skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Draft Assembly of Elite Inbred Line PH207 Provides Insights into Genomic and Transcriptome Diversity in Maize

Abstract

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 of these two assemblies revealed over 2500 genes present in only one of the two genotypes and 136 gene families that have undergone extensive expansion or contraction. Transcriptome profiling revealed extensive expression variation, with as many as 10,564 differentially expressed transcripts and 7128 transcripts expressed in only one of the two genotypes in a single tissue. Genotype-specific genes were more likely to have tissue/condition-specific expression and lower transcript abundance. The availability of a high-quality genome assembly for the elite maize inbred PH207 expands our knowledge of the breadth of natural genome and transcriptome variation in elite maize inbred lines across heteroticmore » pools.« less

Authors:
ORCiD logo [1]; ORCiD logo [2]; ORCiD logo [1]; ORCiD logo [3];  [4];  [5];  [5];  [5];  [6];  [7]; ORCiD logo [7];  [7];  [8]; ORCiD logo [9]; ORCiD logo [10];  [11];  [12]; ORCiD logo [12]; ORCiD logo [13]; ORCiD logo [14]
  1. Univ. of Minnesota, St. Paul, MN (United States). Department of Agronomy and Plant Genetics
  2. Univ. of Minnesota, St. Paul, MN (United States). Department of Plant Pathology
  3. Michigan State Univ., East Lansing, MI (United States). Department of Plant Biology
  4. Calico Labs, San Francisco, CA (United States)
  5. NRGENE Ltd., Ness-Ziona (Israel)
  6. Cornell Univ., Ithaca, NY (United States). Institute for Genome Diversity
  7. Univ. of Illinois, Urbana, IL (United States). Roy J. Carver Biotechnology Center
  8. Dow AgroSciences, Indianapolis, IN (United States)
  9. Univ. of Minnesota, St. Paul, MN (United States). Department of Plant Biology
  10. Cornell Univ., Ithaca, NY (United States). Institute for Genome Diversity; U.S. Department of Agriculture/Agricultural Research Services, Ithaca, NY (United States)
  11. Michigan State Univ., East Lansing, MI (United States). Department of Plant Biology; DOE Great Lakes Bioenergy Research Center, East Lansing, MI (United States)
  12. Univ. of Wisconsin, Madison, WI (United States); DOE Great Lakes Bioenergy Research Center, Madison, WI (United States)
  13. Michigan State Univ., East Lansing, MI (United States). Department of Plant Biology and Center for Genomics-Enabled Plant Sciences
  14. Univ. of Illinois, Urbana, IL (United States). Roy J. Carver Biotechnology Center and Department of Crop Sciences
Publication Date:
Research Org.:
Univ. of Wisconsin, Madison, WI (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1427680
Grant/Contract Number:  
FC02-07ER64494
Resource Type:
Accepted Manuscript
Journal Name:
Plant Cell
Additional Journal Information:
Journal Volume: 28; Journal Issue: 11; Journal ID: ISSN 1040-4651
Publisher:
American Society of Plant Biologists
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Hirsch, Candice N., Hirsch, Cory D., Brohammer, Alex B., Bowman, Megan J., Soifer, Ilya, Barad, Omer, Shem-Tov, Doron, Baruch, Kobi, Lu, Fei, Hernandez, Alvaro G., Fields, Christopher J., Wright, Chris L., Koehler, Klaus, Springer, Nathan M., Buckler, Edward, Buell, C. Robin, de Leon, Natalia, Kaeppler, Shawn M., Childs, Kevin L., and Mikel, Mark A. Draft Assembly of Elite Inbred Line PH207 Provides Insights into Genomic and Transcriptome Diversity in Maize. United States: N. p., 2016. Web. doi:10.1105/tpc.16.00353.
Hirsch, Candice N., Hirsch, Cory D., Brohammer, Alex B., Bowman, Megan J., Soifer, Ilya, Barad, Omer, Shem-Tov, Doron, Baruch, Kobi, Lu, Fei, Hernandez, Alvaro G., Fields, Christopher J., Wright, Chris L., Koehler, Klaus, Springer, Nathan M., Buckler, Edward, Buell, C. Robin, de Leon, Natalia, Kaeppler, Shawn M., Childs, Kevin L., & Mikel, Mark A. Draft Assembly of Elite Inbred Line PH207 Provides Insights into Genomic and Transcriptome Diversity in Maize. United States. doi:10.1105/tpc.16.00353.
Hirsch, Candice N., Hirsch, Cory D., Brohammer, Alex B., Bowman, Megan J., Soifer, Ilya, Barad, Omer, Shem-Tov, Doron, Baruch, Kobi, Lu, Fei, Hernandez, Alvaro G., Fields, Christopher J., Wright, Chris L., Koehler, Klaus, Springer, Nathan M., Buckler, Edward, Buell, C. Robin, de Leon, Natalia, Kaeppler, Shawn M., Childs, Kevin L., and Mikel, Mark A. Tue . "Draft Assembly of Elite Inbred Line PH207 Provides Insights into Genomic and Transcriptome Diversity in Maize". United States. doi:10.1105/tpc.16.00353. https://www.osti.gov/servlets/purl/1427680.
@article{osti_1427680,
title = {Draft Assembly of Elite Inbred Line PH207 Provides Insights into Genomic and Transcriptome Diversity in Maize},
author = {Hirsch, Candice N. and Hirsch, Cory D. and Brohammer, Alex B. and Bowman, Megan J. and Soifer, Ilya and Barad, Omer and Shem-Tov, Doron and Baruch, Kobi and Lu, Fei and Hernandez, Alvaro G. and Fields, Christopher J. and Wright, Chris L. and Koehler, Klaus and Springer, Nathan M. and Buckler, Edward and Buell, C. Robin and de Leon, Natalia and Kaeppler, Shawn M. and Childs, Kevin L. and Mikel, Mark A.},
abstractNote = {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 of these two assemblies revealed over 2500 genes present in only one of the two genotypes and 136 gene families that have undergone extensive expansion or contraction. Transcriptome profiling revealed extensive expression variation, with as many as 10,564 differentially expressed transcripts and 7128 transcripts expressed in only one of the two genotypes in a single tissue. Genotype-specific genes were more likely to have tissue/condition-specific expression and lower transcript abundance. The availability of a high-quality genome assembly for the elite maize inbred PH207 expands our knowledge of the breadth of natural genome and transcriptome variation in elite maize inbred lines across heterotic pools.},
doi = {10.1105/tpc.16.00353},
journal = {Plant Cell},
number = 11,
volume = 28,
place = {United States},
year = {2016},
month = {11}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Citation Metrics:
Cited by: 39 works
Citation information provided by
Web of Science

