An expanded maize gene expression atlas based on RNA sequencing and its use to explore root development
Abstract
Comprehensive and systematic transcriptome profiling provides valuable insight into biological and developmental processes that occur throughout the life cycle of a plant. We have enhanced our previously published microarray-based gene atlas of maize (Zea mays L.) inbred B73 to now include 79 distinct replicated samples that have been interrogated using RNA sequencing (RNA-seq). The current version of the atlas includes 50 original array-based gene atlas samples, a time-course of 12 stalk and leaf samples postflowering, and an additional set of 17 samples from the maize seedling and adult root system. The entire dataset contains 4.6 billion mapped reads, with an average of 20.5 million mapped reads per biological replicate, allowing for detection of genes with lower transcript abundance. As the new root samples represent key additions to the previously examined tissues, we highlight insights into the root transcriptome, which is represented by 28,894 (73.2%) annotated genes in maize. Additionally, we observed remarkable expression differences across both the longitudinal (four zones) and radial gradients (cortical parenchyma and stele) of the primary root supported by fourfold differential expression of 9353 and 4728 genes, respectively. Among the latter were 1110 genes that encode transcription factors, some of which are orthologs of previously characterizedmore »
- Authors:
-
- Univ. of Wisconsin, Madison, WI (United States)
- Clemson Univ., Clemson, SC (United States)
- Michigan State Univ., East Lansing, MI (United States); DOE Great Lakes Bioenergy Research Center, East Lansing, MI (United States)
- Univ. of Minnesota, St. Paul, MN (United States)
- Univ. of Wisconsin, Madison, WI (United States); DOE Great Lakes Bioenergy Research Center, Madison, WI (United States)
- Publication Date:
- Research Org.:
- Univ. of Wisconsin, Madison, WI (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1363961
- Grant/Contract Number:
- FC02-07ER64494
- Resource Type:
- Accepted Manuscript
- Journal Name:
- The Plant Genome
- Additional Journal Information:
- Journal Volume: 9; Journal Issue: 1; 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; 60 APPLIED LIFE SCIENCES
Citation Formats
Stelpflug, Scott C., Sekhon, Rajandeep S., Vaillancourt, Brieanne, Hirsch, Candice N., Buell, C. Robin, de Leon, Natalia, and Kaeppler, Shawn M. An expanded maize gene expression atlas based on RNA sequencing and its use to explore root development. United States: N. p., 2015.
Web. doi:10.3835/plantgenome2015.04.0025.
Stelpflug, Scott C., Sekhon, Rajandeep S., Vaillancourt, Brieanne, Hirsch, Candice N., Buell, C. Robin, de Leon, Natalia, & Kaeppler, Shawn M. An expanded maize gene expression atlas based on RNA sequencing and its use to explore root development. United States. https://doi.org/10.3835/plantgenome2015.04.0025
Stelpflug, Scott C., Sekhon, Rajandeep S., Vaillancourt, Brieanne, Hirsch, Candice N., Buell, C. Robin, de Leon, Natalia, and Kaeppler, Shawn M. Wed .
"An expanded maize gene expression atlas based on RNA sequencing and its use to explore root development". United States. https://doi.org/10.3835/plantgenome2015.04.0025. https://www.osti.gov/servlets/purl/1363961.
