High-throughput Mapping Tools for Maize Genomics

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A greater understanding of the organization and function of the maize genome is essential if US agriculture is to be successful in meeting the growing needs for maize as food, feed and a source of industrial raw materials as the US moves towards a "plant-based" economy. A team of molecular, quantitative and evolutionary geneticists and bioinformaticists has been assembled to build upon existing NSF investments in plant genomics to develop the novel high-throughput genetic mapping technologies and resources needed to meet this challenge. IDPs (InDel Polymorphisms) are a new class of co-dominant, allele-specific, genetic markers suitable for high-throughput analyses. The project team will identify, develop and genetically map 500 IDP markers specific to two widely used inbred lines (B73 and Mo17). To identify efficient IDP isolation strategies, the rates of IDP identification will be compared from four sources: 1) GenBank genic sequences; 2) Mu transposon flanking sequences; 3) 3' UTRs from ESTs; and 4) previously mapped RFLP markers. In addition, computational and wet lab approaches for the high-throughput acquisition and mapping of IDPs will be developed and optimized. The Mapping Array is a novel chip-based technology designed to genetically map a large number of non-redundant, sequence-defined cDNAs. During Phase I, an existing nylon-based protocol will be adapted to DNA "chips"; hybridization conditions optimized; various sources of "target" sequences (e.g., 3' UTRs, exons, full-length cDNAs and RFLP markers) tested; experimental design parameters determined; and mapping software developed. Upon successful completion of Phase I, 10,000 ESTs will be genetically mapped (Phase II). The sequences of EST 3' UTRs are of great value in distinguishing members of gene families, as potential sources of IDPs and for producing the gene-specific probes needed for the Mapping Array. The project team will sequence the 3' ends of 20,000 of the ESTs being isolated by the NSF-supported maize genome project headquartered at Stanford University. In addition, the insert size associated with each of these 20,000 clones will be ascertained. Because the proposed research will occur at the interface between molecular and computational genetics, it will provide important cross-disciplinary training opportunities for graduate students and post-doctoral scientists.