Draft assembly of elite inbred line PH207 provides insights into genomic and transcriptome diversity in maize

Candice N. Hirsch; Cory D. Hirsch; Alex B. Brohammer; Megan J. Bowman; Ilya Soifer; Omer Barad; Doron Shem-Tov; Kobi Baruch; Fei Lu; Alvaro G. Hernandez; Christopher J. Fields; Chris L. Wright; Klaus Koehler; Nathan M. Springer; Edward Buckler; C. Robin Buell; Natalia de Leon; Shawn M. Kaeppler; Kevin L. Childs; Mark A. Mikel

doi:10.1105/tpc.16.00353

Draft assembly of elite inbred line PH207 provides insights into genomic and transcriptome diversity in maize

Candice N. Hirsch, Cory D. Hirsch, Alex B. Brohammer, Megan J. Bowman, Ilya Soifer, Omer Barad, Doron Shem-Tov, Kobi Baruch, Fei Lu, Alvaro G. Hernandez, Christopher J. Fields, Chris L. Wright, Klaus Koehler, Nathan M. Springer, Edward Buckler, C. Robin Buell, Natalia de Leon, Shawn M. Kaeppler, Kevin L. Childs, Mark A. Mikel

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127 Scopus citations

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 heterotic pools.

Original language	English (US)
Pages (from-to)	2700-2714
Number of pages	15
Journal	Plant Cell
Volume	28
Issue number	11
DOIs	https://doi.org/10.1105/tpc.16.00353
State	Published - Nov 2016

Bibliographical note

Funding Information:
This work was funded in part by the DOE Great Lakes Bioenergy Research Center (DOE BER Office of Science DE-FC02-07ER64494), by Dow AgroSciences, and by the National Science Foundation (Grant IOS- 1126998 to K.L.C.). The Minnesota Supercomputing Institute at the University of Minnesota provided computational resources that contributed to the research results reported in this article.C.D.H.was supported by a National Science Foundation National Plant Genome Initiative Postdoctoral Fellowship in Biology Fellowship (Grant 1202724). A.B.B. was supported by the DuPont Pioneer Bill Kuhn Honorary Fellowship.

Publisher Copyright:
© 2016 American Society of Plant Biologists. All rights reserved.

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Hirsch, C. N., Hirsch, C. D., Brohammer, A. B., Bowman, M. J., Soifer, I., Barad, O., Shem-Tov, D., Baruch, K., Lu, F., Hernandez, A. G., Fields, C. J., Wright, C. L., Koehler, K., Springer, N. M., Buckler, E., Buell, C. R., de Leon, N., Kaeppler, S. M., Childs, K. L., & Mikel, M. A. (2016). Draft assembly of elite inbred line PH207 provides insights into genomic and transcriptome diversity in maize. Plant Cell, 28(11), 2700-2714. https://doi.org/10.1105/tpc.16.00353

Hirsch, CN , Hirsch, CD, Brohammer, AB, Bowman, MJ, Soifer, I, Barad, O, Shem-Tov, D, Baruch, K, Lu, F, Hernandez, AG, Fields, CJ, Wright, CL, Koehler, K, Springer, NM, Buckler, E, Buell, CR, de Leon, N, Kaeppler, SM, Childs, KL & Mikel, MA 2016, 'Draft assembly of elite inbred line PH207 provides insights into genomic and transcriptome diversity in maize', Plant Cell, vol. 28, no. 11, pp. 2700-2714. https://doi.org/10.1105/tpc.16.00353

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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 heterotic pools.",

author = "Hirsch, {Candice N.} and Hirsch, {Cory D.} and Brohammer, {Alex B.} and Bowman, {Megan J.} and Ilya Soifer and Omer Barad and Doron Shem-Tov and Kobi Baruch and Fei Lu and Hernandez, {Alvaro G.} and Fields, {Christopher J.} and Wright, {Chris L.} and Klaus Koehler and Springer, {Nathan M.} and Edward Buckler and Buell, {C. Robin} and {de Leon}, Natalia and Kaeppler, {Shawn M.} and Childs, {Kevin L.} and Mikel, {Mark A.}",

note = "Funding Information: This work was funded in part by the DOE Great Lakes Bioenergy Research Center (DOE BER Office of Science DE-FC02-07ER64494), by Dow AgroSciences, and by the National Science Foundation (Grant IOS- 1126998 to K.L.C.). The Minnesota Supercomputing Institute at the University of Minnesota provided computational resources that contributed to the research results reported in this article.C.D.H.was supported by a National Science Foundation National Plant Genome Initiative Postdoctoral Fellowship in Biology Fellowship (Grant 1202724). A.B.B. was supported by the DuPont Pioneer Bill Kuhn Honorary Fellowship. Publisher Copyright: {\textcopyright} 2016 American Society of Plant Biologists. All rights reserved.",

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AU - Soifer, Ilya

AU - Barad, Omer

AU - Shem-Tov, Doron

AU - Baruch, Kobi

AU - Lu, Fei

AU - Hernandez, Alvaro G.

AU - Fields, Christopher J.

AU - Wright, Chris L.

AU - Koehler, Klaus

AU - Springer, Nathan M.

AU - Buckler, Edward

AU - Buell, C. Robin

AU - de Leon, Natalia

AU - Kaeppler, Shawn M.

AU - Childs, Kevin L.

AU - Mikel, Mark A.

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Draft assembly of elite inbred line PH207 provides insights into genomic and transcriptome diversity in maize

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