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.; 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:10.5061/dryad.dk22g4h

Title: Data from: Multiple maize reference genomes impact the identification of variants by GWAS in a diverse inbred panel

Dataset
Other Related Research

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. Using 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 profile 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 assembly. GWAS was conducted in the 942 inbred panel using both the SNP and expression data values to map sugarcane mosaic virus (SCMV) resistance. Highlighting the impact of alternative reference genomes in gene discovery, GWAS results for SCMV resistance using expression values as a surrogate measure of PAV resulted in robust detection of the physical location of a known resistance gene when using the B73 reference that contains the gene, but not when using the PH207 reference. This study provides the valuable resource of the Oh43-type PHJ89 genomemore »« less

Authors:

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

Univ. of Wisconsin, Madison, WI (United States); OSTI
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 Wisconsin, Madison, WI (United States)
Univ. of Illinois at Urbana-Champaign, IL (United States)

Publication Date:: Wed Feb 13 04:00:00 UTC 2019

DOE Contract Number:: FC02-07ER64494

Research Org.:: Great Lakes Bioenergy Research Center, Madison, WI (United States); Univ. of Wisconsin, Madison, WI (United States)

Sponsoring Org.:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Subject:: 59 BASIC BIOLOGICAL SCIENCES

OSTI Identifier:: 1874035

DOI:: https://doi.org/10.5061/dryad.dk22g4h

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. Data from: Multiple maize reference genomes impact the identification of variants by GWAS in a diverse inbred panel.  United States: N. p., 2019. 
        Web.  doi:10.5061/dryad.dk22g4h.

Copy to clipboard


                    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. Data from: Multiple maize reference genomes impact the identification of variants by GWAS in a diverse inbred panel.  United States.  doi:https://doi.org/10.5061/dryad.dk22g4h

Copy to clipboard


                    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. 2019.  
"Data from: Multiple maize reference genomes impact the identification of variants by GWAS in a diverse inbred panel".  United States.  doi:https://doi.org/10.5061/dryad.dk22g4h.  https://www.osti.gov/servlets/purl/1874035. Pub date:Wed Feb 13 04:00:00 UTC 2019

Copy to clipboard


                    
@article{osti_1874035,

  title        = {Data from: Multiple maize reference genomes impact the identification of variants by GWAS 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. Using 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 profile 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 assembly. GWAS was conducted in the 942 inbred panel using both the SNP and expression data values to map sugarcane mosaic virus (SCMV) resistance. Highlighting the impact of alternative reference genomes in gene discovery, GWAS results for SCMV resistance using expression values as a surrogate measure of PAV resulted in robust detection of the physical location of a known resistance gene when using the B73 reference that contains the gene, but not when using 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 using three different reference genomes.},

  doi          = {10.5061/dryad.dk22g4h},

  journal      = {},

  number       = ,

  volume       = ,

  place        = {United States},

  year         = {Wed Feb 13 04:00:00 UTC 2019},

  month        = {Wed Feb 13 04:00:00 UTC 2019}

}

Copy to clipboard

Dataset:

View Dataset

DOI: https://doi.org/10.5061/dryad.dk22g4h

Save / Share:

Export Metadata

Save to My Library

Similar records in DOE Data Explorer and OSTI.GOV collections:

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

Journal Article Gage, Joseph L. ; Vaillancourt, Brieanne ; Hamilton, John P. ; ... - The Plant Genome

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 identifiedmore »« less
Data from: Draft assembly of elite inbred line PH207 provides insights into genomic and transcriptome diversity in maize

Dataset Hirsch, Candice N. ; Hirsch, Cory D. ; Brohammer, Alex B. ; ...

Intense artificial selection over the last 100 years has produced elite maize (Zea mays) inbred lines that combine to produce high-yielding hybrids. To further our understanding of how genome and transcriptome variation contribute to the production of high-yielding hybrids, we generated a draft genome assembly of the inbred line PH207 to complement and compare with the existing B73 reference sequence. B73 is a founder of the Stiff Stalk germplasm pool, while PH207 is a founder of Iodent germplasm, both of which have contributed substantially to the production of temperate commercial maize and are combined to make heterotic hybrids. Comparison ofmore »« less
Data from: Insights into the maize pan-genome and pan-transcriptome

Dataset Hirsch, Candice N. ; Foerster, Jillian M. ; Johnson, James M. ; ...

Genomes at the species level are dynamic, with genes present in every individual (core) and genes in a subset of individuals (dispensable) that collectively constitute the pan-genome. Using transcriptome sequencing of seedling RNA from 503 maize (Zea mays) inbred lines to characterize the maize pan-genome, we identified 8681 representative transcript assemblies (RTAs) with 16.4% expressed in all lines and 82.7% expressed in subsets of the lines. Interestingly, with linkage disequilibrium mapping, 76.7% of the RTAs with at least one single nucleotide polymorphism (SNP) could be mapped to a single genetic position, distributed primarily throughout the nonpericentromeric portion of the genome.more »« less
Genomic Diversity of Pseudomonas spp.

Dataset Loper, Joyce
Data for Mitochondrial Genome Diversity across the Subphylum Saccharomycotina

Dataset Hittinger, Chris Todd

Underlying data for "Mitochondrial Genome Diversity across the Subphylum Saccharomycotina"

Similar Records