Abstract
Aim Grasslands have been pivotal in the development of herbivore breeding since the Neolithic and are still nowadays the most widespread agricultural land-use across Europe. However, it remains unclear whether the current large-scale genetic variation of plant species found in natural grasslands of Europe is the result of human activities or natural processes.
Location Europe.
Taxon Lolium perenne L (perennial ryegrass).
Methods We reconstructed the phylogeographic history of L. perenne, a dominant grassland species, using 481 natural populations including 11 populations from closely related taxa. We combined the Genotyping-by-Sequencing (GBS) and Pool-sequencing (Pool-seq) methods to obtain high-quality allele frequency calls of ~ 500 k SNP loci. We performed genetic structure analyses and demographic reconstructions based on the site frequency spectrum (SFS). We additionally used the same genotyping protocol to assess the genomic diversity of a set of 32 cultivars representative of the L. perenne cultivars widely used for forage purposes.
Results Expansion across Europe took place during the Würm glaciation (12-110 kya), a cooling period that decreased the dominance of trees in favour of grasses. Splits and admixtures in L. perenne fit historical sea level changes in the Mediterranean basin. The development of agriculture in Europe (7-3.5 kya), that caused an increase in the abundance of grasslands, did not have an effect on the demographic patterns of L. perenne. We found little differentiation between modern cultivars and certain natural variants. However, modern cultivars do not represent the wide genetic variation found in natural populations.
Main conclusions Demographic events in L. perenne can be explained by the changing climatic conditions during the Pleistocene. Natural populations maintain a wide genomic variability at continental scale that has been underused by recent breeding activities. This variability constitutes valuable standing genetic variation for future adaptation of grasslands to climate change, safeguarding the agricultural services they provide.
Acknowledgements
J.L. Blanco-Pastor has received the support of the EU in the framework of the Marie-Curie FP7 COFUND People Program, through the award of an AgreenSkills+ fellowship (under grant agreement n° 609398). This work was funded in the frame of the project GrassLandscape awarded by the 2014 FACCE-JPI ERA-NET+ call Climate Smart Agriculture. Funding was granted by the European Commission (EC grant agreement n° 618105), by the Agence Nationale de la Recherche (ANR) and the Institut National de la Recherche Agronomique (INRA – métaprogramme ACCAF) in France, the Biotechnology and Biological Sciences Research Council (BBSRC) in the United-Kingdom, the Bundesantalt für Landwirtschaft und Ernährung (BLE) in Germany.
The authors thank the curators from the genebanks which contributed perennial ryegrass seed samples for the needs of the project. Perennial ryegrass is one of the plant species covered under the Multilateral System of the International Treaty on Plant Genetic Resources for Food and Agriculture. All genetic materials used in this study were made available to the authors after signature of a Standard Material Transfer Agreement (SMTA) by the provider and the recipient. Implementation and signature of a SMTA provides compliance with the provisions of the Nagoya Protocol for parties wishing to provide and receive genetic material under the Multilateral System. The authors declare no conflict of interest.