Deep diving in the genomic diversity of (meta)populations (GA-GENOMICS)

GA-Genomics is one of the multidisciplinary 'coordinated actions' in which ILVO invests a substantial research budget in a 'big challenge' that is described in the ILVO2020 programme. The goal is to build an ILVO-wide expertise platform (the Genomics Platform) on Next Generation Sequencing (NGS) technologies to support genomics research. These DNA sequencing technologies make it possible to genetically characterise organisms and populations with an unprecedented resolution, speed and completeness. Several very diverse and agronomically important populations were chosen as case studies. Examples are populations of perennial ryegrass (relevant to breeding), comb jelly (in the context of containing an invasive species), and various micro-organisms (in various contexts: soil optimisation, animal production with a lower ecological footprint or biodegradation of microplastics). The general research questions are: What is the genetic diversity in populations? How does the genetic constitution change under the influence of natural or artificial selection and/or adaptation? Which mechanisms are involved? How can the genetic diversity be exploited to optimise production systems? How do bacterial metapopulations react to different environmental circumstances? Which interesting functional properties do these populations have?

The research team of more than 20 researchers and 4 PhD students will implement a technological platform with generic genomics tools, including Next Generation Sequencing (NGS). The selected case studies are embedded in the current research programme at ILVO:

1) Design and testing of an innovative conceptual breeding approach in perennial ryegrass

2) Analysis of the population dynamics of comb jelly populations from the North Sea

3) The effect of soil treatments on the rhizosphere microbiome and the influence on plant health

4) Characterisation of the microplastics microbiome in relation to biodegradation

5) The effect of interventions in feeding on the microbiome of rumen of cattle and the influence on methane emissions

6) Antibiotics resistance development in the gut microbiome of weaned piglets

7) The development of high-throughput GMO detection methods

In the plant and animal populations under study, we want to develop methods to identify drivers of selection and/or adaptation and use these to make hypotheses on the relationship between candidate genes and physiological processes. In bacterial metapopulations we want to link observed taxonomical shifts with environmental factors or treatments. We will make an overview of 'all' gene functions present in the (meta)genome and we will investigate relevant biological properties of a microbial community.

In agriculture and fisheries, research on population dynamics is important for the development of sustainable production systems. Examples are plant breeding, containment of invasive species, microbial communities that promote plant health, animal production with a lower ecological footprint, or microbial biodegradation of pollutants. The knowledge gained through population genetics studies can be exploited for the development of selection or management strategies to steer and optimise the composition of the (meta)population. Newly gained expertise on the generation and data analysis of NGS data will benefit current and future research at ILVO. A critical level of know-how will be developed in Next Generation Sequencing and genome-wide DNA analyses. The establishment of the Genomics Platform will guarantee that ILVO becomes an attractive partner in domains where high-throughput DNA sequencing technologies are being implemented.