High-Throughput Genome-Wide Genotyping To Optimize the Use of Natural Genetic Resources in the Grassland Species Perennial Ryegrass (Lolium perenne L.)

Thomas Keep, Jean Paul Sampoux, José Luis Blanco-Pastor, Klaus J. Dehmer, Matthew J. Hegarty, Thomas Ledauphin, Isabelle Litrico, Hilde Muylle, Isabel Roldán-Ruiz, Anna M. Roschanski, Tom Ruttink, Fabien Surault, Evelin Willner, Philippe Barre

Research output: Contribution to journalArticlepeer-review

18 Citations (SciVal)
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The natural genetic diversity of agricultural species is an essential genetic resource for breeding programs aiming to improve their ecosystem and production services. A large natural ecotype diversity is usually available for most grassland species. This could be used to recombine natural climatic adaptations and agronomic value to create improved populations of grassland species adapted to future regional climates. However describing natural genetic resources can be long and costly. Molecular markers may provide useful information to help this task. This opportunity was investigated for Lolium perenne L., using a set of 385 accessions from the natural diversity of this species collected right across Europe and provided by genebanks of several countries. For each of these populations, genotyping provided the allele frequencies of 189,781 SNP markers. GWAS were implemented for over 30 agronomic and/or putatively adaptive traits recorded in three climatically contrasted locations (France, Belgium, Germany). Significant associations were detected for hundreds of markers despite a strong confounding effect of the genetic background; most of them pertained to phenology traits. It is likely that genetic variability in these traits has had an important contribution to environmental adaptation and ecotype differentiation. Genomic prediction models calibrated using natural diversity were found to be highly effective to describe natural populations for almost all traits as well as commercial synthetic populations for some important traits such as disease resistance, spring growth or phenological traits. These results will certainly be valuable information to help the use of natural genetic resources of other species.

Original languageEnglish
Pages (from-to)3347-3364
Number of pages18
JournalG3 (Bethesda, Md.)
Issue number9
Early online date21 Jul 2020
Publication statusPublished - 01 Sept 2020


  • association study
  • forage species
  • genebank
  • genomic prediction
  • GenPred
  • GWAS
  • natural diversity
  • Shared data resources
  • Forage species
  • Prediction
  • Association study
  • Genebank
  • Natural diversity
  • Resources
  • Genomic
  • Shared data
  • Grassland
  • Lolium/genetics
  • Europe
  • Plant Breeding
  • Genotype
  • Genetic Variation
  • Ecosystem
  • Germany


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