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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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Published in: | Nature communications 2016-02, Vol.7 (1), p.10527-10527, Article 10527 |
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creator | Crowell, Samuel Korniliev, Pavel Falcão, Alexandre Ismail, Abdelbagi Gregorio, Glenn Mezey, Jason McCouch, Susan |
description | 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. |
doi_str_mv | 10.1038/ncomms10527 |
format | article |
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Panicle architecture is an important determinant of crop yield and a target of selection by plant breeders. Here, Crowell
et al.
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Panicle architecture is an important determinant of crop yield and a target of selection by plant breeders. Here, Crowell
et al.
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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.</abstract><cop>London</cop><pub>Nature Publishing Group UK</pub><pmid>26841834</pmid><doi>10.1038/ncomms10527</doi><tpages>1</tpages><orcidid>https://orcid.org/0000-0002-1961-3072</orcidid><oa>free_for_read</oa></addata></record> |
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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) |
title | Genome-wide association and high-resolution phenotyping link Oryza sativa panicle traits to numerous trait-specific QTL clusters |
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