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

Research output: Contribution to journalArticle

63 Citations (Scopus)

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 languageEnglish (US)
Pages (from-to)2700-2714
Number of pages15
JournalPlant Cell
Volume28
Issue number11
DOIs
StatePublished - Nov 2016

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Transcriptome
transcriptome
inbred lines
Zea mays
genome assembly
genomics
corn
Genome
Genotype
genotype
germplasm
artificial selection
genome
genes
Genes
transcriptomics
Gene Expression Profiling
complement
tissues

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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.

In: Plant Cell, Vol. 28, No. 11, 11.2016, p. 2700-2714.

Research output: Contribution to journalArticle

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
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. / Draft assembly of elite inbred line PH207 provides insights into genomic and transcriptome diversity in maize. In: Plant Cell. 2016 ; Vol. 28, No. 11. pp. 2700-2714.
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