@article{osti_1363961,
title = {An expanded maize gene expression atlas based on RNA sequencing and its use to explore root development},
author = {Stelpflug, Scott C. and Sekhon, Rajandeep S. and Vaillancourt, Brieanne and Hirsch, Candice N. and Buell, C. Robin and de Leon, Natalia and Kaeppler, Shawn M.},
abstractNote = {Comprehensive and systematic transcriptome profiling provides valuable insight into biological and developmental processes that occur throughout the life cycle of a plant. We have enhanced our previously published microarray-based gene atlas of maize (Zea mays L.) inbred B73 to now include 79 distinct replicated samples that have been interrogated using RNA sequencing (RNA-seq). The current version of the atlas includes 50 original array-based gene atlas samples, a time-course of 12 stalk and leaf samples postflowering, and an additional set of 17 samples from the maize seedling and adult root system. The entire dataset contains 4.6 billion mapped reads, with an average of 20.5 million mapped reads per biological replicate, allowing for detection of genes with lower transcript abundance. As the new root samples represent key additions to the previously examined tissues, we highlight insights into the root transcriptome, which is represented by 28,894 (73.2%) annotated genes in maize. Additionally, we observed remarkable expression differences across both the longitudinal (four zones) and radial gradients (cortical parenchyma and stele) of the primary root supported by fourfold differential expression of 9353 and 4728 genes, respectively. Among the latter were 1110 genes that encode transcription factors, some of which are orthologs of previously characterized transcription factors known to regulate root development in Arabidopsis thaliana (L.) Heynh., while most are novel, and represent attractive targets for reverse genetics approaches to determine their roles in this important organ. As a result, this comprehensive transcriptome dataset is a powerful tool toward understanding maize development, physiology, and phenotypic diversity.},
doi = {10.3835/plantgenome2015.04.0025},
journal = {The Plant Genome},
number = 1,
volume = 9,
place = {United States},
year = {Wed Dec 30 00:00:00 EST 2015},
month = {Wed Dec 30 00:00:00 EST 2015}
}
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- Anderson, Sarah N.; Stitzer, Michelle C.; Zhou, Peng
- G3: Genes|Genomes|Genetics, Vol. 9, Issue 11
Besides and beyond Flowering: Other Roles of EuAP2 Genes in Plant Development
journal, December 2019
- Solomon, Charles U.; Drea, Sinéad
- Genes, Vol. 10, Issue 12
Maize nested introgression library provides evidence for the involvement of liguleless1 in resistance to northern leaf blight
posted_content, October 2019
- Kolkman, Judith M.; Strable, Josh; Harline, Kate
- G3: Genes|Genomes|Genetics
Drought-tolerant and drought-sensitive genotypes of maize (Zea mays L.) differ in contents of endogenous brassinosteroids and their drought-induced changes
journal, May 2018
- Tůmová, Lenka; Tarkowská, Danuše; Řehořová, Kateřina
- PLOS ONE, Vol. 13, Issue 5
Functions of maize genes encoding pyruvate phosphate dikinase in developing endosperm
journal, December 2017
- Lappe, Ryan R.; Baier, John W.; Boehlein, Susan K.
- Proceedings of the National Academy of Sciences, Vol. 115, Issue 1
Interpretation of differential gene expression results of RNA-seq data: review and integration
journal, August 2018
- McDermaid, Adam; Monier, Brandon; Zhao, Jing
- Briefings in Bioinformatics, Vol. 20, Issue 6
Dicer-like 5 deficiency confers temperature-sensitive male sterility in maize
posted_content, May 2020
- Teng, Chong; Zhang, Han; Hammond, Reza
- Nature Communications
Gene Expression Maps in Plants: Current State and Prospects
journal, August 2019
- Klepikova, Anna V.; Penin, Aleksey A.
- Plants, Vol. 8, Issue 9
Discovering and Constructing ceRNA-miRNA-Target Gene Regulatory Networks during Anther Development in Maize
journal, July 2019
- Li, Ziwen; An, Xueli; Zhu, Taotao
- International Journal of Molecular Sciences, Vol. 20, Issue 14
Cloning and characterization of BES1/BZR1 transcription factor genes in maize
journal, July 2018
- Yu, Haoqiang; Feng, Wenqi; Sun, Fuai
- Plant Growth Regulation, Vol. 86, Issue 2
The limited role of differential fractionation in genome content variation and function in maize ( Zea mays L .) inbred lines
journal, December 2017
- Brohammer, Alex B.; Kono, Thomas J. Y.; Springer, Nathan M.
