LOW-FREQUENCY OF MICROSATELLITES IN THE AVIAN GENOME

A better insight into the occurrence of microsatellites in a range of taxa may help to understand the evolution of simple repeats. Previous studies have found the relative abundance of several repeat motifs to differ among mammals, invertebrates, and plants. Absolute numbers of m icrosatellites also tend to correlate positively with genome size. We analyzed the occurrence, frequency, and distribution of microsatellite s in birds, a taxol 1 with one of the smallest known genome sizes amon g vertebrates. Dot-blot hybridization revealed that about half of 22 d ifferent di-, tri-, and tetranucleotide repeat motifs were clearly mor e common il 1 human than in three species of birds: chicken, woodpecke r, and swallow. For the remaining motifs no clear difference was found . From searching avian database sequences we estimated there to be 30, 000-70,000 microsatellites longer than 20 bp in the avian genome. The number of (CA)(greater than or equal to 10) would be around 7000-9000 and the number of (CA)(greater than or equal to 14) about 3000. The ca lculated density of avian microsatellites [total, one every 20-39 kb; (CA)(greater than or equal to 10), one every 136-150 kb) is much lower than that estimated for the human genome [one every 6 and 30 kb, resp ectively). This may be explained by the Fact that the avian genome con tains relatively less noncoding DNA than most mammals and that avian S INE/LINE elements do not terminate in poly(A) tails, which are known t o provide a resource for the evolution of simple repeats in mammals. W e found no association between microsatellites and SINEs in birds. Pri med in situ labeling suggested fairly even distribution of (CA)(n) rep eats over chicken macrochromosomes and intermediate chromosomes, where as the microchromosomes, a large part of the Z and W chromosomes, and most telomeres and centromeres had very low concentrations of (CA), mi crosatellites. The scarcity of microsatellites on the microchromosomes is compatible to these regions likely being unusually rich In coding sequences. The low microsatellite density in the genome in general and on the microchromosomes in particular imposes an obstacle for the dev elopment of marker-rich genetic maps of chicken and other birds, and f or the localization of quantitative trait genes.