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Canonical correlations reveal adaptive loci and phenotypic responses to climate in perennial ryegrass

(2021) MOLECULAR ECOLOGY RESOURCES. 21(3). p.849-870
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Abstract
Germplasm from perennial ryegrass (Lolium perenne L.) natural populations is useful for breeding because of its adaptation to a wide range of climates. Climate‐adaptive genes can be detected from associations between genotype, phenotype and climate but an integrated framework for the analysis of these three sources of information is lacking. We used two approaches to identify adaptive loci in perennial ryegrass and their effect on phenotypic traits. First, we combined Genome‐Environment Association (GEA) and GWAS analyses. Then, we implemented a new test based on a Canonical Correlation Analysis (CANCOR) to detect adaptive loci. Furthermore, we improved the previous perennial ryegrass gene set by de novo gene prediction and functional annotation of 39,967 genes. GEA‐GWAS revealed eight outlier loci associated with both environmental variables and phenotypic traits. CANCOR retrieved 633 outlier loci associated with two climatic gradients, characterized by cold‐dry winter versus mild‐wet winter and long rainy season versus long summer, and pointed out traits putatively conferring adaptation at the extremes of these gradients. Our CANCOR test also revealed the presence of both polygenic and oligogenic climatic adaptations. Our gene annotation revealed that 374 of the CANCOR outlier loci were positioned within or close to a gene. Co‐association networks of outlier loci revealed a potential utility of CANCOR for investigating the interaction of genes involved in polygenic adaptations. The CANCOR test provides an integrated framework to analyse adaptive genomic diversity and phenotypic responses to environmental selection pressures that could be used to facilitate the adaptation of plant species to climate change.
Keywords
Biotechnology, Genetics, Ecology, Evolution, Behavior and Systematics, adaptation, agriculture, climate change, ecological genetics, landscape genetics, quantitative genetics, GENOME-WIDE ASSOCIATION, QUANTITATIVE TRAIT LOCI, LOLIUM-PERENNE, R PACKAGE, FLOWERING TIME, LEAF-AREA, ADAPTATION, SELECTION, L., COLLECTION

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Citation

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MLA
Blanco‐Pastor, José Luis, et al. “Canonical Correlations Reveal Adaptive Loci and Phenotypic Responses to Climate in Perennial Ryegrass.” MOLECULAR ECOLOGY RESOURCES, vol. 21, no. 3, 2021, pp. 849–70, doi:10.1111/1755-0998.13289.
APA
Blanco‐Pastor, J. L., Barre, P., Keep, T., Ledauphin, T., Escobar‐Gutiérrez, A., Roschanski, A. M., … Sampoux, J. (2021). Canonical correlations reveal adaptive loci and phenotypic responses to climate in perennial ryegrass. MOLECULAR ECOLOGY RESOURCES, 21(3), 849–870. https://doi.org/10.1111/1755-0998.13289
Chicago author-date
Blanco‐Pastor, José Luis, Philippe Barre, Thomas Keep, Thomas Ledauphin, Abraham Escobar‐Gutiérrez, Anna Maria Roschanski, Evelyn Willner, et al. 2021. “Canonical Correlations Reveal Adaptive Loci and Phenotypic Responses to Climate in Perennial Ryegrass.” MOLECULAR ECOLOGY RESOURCES 21 (3): 849–70. https://doi.org/10.1111/1755-0998.13289.
Chicago author-date (all authors)
Blanco‐Pastor, José Luis, Philippe Barre, Thomas Keep, Thomas Ledauphin, Abraham Escobar‐Gutiérrez, Anna Maria Roschanski, Evelyn Willner, Klaus J. Dehmer, Matthew Hegarty, Hilde Muylle, Elisabeth Veeckman, Klaas Vandepoele, Tom Ruttink, Isabel Roldàn-Ruiz, Stéphanie Manel, and Jean‐Paul Sampoux. 2021. “Canonical Correlations Reveal Adaptive Loci and Phenotypic Responses to Climate in Perennial Ryegrass.” MOLECULAR ECOLOGY RESOURCES 21 (3): 849–870. doi:10.1111/1755-0998.13289.
Vancouver
1.
Blanco‐Pastor JL, Barre P, Keep T, Ledauphin T, Escobar‐Gutiérrez A, Roschanski AM, et al. Canonical correlations reveal adaptive loci and phenotypic responses to climate in perennial ryegrass. MOLECULAR ECOLOGY RESOURCES. 2021;21(3):849–70.
IEEE
[1]
J. L. Blanco‐Pastor et al., “Canonical correlations reveal adaptive loci and phenotypic responses to climate in perennial ryegrass,” MOLECULAR ECOLOGY RESOURCES, vol. 21, no. 3, pp. 849–870, 2021.
@article{8682265,
  abstract     = {Germplasm from perennial ryegrass (Lolium perenne L.) natural populations is useful for breeding because of its adaptation to a wide range of climates. Climate‐adaptive genes can be detected from associations between genotype, phenotype and climate but an integrated framework for the analysis of these three sources of information is lacking. We used two approaches to identify adaptive loci in perennial ryegrass and their effect on phenotypic traits. First, we combined Genome‐Environment Association (GEA) and GWAS analyses. Then, we implemented a new test based on a Canonical Correlation Analysis (CANCOR) to detect adaptive loci. Furthermore, we improved the previous perennial ryegrass gene set by de novo gene prediction and functional annotation of 39,967 genes. GEA‐GWAS revealed eight outlier loci associated with both environmental variables and phenotypic traits. CANCOR retrieved 633 outlier loci associated with two climatic gradients, characterized by cold‐dry winter versus mild‐wet winter and long rainy season versus long summer, and pointed out traits putatively conferring adaptation at the extremes of these gradients. Our CANCOR test also revealed the presence of both polygenic and oligogenic climatic adaptations. Our gene annotation revealed that 374 of the CANCOR outlier loci were positioned within or close to a gene. Co‐association networks of outlier loci revealed a potential utility of CANCOR for investigating the interaction of genes involved in polygenic adaptations. The CANCOR test provides an integrated framework to analyse adaptive genomic diversity and phenotypic responses to environmental selection pressures that could be used to facilitate the adaptation of plant species to climate change.},
  author       = {Blanco‐Pastor, José Luis and Barre, Philippe and Keep, Thomas and Ledauphin, Thomas and Escobar‐Gutiérrez, Abraham and Roschanski, Anna Maria and Willner, Evelyn and Dehmer, Klaus J. and Hegarty, Matthew and Muylle, Hilde and Veeckman, Elisabeth and Vandepoele, Klaas and Ruttink, Tom and Roldàn-Ruiz, Isabel and Manel, Stéphanie and Sampoux, Jean‐Paul},
  issn         = {1755-098X},
  journal      = {MOLECULAR ECOLOGY RESOURCES},
  keywords     = {Biotechnology,Genetics,Ecology,Evolution,Behavior and Systematics,adaptation,agriculture,climate change,ecological genetics,landscape genetics,quantitative genetics,GENOME-WIDE ASSOCIATION,QUANTITATIVE TRAIT LOCI,LOLIUM-PERENNE,R PACKAGE,FLOWERING TIME,LEAF-AREA,ADAPTATION,SELECTION,L.,COLLECTION},
  language     = {eng},
  number       = {3},
  pages        = {849--870},
  title        = {Canonical correlations reveal adaptive loci and phenotypic responses to climate in perennial ryegrass},
  url          = {http://dx.doi.org/10.1111/1755-0998.13289},
  volume       = {21},
  year         = {2021},
}

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