Save / Share:

Works referencing / citing this record:

A gene encoding maize caffeoyl-CoA O-methyltransferase confers quantitative resistance to multiple pathogens
journal, July 2017

  • Yang, Qin; He, Yijian; Kabahuma, Mercy
  • Nature Genetics, Vol. 49, Issue 9
  • DOI: 10.1038/ng.3919

New de novo assembly of the Atlantic bottlenose dolphin ( Tursiops truncatus ) improves genome completeness and provides haplotype phasing
journal, January 2019

  • Martinez-Viaud, Karine A.; Lawley, Cindy Taylor; Vergara, Milmer Martinez
  • GigaScience, Vol. 8, Issue 3
  • DOI: 10.1093/gigascience/giy168

Computational aspects underlying genome to phenome analysis in plants
journal, January 2019

  • Bolger, Anthony M.; Poorter, Hendrik; Dumschott, Kathryn
  • The Plant Journal, Vol. 97, Issue 1
  • DOI: 10.1111/tpj.14179

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
  • DOI: 10.1111/tpj.14184

Tandem Duplicate Genes in Maize Are Abundant and Date to Two Distinct Periods of Time
journal, July 2018

  • Kono, Thomas J. Y.; Brohammer, Alex B.; McGaugh, Suzanne E.
  • G3: Genes|Genomes|Genetics, Vol. 8, Issue 9
  • DOI: 10.1534/g3.118.200580

Heritable Epigenomic Changes to the Maize Methylome Resulting from Tissue Culture
journal, May 2018