Each N2 mouse was genotyped using a total of 112 microsatellites with an average interval space between markers of 15 cM based on Kosambi's distances created by the MapManager QTX programme.
In a first phase, DNA samples from 68 individuals belonging to Families 1 and 2 were genotyped for a panel of 1000 microsatellite markers with average spacing of 4 cM along the genome (DeCode Genetics).
All four strains had moderate to high levels of microsatellite genetic variation, with average numbers of alleles per locus ranging from 6.8 to 9.4, effective numbers of alleles per locus ranging from 4.33 to 5.99 and observed heterozygosities ranging from 0.75 to 0.81.
The 405.73 Mb available genome sequences of foxtail millet were searched for microsatellites, and a total of 28 342 microsatellites comprising different kinds of desirable repeat-motifs (from DNRs to HNRs) were identified with average frequency of about 69 microsatellites per megabase of genomic sequences.
However, highly conserved microsatellites (NP3Ms) had a slightly different distribution (table 1), with megabase portions of the human genome containing substantially more of these microsatellites than average, providing clues that at least some microsatellites are not randomly maintained.
The novel polymorphic microsatellites produced an average of 4.9 alleles/locus, an average observed heterozygosity of 0.4296 and an average PIC (polymorphism information content) value of 0.4483.
Database analyses of genomic sequences have investigated the genome-wide frequency and distribution of microsatellites; such analyses find that the frequencies of microsatellites with different repeat motifs, as well as their average and maximum repeat lengths, vary widely both between and within motif size classes (di-, tetra-,etra-, or penta-nucleotide) [ 7, 8, 64- 68].
Testing for polymorphism in three reference parents and five doubled haploids resulted in the development of 89 polymorphic microsatellites markers with an average of 4.52 alleles (range 2 7), 40% of which were duplicated as determined by the observance of multiple alleles in clonal lines (see Additional File 1).
All microsatellite markers showed a high level of polymorphism (5 15 alleles per microsatellite marker, with an average of 9.11 alleles per locus).
