U.S. Department of EnergyOffice of Scientific and Technical Information
Data from: An updated gene atlas for maize reveals organ-specific and stress-induced genes
Abstract
Maize(Zea mays L.), a model species for genetic studies, is one of the two most important crop species worldwide.The genome sequence of the reference genotype, B73, representative of the stiff stalk heterotic group was recently updated (AGPv4) using long‐read sequencing and optical mapping technology. To facilitate the use of AGPv4 and to enable functional genomic studies and association of genotype with phenotype, we determined expression abundances for replicated mRNA‐sequencing datasets from 79 tissues and five abiotic/biotic stress treatments revealing 36,207 expressed genes. Characterization of the B73 transcriptome across six organs revealed 4,154 organ‐specific and 7,704 differentially expressed genes following stress treatment. Gene co‐expression network analyses revealed 12 modules associated with distinct biological processes containing 13,590 genes providing a resource for further association of gene function based on co‐expression patterns. Presence/absence variants (PAVs) previously identified using whole genome resequencing data from 61 additional inbred lines were enriched in organ‐specific and stress‐induced differentially expressed genes, suggesting PAVs may function in phenological variation and adaptation to environment. Relative to core genes conserved across the 62 profiled inbreds, PAVs have lower expression abundances which are correlated with their frequency of dispersion across inbreds and on average, have significantly fewer co‐expression network connections suggesting thatmore »
- Authors:
-
- Michigan State Univ., East Lansing, MI (United States); OSTI
- Michigan State Univ., East Lansing, MI (United States)
- Univ. of Toronto, ON (Canada)
- Publication Date:
- 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:
- 1873860
- DOI:
- https://doi.org/10.5061/dryad.5p58q34
Citation Formats
Hoopes, Genevieve M., Hamilton, John P., Wood, Joshua C., Esteban, Eddi, Pasha, Asher, Vaillancourt, Brieanne, Provart, Nicholas J., and Buell, C. Robin. Data from: An updated gene atlas for maize reveals organ-specific and stress-induced genes. United States: N. p., 2018.
Web. doi:10.5061/dryad.5p58q34.
Hoopes, Genevieve M., Hamilton, John P., Wood, Joshua C., Esteban, Eddi, Pasha, Asher, Vaillancourt, Brieanne, Provart, Nicholas J., & Buell, C. Robin. Data from: An updated gene atlas for maize reveals organ-specific and stress-induced genes. United States. doi:https://doi.org/10.5061/dryad.5p58q34
Hoopes, Genevieve M., Hamilton, John P., Wood, Joshua C., Esteban, Eddi, Pasha, Asher, Vaillancourt, Brieanne, Provart, Nicholas J., and Buell, C. Robin. 2018.
"Data from: An updated gene atlas for maize reveals organ-specific and stress-induced genes". United States. doi:https://doi.org/10.5061/dryad.5p58q34. https://www.osti.gov/servlets/purl/1873860. Pub date:Fri Dec 14 04:00:00 UTC 2018
@article{osti_1873860,
title = {Data from: An updated gene atlas for maize reveals organ-specific and stress-induced genes},
author = {Hoopes, Genevieve M. and Hamilton, John P. and Wood, Joshua C. and Esteban, Eddi and Pasha, Asher and Vaillancourt, Brieanne and Provart, Nicholas J. and Buell, C. Robin},
abstractNote = {Maize(Zea mays L.), a model species for genetic studies, is one of the two most important crop species worldwide.The genome sequence of the reference genotype, B73, representative of the stiff stalk heterotic group was recently updated (AGPv4) using long‐read sequencing and optical mapping technology. To facilitate the use of AGPv4 and to enable functional genomic studies and association of genotype with phenotype, we determined expression abundances for replicated mRNA‐sequencing datasets from 79 tissues and five abiotic/biotic stress treatments revealing 36,207 expressed genes. Characterization of the B73 transcriptome across six organs revealed 4,154 organ‐specific and 7,704 differentially expressed genes following stress treatment. Gene co‐expression network analyses revealed 12 modules associated with distinct biological processes containing 13,590 genes providing a resource for further association of gene function based on co‐expression patterns. Presence/absence variants (PAVs) previously identified using whole genome resequencing data from 61 additional inbred lines were enriched in organ‐specific and stress‐induced differentially expressed genes, suggesting PAVs may function in phenological variation and adaptation to environment. Relative to core genes conserved across the 62 profiled inbreds, PAVs have lower expression abundances which are correlated with their frequency of dispersion across inbreds and on average, have significantly fewer co‐expression network connections suggesting that a subset of PAVs may be on an evolutionary path to pseudogenization. To facilitate use by the community, we developed the Maize Genomics Resource website(maize.plantbiology.msu.edu) for viewing and data‐mining these resources and deployed two new views on the Maize electronic Fluorescent Pictograph Browser (bar.utoronto. ca/efp_maize)},
doi = {10.5061/dryad.5p58q34},
journal = {},
number = ,
volume = ,
place = {United States},
year = {Fri Dec 14 04:00:00 UTC 2018},
month = {Fri Dec 14 04:00:00 UTC 2018}
}