- The Plant Journal, Vol. 93, Issue 1
The genetic architecture of amylose biosynthesis in maize kernel
journal, September 2017
- Li, Changsheng; Huang, Yongcai; Huang, Ruidong
- Plant Biotechnology Journal, Vol. 16, Issue 2
Genome-wide identification, systematic analysis and characterization of SRO family genes in maize (Zea mays L.)
journal, September 2018
- Jiang, Huanhuan; Xiao, Yao; Zhu, Suwen
- Acta Physiologiae Plantarum, Vol. 40, Issue 10
Genome-wide association study of maize plant architecture using F1 populations
journal, December 2018
- Zhao, Yang; Wang, Hengsheng; Bo, Chen
- Plant Molecular Biology, Vol. 99, Issue 1-2
Transcriptome analysis of maize seedling roots in response to nitrogen-, phosphorus-, and potassium deficiency
journal, January 2020
- Ma, Nana; Dong, Lina; Lü, Wei
- Plant and Soil, Vol. 447, Issue 1-2
An updated gene atlas for maize reveals organ‐specific and stress‐induced genes
journal, January 2019
- Hoopes, Genevieve M.; Hamilton, John P.; Wood, Joshua C.
- The Plant Journal, Vol. 97, Issue 6
Genomic-Enabled Prediction Kernel Models with Random Intercepts for Multi-environment Trials
journal, February 2018
- Cuevas, Jaime; Granato, Italo; Fritsche-Neto, Roberto
- G3: Genes|Genomes|Genetics, Vol. 8, Issue 4
MLKS2 is an ARM domain and F-actin-associated KASH protein that functions in stomatal complex development and meiotic chromosome segregation
journal, January 2019
- Gumber, Hardeep K.; McKenna, Joseph F.; Tolmie, Andrea F.
- Nucleus, Vol. 10, Issue 1
MaizeGDB 2018: the maize multi-genome genetics and genomics database
journal, November 2018
- Portwood, John L.; Woodhouse, Margaret R.; Cannon, Ethalinda K.
- Nucleic Acids Research, Vol. 47, Issue D1
A calcium-dependent protein kinase, ZmCPK32, specifically expressed in maize pollen to regulate pollen tube growth
journal, May 2018
- Li, Jie; Li, Yihao; Deng, Yanling
- PLOS ONE, Vol. 13, Issue 5
Transcriptomic response to divergent selection for flowering times reveals convergence and key players of the underlying gene regulatory network
preprint, June 2019
- Tenaillon, Maud I.; Seddiki, Khawla; Mollion, Maeva
ZmRAP2.7, an AP2 Transcription Factor, Is Involved in Maize Brace Roots Development
journal, July 2019
- Li, Jieping; Chen, Fanjun; Li, Yanqing
- Frontiers in Plant Science, Vol. 10
A comparative transcriptional landscape of maize and sorghum obtained by single-molecule sequencing
journal, April 2018
- Wang, Bo; Regulski, Michael; Tseng, Elizabeth
- Genome Research, Vol. 28, Issue 6
Evolutionarily informed deep learning methods for predicting relative transcript abundance from DNA sequence
journal, March 2019
- Washburn, Jacob D.; Mejia-Guerra, Maria Katherine; Ramstein, Guillaume
- Proceedings of the National Academy of Sciences, Vol. 116, Issue 12
A Comprehensive Analysis of Alternative Splicing in Paleopolyploid Maize
journal, May 2017
- Mei, Wenbin; Liu, Sanzhen; Schnable, James C.
- Frontiers in Plant Science, Vol. 8
Expansion and diversification of the gibberellin receptor GIBBERELLIN INSENSITIVE DWARF1 (GID1) family in land plants
journal, June 2018
- Gazara, Rajesh K.; Moharana, Kanhu C.; Bellieny-Rabelo, Daniel
- Plant Molecular Biology, Vol. 97, Issue 4-5
MATRILINEAL, a sperm-specific phospholipase, triggers maize haploid induction
journal, January 2017
- Kelliher, Timothy; Starr, Dakota; Richbourg, Lee
- Nature, Vol. 542, Issue 7639
The RNA-Seq-based high resolution gene expression atlas of chickpea ( Cicer arietinum L.) reveals dynamic spatio-temporal changes associated with growth and development: RNA-Seq based chickpea gene expression atlas
journal, May 2018
- Kudapa, Himabindu; Garg, Vanika; Chitikineni, Annapurna
- Plant, Cell & Environment
Integration of quantitated expression estimates from polyA-selected and rRNA-depleted RNA-seq libraries
journal, June 2017
- Bush, Stephen J.; McCulloch, Mary E. B.; Summers, Kim M.
