Efficient validation of single nucleotide polymorphisms in plants by allele-specific PCR, with an example from barley

被引：28

作者：

Soleimani, VD

Baum, BR ^{[1
]}

Johnson, DA

机构：

[1] Agr & Agri Food Canada, Cent Expt Farm, Ottawa, ON K1A 0C6, Canada

[2] Univ Ottawa, Ottawa Carleton Inst Biol, Ottawa, ON K1N 6N5, Canada

来源：

PLANT MOLECULAR BIOLOGY REPORTER | 2003年 / 21卷 / 03期

关键词：

allele-specific PCR; SNP validation;

D O I：

10.1007/BF02772803

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Although the increasing number of expressed sequence tags (ESTs) from the public domain has facilitated the detection of single nucleotide polymorphisms (SNPs), further validation is needed before they can be used as markers. For SNP validation, we have compared 2 independent methods: (1) the primer extension method followed by capillary electrophoresis on an ABI PRISM 3100 Genetic Analyzer and (2) nested PCR followed by agarose-based visualization. We present an assessment of the efficiency and costs associated with these methods, based on a sample of barley cultivars.

引用

收藏

页码：281 / 288

页数：8

相关论文

共 22 条

[1] Reliable identification of large numbers of candidate SNPs from public EST data [J].

Buetow, KH ;

Edmonson, MN ;

Cassidy, AB .

NATURE GENETICS, 1999, 21 (03) :323-325

[2]

Chen XN, 1999, GENOME RES, V9, P492

[3] SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines [J].

Ching, A ;

Caldwell, KS ;

Jung, M ;

Dolan, M ;

Smith, OS ;

Tingey, S ;

Morgante, M ;

Rafalski, AJ .

BMC GENETICS, 2002, 3 (1)

[4]

*CLEMS U GEN I, 2003, BARL EST PROJ

[5] Identification of 96 single nucleotide polymorphisms in eight genes involved in iron metabolism: efficiency of bioinformatic extraction compared with a systematic sequencing approach [J].

Douabin-Gicquel, V ;

Soriano, N ;

Ferran, H ;

Wojcik, F ;

Palierne, E ;

Tamim, S ;

Jovelin, T ;

McKie, AT ;

Le Gall, JY ;

David, V ;

Mosser, J .

HUMAN GENETICS, 2001, 109 (04) :393-401

[6]

Giesendorf BAJ, 1998, CLIN CHEM, V44, P482

[7] HIGH-DENSITY MULTIPLEX DETECTION OF NUCLEIC-ACID SEQUENCES - OLIGONUCLEOTIDE LIGATION ASSAY AND SEQUENCE-CODED SEPARATION [J].

GROSSMAN, PD ;

BLOCH, W ;

BRINSON, E ;

CHANG, CC ;

EGGERDING, FA ;

FUNG, S ;

IOVANNISCI, DA ;

WOO, S ;

WINNDEEN, ES .

NUCLEIC ACIDS RESEARCH, 1994, 22 (21) :4527-4534

[8] Patterns of single-nucleotide polymorphisms in candidate genes for blood-pressure homeostasis [J].

Halushka, MK ;

Fan, JB ;

Bentley, K ;

Hsie, L ;

Shen, NP ;

Weder, A ;

Cooper, R ;

Lipshutz, R ;

Chakravarti, A .

NATURE GENETICS, 1999, 22 (03) :239-247

[9]

Hamajima N, 2001, Expert Rev Mol Diagn, V1, P119, DOI 10.1586/14737159.1.1.119

[10] DNA METHYLATION AND MUTATION [J].

HOLLIDAY, R ;

GRIGG, GW .

MUTATION RESEARCH, 1993, 285 (01) :61-67