Evolutionary Applications in Agriculture: Evolutionary Concepts for the management of Agro-Ecosystems

Modern agro-ecosystem management must resolve the potentially conflicting objectives of short-term, intensive production and long-term sustainability whilst simultaneously reducing negative environmental impacts. This module aims at providing students with the key theoretical background elements needed to comprehend and assess the agro-ecosystem within an evolutionary framework.
Relevant evolutionary concepts will be used to shed light on processes such as: domestication and its impact on cultivated plants; adaptive potential to biotic or abiotic stresses; identification of candidate genes for adaptation; community dynamics influencing host/pathogen, plant/microbiome or arthropod-related interactions; the spread of invasive species. To achieve this goal, students will be introduced to the essential theoretical background from population genetics, molecular evolution and phylogeny, as well as community dynamics and interactions.
First week: Genetic resources in agriculture and conservation biology (molecular diversity): Characterizing genetic/genomic diversity via high-throughput molecular methods, Understanding evolutionary processes shaping allelic distribution, Quantifying molecular diversity, Conducting taxon identification and phylogenetics analyses for diagnostics and classification
Second week: Molecular breeding, dynamics of adaptation, candidate gene identification (footprints of selection): Establishing a null hypothesis to detect selection for adaptation to biotic and abiotic conditions, Detecting selection at the genome level for adaptation to biotic and abiotic conditions
Third week: Domestication history, epidemiology, emergence and spreaging of resistances: Understanding how molecular diversity is shaped by organism reproductive traits, Deciphering the history of populations at different time and space scales, Retracing phylogeography and geographical expansion to understand the past and predict the future
Fourth week: Community evolutionary dynamics (interactions): Understanding co-evolution and how it can be tested, Knowing the importance of soil microbiome and how metagenomics allows to characterize it, Understanding that the plant level is not the sole relevant level
Keywords: molecular diversity, evolution, selection footprint, co-evolution, barcoding, microbiome