A pipeline for high throughput detection and mapping of SNPs from EST databases

Molecular Breeding

Volumn 26, Issue 1, 2010, Pages 65-75

  Anithakumari, A M ^a   Tang, Jifeng ^b   van Eck, Herman J ^a   Visser, Richard G F ^a   Leunissen, Jack A M ^a   Vosman, Ben ^a   van der Linden, C Gerard ^a  

^a WAGENINGEN UNIVERSITY   (Netherlands)

^b KEYGENE N V   (Netherlands)

Author keywords

EST database; Illumina GoldenGate assay; Potato; QualitySNP

Indexed keywords

DATABASE SYSTEMS; GENES; MAPPING; POPULATION STATISTICS;

EST DATABASE; GENETIC VARIATION; GENOTYPING; HIGH-THROUGHPUT DETECTION; ILLUMEN GOLDENGATE ASSAY; ILLUMINA; MAPPING POPULATIONS; POTATO; QUALITYSNP; SINGLE NUCLEOTIDE POLYMORPHISMS;

PIPELINES;

SOLANUM TUBEROSUM;

EID: 77952424242     PISSN: 13803743     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11032-009-9377-5     Document Type: Article

References (37)

1. Ablett G, Hill H, Henry R (2006) Sequence polymorphism discovery in wheat microsatellite flanking regions using pyrophosphate sequencing. Mol Breeding 17: 281-289.
2. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215: 403-410.
3. Barker G, Batley J, O'Sullivan H, Edwards KJ, Edwards D (2003) Redundancy based detection of sequence polymorphisms in expressed sequence tag data using autoSNP. Bioinformatics 19: 421-422.
4. Bryan GT, Wu KS, Farrall L, Jia Y, Hershey HP, McAdams SA, Faulk KN, Donaldson GK, Tarchini R, Valent B (2000) A single amino acid difference distinguishes resistant and susceptible alleles of the rice blast resistance gene Pi-ta. Plant Cell 12: 2033-2045.
5. Ching A, Caldwell K, Jung M, Dolan M, Smith O, Tingey S, Morgante M, Rafalski A (2002) SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines. BMC Genetics 3: 19.
6. Choi IY, Hyten DL, Matukumalli LK, Song Q, Chaky JM, Quigley CV, Chase K, Lark KG, Reiter RS, Yoon MS, Hwang EY, Yi SI, Young ND, Shoemaker RC, van Tassell CP, Specht JE, Cregan PB (2007) A soybean transcript map: gene distribution, haplotype and single-nucleotide polymorphism analysis. Genetics 176: 685-696.
7. Collard BCY, Jahufer MZZ, Brouwer JB, Pang ECK (2005) An introduction to markers, quantitative trait loci (QTL) mapping and marker-assisted selection for crop improvement: The basic concepts. Euphytica 142: 169-196.
8. Fan JBOA, Shen R, Kermani BG, Garcia F, Gunderson KL, Hansen M, Steemers F, Butler SL, Deloukas P, Galver L, Hunt S, McBride C, Bibikova M, Rubano T, Chen J, Wickham E, Doucet D, Chang W, Campbell D, Zhang B, Kruglyak S, Bentley D, Haas J, Rigault P, Zhou L, Stuelpnagel J, Chee MS, Wickham E, Doucet D, Chang W, Campbell D, Zhang B, Kruglyak S, Bentley D, Haas J, Rigault P, Zhou L, Stuelpnagel J, Chee MS (2003) Highly parallelSNP genotyping. Cold Spring Harb Symp Quant Biol 68: 69-78.
9. Feingold S, Lloyd J, Norero N, Bonierbale M, Lorenzen J (2005) Mapping and characterization of new EST-derived microsatellites for potato (Solanum tuberosum L.). Theor and Appl Gen 111: 456-466.
10. Hanneman RE PS (1967) Crossability of 24-chromosome potato hybrids with 48-chromosome cultivars. Potato Research 10: 62-73.
11. Hoskins RA, Phan AC, Naeemuddin M, Mapa FA, Ruddy DA, Ryan JJ, Young LM, Wells T, Kopczynski C, Ellis MC (2001) Single nucleotide polymorphism markers for genetic mapping in Drosophila melanogaster. Genome Res 11: 1100-1113.
12. Hyten DL, Song Q, Choi IY, Yoon MS, Specht JE, Matukumalli LK, Nelson RL, Shoemaker RC, Young ND, Cregan PB (2008) High-throughput genotyping with the GoldenGate assay in the complex genome of soybean. Theor and Appl Gen 116: 945-952.
13. Jacobsen E (1978) Die chromosomen verdopplung in der zuchtung dihaploider kartoffeln. PhD thesis, Rheinischen Friedrich Wilhelm Universitat, Bonn. 159 pp.
14. Jacobsen E (1980) Increase of diplandroid formation and seed set in 4× × 2× crosses in potatoes by genetical manipulation of dihaploid and some theoretical consequences. Zeitschrift für Pflanzenzuchtung 85: 110-121.
15. Jander G, Norris SR, Rounsley SD, Bush DF, Levin IM, Last RL (2002) Arabidopsis map-based cloning in the post-genome era. Plant Physiol 129: 440-450.
16. Marth GT (1999) A general approach to single-nucleotide polymorphism discovery. Nature Genet 23: 452-456.
