Mining single-nucleotide polymorphisms from hexaploid wheat ESTs
作者： Daryl J Somers , Robert Kirkpatrick , Mariko Moniwa , Andrew Walsh
DOI: 10.1139/G03-027
关键词: Microsatellite 、 Genetic diversity 、 SNP genotyping 、 Genetic variation 、 Expressed sequence tag 、 Genetics 、 Gene mapping 、 Single-nucleotide polymorphism 、 Contig 、 Biology
摘要: Single-nucleotide polymorphisms (SNPs) represent a new form of functional marker, particularly when they are derived from expressed sequence tags (ESTs). A bioinformatics strategy was developed to discover SNPs within large wheat EST database and demonstrate the utility in genetic mapping diversity applications. collection > 90000 ESTs assembled into contiguous sequences (contigs), 45 random contigs were then visually inspected identify primer pairs capable amplifying specific alleles. We estimate that homoeologue variants occurred 1 24 bp frequency between genotypes SNP/540 (theta = 0.0069). Furthermore, we one diagnostic SNP test can be every contig with 10-60 members. Thus, databases an abundant source markers. Polymorphism information content for ranged 0.04 0.50 could mapped framework microsatellite markers using segregating populations. The results showed discovered ESTs, validated, applied conventional studies.
nrcresearchpress.com参考文章(24)
Dinakar Bhattramakki, Maureen Dolan, Mike Hanafey, Robin Wineland, Dave Vaske, James C. Register III, Scott V. Tingey, Antoni Rafalski, Insertion-deletion polymorphisms in 3' regions of maize genes occur frequently and can be used as highly informative genetic markers. Plant Molecular Biology. ,vol. 48, pp. 539- 547 ,(2002) , 10.1023/A:1014841612043
Vladimir Kanazin, Hope Talbert, Deven See, Phil DeCamp, Eviatar Nevo, Tom Blake, Discovery and assay of single-nucleotide polymorphisms in barley (Hordeum vulgare). Plant Molecular Biology. ,vol. 48, pp. 529- 537 ,(2002) , 10.1023/A:1014859031781
Gabor T. Marth, Ian Korf, Mark D. Yandell, Raymond T. Yeh, Zhijie Gu, Hamideh Zakeri, Nathan O. Stitziel, LaDeana Hillier, Pui-Yan Kwok, Warren R. Gish, A general approach to single-nucleotide polymorphism discovery Nature Genetics. ,vol. 23, pp. 452- 456 ,(1999) , 10.1038/70570
R. L. Gaut, J. F. Doebley, B. S. Gaut, M. I. Tenaillon, M. C. Sawkins, A. D. Long, Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp. mays L.) Proceedings of the National Academy of Sciences of the United States of America. ,vol. 98, pp. 9161- 9166 ,(2001) , 10.1073/PNAS.151244298
N.D. Coles, C.E. Coleman, S.A Christensen, E.N. Jellen, M.R. Stevens, A. Bonifacio, J.A. Rojas-Beltran, D.J. Fairbanks, P.J. Maughan, Development and use of an expressed sequenced tag library in quinoa (Chenopodium quinoa Willd.) for the discovery of single nucleotide polymorphisms Plant Science. ,vol. 168, pp. 439- 447 ,(2005) , 10.1016/J.PLANTSCI.2004.09.007
T. R. Endo, B. S. Gill, The Deletion Stocks of Common Wheat Journal of Heredity. ,vol. 87, pp. 295- 307 ,(1996) , 10.1093/OXFORDJOURNALS.JHERED.A023003
Marco Maccaferri, Maria Corinna Sanguineti, Enrico Noli, Roberto Tuberosa, Population structure and long-range linkage disequilibrium in a durum wheat elite collection Molecular Breeding. ,vol. 15, pp. 271- 290 ,(2005) , 10.1007/S11032-004-7012-Z
Daryl J. Somers, Peter Isaac, Keith Edwards, A high-density microsatellite consensus map for bread wheat ( Triticum aestivum L.) Theoretical and Applied Genetics. ,vol. 109, pp. 1105- 1114 ,(2004) , 10.1007/S00122-004-1740-7
David Edwards, Jacqueline Batley, Plant bioinformatics: From genome to phenome Trends in Biotechnology. ,vol. 22, pp. 232- 237 ,(2004) , 10.1016/J.TIBTECH.2004.03.002
D. L. Remington, J. M. Thornsberry, Y. Matsuoka, L. M. Wilson, S. R. Whitt, J. Doebley, S. Kresovich, M. M. Goodman, E. S. Buckler, Structure of linkage disequilibrium and phenotypic associations in the maize genome Proceedings of the National Academy of Sciences of the United States of America. ,vol. 98, pp. 11479- 11484 ,(2001) , 10.1073/PNAS.201394398