Award Abstract #0110134
A Radiation Hybrid System for the Genetic and Physical Mapping of the Corn Genome

NSF Org:	DBI Division of Biological Infrastructure
Initial Amendment Date:	September 13, 2001
Latest Amendment Date:	October 5, 2006
Award Number:	0110134
Award Instrument:	Continuing grant
Program Manager:	Diane Jofuku Okamuro DBI Division of Biological Infrastructure BIO Directorate for Biological Sciences
Start Date:	October 1, 2001
Expires:	September 30, 2007 (Estimated)
Awarded Amount to Date:	$3208737
Investigator(s):	Ronald Phillips phill005@umn.edu (Principal Investigator) Howard Rines (Co-Principal Investigator)
Sponsor:	University of Minnesota-Twin Cities 200 OAK ST SE MINNEAPOLIS, MN 55455 612/624-5599
NSF Program(s):	PLANT GENOME RESEARCH PROJECT
Field Application(s):
Program Reference Code(s):	BIOT, 9251, 9232, 9109
Program Element Code(s):	1329

ABSTRACT



The large and complex genome of corn has impeded integrated mapping and sequencing efforts. The anticipated isolation of all the corn genes, however, indicates the pressing need for efficient mapping systems and/or a reduction in genome complexity. This research addresses the need by developing multifunctional genetic materials that include the ability to rapidly physically map DNA sequences to chromosomes and chromosome segments of 1 Mbp or less. These materials coupled with microarray technology will allow the mapping of thousands of sequences in a single set of experiments. The complete set of oat-corn chromosome addition lines has been recovered. Hybridization of sequences to DNA of the 10 additions allows placement of sequences to chromosome including duplicated sequences or multigene families. Radiation hybrid (RH) lines are then produced by gamma irradiation of the addition lines. The research will focus on obtaining fertile lines for all 10 addition plants and on creating RH mapping panels for all 10 chromosomes. Preliminary data indicates the feasibility for efficient physical mapping of genes (ESTs and known genes) to chromosome and chromosome segment, and the identification and mapping of duplicated sequences. The ESTs isolated at Stanford University will initially be mapped. An RH physical map will complement other corn physical mapping systems by providing a scaffold at the subchromosomal fragment level. The specific objectives of this renewal are to (1) recover a complete set of fertile oat-corn addition lines and characterize the phenotype, cytology, chromosome stability and transmission of the addition and RH lines; (2) produce RH mapping panels for all 10 individual chromosomes for both low and high resolution mapping; (3) enable high-throughput mapping of ESTs to chromosomal regions for candidate gene discovery and comparative genome studies.

Deliverables:

1. Fertile oat-corn addition lines for each corn chromosome; seed, tissue or DNA of the addition lines for distribution.

2. DNA panels of radiation hybrid lines for low and high-resolution mapping of each chromosome.

3. Radiation hybrid mapping panels for each chromosome, along with appropriate resources that will allow other researchers to physically map genes to within one to five megabases.

4. A database of sequences mapped to chromosome and to radiation hybrid lines as the lines become available. Data to be provided to existing web resources.

5. Data about relative quantities of repetitive sequences per chromosome measured using microarray technology with genomic DNA from the oat-corn addition lines.

6. Web resources describing genetic materials, radiation hybrid mapping, and sequences mapped.

Project address:

University of Minnesota, Dept. of Agronomy and Plant Genetics 411 Borlaug Hall, 1991 Upper Buford Circle, St. Paul, MN 55108

Internet Addresses (Web and E-mail) for Project Information:

http://agronomy.coafes.umn.edu/cornpep/nsf/

PUBLICATIONS PRODUCED AS A RESULT OF THIS RESEARCH

Kynast,R.G.; Okagaki,R.J.; Galatowitsch,M.W.; Granath,S.R.; Jacobs,M.S.; Stec,A.O.; Rines,H.W.; and Phillips,R.L.. "Dissecting the maize genome by using chromosome addition and radiation hybrid lines.," Proc Natl. Acad. Sci. USA, v.101, 2004, p. 9921.

Kynast,R.G; Okagaki,R.J.; Rines,H.W.; and Phillips,R.L.. "Maize individualized chromosomes and derived radiation hybrid lines and their use in functional genomics.," Functional Integr. Genomics, v.2, 2002, p. 60.

Kynast,R.G; Riera-Lizarazu,O.; Vales,I.M; Okagaki,R.J; Maquieira,S.D; Ananiev,E.V; Odland,W.E; Russell,C.D; Stec,A.O; Livingston,S.M; Zaia,H.A; Rines,H.W; and Phillips,R.L.. "A complete set of maize individual chromosome additions to the oat genome.," Plant Physiology, v.125, 2001, p. 1216.

Odland,W.; Baumgartner,A.; and Phillips,R.. "Ancestral rice blocks define multiple related regions in the maize genome.," The Plant Genome, a suppl. to Crop Science, v.46, 2006, p. S41.

Okagaki,R.J.; Kynast,R.G.; Livingston,S.M.; Russell,C.D.; Rines,H.W.; and Phillips,R.L.. "Mapping maize sequences to chromosomes using oat-maize chromosome addition materials.," Plant Physiology, v.125, 2001, p. 1228.

Vales,I.M.; Riera-Lizarazu,O.; Rines,H.W.; and Phillips,R.L.. "Transmission of maize chromosome 9 rearrangements in oat-maize radiation hybrids.," Genome, v.47, 2004, p. 1202.

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