VII. MAIZE PROBE BANK

DNA clones in the public bank and distribution center at the UMC Maize RFLP Lab now total over 6400, of which we distribute more than 4700 (Table 1). This includes the large sets of sequenced cDNAs generated by Chris Baysdorfer, California State University - Hayward (designated csu), and by Tim Helentjaris (designated uaz or 5C, 6C, etc.), which represent the largest collection of candidate genes publicly available for maize. Over the last four years the UMC Maize Probe Bank has filled more than 540 requests for more than 16,000 clones to 31 countries, including 71 sets of the UMC Core Marker probes (Table 2), which have become the standard landmark probe set for gene and QTL trait mapping in maize. The UMC Core Marker set has become the standard landmark set for mapping genes, phenotypes and QTLs in maize. We are particularly pleased with the growth of interest in using maize clones in "developing" countries. During the period 1993-1996 we received a total of 69 probe requests, including 15 requests for core marker probe sets, from scientists in 15 "developing" countries for a total of 3338 probes distributed. China (PRC) led the list with a total of 1601 probes requested and received. The number of probes sent to scientists in China has increased each year, indicative of the continuing demand for probe distribution. Brazil was second with 979 probes requested. Third in probes requested was Mexico. In addition to the probe banking and distribution functions, the UMC RFLP Lab will place on the UMC Maize map any clones of defined function contributed by individual scientists. This greatly enriches the UMC Maize Genetic Map as a tool to define correlations of sequence to function. To date, we have placed 250 loci from 193 different "contributed" probes. Information about genes, probes, and maps is constantly updated on MaizeDB. Most of the sets of clones of other species being held by us are a backup to their primary storage site and for our use in cross-species mapping experiments.

Three major, current research efforts will have a major impact on probe resources for maize. The first is the development of SSR probes. The current total of available SSR primer sets for maize is 195. This number is increasing due to the efforts of Lynn Senior, USDA-ARS; Ben Burr, Brookhaven Natl. Labs., and others. As this number expands, coverage of the genome will soon reach a stage that some of the applications currently conducted with RFLPs may be replaced with SSRs. The second development is the expanded use of AFLP technology. For many private and large scale public efforts the cost effectiveness of AFLPs is very attractive. The major drawback for maize is the lack of codominant information for most AFLP alleles. The third development is the initiation of large-scale EST sequencing projects for maize. Four different private concerns are reportedly sequencing greater than 100,000 ESTs for maize. While the sequences and clones are currently being held as proprietary information by the companies, these efforts or a public EST effort in maize have the potential to place into the public sector a number of defined sequence probes much greater than currently available.

The activities of the RFLP Lab and the Probe Bank are meaningful as they contribute to the research needs of the community. The easiest avenue to request clones is through the "PROBE Requests" form in MaizeDB http://www.agron.missouri.edu or by email to musket@teosinte.agron.missouri.edu.

To contribute clones for distribution or to be mapped onto the UMC Maize Genetic Map contact Theresa Musket at the email listed above and she will inform you of the information and materials needed.

These activities are supported by USDA-ARS CRIS projects "Genetic Mechanisms and Molecular Genetic Resources for Corn" and "Maize Genome Database"; supplemental support from USDA Plant Genome and Germplasm Programs; USDA-NRI Plant Genome Panel Grant, "Maize cDNAs and Mutants Mapped in Concert; FAO/IAEA Coordinated Research Program, "Molecular Markers for Maize, Rye and Rice", and helpful contributions from CIMMYT, DeKalb Genetics Corporation, Monsanto-Ceregen, Mycogen Plant Sciences, and Pioneer Hi-Bred International Inc.

Table 1. Clones maintained by UMC RFLP Lab and Probe Bank.
Clone Set Abbreviation Type of Clone Total Number in Set Distribution by UMC
Asgrow asg maize genomic 85 Yes
Brookhaven National Laboratories bnl maize genomic 109 Yes
Brookhaven National Laboratories bnl maize cDNA 12 Yes
California State University-Hayward csu maize cDNA 1197 Yes
Cornell University bcd, cdo, rg, rz barley, oat, rice 151 No
Iowa State University isu maize cDNA 136 Yes
Mycogen Plant Sciences agr maize cDNA 413 Yes
Northrup King npi maize 30 No
Contributed Clones mostly maize 165 49 Yes, 116 No
Pioneer Hi-Bred International php maize genomic 161 Yes
Pioneer Hi-Bred International npi maize both 236 Yes
Rice Genome Research Program rgp rice 371 No
Texas A&M University txs sorghum genomic 145 No
University of Arizona uaz 5C, 6C, 7C maize cDNA 1920 Yes
University of Hohenheim Ch6S maize genomic 339 No
University of Minnesota  umn oat 29 No
University of Missouri  umc maize both 249 237 Yes, 12 No
University of Missouri-Rice  pOs rice genomic 18 Yes
University of Missouri-Rye  ScG rye genomic 171 Yes
University of Missouri-Tripsacum tda tripsacum genomic 476 20 Yes, 456 No
Total Number of Clones: 6413
Total Distributable Clones: 4752

Table 2. Clone distribution.
1993 1994 1995 1996
 

Country

No. of Requests No. of Clones No. of Core Sets No. of Requests No. of Clones No. of Core Sets No. of Requests No. of Clones No. of Core Sets No. of Requests No. of Clones No. of Core Sets
Argentina 1 12 1 1
Australia 1 2 7 18
Belgium 1 214 1 7
Brazil 1 210 1 214 4 387 3 7 168 1
Canada 1 2 1 2 3 4
China 7 277 1 2 354 2 5 426 3 9 544 3
Colombia 1 1 1 1
Costa Rica 1 1
Cuba 1 48
England 1 2
France 6 298 1 3 446 2 12 572 3 12 150
Germany 3 128 1 12 147 1 3 4
Hungary 1 118 1 1
India 1 1
Indonesia 1 20
Israel 1 118 1 4 2 113 1 1 92
Italy 1 7 1 13 2 207 1 3 56
Japan 11 624 4 9 292 1
Korea 2 183 1 3 4
Mexico 4 193 1 50 5 31 5 64
Netherlands 1 100
Poland 1 10
South Africa 3 25
Spain 1 1 2 10
Switzerland 2 2 2 2
Taiwan 1 5 1 4 1 112 1
Thailand 1 90 1
United Kingdom 1 92 2 134 1 2 17 6 101 1
Uruguay 1 1
USA 43 2093 58 1940 9 134 2506 17 121 1905 12
Yugoslavia 1 90 1
TOTALS: 66 3411 2 77 3517 15 203 5455 36 203 3688 18

Theresa Musket, Georgia Davis, Mary Polacco, Mike McMullen, and Ed Coe
 


Please Note: Notes submitted to the Maize Genetics Cooperation Newsletter may be cited only with consent of the authors

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