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; 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.

doi:10.1105/tpc.16.00353

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

Journal Article · Tue Nov 01 00:00:00 EDT 2016 · The Plant Cell

DOI:https://doi.org/10.1105/tpc.16.00353· OSTI ID:1427680

^[1]; ^[2]; ^[3]; ^[4]; Soifer, Ilya ^[5]; Barad, Omer ^[6]; Shem-Tov, Doron ^[6]; Baruch, Kobi ^[6]; Lu, Fei ^[7]; Hernandez, Alvaro G. ^[8]; ^[8]; Wright, Chris L. ^[8]; Koehler, Klaus ^[9]; ^[10]; ^[11]; Buell, C. Robin ^[12]; de Leon, Natalia ^[13]; ^[13]; ^[14]; ^[15]

Univ. of Minnesota, St. Paul, MN (United States). Department of Agronomy and Plant Genetics; University of Minnesota
Univ. of Minnesota, St. Paul, MN (United States). Department of Plant Pathology
Univ. of Minnesota, St. Paul, MN (United States). Department of Agronomy and Plant Genetics
Michigan State Univ., East Lansing, MI (United States). Department of Plant Biology
Calico Labs, San Francisco, CA (United States)
NRGENE Ltd., Ness-Ziona (Israel)
Cornell Univ., Ithaca, NY (United States). Institute for Genome Diversity
Univ. of Illinois, Urbana, IL (United States). Roy J. Carver Biotechnology Center
Dow AgroSciences, Indianapolis, IN (United States)
Univ. of Minnesota, St. Paul, MN (United States). Department of Plant Biology
Cornell Univ., Ithaca, NY (United States). Institute for Genome Diversity; U.S. Department of Agriculture/Agricultural Research Services, Ithaca, NY (United States)
Michigan State Univ., East Lansing, MI (United States). Department of Plant Biology; DOE Great Lakes Bioenergy Research Center, East Lansing, MI (United States)
Univ. of Wisconsin, Madison, WI (United States); DOE Great Lakes Bioenergy Research Center, Madison, WI (United States)
Michigan State Univ., East Lansing, MI (United States). Department of Plant Biology and Center for Genomics-Enabled Plant Sciences
Univ. of Illinois, Urbana, IL (United States). Roy J. Carver Biotechnology Center and Department of Crop Sciences

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.

View Accepted Manuscript (DOE)

Research Organization:: Univ. of Wisconsin, Madison, WI (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)

Grant/Contract Number:: FC02-07ER64494

OSTI ID:: 1427680

Journal Information:: The Plant Cell, Journal Name: The Plant Cell Journal Issue: 11 Vol. 28; ISSN 1040-4651

Publisher:: American Society of Plant BiologistsCopyright Statement

Country of Publication:: United States

Language:: English

References (1)

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. Dryad https://doi.org/10.5061/dryad.8vj84	dataset	January 2017

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