17. Masouleh AK, Waters DLE, Reinke RF, Henry RJ (2009) A high-throughput assay for rapid and simultaneous analysis of perfect markers for important quality and agronomic traits in rice using multiplexed MALDI-TOF mass spectrometry. Plant Biotechnol J 7: 355-363.
18. McNally KL, Bruskiewich R, Mackill D, Buell CR, Leach JE, Leung H (2006) Sequencing multiple and diverse rice varieties. Connecting whole-genome variation with phenotypes. Plant Physiol 141: 26-31.
19. Milbourne D, Meyer RC, Collins AJ, Ramsay LD, Gebhardt C (1998) Isolation, characterisation and mapping of simple sequence repeat loci in potato. Mol Gen Genet 259: 233-245.
20. Rafalski A (2002) Applications of single nucleotide polymorphisms in crop genetics. Curr Opin Plant Biol 5: 94-100.
21. Rostoks N, Borevitz J, Hedley P, Russell J, Mudie S, Morris J, Cardle L, Marshall D, Waugh R (2005) Single-feature polymorphism discovery in the barley transcriptome. Genome Biol 6: R54.
22. Rostoks N, Ramsay L, MacKenzie K, Cardle L, Bhat PR, Roose ML, Svensson JT, Stein N, Varshney RK, Marshall DF, Graner A, Close TJ, Waugh R (2006) Recent history of artificial outcrossing facilitates whole-genome association mapping in elite inbred crop varietes. Proc Natl Acad Sci USA 103: 18656-18661.
23. Sachidanandam R, David Weissman SCS, Kakol JerzyM, Lincoln D, The International SNP Map Working Group et al (2001) A map of human genome sequence variation containing 1. 42 million single nucleotide polymorphisms. Nature 409: 928-933.
24. Schlotterer C (2004) The evolution of molecular markers-just a matter of fashion? Nature Reviews Genetics 5: 63-69.
25. Shen Y-J, Jiang H, Jin J-P, Zhang Z-B, Xi B, He Y-Y, Wang G, Wang C, Qian L, Li X, Yu Q-B, Liu H-J, Chen D-H, Gao J-H, Huang H, Shi T-L, Yang Z-N (2004) Development of genome-wide DNA polymorphism database for map-based cloning of rice genes. Plant Physiol 135: 1198-1205.
26. Shen R, Fan J-B, Campbell D, Chang W, Chen J, Doucet D, Yeakley J, Bibikova M, Wickham Garcia E, McBride C, Steemers F, Garcia F, Kermani BG, Gunderson K, Oliphant A (2005) High-throughput SNP genotyping on universal bead arrays. Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis 573: 70-82.
27. Somers DJ, Kirkpatrick R, Moniwa M, Walsh A (2003) Mining single-nucleotide polymorphisms from hexaploid wheat ESTs. Genome 46: 431-437.
28. Syvanen A-C (2005) Toward genome-wide SNP genotyping. Nature Genet 37: S5-S10.
29. Tang J, Vosman B, Voorrips R, van der Linden CG, Leunissen J (2006) QualitySNP: a pipeline for detecting single nucleotide polymorphisms and insertions/deletions in EST data from diploid and polyploid species. BMC Bioinformatics 7: 438.
30. van Ooijen JW (2006) JoinMap 4. 0, software for the calculation of genetic linkage maps in experimental populations. Plant Research International, Wageningen.
31. van Os HV, Andrzejewski S, Bakker E, Barrena I, Bryan G, Caromel B, Ghareeb B, Isidore E, Jong WD, Koert Pv, Lefebvre V, Milbourne D, Ritter E, Rouppe van der Voort JNAM, Rousselle-Bourgeois F, Vliet Jv, Waugh R, Visser RG, Bakker J, Eck HJV (2006) Construction of a 10, 000 marker ultra-dense genetic recombination map of potato: providing a framework for accelerated gene isolation and a genome-wide physical map. Genetics 173: 1075-1087.
32. Vision TJ, Brown DG, Shmoys DB, Durrett RT, Tanksley SD (2000) Selective mapping: a strategy for optimizing the construction of high-density linkage maps. Genetics 155: 407-420.
33. Voorrips RE (2002) MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered 93: 77-78.
34. Vos P, Hogers R, Bleeker M, Reijans M, Lee Tvd, Hornes M, Friters A, Pot J, Paleman J, Kuiper M, Zabeau M (1995) AFLP: a new technique for DNA fingerprinting. Nucl Acids Res 23: 4407-4414.
35. Werij JS, Kloosterman B, Celis-Gamboa C, De Vos CHR, America T, Visser RGF, Bachem CWB (2007) Unravelling enzymatic discoloration in potato through a combined approach of candidate genes, QTL, and expression analysis. Theor Appl Gen 115: 245-252.
36. Wheeler DL, Church DM, Federhen S, Lash AE, Madden TL, Pontius JU, Schuler GD, Schriml LM, Sequeira E, Tatusova TA, Wagner L (2003) Database resources of the National Center for Biotechnology. Nucl Acids Res 31: 28-33.
37. Zhu YL, Song QJ, Hyten DL, van Tassell CP, Matukumalli LK, Grimm DR, Hyatt SM, Fickus EW, Young ND, Cregan PB (2003) Single-nucleotide polymorphisms in soybean. Genetics 163: 1123-1134.