- BMC Bioinformatics, Vol. 18, Issue 1
Using multiple reference genomes to identify and resolve annotation inconsistencies
journal, April 2020
- Monnahan, Patrick J.; Michno, Jean-Michel; O’Connor, Christine
- BMC Genomics, Vol. 21, Issue 1
Genome-wide analysis of the basic Helix-Loop-Helix (bHLH) transcription factor family in maize
journal, October 2018
- Zhang, Tingting; Lv, Wei; Zhang, Haisen
- BMC Plant Biology, Vol. 18, Issue 1
Utilization of Tissue Ploidy Level Variation in de Novo Transcriptome Assembly of Pinus sylvestris
journal, August 2019
- Ojeda, Dario I.; Mattila, Tiina M.; Ruttink, Tom
- G3: Genes|Genomes|Genetics, Vol. 9, Issue 10
qKW9 encodes a pentatricopeptide repeat protein affecting photosynthesis and grain filling in maize
posted_content, November 2019
- Huang, Juan; Lu, Gang; Liu, Lei
Besides and Beyond Flowering: Other Roles of euAP2 Genes in Plant Development
posted_content, January 2019
- Solomon, Charles U.; Drea, Sinead
- Preprints.org
Dynamic patterns of transcript abundance of transposable element families in maize
posted_content, June 2019
- Anderson, Sarah N.; Stitzer, Michelle C.; Zhou, Peng
- G3: Genes|Genomes|Genetics
Besides and Beyond Flowering: Other Roles of euAP2 Genes in Plant Development
posted_content, January 2019
- Solomon, Charles U.; Drea, Sinead
- Preprints.org
Dicer-like 5 deficiency confers temperature-sensitive male sterility in maize
journal, June 2020
- Teng, Chong; Zhang, Han; Hammond, Reza
- Nature Communications, Vol. 11, Issue 1
Stress-induced and epigenetic-mediated maize transcriptome regulation study by means of transcriptome reannotation and differential expression analysis
journal, July 2016
- Forestan, Cristian; Aiese Cigliano, Riccardo; Farinati, Silvia
- Scientific Reports, Vol. 6, Issue 1
Expansion and diversification of the gibberellin receptor GIBBERELLIN INSENSITIVE DWARF1 (GID1) family in land plants
posted_content, November 2017
- Gazara, Rajesh K.; Moharana, Kanhu C.; Bellieny-Rabelo, Daniel
- bioRxiv
MLKS2 is an ARM domain and F-actin-associated KASH protein that functions in stomatal complex development and meiotic chromosome segregation
posted_content, May 2019
- Gumber, Hardeep K.; McKenna, Joseph F.; Tolmie, Andrea F.
- Nucleus
MLKS2 is an ARM domain and F-actin-associated KASH protein that functions in stomatal complex development and meiotic chromosome segregation
journal, January 2019
- Gumber, Hardeep K.; McKenna, Joseph F.; Tolmie, Andrea F.
- Nucleus, Vol. 10, Issue 1
Genome-wide analysis of the basic Helix-Loop-Helix (bHLH) transcription factor family in maize
journal, October 2018
- Zhang, Tingting; Lv, Wei; Zhang, Haisen
- BMC Plant Biology, Vol. 18, Issue 1
Genome-wide association analysis of stalk biomass and anatomical traits in maize
journal, January 2019
- Mazaheri, Mona; Heckwolf, Marlies; Vaillancourt, Brieanne
- BMC Plant Biology, Vol. 19, Issue 1
A maize polygalacturonase functions as a suppressor of programmed cell death in plants
journal, July 2019
- He, Yijian; Karre, Shailesh; Johal, Gurmukh S.
