Maize simple repetitive DNA sequences: abundance and allele variation

Abstract

Microsatellites or simple sequence repeats, first demonstrated in human and other mammalian genomes, are being identified in many plant species. A database survey of 576 maize sequences from the GenBank and EMBL databases was made to determine the abundance of maize microsatellites. Two hundred potential microsatellites were identified. The relative abundance of the different repetitive motifs varied considerably and all possible dinucleotide and trinucleotide motif types were found. The three most abundant classes of microsatellites identified in this search were (AG/CT)n, (CCT/GGA)n, and (CCG/GGC)n repeats. Allelic variation was surveyed with 9 maize inbred lines representing diverse pedigrees. Amplification of DNA from these lines and analysis using high resolution agarose gels showed that 69 of the 200 potential microsatellites were polymorphic and yielded 2-4 alleles. A more complete screen of these loci against a wider array of maize germplasm using denaturing sequencing gels is now being conducted to more thoroughly evaluate these loci.