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

(2020) G3 Genes|Genomes|Genetics. 10(9). p.3347-3364
Author
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Abstract
<jats:title>Abstract</jats:title><jats:p>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.</jats:p>
Keywords
Genetics (clinical), Genetics, Molecular Biology

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MLA
Keep, Thomas, et al. “High-Throughput Genome-Wide Genotyping To Optimize the Use of Natural Genetic Resources in the Grassland Species Perennial Ryegrass (Lolium PerenneL.).” G3 Genes|Genomes|Genetics, vol. 10, no. 9, Oxford University Press (OUP), 2020, pp. 3347–64, doi:10.1534/g3.120.401491.
APA
Keep, T., Sampoux, J.-P., Blanco-Pastor, J. L., Dehmer, K. J., Hegarty, M. J., Ledauphin, T., … Barre, P. (2020). High-Throughput Genome-Wide Genotyping To Optimize the Use of Natural Genetic Resources in the Grassland Species Perennial Ryegrass (Lolium perenneL.). G3 Genes|Genomes|Genetics, 10(9), 3347–3364. https://doi.org/10.1534/g3.120.401491
Chicago author-date
Keep, Thomas, Jean-Paul Sampoux, José Luis Blanco-Pastor, Klaus J Dehmer, Matthew J Hegarty, Thomas Ledauphin, Isabelle Litrico, et al. 2020. “High-Throughput Genome-Wide Genotyping To Optimize the Use of Natural Genetic Resources in the Grassland Species Perennial Ryegrass (Lolium PerenneL.).” G3 Genes|Genomes|Genetics 10 (9): 3347–64. https://doi.org/10.1534/g3.120.401491.
Chicago author-date (all authors)
Keep, Thomas, 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, and Philippe Barre. 2020. “High-Throughput Genome-Wide Genotyping To Optimize the Use of Natural Genetic Resources in the Grassland Species Perennial Ryegrass (Lolium PerenneL.).” G3 Genes|Genomes|Genetics 10 (9): 3347–3364. doi:10.1534/g3.120.401491.
Vancouver
1.
Keep T, Sampoux J-P, Blanco-Pastor JL, Dehmer KJ, Hegarty MJ, Ledauphin T, et al. High-Throughput Genome-Wide Genotyping To Optimize the Use of Natural Genetic Resources in the Grassland Species Perennial Ryegrass (Lolium perenneL.). G3 Genes|Genomes|Genetics. 2020;10(9):3347–64.
IEEE
[1]
T. Keep et al., “High-Throughput Genome-Wide Genotyping To Optimize the Use of Natural Genetic Resources in the Grassland Species Perennial Ryegrass (Lolium perenneL.),” G3 Genes|Genomes|Genetics, vol. 10, no. 9, pp. 3347–3364, 2020.
@article{01HP3VAZFQE7QAPN1QQ2MHZB58,
  abstract     = {{<jats:title>Abstract</jats:title><jats:p>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.</jats:p>}},
  author       = {{Keep, Thomas and Sampoux, Jean-Paul and Blanco-Pastor, José Luis and Dehmer, Klaus J and Hegarty, Matthew J and Ledauphin, Thomas and Litrico, Isabelle and Muylle, Hilde and Roldán-Ruiz, Isabel and Roschanski, Anna M and Ruttink, Tom and Surault, Fabien and Willner, Evelin and Barre, Philippe}},
  issn         = {{2160-1836}},
  journal      = {{G3 Genes|Genomes|Genetics}},
  keywords     = {{Genetics (clinical),Genetics,Molecular Biology}},
  language     = {{eng}},
  number       = {{9}},
  pages        = {{3347--3364}},
  publisher    = {{Oxford University Press (OUP)}},
  title        = {{High-Throughput Genome-Wide Genotyping To Optimize the Use of Natural Genetic Resources in the Grassland Species Perennial Ryegrass (<i>Lolium perenne</i>L.)}},
  url          = {{http://doi.org/10.1534/g3.120.401491}},
  volume       = {{10}},
  year         = {{2020}},
}

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