Maize is probably the most diverse of all crop species. The most significant practical consequence of the huge genetic diversity within maize is the phenomenon of hybrid vigor (heterosis). Distantly related lines tend to produce highly vigorous F1 hybrids, which are planted across the entire Corn Belt. Yet, the molecular basis of hybrid vigor is not understood. However, analysis of allelic regions between inbreds has indicated that the same interval differs in sequence and gene content. Therefore, it has been hypothesized that hybrid vigor could be explained on the basis of different, yet complementing, gene sets in the two inbreds. To investigate the extent of occurrence of such plus-minus type changes, the genomic organization of two gene-dense genomic regions, bz and fie2-orp2, will be investigated in a group of 12 inbred lines, races, and relatives of maize. Twelve size-fractionated, NotI BAC libraries will be constructed and bz and fie2 clones will be isolated and sequenced from each library. Thus, >1 Mb of DNA sequence will be generated and deposited in central sequence repositories. The distribution of polymorphism will be examined with respect to differences among heterotic groups and to the potential role of inbreeding in genome rearrangement. BAC data will be analyzed with population genetic methods to contrast evolutionary histories between genes and examine the relationship between linkage disequilibrium and recombination.
Specific deliverables are:
1. BAC libraries specific to the bz and fie2-orp2 regions from 12 accessions
2. 1 Mb sequence data deposited in GenBank and maizeGDB
3. Characterization of gene presence/absence and polymorphisms in the selected regions
4. Analysis of recombination rates across multiple accessions for the specific regions
PUBLICATIONS PRODUCED AS A RESULT OF THIS RESEARCH
Lai, Jinsheng, Yubin Li, Jo Messing, and Hugo K. Dooner. "Gene movement by Helitron transposons contributes to the haplotype variability of maize," Proc. Natl. Acad. Sci. USA, v.102, 2005, p. 968.
Wang, QH; Dooner, HK. "Remarkable variation in maize genome structure inferred from haplotype diversity at the bz locus," PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, v.103, 2006, p. 17644. View record at Web of Science
Qinghua Wang and Hugo K. Dooner. "Variability of bz haplotypes in maize and its wild relatives," Annual Maize Genetics Conference, Program and Abstracts, v.49, 2007, p. 100.
Du, C., J. Caronna, L. He, and H.K. Dooner. "Computational prediction and molecular confirmation of Helitron transposons in the maize genome," BMC Genomics, v.9, 2008, p. 51.
Dooner, H.K., and Weil, C.F.. "Give-and-take: interactions between DNA transposons and their host plant genomes," Curr. Opin. Genet. Devel., v.17, 2007, p. 486.
Messing, J. and H.K. Dooner. "Organization and variability of the maize genome," Curr. Opin. Plant Biol., v.9, 2006, p. 157.
Hollister, JD; Gaut, BS. "Population and evolutionary dynamics of Helitron transposable elements in Arabidopsis thaliana," MOLECULAR BIOLOGY AND EVOLUTION, v.24, 2007, p. 2515. View record at Web of Science
Sweredoski, M; DeRose-Wilson, L; Gaut, BS. "A comparative computational analysis of nonautonomous Helitron elements between maize and rice," BMC GENOMICS, v.9, 2008. View record at Web of Science
Lockton, S; Gaut, BS. "The Contribution of Transposable Elements to Expressed Coding Sequence in Arabidopsis thaliana," JOURNAL OF MOLECULAR EVOLUTION, v.68, 2009, p. 80. View record at Web of Science
Du, C., N. Fefelova, J. Caronna, L. He, and H.K. Dooner. "The polychromatic Helitron landscape of the maize genome," Proc. Natl. Acad. Sci., v.106, 2009, p. 19916-19.
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