title: Genome-wide association and high-resolution phenotyping link Oryza sativa panicle traits to numerous trait-specific QTL clusters.
abstract: Rice panicle architecture is a key target of selection when breeding for yield and grain quality. However, panicle phenotypes are difficult to measure and susceptible to confounding during genetic mapping due to correlation with flowering and subpopulation structure. Here we quantify 49 panicle phenotypes in 242 tropical rice accessions with the imaging platform PANorama. Using flowering as a covariate, we conduct a genome-wide association study (GWAS), detect numerous subpopulation-specific associations, and dissect multi-trait peaks using panicle phenotype covariates. Ten candidate genes in pathways known to regulate plant architecture fall under GWAS peaks, half of which overlap with quantitative trait loci identified in an experimental population. This is the first study to assess inflorescence phenotypes of field-grown material using a high-resolution phenotyping platform. Herein, we establish a panicle morphocline for domesticated rice, propose a genetic model underlying complex panicle traits, and demonstrate subtle links between panicle size and yield performance.
authors: Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA.
authors: Samuel
authors: S
authors: Crowell
authors: Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14853, USA.
authors: Pavel
authors: P
authors: Korniliev
authors: Department of Information Systems, Institute of Computing, University of Campinas, São Paulo CEP 13083-852, Brazil.
authors: Alexandre
authors: A
authors: Falcão
authors: Crop and Environmental Sciences Division, International Rice Research Institute, DAPO Box 7777, Metro Manila 1301, Philippines.
authors: Abdelbagi
authors: http://orcid.org/0000-0002-1961-3072
authors: A
authors: Ismail
authors: Plant Breeding, Genetics and Biotechnology Division, International Rice Research Insititute, Los Baños, Laguna 4031, Philippines.
authors: Glenn
authors: G
authors: Gregorio
authors: Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14853, USA.
authors: Jason
authors: J
authors: Mezey
authors: Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA.|Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14853, USA.|Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, 162 Emerson Hall, Ithaca, New York 14853, USA.
authors: Susan
authors: S
authors: McCouch
mesh_terms: D002874:Chromosome Mapping; D018745:Genome, Plant / Q000235:genetics*; D055106:Genome-Wide Association Study; D056626:Inflorescence / Q000235:genetics*; D012275:Oryza / Q000235:genetics*; D010641:Phenotype; D040641:Quantitative Trait Loci