Y-chromosomal SNPs in Finno-Ugric-speaking populations analyzed by minisequencing on microarrays

An increasing number of single nucleotide polymorphisms (SNPs) on the Y chr omosome are being identified. To utilize the full potential of the SNP mark ers in population genetic studies, new genotyping methods with high through put are required. We describe a microarray system based on the minisequenci ng single nucleotide primer extension principle for multiplex genotyping of Y-chromosomal SNP markers. The system was applied for screening a panel of 25 Y-chromosomal SNPs in a unique collection of samples representing five Finno-Ugric populations. The specific minisequencing reaction provides 5-fo ld to infinite discrimination between the Y-chromosomal genotypes, and the microarray format of the system allows parallel and simultaneous analysis o f large numbers of SNPs and samples. In addition to the SNP markers, five Y -chromosomal microsatellite loci were typed. Altogether 10,000 genotypes we re generated to assess the genetic diversity in these population samples. S ix of the 25 SNP markers (M9, Tat, SRY10831, M17, M12, 92R7) were polymorph ic in the analyzed populations, yielding six distinct SNP haplotypes. The m icrosatellite data were used to study the genetic structure of two major SN P haplotypes in the Finns and the Saami in more detail. We found that the m ost common haplotypes are shared between the Finns and the Saami, and that the SMP haplotypes show regional differences within the Finns and the Saami , which supports the hypothesis of two separate settlement waves to Finland .