First successful assay of Y-SNP typing by SNaPshot minisequencing on ancient DNA.
Bouakaze C, Keyser C, Amory S, Crubézy E, Ludes B.
Institute of Legal Medicine, EA3428, Strasbourg, France, caroline.bouakaze@ulp.u-strasbg.fr.
In the present study, a set of 13 Y-chromosomal single nucleotide polymorphisms (Y-SNPs) selected for the identification of the most frequent Asian Y-haplogroups was included in an allele-specific primer extension assay. Single nucleotide polymorphism (SNP) genotyping was accomplished by co-amplification of these 13 DNA fragments within 2 multiplex PCRs followed by detection with 1 minisequencing reaction using the SNaPshottrade mark Multiplex kit and analysis of extension products by capillary electrophoresis. First developed on modern samples, the assay was optimized for the analysis of 11 ancient DNA (aDNA) samples from the Krasnoyarsk region (southern Siberia) that were dated from 5,500-1,800 years before present (YBP). SNP typing was successful for most of them, which were all assigned to Y-haplogroup R1a1 except one. These results show that SNPs are well-suited for the analysis of aged and degraded DNA samples. Moreover, we found that the SNaPshot minisequencing methodology is a convenient, robust, and efficient method for SNP typing. To our knowledge, this study reports the first successful investigation of Y-SNPs on aDNA samples. The potential use of Y-SNPs in both evolutionary and forensic fields is also discussed.
http://www.ncbi.nlm.nih.gov/sites/entrez?tmpl=NoSidebarfile&db=PubMed&cmd=Retrieve&list_uids=17534642&dopt=Abstract Archaeological samples consisted of 11 femoral-diaphyseal bone fragments from unrelated male individuals. These samples originated from the Krasnoyarsk Museum, southern
Siberia. One of them was attributed to the Afanassievo culture (3,500–2,500 B.C.), 3 to the Andronovo culture (2,500–1,500 B.C.), 6 to the Tagar culture (800–200 B.C.)
and the remaining 1 to the Tachtyk culture (200 B.C.–200 A.D.).
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The typing always failed for 2 samples, the oldest sample belonging to the Afanasievo culture (3,500–2,500 B.C.) and 1 belonging to the Tagar culture (800–200 B.
C.). This can be explained by the fact that the DNA content of these two bone samples was too low according to quantitation
results (Table S3 of the ESM). Among the nine remaining samples, eight were assigned to Y-haplogroup R1a1 and one to Y-haplogroup C(xC3).
В подготовке находится статья этого коллектива по тем-же образцам с анализом по STR и mtDNA маркерам, что повзволит сузить круг возможных родственных популяций.
R1a1 одна из основных индоевропейских гаплогрупп, (но также есть с высокой частотой и у киргизов, повидимому из-за субстрата)
http://en.wikipedia.org/wiki/Haplogroup_R1a1_%28Y-DNA%29
С - типично монголоидная группа
http://en.wikipedia.org/wiki/Haplogroup_C_%28Y-DNA%29
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