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Title: HOW MANY GENES WILL NOT BE IN MAIZE INBRED B73?

Author
item OKAGAKI, R - UNIVERSITY OF MINNESOTA
item SCHMIDT, C - UNIVERSITY OF MINNESOTA
item STEC, A - UNIVERSITY OF MINNESOTA
item Rines, Howard
item PHILLIPS, R - UNIVERSITY OF MINNESOTA

Submitted to: Maize Genetics Cooperation Newsletter
Publication Type: Abstract Only
Publication Acceptance Date: 2/20/2006
Publication Date: 3/31/2006
Citation: Okagaki, R.J., Schmidt, C.M., Stec, A.O., Rines, H.W., Phillips, R.L. 2006. How many genes will not be in maize inbred B73? Maize Genetics Cooperation Newsletter. 80:38. Available: http://www.agron.missouri.edu/mnl/80/38okagi.pdf

Interpretive Summary:

Technical Abstract: We are finding evidence that the genome sequences for numerous maize ESTs are not present in the B73 maize genome. These gene-like sequences can be found in other maize lines, but they appear to be missing in B73. Approximately 16,000 EST sequences that had been annotated as having come from A188 were downloaded from GenBank. EST sequences longer than 300 nucleotides were then searched against the maize B73 genomic sequences in the TIGR Maize Database, AZM Release 5.0. Approximately 500 EST sequences longer than 300 basepairs did not match a B73 genomic sequence with a probability value of e-10 or less, and thus may identify a maize gene that is not in the B73 genome. After repeating the process using the entire contig sequences developed by TIGR, PCR primers were developed against the remaining 63 EST sequences. PCR assays were used to detect the presence of these sequences in genomic DNA from A188, B73, and 12 other maize lines. We obtained results with 53 sets of primers. No products from B73 genomic DNA were detected with 17 primer sets, and 28 primer sets failed to amplify products from at least one of the maize lines. Twenty-five primer sets amplified products from all 14 lines tested. We are in the process of confirming these results by Southern blot analysis. To date, Southern blot analysis has confirmed the absence of 5 sequences in B73 out of the 10 sequences tested. Extrapolation of these results to the approximately 50,000 maize genes suggests there could be many gene-like sequences in A188 that are missing in B73.