Frequencies and sequence characteristics of di-, tri-, and tetra-nucleotide microsatellites in wheat

Microsatellites have emerged as an important source of genetic markers for eukaryotic genomes. In this report, two wheat (Triticum aestivum L.) genomic libraries were screened for several di-, tri-, and tetranucleotide tandem repeats. Clones containing (AC)n, (AG)n, (TCT)n, and (TTG)n repeats were isolated and sequenced. On average, there was one (AC)n microsatellite every 292 kbp and one (AG)n microsatellite every 212 kbp. The trinucleotide tandem repeats (TCT)n and (TTG)n were about 10 times less common than the two dinucleotide tandem repeats tested and tetranucleotide tandem repeats were rare. Many of the microsatellites had more than 10 repeats. The maximum repeat number found for (AC)n was 36 and for (TCT)n was more than 50. The prevailing category of (AG)n microsatellites from (AG)n isolates was perfect repeats. About half of the (AC)n microsatellites were compound repeats, while most of the (TCT)n microsatellites were imperfect repeats. In a small sample, (TTG)n microsatellites consisted mainly of compound repeats. The most frequently associated repeats were (AC)n with (AG)n, (TCT)n with (TCC)n, and (TTG)n with (TGG)n. Among 32 pairs of microsatellite primers surveyed, seven produced polymorphic products in the expected size range and these loci were mapped using a hexaploid wheat mapping population or aneuploid stocks.