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Project Documentation & Protocols: Maize Mapping Project: General Information (Feb. 2002)

An Integrated Genetic and Physical Map for Maize, to provide the draft foundation for complete or partial sequencing of this most important US crop, is approximately half complete. The target is to define contiguous, overlapping physical pieces (contigs) of the maize genome to the greatest extent possible. Maize has 10 chromosomes, making 10 the minimum number of such contigs, but the size of the genome (2.5 billion base pairs) and its complexity suggest rather that a number between 2,000 and 5,000 contigs may be attainable with realistic investments of time and effort by mid-2003.

  • At the halfway stage, the contig count has been dropping and is down to 7,315 BAC contigs and 7,730 singles among 192,000 fingerprinted clones (9X from two libraries). The analysis includes BAC addresses of 7,974 DNA markers, of which 135 are anchored to the genetic map so far.
  • Markers and anchors have been mined from 10,300 unigenes. An integrated map interface (iMAP) is available...

High-resolution Genetic Mapping Resources for the integrated map are prepared and are available to researchers.

  • Intermated B73/Mo17 (IBM) Map with 1800 RFLP and SSR markers is provided, on a population of 302 lines equivalent in resolution to 906 recombinant inbred lines, with map scores.
  • Seed supplies of IBM increased, quality checked, and made available. DNA from a 94-line subset is available for community mapping.
  • SSR Maps are provided, with 1,354 new SSRs among 3 populations.
  • Screening images are provided for RFLP and SSR markers.
  • Pool analysis of markers from probes mapped in sorghum and rice is in progress.

Physical Mapping Materials and Data for the integrated map have been derived and are available to researchers.

  • Three BAC libraries prepared with three different enzymes, containing ~27 genome equivalents, are available as filters and as clones.
  • Fingerprinting of 450,000 BACs, addressing, and anchoring of BAC contigs is approximately half completed and the data are available.
  • Addressing of BAC filters with complex markers (telomere, centromere, knob, ribosomal probes) is completed.
  • Pools of BACs from a 48x48x48 array in 6 dimensions are made and validated. Addresses with ~100 SSRs are defined and deconvoluted.

Development and Enhancement of Curation and Access to Maize Genomics Data, the basis for high-throughput and for high-fidelity processes and products, provide the tools, the analytical base, and the presentation utilities for the project.

  • Automated applications for SSR and RFLP scoring, and for preparation of map files, are completed and in use. Applications are to be extended to SNPs, INDELs, and AFLPs, for which data will be scored and ported automatically. Utilities for base calling and trimming of sequences, and an SSR Finder linked with Primer3 and BLAST, are completed and in use. WWW interfaces for community input of map data, and for a beta-version Mapped Sequence Locator to return map location, are completed.
  • Comparison Map (cMap) display is deployed for genetic maps, with popups for screening data and for dynamic retrieval of marker links.
  • Integrated Map (iMAP) displaying genetic markers associated with contigs is completed and available, and provides access to probes and other research links. iMap operates in a database environment, where updating of physical and genetic map content is designed to be inherently incorporated.

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