Skip to main content
ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #344787

Research Project: Development and Application of Genetic, Genomic, and Bioinformatic Resources in Maize

Location: Plant, Soil and Nutrition Research

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

Author
item HIRSCH, CANDICE - University Of Minnesota
item HIRSCH, CORY - University Of Minnesota
item BROHAMMER, ALEX - University Of Minnesota
item BOWMAN, MEGAN - Michigan State University
item SOIFER, ILYA - University Of Calicut
item BARAD, OMER - Nrgene
item SHEM-TOV, DORON - Nrgene
item BARUCH, KOBI - Nrgene
item LU, FEI - Cornell University - New York
item HERNANDEZ, ALVARO - University Of Illinois
item FIELDS, CHRISTOPHER - University Of Illinois
item WRIGHT, CHRIS - University Of Illinois
item KOEHLER, KLAUS - Dow Agro Sciences
item SPRINGER, NATHAN - University Of Minnesota
item Buckler, Edward - Ed
item BUELL, ROBIN - Michigan State University
item DE LEON, NATALIA - University Of Wisconsin
item KAEPPLER, SHAWN - University Of Wisconsin
item CHILDS, KEVIN - Michigan State University
item MIKEL, MARK - University Of Illinois

Submitted to: The Plant Cell
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/31/2016
Publication Date: 11/1/2016
Citation: Hirsch, C., Hirsch, C., Brohammer, A., Bowman, M., Soifer, I., Barad, O., Shem-Tov, D., Baruch, K., Lu, F., Hernandez, A., Fields, C., Wright, C., Koehler, K., Springer, N., Buckler IV, E.S., Buell, R., De Leon, N., Kaeppler, S., Childs, K., Mikel, M. 2016. Draft assembly of elite inbred line PH207 provides insights into genomic and transcriptome diversity in maize. The Plant Cell. 28(11):2700-2714.

Interpretive Summary: Eight years ago, for a cost of nearly $30 million, the first maize genome was sequenced. In this study, a second high quality maize genome has been sequenced and released to the public, using novel technologies at much lower cost. Maize breeding is based on developing hybrids, and this variety is the founder of one of the most important groups of varieties used in making hybrids. This genome sequence revealed tremendous variation in the gene content between natural varieties and how those genes are regulated. Over 2,500 genes were only present in one of the two lines, and over 25% of the genes showed differences in regulation. This tremendous genomic diversity is key to diversity and productivity seen in maize hybrids.

Technical 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.