Category Archives: Genomics

Nuclear microsatellite (nSSR) development for diploid annual mercury

Over 3,000 microsatellite sequences have been made available for marker development by Katie Ridou, the bioinformatician responsible of Mercurialis genome assembly. These sequences include only microsatellite regions with enough flanking sequence to design 20-bp PCR primers. Jonathan El Assad is using standard methods to PCR-test several primer pairs in a diverse panel of diploid Mercurialis annua covering its full range. The target is to develop a set of about 20 microsatellites that could be used in 2-3 multiplexes. This tool would be very useful to increase our understanding of Mercurialis annua demographic history and to evaluate the levels of inbreeding in current experimental evolution and quantitative genetics experiments.

ERA-CAPS project submitted

A new collaborative proposal has been submitted to CAPS-ERANET under the title ‘Molecular adaptation to biotic and abiotic stressors in the context of range expansion and rapid climate change’. This project is participated by most of the Mercurialis community, including:

University of Lausanne (DEE and DBMV Departments), Lausanne – Switzerland
National Institute for Agricultural and Food Research and Technology (INIA), Madrid – Spain
Centre for Ecological Research (CREAF-UAB), Barcelona – Spain
Université Catholique de Louvain (UCL), Louvain-la-Neuve – Belgium
Heidelberg University (COS-HD), Heidelberg – Germany
Institute of Soil Science and Plant Cultivation – State Research Institute (IUNG), Pulawy – Poland
Tel Aviv University (TAU), Tel Aviv – Israel
National Research Council (CNR), Firenze – Italy
Université Montpellier 2 (ISEM-UM2), Montpellier – France
Université Lille 1 (GEPV-Lille), Lille – France

The project summary follows:

Plants that have expanded their geographic ranges tend to show lower genetic diversity at their new range margins, and thus may have lost their adaptive potential as a result of the repeated genetic bottlenecks that occur during colonisation. In outcrossing species, however, range-edge populations might maintain sufficient genetic variation for continued responses to selection, either because colonisation bottlenecks are less severe for outcrossers, or because outcrossing facilitates continued gene flow into range-edge populations from elsewhere. We propose to test this hypothesis by studying the impact of range expansions and natural selection on the genome and patterns of gene expression of the European plant Mercurialis annua, a wind-pollinated dioecious (and thus outcrossing) annual plant that currently occupies a wide environmental range in Europe following range expansion from an eastern Mediterranean refugium. To test recent theory about how local adaptation interacts with range shifts at the genomic level, we will carry out genome and transcriptome analysis of natural and evolved genotypes in a set of common gardens established along range-expansion routes and environmental gradients across Europe and the eastern Mediterranean Basin. Specifically, we will evaluate the consequences of range expansions on the accumulation of deleterious vs. beneficial mutations in the context of genes and gene networks associated with responses to biotic and abiotic stressors in regions with contrasting climates. We will also estimate the potential for evolution in range-edge populations and their level of genomic and transcriptomic differentiation from ancestral populations. We will relate our results to phenotypic differentiation and fitness, addressing the question as to whether adaptive molecular variants are typically new mutations or arise from standing genetic variation. Finally, our project will assess the merit of active transplantation of genotypes among different geographical regions (i.e., genetic admixture) to facilitate new and rapid adaptive evolutionary responses to extremes in climatic tolerance. This will allow an evaluation of the effects on plant performance of potential heterosis and outbreeding depression (i.e., positive and negative genetic interactions) brought about by such admixture. Our project will establish at a genomic and transcriptomic level how plant populations respond to challenges from abiotic and biotic stressors brought about by climate change in the European context.

Let’s cross fingers!

Full exome capture experiment

A new full-exome capture assay (ca. 48 Mbp of sequence) has been designed and will be used for sequencing of 48 Mercurialis accessions in the framework of a Senior Marie Curie Project by Dr. Santiago C. González-Martínez. This assay covers the over one hundred thousand exons found in the M. annua diploid genome and were identified using state-of-the-art bioinformatics by postdoc Kate Ridou. The assay is also intended to sequence sex-linked regions and random non-coding portions of the Mercurialis genome. The 48 accessions that will be sequenced with this assay have been collected from both ancestral and colonization-front of the species (see map below). Deep sequencing of these materials would allow to determine the genetic make-up of colonization-front populations in diploid Mercurialis annua.


The 48 accessions included in the M. annua gene capture experiment

Pre-proposal submitted to the ERA-CAPS 2nd call

Under the title ‘Molecular adaptation in range expansions: predicting fitness of future plant communities’, members of the Mercurialis Genomics Network has just submitted a pre-proposal for the current call for projects of the ERA-CAPS (an ERA-NET from the seventh framework EU program for Coordinating Action in Plant Sciences). ERA-CAPS main objective is to promote sustainable collaboration in plant sciences through coordinating and funding excellent transnational research, including food security, adaptation to climate change, and biotic and abiotic stress response. The specific objectives of the project are to:

1) Evaluate the consequences of range expansions on the accumulation of deleterious vs. beneficial mutations, and thus on the process of local adaptation to new biotic and abiotic stress (e.g. herbivory, drought), in a gene network context.

2) Estimate the potential for evolution in colonization-front populations, their level of genomic and transcriptomic differentiation from ancestral populations, and the origin of adaptive molecular variants (new mutations vs. standing genetic variation), and relate this to phenotypic differentiation and phenotypic innovations.

3) Assess the merit of assisted migration (increase of genetic variation vs. outbreeding depression) to allow new adaptive responses in populations facing extremes in their climatic tolerance and evaluate, through environmental modelling, the fate of standing populations confronted with increasing pressure due to climate change.

These goals will be achieved by a combination of experimental evolution, genomic and quantitative genetic approaches using Mercurialis annua as model organism.