• Integrated Physical and Genetic Map

• Genetic Mapping: High-Resolution Maize Population

• Physical Mapping

• Bioinformatics

INTEGRATED PHYSICAL AND GENETIC MAP

Goals

• Anchor ESTs and other markers to both the physical map and the genetic map
• Display the genetic and physical map with ready links to source information

Completed and Deliverable resources / Status September 23 2002

• Integrated Map Components

• Genetic Maps
      -IBM : 1800 RFLP and SSR markers
      -IBM Neighbors: IBM framework loci serve as fixed backbone onto which loci from other maps are assigned order and approximate coordinates

• Physical Map
     - Updated regularly with most recent FPC data
     - Currently: 250,065 BAC clones, 4847 contigs

• Anchoring the Physical Components and Genetic Markers

• BAC screening
√ Hybridization of filters (165,254 BACs = 10X)
-Core markers (90): 22 are single-copy and potential anchors
-Maize ESTs (9,371): MMP/Dupont/Incyte Genomics partnership

Overgo probes derived from Cornsensus unigene set
40% localize to a single contig
29% localize to two contigs

1207 sorghum, 211 maize, 305 rice markers
274 sequences are on maize map, 1870 on sorghum map
56% localize to one or more contigs

   √ PCR-based analysis of DNA pools (110,592 BACs = 6X)
               - 700 SSRs with genetic locations to date, others in process
               - 50 single-copy RFLPs

• Sequence mining for new markers

- SSR development
      Map genetically on IBM
      Map physically using BAC DNA pools

- SNP development
      Targeted at Cornsensus unigenes that hit single contigs in FPC
      2000 to be developed
     1000 to be mapped

• Resource availability

-Cornsensus unigenes in GenBank in High-Throughput cDNA (HTC) section
-Overgo primer sequences in MaizeDB
-BAC addresses at http://www.maizemap.org/resources.htm

• Integrated Map Display

• Side-by-side display of genetic map and unambiguously anchored BAC contigs
             -IBM map currently available
             -IBM Neighbors map available soon
• Database environment
• Information retrieved dynamically via pop-up windows
             -Links to genetic marker information
             -Links to BAC contigs in FPC
• Web address: http://www.maizemap.org/iMapDB/iMap.html

BACK TO TOP

GENETIC MAPPING: HIGH-RESOLUTION MAIZE POPULATION

Goals

• Construct a high-resolution genetic map of maize as an anchor for mapping BAC clones and maize mutants
• Produce high-efficiency markers for mapping
• Make mapping materials and seed available

Completed and Deliverable resources / Status September 23 2002

• IBM Map Preparation and community mapping resources
• 1317 RFLP probes screened
• 1006 RFLP markers mapped on 302 lines of Intermated B73/Mo17 (IBM) population, equivalent in resolution to 906 recombinant inbred lines
• IBM map posted includes 1006 RFLP and 787 SSR markers, to be enhanced with new data and periodic iterations
• Map scores and screening images posted at http://www.maizemap.org/
• Seed for 302-line IBM population reproduced, quality-checked, and made available (http://w3.ag.uiuc.edu/maize-coop/IBM-Stocks.html)
• IBM DNA from 94 mapping lines (equivalent in resolution to 282 recombinant inbred lines) is available in 96-well format with 3 quality-control primers (http://www.maizemap.org/dna_kits.htm)
• Community IBM Mapping Data Entry (CIMDE), on-line map score entry for 94-line set is available (http://www.maizemap.org/CIMDE/cimde.html). Community mapping data from the Chromatin Project, and from other sources that so choose, will be incorporated into IBM Neighbors map
• RFLP markers
• In addition to mapped historical markers, 276 new markers from PstI and Mutator-adjacent sequences were produced and mapped
• SSR markers
• 1354 UMC SSRs and all public SSRs, with released original sequence, primer sequence, repeat motif, map position, and screening image against 11 diverse inbred lines at http://www.agron.missouri.edu/ssr.html
• SSR maps of 3 populations are posted; 900 UMC SSR loci, of which 580 are on IBM, are mapped on multiple populations; 787 loci for 2074 public SSRs are mapped on IBM, 1146 are on IBM neighbors
• SSR and RFLP screening images are publicly available
• SNP markers
• SNPs under development focus on unigenes that hit only a single contig
• Genomic sequencing across 12 lines has been completed for regions corresponding to 1600 unigenes
• Target completion of the SNP project is Fall 2003, with a goal of SNP discovery in 3000 unigenes and mapping of 1000 on the IBM population
• Genotyping
• Software for automated genotyping and validation of RFLP, SSR, and INDEL scoring, and preparation of mapping files, is completed and in use
• SNP assay by primer extension and detection on the ABI 3700 generates data automatically genotyped and processed for mapping
• WWW interface for input of community map scores for the 94-line IBM map population is available
• Mutant mapping
• 380 Mutants analyzed, 331 mutants mapped vs. SSRs.
• Samples of segregating F2 seed for over 1300 mutants, often involving two or more inbred lines, may be requested from CoeE@missouri.edu
• Ontology
• The Plant Ontology Consortium ™ (POC) has been instituted, and systematizations of terminology are in progress in collaboration with MaizeDB, TAIR, Gramene, and the International Rice Research Institute (IRRI)

