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

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

doi:10.5061/dryad.8vj84

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

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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 2,500 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 7,128 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:

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

Univ. of Minnesota, Minneapolis, MN (United States); OSTI
Univ. of Minnesota, Minneapolis, MN (United States)
Michigan State Univ., East Lansing, MI (United States)
Calico Labs, San Francisco, CA (United States)
NRGENE Ltd., Ness-Ziona (Israel)
Cornell Univ., Ithaca, NY (United States)
Univ. of Illinois at Urbana-Champaign, IL (United States)
Dow AgroSciences, Indianapolis, IN (United States)
Univ. of Wisconsin, Madison, WI (United States)

Publication Date:: Wed Nov 01 04:00:00 UTC 2017

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:: 1873894

DOI:: https://doi.org/10.5061/dryad.8vj84

Citation Formats


                    Hirsch, Candice N., Hirsch, Cory D., Brohammer, Alex B., Bowman, Megan J., Soifer, Ilya, Barad, Omer, Sehm-Tov, Doron, Baruch, Kobi, Lu, Fei, Hernandez, Alvaro G., Fields, Christopher J., Wright, Chris L., Koehler, Klaus, Springer, Nathan M., Buckler, Edward S., Buell, C. Robin, de Leon, Natalia, Kaeppler, Shawn M., Childs, Kevin, and Mikel, Mark A. Data from: Draft assembly of elite inbred line PH207 provides insights into genomic and transcriptome diversity in maize.  United States: N. p., 2017. 
        Web.  doi:10.5061/dryad.8vj84.

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                    Hirsch, Candice N., Hirsch, Cory D., Brohammer, Alex B., Bowman, Megan J., Soifer, Ilya, Barad, Omer, Sehm-Tov, Doron, Baruch, Kobi, Lu, Fei, Hernandez, Alvaro G., Fields, Christopher J., Wright, Chris L., Koehler, Klaus, Springer, Nathan M., Buckler, Edward S., Buell, C. Robin, de Leon, Natalia, Kaeppler, Shawn M., Childs, Kevin, & Mikel, Mark A. Data from: Draft assembly of elite inbred line PH207 provides insights into genomic and transcriptome diversity in maize.  United States.  doi:https://doi.org/10.5061/dryad.8vj84

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                    Hirsch, Candice N., Hirsch, Cory D., Brohammer, Alex B., Bowman, Megan J., Soifer, Ilya, Barad, Omer, Sehm-Tov, Doron, Baruch, Kobi, Lu, Fei, Hernandez, Alvaro G., Fields, Christopher J., Wright, Chris L., Koehler, Klaus, Springer, Nathan M., Buckler, Edward S., Buell, C. Robin, de Leon, Natalia, Kaeppler, Shawn M., Childs, Kevin, and Mikel, Mark A. 2017.  
"Data from: Draft assembly of elite inbred line PH207 provides insights into genomic and transcriptome diversity in maize".  United States.  doi:https://doi.org/10.5061/dryad.8vj84.  https://www.osti.gov/servlets/purl/1873894. Pub date:Wed Nov 01 04:00:00 UTC 2017

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@article{osti_1873894,

  title        = {Data from: 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 Sehm-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 S. and Buell, C. Robin and de Leon, Natalia and Kaeppler, Shawn M. and Childs, Kevin 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 2,500 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 7,128 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          = {10.5061/dryad.8vj84},

  journal      = {},

  number       = ,

  volume       = ,

  place        = {United States},

  year         = {Wed Nov 01 04:00:00 UTC 2017},

  month        = {Wed Nov 01 04:00:00 UTC 2017}

}

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DOI: https://doi.org/10.5061/dryad.8vj84

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