Detection of locally adapted genomic regions in wild rice (Oryza rufipogon) using environmental association analysis
Detection of locally adapted genomic regions in wild rice (Oryza rufipogon) using environmental association analysis
Oryza rufipogon is the wild progenitor of cultivated rice Oryza sativa and exhibits high levels of genetic diversity across its distribution, making it a useful resource for the identification of abiotic stress-tolerant varieties and genes that could limit future climate-changed-induced yield losses. To investigate local adaptation in O. rufipogon, we analyzed single nucleotide polymorphism (SNP) data from a panel of 286 samples located across a diverse range of climates. Environmental association analysis (EAA), a genome-wide association study (GWAS)-based method, was used and revealed 15 regions of the genome significantly associated with various climate factors. Genes within these environmentally associated regions have putative functions in abiotic stress response, phytohormone signaling, and the control of flowering time. This provides an insight into potential local adaptation in O. rufipogon and reveals possible locally adaptive genes that may provide opportunities for breeding novel rice varieties with climate change-resilient phenotypes.
Genome, Plant, Genome-Wide Association Study, Genomics/methods, Oryza/genetics, Plant Breeding, Plant Genetics and Genomics, wild rice, climate, Oryza rufipogon, abiotic stress, local adaptation, domestication, genomics, environmental association analysis
Bedford, James A.
c8db1d0c-7b73-42b8-9e22-e96cd8140cca
Carine, Mark
eeaed5aa-bc4b-43ec-a667-b6c45e3217ed
Chapman, Mark A.
8bac4a92-bfa7-4c3c-af29-9af852ef6383
October 2023
Bedford, James A.
c8db1d0c-7b73-42b8-9e22-e96cd8140cca
Carine, Mark
eeaed5aa-bc4b-43ec-a667-b6c45e3217ed
Chapman, Mark A.
8bac4a92-bfa7-4c3c-af29-9af852ef6383
Bedford, James A., Carine, Mark and Chapman, Mark A.
(2023)
Detection of locally adapted genomic regions in wild rice (Oryza rufipogon) using environmental association analysis.
G3: Genes, Genomes, Genetics, 13 (10), [jkad194].
(doi:10.1093/g3journal/jkad194).
Abstract
Oryza rufipogon is the wild progenitor of cultivated rice Oryza sativa and exhibits high levels of genetic diversity across its distribution, making it a useful resource for the identification of abiotic stress-tolerant varieties and genes that could limit future climate-changed-induced yield losses. To investigate local adaptation in O. rufipogon, we analyzed single nucleotide polymorphism (SNP) data from a panel of 286 samples located across a diverse range of climates. Environmental association analysis (EAA), a genome-wide association study (GWAS)-based method, was used and revealed 15 regions of the genome significantly associated with various climate factors. Genes within these environmentally associated regions have putative functions in abiotic stress response, phytohormone signaling, and the control of flowering time. This provides an insight into potential local adaptation in O. rufipogon and reveals possible locally adaptive genes that may provide opportunities for breeding novel rice varieties with climate change-resilient phenotypes.
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Accepted/In Press date: 17 August 2023
e-pub ahead of print date: 24 August 2023
Published date: October 2023
Additional Information:
Funding Information:
This work was supported by the Natural Environmental Research Council for the INSPIRE DTP at the University of Southampton (grant number NE/S007210/1).
Publisher Copyright:
© The Author(s) 2023.
Keywords:
Genome, Plant, Genome-Wide Association Study, Genomics/methods, Oryza/genetics, Plant Breeding, Plant Genetics and Genomics, wild rice, climate, Oryza rufipogon, abiotic stress, local adaptation, domestication, genomics, environmental association analysis
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Local EPrints ID: 483158
URI: http://eprints.soton.ac.uk/id/eprint/483158
PURE UUID: fdf2682d-52ab-4ff6-ac98-ebdc1b1426a7
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Date deposited: 25 Oct 2023 17:06
Last modified: 18 Mar 2024 03:24
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Author:
Mark Carine
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