Thematic Newsletter Genomics - May 2015

A year ago, ILVO started the “Genomics Platform”. More than 30 researchers from a variety of disciplines work together to make Next Generation DNA Sequencing (NGS) technologies and bioinformatics more accessible, with measurable results. In this thematic newsletter we present a selection of the research themes that have made a great leap from using genomics. From improved disease resistance in plants to biodegrading plastic waste in the sea, from antibiotic resistance to reducing methane emissions, from food safety to GMO detection, from chromosome studies to molecular markers for flower colour, plant architecture and cell wall digestibility, from invasive species to new strategies for breeding… What do all of these diverse studies have in common: genomics. Page through these research results and be surprised by the applications of genomics. Want to know more? Contact the coordinator or visit www.ilvogenomics.be.

New Research Projects

Detection with thousands of droplets. Searching for STEC shedding cattle using the Digital Droplet PCR.

E. coliCan STEC, a pathogenic gut bacterium in cattle that makes people ill, be detected and quantified using a new genome-based technique? With a new research study, ILVO aims to answer that question. If infected cattle within the herd can be effectively detected this research will contribute to a reduction in human infections after contact with infected cattle or contaminated food.

Searching mutations in a haystack. Development of computational tools for population genomics in perennial ryegrass.

Engels raaigrasGenetic variation leads to phenotypic variation. But how can we use the genetic code to predict which genetic variation is relevant for optimizing agricultural traits? By sequencing specific parts of the genome of hundreds of individuals, we can determine the genetic diversity that is present in a population and make predictions on the effect that naturally occurring mutations have on the development and agronomic performance of plants. In this way, genome analysis can help the selection of plants with the best genetic characteristics for growth, yield, quality, or optimal flowering based on their genome sequence.

Methane-belching cows: Determination of the influence of cow-specific factors on the composition of the methanogenic population in the rumen. 

koeThe methane production of lactating cows is largely influenced by diet composition and can thus be partly reduced by certain feed additives and mitigation strategies. This has already been extensively investigated in the recent decade. But to what extent is the methane production influenced by the cow itself? In a unique experiment, the rumen content of four cows was transferred between cows. This experiment allows us to study the influence of the host on the rumen microbial composition with Next-Generation Sequencing. This experiment will offer a more profound insight into the complex relation between host-microbiome-methane production. 

The American comb jelly in the North Sea: a temporary plague or a long-term problem? Population genomics of an invasive comb jelly species.

Amerikaanse ribkwalFor the past decade, the American comb jelly (Mnemiopsis leidyi) has been observed every summer in the North Sea. Is its presence the result of annual reintroduction or migration? Or are there permanent populations established in our region? Genetic techniques, and more specifically genetic fingerprinting based on thousands of markers scattered across the genome, is the method of choice to reconstruct the origin and distribution of the species.

Expertise in expression. Transcriptome sequencing in azalea

azaleaGenetic information is of importance for a plant only when genes are effectively activated, and are thus expressed. ILVO studies the expression of genes related to flower colour, branching, and resistance to broad mites in azalea. This fundamental knowledge will provide insights into how to steer biological processes and eventually lead to more targeted breeding via selecting parents with specific genetic traits.

Survival in a grass field: Population genomics of perennial ryegrass.
overleven in een grasveldWhich plants survive in our grasslands, and which plants disappear? Which factors determine this selection? Does this have an effect on the crop yield? These are the questions keeping ryegrass breeders awake at night. ILVO researchers use genetic research to search for an answer.

Detection of unauthorized GMOs in the food/feed chain using NGS technology
UGM?European legislation governs the introduction and control of all genetically modified organisms (GMOs) in order to guarantee food safety, food traceability and the consumer’s freedom of choice. The potential presence of GMOs in the food/feed chain is routinely assessed by the enforcement laboratories, who currently use qPCR as detection method. In a first step, screening methods are usually used to detect GMOs. In case of positive detection, genetically modified (GM) events are subsequently identified and quantified using event-specific real-time PCR methods. The number of authorized GMOs in the European food and feed chain is increasing, which makes their detection more complex, laborious and time-consuming. To improve the GMO routine analysis, the development of an approach allowing to generate all the data required to indubitably conclude on the GM event presence in any given sample in one experiment is becoming necessary. In this project, the relevance of using Next Generation Sequencing (NGS) technology to detect GMOs as well as its applicability in routine analysis will be investigated.

Metagenomics@HOME: peptidome-based functional analysis of metagenomics and metaproteomics data sets.
metagenomicsNew sequencing technologies make it possible to gather information about large amounts of genetic material. However, the interpretation of the massive collection of biological data requires novel analysis methods. ILVO and Ghent University (UGent) are collaborating on a completely automated “Unipept Metagenomics en Metaproteomics Analysis Pipeline”. This web application allows for efficient analysis and visualisation of metagenomics and metaproteomics data sets.

 

Rcent Results

Hidden dangers in pig feed. Quantifying the effect of cross contamination of antibiotics on the microbial community in pigs.
varkensEven very low concentrations of antibiotics in pig feed can disturb the intestinal microbial communities and stimulate resistance development. This was the conclusion of recent research on resistant bacteria and resistance transfer, conducted at ILVO in partnership with Ghent University and CODA. Appropriate measurements during feed production, transport and administration remain of utmost importance in the battle against resistance transfer.


Living in the Plastic Age. Colonisation of marine plastic debris by bacteria

plasticDo bacteria colonise plastic debris at sea? If so, what are the major factors that influence this colonisation? Using next-generation sequencing techniques, the bacterial colonisation on plastic and the surrounding environment was studied and compared. Ultimately, the aim is to detect bacteria that have genes that enable them to break down plastic. These tiny organisms could help to solve the plastic pollution in our oceans and seas.

Zooming in on rose chromosomes. Development of cytogenetic chromosome markers for rose using genome sequencing and FISH techniques.

chromosomen van roosGenetic techniques are becoming more and more important in plant breeding, including for roses. This is complicated by the small size of rose chromosomes, which are also difficult to distinguish from each other. ILVO attempts to distinguish individual chromosomes using specific markers based on repetitive DNA sequences.

Bacteria: beneficial and damaging species. Genetic properties of bacteria revealed by analysing their genomes.

goedzakken en slechterikkenBacteria have had a bad name because they can cause problems in plant and animal production and in the storage and consumption of food. But some of them have positive effects. Which bacteria do what and why? At ILVO, we investigate this by studying their complete genome, sometimes with surprising results.

Bacteria around the roots of strawberry and lettuce: influence of soil additives on the rhizosphere microbiome and the correlation with plant health

rhizosphere slaHow do soil treatments influence a plant and its associated bacteria? ILVO studied the effect of biochar addition on lettuce and strawberry plants. Using next-generation sequencing techniques, shifts in bacterial community composition at the level of the plant roots were analysed and correlated with plant growth and disease resistance.

 

Less lignin in grass, more protein in milk. An improved cell wall digestibility of perennial ryegrass using marker-assisted breeding.

grasHow can more energy be released from ryegrass so the cow can convert grass protein into milk protein more efficiently? This research question from the feed industry is answered from an unexpected angle, namely from DNA research in the context of breeding.