Genome-wide association and high-resolution phenotyping link Oryza sativa panicle traits to numerous trait-specific QTL clusters

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 phen...

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Bibliographic Details
Published in:Nature communications 2016-02, Vol.7 (1), p.10527-10527, Article 10527
Main Authors: Crowell, Samuel, Korniliev, Pavel, Falcão, Alexandre, Ismail, Abdelbagi, Gregorio, Glenn, Mezey, Jason, McCouch, Susan
Format: Article
Language:English
Subjects:
631/208/205/2138
631/208/729/743
631/449/2491
Chromosome Mapping
Genome, Plant - genetics
Genome-Wide Association Study
Humanities and Social Sciences
Inflorescence - genetics
multidisciplinary
Oryza - genetics
Phenotype
Quantitative Trait Loci
Science
Science (multidisciplinary)
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Summary: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. Panicle architecture is an important determinant of crop yield and a target of selection by plant breeders. Here, Crowell et al. combine image-based phenotyping with high-density array-based genotyping to perform a genome-wide association study revealing a number of candidate genes linked to panicle variation in rice.
ISSN:2041-1723
2041-1723
DOI:10.1038/ncomms10527