Multiple Maize Reference Genomes Impact the Identification of Variants by Genome-Wide Association Study in a Diverse Inbred Panel
Abstract
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 themore »
- Authors:
-
- 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)
- Publication Date:
- Research Org.:
- Univ. of Wisconsin, Madison, WI (United States); Univ. of California, Oakland, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC)
- OSTI Identifier:
- 1609251
- Grant/Contract Number:
- FC02-07ER64494; AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- The Plant Genome
- Additional Journal Information:
- Journal Volume: 12; Journal Issue: 2; Journal ID: ISSN 1940-3372
- Publisher:
- Alliance of Crop, Soil, and Environmental Science Societies
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; Plant Sciences; Genetics & Heredity
Citation Formats
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, and de Leon, Natalia. Multiple Maize Reference Genomes Impact the Identification of Variants by Genome-Wide Association Study in a Diverse Inbred Panel. United States: N. p., 2019.
Web. doi:10.3835/plantgenome2018.09.0069.
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. Multiple Maize Reference Genomes Impact the Identification of Variants by Genome-Wide Association Study in a Diverse Inbred Panel. United States. https://doi.org/10.3835/plantgenome2018.09.0069
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, and de Leon, Natalia. Sat .
"Multiple Maize Reference Genomes Impact the Identification of Variants by Genome-Wide Association Study in a Diverse Inbred Panel". United States. https://doi.org/10.3835/plantgenome2018.09.0069. https://www.osti.gov/servlets/purl/1609251.
@article{osti_1609251,
title = {Multiple Maize Reference Genomes Impact the Identification of Variants by Genome-Wide Association Study in a Diverse Inbred Panel},
author = {Gage, Joseph L. and Vaillancourt, Brieanne and Hamilton, John P. and Manrique-Carpintero, Norma C. and Gustafson, Timothy J. and Barry, Kerrie and Lipzen, Anna and Tracy, William F. and Mikel, Mark A. and Kaeppler, Shawn M. and Buell, C. Robin and de Leon, Natalia},
abstractNote = {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.},
doi = {10.3835/plantgenome2018.09.0069},
journal = {The Plant Genome},
number = 2,
volume = 12,
place = {United States},
year = {Sat Jun 01 00:00:00 EDT 2019},
month = {Sat Jun 01 00:00:00 EDT 2019}
}
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Data from: Multiple maize reference genomes impact the identification of variants by GWAS in a diverse inbred panel
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Works referencing / citing this record:
Data from: Multiple maize reference genomes impact the identification of variants by GWAS in a diverse inbred panel
dataset, January 2019
- Gage, Joseph L.; Vaillancourt, Brieanne; Hamilton, John P.
- Dryad
Data from: Multiple maize reference genomes impact the identification of variants by GWAS in a diverse inbred panel
dataset, January 2019
- Gage, Joseph L.; Vaillancourt, Brieanne; Hamilton, John P.
- Dryad