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The scanned maize sequences represent the whole large sequences available for maize in the public database, i.e., excluding the trace files and the gene-only sequences.
For selecting the markers for MAS, sequences presented only in maize rather than in rice were identified by BLAST, and used for primer design using Primer Premier 5.0.
An MNCP score of ≤1 means that the motif is more frequently present in a random set of maize sequences than the user data set of co-expressed genes.
Subfamily 1 consists of rice, wheat, switchgrass, sorghum, and maize sequences.
Silico3 was predicted from the B73 maize sequences.
Maize sequences for design of this chip were predominantly selected from the The Institute for Genomic Research TIGRR) maize gene index [ 33].
Maize sequences were identified by local BLASTP program as described above.
The majority of features present in the Maize Array Project are designed to EST contigs present in the TIGR maize sequence database [ 40].
The public maize sequence sets fall into three classes: (A) maize whole genome sequences, (B) maize repeats, and (c) maize gene enrichment sequences.
For maize, BAC contigs and annotation data were download from the maize sequence ftp site [ 43].
The PCR primers (see Table 2) were designed based on maize cDNA and genomic sequences from the Maize Sequence Database.
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