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Plant Cell. 2016 Nov;28(11):2700-2714. Epub 2016 Nov 1.

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

Author information

1
Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108 cnhirsch@umn.edu.
2
Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108.
3
Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108.
4
Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824.
5
Calico Labs, San Francisco, California 94080.
6
NRGENE Ltd., Ness-Ziona 7403648, Israel.
7
Instiute for Genome Diversity, Cornell University, Ithaca, New York 14850.
8
Roy J. Carver Biotechnology Center, University of Illinois, Urbana, Illinois 61801.
9
Dow AgroSciences, Indianapolis, Indiana 46268.
10
Department of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108.
11
U.S. Department of Agriculture/Agricultural Research Services, Ithaca, New York 14850.
12
DOE Great Lakes Bioenergy Research Center, East Lansing, Michigan 48824.
13
Department of Agronomy, University of Wisconsin-Madison, Madison, Wisconsin 53706.
14
DOE Great Lakes Bioenergy Research Center, Madison, Wisconsin 53706.
15
Center for Genomics-Enabled Plant Sciences, Michigan State University, East Lansing, Michigan 48824.
16
Department of Crop Sciences, University of Illinois, Urbana, Illinois 61801.

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.

PMID:
27803309
PMCID:
PMC5155341
DOI:
10.1105/tpc.16.00353
[Indexed for MEDLINE]
Free PMC Article

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