title: Genome-wide association mapping for phenotypic plasticity in rice.
abstract: Phenotypic plasticity of plants in response to environmental changes is important for adapting to changing climate. Less attention has been paid to exploring the advantages of phenotypic plasticity in resource-rich environments to enhance the productivity of agricultural crops. Here, we examined genetic variation for phenotypic plasticity in indica rice (Oryza sativa L.) across two diverse panels: (1) a Phenomics of Rice Adaptation and Yield (PRAY) population comprising 301 accessions; and (2) a Multi-parent Advanced Generation Inter-Cross (MAGIC) indica population comprising 151 accessions. Altered planting density was used as a proxy for elevated atmospheric CO2response. Low planting density significantly increased panicle weight per plant compared with normal density, and the magnitude of the increase ranged from 1.10 to 2.78 times among accessions for the PRAY population and from 1.05 to 2.45 times for the MAGIC population. Genome-wide-association studies validate three Environmental Responsiveness (ER) candidate alleles (qER1-3) that were associated with relative response of panicle weight to low density. Two of these alleles were tested in 13 genotypes to clarify their biomass responses during vegetative growth under elevated CO2in Japan. Our study provides evidence for polymorphisms that control rice phenotypic plasticity in environments that are rich in resources such as light and CO2.
authors.affiliation: Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, Iwate, 020-8550, Japan.
authors.forename: Shinji
authors.initials: S
authors.lastname: Kikuchi
authors.affiliation: Crop and Environmental Sciences Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, the Philippines.|Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA.
authors.forename: Raju
authors.initials: R
authors.lastname: Bheemanahalli
authors.affiliation: Crop and Environmental Sciences Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, the Philippines.|Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA.
authors.forename: Krishna S V
authors.identifier: http://orcid.org/0000-0002-1501-0960
authors.initials: KSV
authors.lastname: Jagadish
authors.affiliation: Agro-Environmental Research Division, NARO Tohoku Agricultural Research Center, Morioka, Iwate, 020-0198, Japan.
authors.forename: Etsushi
authors.initials: E
authors.lastname: Kumagai
authors.affiliation: Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, Iwate, 020-8550, Japan.
authors.forename: Yusuke
authors.initials: Y
authors.lastname: Masuya
authors.affiliation: Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, Iwate, 020-8550, Japan.
authors.forename: Eiki
authors.initials: E
authors.lastname: Kuroda
authors.affiliation: Crop and Environmental Sciences Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, the Philippines.
authors.forename: Chitra
authors.initials: C
authors.lastname: Raghavan
authors.affiliation: Crop and Environmental Sciences Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, the Philippines.|Département BIOS, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Umr AGAP, 34398, Montpellier, France.
authors.forename: Michael
authors.initials: M
authors.lastname: Dingkuhn
authors.affiliation: Iwate Biotechnology Research Center, 22-174-4, Narita, Kitakami, Iwate, 024-0003, Japan.
authors.forename: Akira
authors.initials: A
authors.lastname: Abe
authors.affiliation: Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, Iwate, 020-8550, Japan.
authors.forename: Hiroyuki
authors.identifier: http://orcid.org/0000-0002-7328-0483
authors.initials: H
authors.lastname: Shimono
mesh_terms: D018533:Biomass; D002245:Carbon Dioxide / Q000378:metabolism; D055106:Genome-Wide Association Study; D005838:Genotype; D006239:Haplotypes / Q000235:genetics; D012275:Oryza / Q000235:genetics*; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D040641:Quantitative Trait Loci / Q000235:genetics; D015203:Reproducibility of Results
chemical_list: D002245:Carbon Dioxide
keywords: climate change; elevated carbon dioxide; genome-wide association study; phenotypic plasticity; rice