- BMC Plant Biology, Vol. 19, Issue 1
Identification and characterization of genes encoding the nuclear envelope LINC complex in the monocot species Zea mays
journal, January 2019
- Gumber, Hardeep K.; McKenna, Joseph F.; Estrada, Amado L.
- Journal of Cell Science, Vol. 132, Issue 3
Characterization of the maize lipoxygenase gene family in relation to aflatoxin accumulation resistance
journal, July 2017
- Ogunola, Oluwaseun F.; Hawkins, Leigh K.; Mylroie, Erik
- PLOS ONE, Vol. 12, Issue 7
Dynamic Patterns of Transcript Abundance of Transposable Element Families in Maize
journal, September 2019
- Anderson, Sarah N.; Stitzer, Michelle C.; Zhou, Peng
- G3: Genes|Genomes|Genetics, Vol. 9, Issue 11
Besides and Beyond Flowering: Other Roles of euAP2 Genes in Plant Development
posted_content, January 2019
- Solomon, Charles U.; Drea, Sinead
- Preprints.org
Genetic Diversity and Molecular Evolution of a Violaxanthin De-epoxidase Gene in Maize
journal, July 2016
- Xu, Jing; Li, Zhigang; Yang, Haorui
- Frontiers in Genetics, Vol. 7
A Comprehensive Analysis of Alternative Splicing in Paleopolyploid Maize
journal, May 2017
- Mei, Wenbin; Liu, Sanzhen; Schnable, James C.
- Frontiers in Plant Science, Vol. 8
Structural Characterization of Maize SIRK1 Kinase Domain Reveals an Unusual Architecture of the Activation Segment
journal, May 2017
- Aquino, Bruno; Couñago, Rafael M.; Verza, Natalia
- Frontiers in Plant Science, Vol. 8
Comparative Genomics, Whole-Genome Re-sequencing and Expression Profile Analysis of Nucleobase:Cation Symporter 2 (NCS2) Genes in Maize
journal, June 2018
- Chai, Wenbo; Peng, Xiaojian; Liu, Bin
- Frontiers in Plant Science, Vol. 9
Cell Type-Specific Transcriptomics of Lateral Root Formation and Plasticity
journal, February 2019
- Kortz, Annika; Hochholdinger, Frank; Yu, Peng
- Frontiers in Plant Science, Vol. 10
Proteases Underground: Analysis of the Maize Root Apoplast Identifies Organ Specific Papain-Like Cysteine Protease Activity
journal, April 2019
- Schulze Hüynck, Jan; Kaschani, Farnusch; van der Linde, Karina
- Frontiers in Plant Science, Vol. 10
ZmRAP2.7, an AP2 Transcription Factor, Is Involved in Maize Brace Roots Development
journal, July 2019
- Li, Jieping; Chen, Fanjun; Li, Yanqing
- Frontiers in Plant Science, Vol. 10
Discovering and Constructing ceRNA-miRNA-Target Gene Regulatory Networks during Anther Development in Maize
journal, July 2019
- Li, Ziwen; An, Xueli; Zhu, Taotao
- International Journal of Molecular Sciences, Vol. 20, Issue 14
Gene Expression Maps in Plants: Current State and Prospects
journal, August 2019
- Klepikova, Anna V.; Penin, Aleksey A.
- Plants, Vol. 8, Issue 9
Seed Weight as a Covariate in Association and Prediction Studies for Biomass Traits in Maize Seedlings
journal, February 2020
- Galic, Vlatko; Mazur, Maja; Brkic, Andrija
- Plants, Vol. 9, Issue 2
Genome-wide identification of ZmHMAs and association of natural variation in ZmHMA2 and ZmHMA3 with leaf cadmium accumulation in maize
journal, October 2019
- Cao, Yanhua; Zhao, Xiongwei; Liu, Yajuan
- PeerJ, Vol. 7