BACK TO TOP

PHYSICAL MAPPING

Goals

• Create libraries of cloned genomic maize DNAs with deep genome coverage
• Fingerprint and assemble the BACS into contigs
• Display contig assembly by FPC
• Make BAC filters and libraries available for screening and sequencing

Deliverable Resources/ Status September 23 2002

• BAC libraries from B73 DNA

Enzyme	# of 384-well plates	Avg insert size (kb)	Genome equivalents
HindIIIa	645	137	12.6
EcoRIb	288	163	7
MboIb,c	288	167	7

a Constructed by the Wing laboratory at the Clemson University Genomics Institute (CUGI)

b Constructed by the de Jong laboratory at the Children's Hospital of Oakland Research Institute (CHORI)

c Funded by Jo Messing's NSF Plant Genome award

• BAC Availability

• Filters: available from CUGI (http://www.genome.clemson.edu/)
-6X HindIII BAC filter set (6 filters, plates 1-288)
-7X EcoRI BAC filter set (6 filters, CHORI 201, plates 1-288)
-7X MboI filter set (6 filters, CHORI 201, plates 289-576)

• Libraries
-HindIII library available from CUGI
-EcoRI and MboI libraries available from CHORI
(http://www.chori.org/bacpac/)

• BAC Fingerprinting / Contig Assembly

• Fingerprinting underway for all clones in all three libraries
• Completion date for fingerprinting and finishing: June 2003
• Projected genome coverage for fingerprinting: 20X
• Progress viewable: http://genome.arizona.edu/fpc/maize/
• As of August 8, 2002, 250,064 fingerprints (13X) and 10,191 markers form 4847 contigs and 11,191 singletons at cutoff 10^-12

• BAC filter hybridization

• Total number of markers addressed to date: 10,191
• Marker types
     -Maize ESTs (Cornsensus)
     -Complex probes: telomere, centromere, knob, ribosomal
     -Core RFLP markers
     -Cross-species probes from cereals
• BAC addresses available at http://www.maizemap.org/resources.htm

• BAC pools

• Six-dimensional pooling scheme
• 288 pools, 110,592 BACs, 6X
• Quality comparisons to filter hybridization results: favorable
• PCR-based screening  
                    -all mapped SSRs
                    -single-copy RFLPs
• Excellent quality of results as judged by comparison to filter hybridization

BACK TO TOP

BIOINFORMATICS

Goals

• LIMS - Laboratory Information Management System

• Components
     -NT server
     -Sybase database management system
     -Visual Basic and Java interfaces

• Additional Software Tools

• WWW CIMDE
   - LIMS tool
   - Receives submitted map scores for 94-line IBM population
   - Returns map positions to submitter
   - Web address: http://www.maizemap.org/CIMDE/cimde.html

-Uses input sequence as query against all public maize
-Returns map location if known, and links to related sequences
-Web address: http://www.maizemap.org/cgi-bin/zmMSL.cgi

• Map Displays

• Integrated Map (iMAP) user interface (see Figure)
    -Side-by-side display of genetic map and anchored contigs
    - http://www.maizemap.org/iMapDB/iMap.html

• Compare Maps display (cMap)
    - Side-by-side display of genetic maps
    - Includes maize, sorghum and rice maps
    - http://www.agron.missouri.edu/cMapDB/cMap.html

• External Links, Semantic Checking

• Links to TIGR and ZmDB EST contigs, to GenBank, and to CSH MTM phenotypes are supplied by MaizeDB
• Semantic checking of probe and locus nomenclature, and for map locations (MSL, cMap, iMap), is supplied by MaizeDB

• Educational Links

• Interactive Maize Plant (IMP): http://www.agron.missouri.edu/IMP/frames_imp2.html
• Controlled Pollinations of Maize/Corn: http://www.agron.missouri.edu/IMP/WEB/pollen.htm)
• Plant Genomics Internships at MU (PGI@MU)
     -Summer research internship program for undergraduates
     -http://www. lsurop.missouri.edu/PGI

• Project information
• Data generated
• Summaries of progress
• http://www.maizemap.org

BACK TO TOP