model organisms (such as yeast and Arabidopsis) representing a narrow spectrum of phenotypes, whereas many organisms that are the focus of ecological research have had limited genomic resources devoted to them. In this course, we will focus on the ways in which ecogenomics unites genomic and ecological approaches, which are: (1) to explore the natural variation found within model or crop species, (2) to analyze close relatives with a broader range of phenotypes (e.g. comparative genomics ), and (3) to generate new genomic resources for the species of interest . We will explore the underlying principles of genomics and how they are being applied for each of these three approaches. We will specifically focus on ecogenomics studies of abiotic stress responses. Specific approaches that will be discussed and demonstrated include: genetic mapping, expression analysis (transcriptomics), phenotyping (metabolomics, microbiome analysis, etc.), gene candidate verification. Analysis tools that will be studied “hands-on” will include: the use of genomic databases and tools, quantitative trait loci (QTL) analysis, physiological experiments and genome-wide association studies. Objectives: Explain the strategy of Ecogenomics in answering biological questions Explain the principles of and difference between association mapping (GWAS) and mapping in biparental populations (QTL mapping) Explain the principle of genomics, transcriptomics, metabolomics, microbiome analysis Discuss the principles of how organisms can adapt or respond to their environment Translate knowledge on genetics and omics into ecological insight or breeding strategies Use online genomics resources Carry out an ecogenomics research project Analyse the results of a Genome Wide Association Study Interpret and present the experimental results