Multiple Maize Reference Genomes Impact the Identification of Variants by Genome-Wide Association Study in a Diverse Inbred Panel

Gage, Joseph L.; Vaillancourt, Brieanne; Hamilton, John P.; Manrique-Carpintero, Norma C.; Gustafson, Timothy J.; Barry, Kerrie; Lipzen, Anna; Tracy, William F.; Mikel, Mark A.; Kaeppler, Shawn M.; Buell, C. Robin; de Leon, Natalia

doi:10.3835/plantgenome2018.09.0069

Title: Multiple Maize Reference Genomes Impact the Identification of Variants by Genome-Wide Association Study in a Diverse Inbred Panel

Journal Article · 01 June 2019 · The Plant Genome

DOI: https://doi.org/10.3835/plantgenome2018.09.0069 · OSTI ID:1609251

Gage, Joseph L. ^[1]; Vaillancourt, Brieanne ^[2]; Hamilton, John P. ^[2]; Manrique-Carpintero, Norma C. ^[2]; Gustafson, Timothy J. ^[3]; Barry, Kerrie ^[4]; Lipzen, Anna ^[4]; Tracy, William F. ^[1]; Mikel, Mark A. ^[5]; Kaeppler, Shawn M. ^[1]; Buell, C. Robin ^[2]; de Leon, Natalia ^[1]

Univ. of Wisconsin, Madison, WI (United States)
Michigan State Univ., East Lansing, MI (United States)
Monsanto Company, DeForest, WI (United States)
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Univ. of Illinois at Urbana, IL (United States)

Use of a single reference genome for genome-wide association studies (GWAS) limits the gene space represented to that of a single accession. This limitation can complicate identification and characterization of genes located within presence–absence variations (PAVs). In this study, we present the draft de novo genome assembly of ‘PHJ89’, an ‘Oh43’-type inbred line of maize (Zea mays L.). From three separate reference genome assemblies (‘B73’, ‘PH207’, and PHJ89) that represent the predominant germplasm groups of maize, we generated three separate whole-seedling gene expression profiles and single nucleotide polymorphism (SNP) matrices from a panel of 942 diverse inbred lines. We identified 34,447 (B73), 39,672 (PH207), and 37,436 (PHJ89) transcripts that are not present in the respective reference genome assemblies. Genome-wide association studies were conducted in the 942 inbred panel with both the SNP and expression data values to map Sugarcane mosaic virus (SCMV) resistance. Highlighting the impact of alternative reference genomes in gene discovery, the GWAS results for SCMV resistance with expression values as a surrogate measure of PAV resulted in robust detection of the physical location of a known resistance gene when the B73 reference that contains the gene was used, but not the PH207 reference. This study provides the valuable resource of the Oh43-type PHJ89 genome assembly as well as SNP and expression data for 942 individuals generated from three different reference genomes.

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Research Organization:: Univ. of Wisconsin, Madison, WI (United States); Univ. of California, Oakland, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: FC02-07ER64494; AC02-05CH11231

OSTI ID:: 1609251

Journal Information:: The Plant Genome, Vol. 12, Issue 2; ISSN 1940-3372

Publisher:: Alliance of Crop, Soil, and Environmental Science SocietiesCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 22 works

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Data from: Multiple maize reference genomes impact the identification of variants by GWAS in a diverse inbred panel Gage, Joseph L.; Vaillancourt, Brieanne; Hamilton, John P. Dryad https://doi.org/10.5061/dryad.dk22g4h	dataset	January 2019
Data from: Multiple maize reference genomes impact the identification of variants by GWAS in a diverse inbred panel Gage, Joseph L.; Vaillancourt, Brieanne; Hamilton, John P. Dryad https://doi.org/10.5061/dryad.dk22g4h	dataset	January 2019

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Title: Multiple Maize Reference Genomes Impact the Identification of Variants by Genome-Wide Association Study in a Diverse Inbred Panel

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