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Genome-wide association study based on multiple imputation with low-depth sequencing data: application to biofuel traits in reed canarygrass

Author: Ramstein, G.P.
Author: Lipka, A.E.
Author: Fei Lu
Author: Costich, D.E
Author: Cherney, J.H.
Author: Buckler, E.S.
Author: Casler, M.D.
Year: 2015
ISSN: 2160-1836
URI: https://hdl.handle.net/10883/19722
Abstract: Genotyping by sequencing allows for large-scale genetic analyses in plant species with no reference genome, but sets the challenge of sound inference in presence of uncertain genotypes. We report an imputation-based genome-wide association study (GWAS) in reed canarygrass (Phalaris arundinacea L., Phalaris caesia Nees), a cool-season grass species with potential as a biofuel crop. Our study involved two linkage populations and an association panel of 590 reed canarygrass genotypes. Plants were assayed for up to 5228 single nucleotide polymorphism markers and 35 traits. The genotypic markers were derived from low-depth sequencing with 78% missing data on average. To soundly infer marker-trait associations, multiple imputation (MI) was used: several imputes of the marker data were generated to reflect imputation uncertainty and association tests were performed on marker effects across imputes. A total of nine significant markers were identified, three of which showed significant homology with the Brachypodium dystachion genome. Because no physical map of the reed canarygrass genome was available, imputation was conducted using classification trees. In general, MI showed good consistency with the complete-case analysis and adequate control over imputation uncertainty. A gain in significance of marker effects was achieved through MI, but only for rare cases when missing data were <45%. In addition to providing insight into the genetic basis of important traits in reed canarygrass, this study presents one of the first applications of MI to genome-wide analyses and provides useful guidelines for conducting GWAS based on genotyping-by-sequencing data.
Format: PDF
Language: English
Publisher: Genetics Society of America
Copyright: CIMMYT manages Intellectual Assets as International Public Goods. The user is free to download, print, store and share this work. In case you want to translate or create any other derivative work and share or distribute such translation/derivative work, please contact CIMMYT-Knowledge-Center@cgiar.org indicating the work you want to use and the kind of use you intend; CIMMYT will contact you with the suitable license for that purpose.
Type: Article
Place of Publication: United States
Pages: 891-909
Issue: 5
Volume: 5
DOI: 10.1534/g3.115.017533
Keywords: Genome-Wide Association Study
Keywords: Multiple Imputation
Keywords: Genotyping by Sequencing
Keywords: Phalaris SPP
Agrovoc: NUCLEOTIDE SEQUENCE
Agrovoc: CHROMOSOME MAPPING
Agrovoc: GRASSES
Agrovoc: GENETIC MARKERS
Agrovoc: BIOFUELS
Agrovoc: BIOENERGY
Journal: G3: Genes, Genomes, Genetics


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  • Maize
    Maize breeding, phytopathology, entomology, physiology, quality, and biotech

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