Assignment of Y-chromosomal SNPs found in Japanese population to Y-chromosomal haplogroup tree

被引：12
作者：
Naitoh, Sae [1 ]
Kasahara-Nonaka, Iku [1 ]
Minaguchi, Kiyoshi [1 ]
Nambiar, Phrabhakaran [2 ]
机构：
[1] Tokyo Dent Coll, Dept Forens Odontol, Chiba 2618502, Japan
[2] Univ Malaya, Dept Gen Dent Practice & Oral & Maxillofacial Ima, Fac Dent, Kuala Lumpur, Malaysia
来源：
JOURNAL OF HUMAN GENETICS | 2013年 / 58卷 / 04期
关键词：
haplogroup; Japanese; !text type='JS']JS[!/text]NP database; non-recombining portions of Y; Y chromosome; Y-chromosomal haplogroup tree; HAPLOTYPES; ORIGINS; IDENTIFICATION; MARKER; AINU;
D O I：
10.1038/jhg.2012.159
中图分类号：
Q3 [遗传学];
学科分类号：
071007 ; 090102 ;
摘要：
The relationship between Y-chromosome single-nucleotide polymorphisms (SNPs) registered in the Japanese SNP (JSNP) database (http://snp.ims.u-tokyo.ac.jp) and Y-binary haplogroup lineages was investigated to identify new Y-chromosomal binary haplogroup markers and further refine Y-chromosomal haplogroup classification in the Japanese population. We used SNPs for which it was possible to construct primers to make Y-specific PCR product sizes small enough to obtain amplification products even from degraded DNA, as this would allow their use not only in genetic but also in archeological and forensic studies. The genotype of 35 JSNP markers were determined, of which 14 were assigned to appropriate positions on the Y-chromosomal haplogroup tree, together with 5 additional new non-JSNP markers. These markers defined 14 new branches (C3/64562 + 13, C3/2613-27, D2a1b/006841*, D2a1b/119166-11A, D2a/022456*, D2a/119166-11A, D2a/119167rec/119167-40rec*, D2a/75888-GC, O3a3c/075888-9T/10T*, O3a3c/075888-9T/9T, O3a3/8425 + 6, O3a3/119166-13A*, O3a3/008002 and O3a4/037852) and 21 new internal markers on the 2008 Y-chromosome haplogroup tree. These results will provide useful information for Y-chromosomal polymorphic studies of East Asian populations, particularly those in and around Japan, in the fields of anthropology, genetics and forensics. Journal of Human Genetics (2013) 58, 195-201; doi: 10.1038/jhg.2012.159; published online 7 February 2013
引用
收藏
页码：195 / 201
页数：7
相关论文
共 22 条
[1]   The case of the unreliable SNP: Recurrent back-mutation of Y-chromosomal marker P25 through gene conversion [J].
Adams, Susan M. ;
King, Turi E. ;
Bosch, Elena ;
Jobling, Mark A. .
FORENSIC SCIENCE INTERNATIONAL, 2006, 159 (01) :14-20
[2]  
Ellis N, 2002, GENOME RES, V12, P339
[3]  
FUJITA T, 1995, BIOTECHNIQUES, V19, P532
[4]   The Himalayas as a directional barrier to gene flow [J].
Gayden, Tenzin ;
Cadenas, Alicia M. ;
Regueiro, Maria ;
Singh, Nanda B. ;
Zhivotovsky, Lev A. ;
Underhill, Peter A. ;
Cavalli-Sforza, Luigi L. ;
Herrera, Rene J. .
AMERICAN JOURNAL OF HUMAN GENETICS, 2007, 80 (05) :884-894
[5]   DNA Commission of the International Society of Forensic Genetics: recommendations on forensic analysis using Y-chromosome STRs [J].
Gill, P ;
Brenner, C ;
Brinkmann, B ;
Budowle, B ;
Carracedo, A ;
Jobling, MA ;
de Knijff, P ;
Kayser, M ;
Krawczak, M ;
Mayr, WR ;
Morling, N ;
Olaisen, B ;
Pascali, V ;
Prinz, M ;
Roewer, L ;
Schneider, PM ;
Sajantila, A ;
Tyler-Smith, C .
INTERNATIONAL JOURNAL OF LEGAL MEDICINE, 2001, 114 (06) :305-309
[6]  
Gusmao L, 2001, ANN HUM GENET, V65, P285, DOI 10.1046/j.1469-1809.2001.6530285.x
[7]   Gene-based SNP discovery as part of the Japanese Millennium Genome Project: identification of 190562 genetic variations in the human genome [J].
Haga, H ;
Yamada, R ;
Ohnishi, Y ;
Nakamura, Y ;
Tanaka, T .
JOURNAL OF HUMAN GENETICS, 2002, 47 (11) :605-610
[8]   Dual origins of the Japanese: common ground for hunter-gatherer and farmer Y chromosomes [J].
Hammer, MF ;
Karafet, TM ;
Park, H ;
Omoto, K ;
Harihara, S ;
Stoneking, M ;
Horai, S .
JOURNAL OF HUMAN GENETICS, 2006, 51 (01) :47-58
[9]  
HAMMER MF, 1995, AM J HUM GENET, V56, P951
[10]   JS']JSNP: a database of common gene variations in the Japanese population [J].
Hirakawa, M ;
Tanaka, T ;
Hashimoto, Y ;
Kuroda, M ;
Takagi, T ;
Nakamura, Y .
NUCLEIC ACIDS RESEARCH, 2002, 30 (01) :158-162
123