Development of versatile gene-based SNP assays in maize (Zea mays L.)

Molecular Breeding

Volumn 29, Issue 3, 2012, Pages 779-790

  Mammadov, Jafar ^a   Chen, Wei ^a   Mingus, Jennifer ^a   Thompson, Steve ^a   Kumpatla, Siva ^a  

^a DOW AGROSCIENCES LLC   (United States)

Author keywords

GoldenGate; Infinium; KASPar; Maize; Single nucleotide polymorphism; TaqMan

Indexed keywords

ASSAYS; GRAIN (AGRICULTURAL PRODUCT); NUCLEOTIDES;

CANDIDATE SEQUENCES; GOLDENGATE; INFINIA; KASPAR; MAIZE; MAIZE (ZEA MAYS L.); MOLECULAR GENETICS; POLYMORPHISM ASSAYS; SINGLE NUCLEOTIDE POLYMORPHISMS; TAQMAN;

GENES;

ZEA MAYS;

EID: 84863255535     PISSN: 13803743     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11032-011-9589-3     Document Type: Article

References (35)

1. Andersen JR, Lübberstedt T (2003) Functional markers in plants. Trends Plant Sci 11: 554-560.
2. Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL, Lewis ZA, Selker EU, Cresko WA, Johnson EA (2008) Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS One 3: e3376.
3. Barbazuk WB, Emrich SJ, Chen HD, Schnable P (2007) SNP discovery via 454 transcriptome sequencing. Plant J 51: 910-918.
4. Barker G, Edwards KJ (2009) A genome-wide analysis of single nucleotide polymorphism diversity in the world's major cereal crops. Plant Biotechnol J 7: 318-325.
5. Chandrasekar A, Riju A, Sithara K, Anoop A, Eapen SJ (2009) Identification of single nucleotide polymorphism in ginger using expressed sequence tags. Bioinformation 4: 119-122.
6. Chen W, Mingus J, Mammadov J, Backlund JE, Greene T, Thompson S, Kumpatla S (2010) KASPar: a simple and cost-effective system for SNP genotyping. In: Final program, abstract and exhibit guide of the XVIII international conference on the status of plant and animal genome research, San Diego, CA, 9-13 Jan 2010.
7. Ching A, Caldwell KS, Jung M, Dolan M, Smith OS, Tingey S, Morgante M, Rafalski AJ (2002) SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines. BMC Genomics 3: 19.
8. Collins DW, Jukes TH (1994) Rates of transition and transversion in coding sequences since the human-rodent divergence. Genomics 20: 386-396.
9. Ebersberger I, Metzler D, Schwarz C, Pääbo S (2002) Genomewide comparison of DNA sequences between humans and chimpanzees. Am J Hum Genet 70: 1490-1497.
10. Fan JB, Oliphant A, 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 (2003) Highly parallel SNP genotyping. Cold Spring Harb Symp Quant Biol 68: 69-78.
11. Ganal M, Polley A, Durstewitz G, Thompson M, Hansen M (2010) A 50 K SNP infinium chip for maize genome analysis. In: Program and abstracts of 52nd annual maize genetics conference, Riva del Garda (Trento), Italy, 18-21 Mar 2010.
12. Gore MA, Chia JM, Elshire RJ, Sun Q, Ersoz ES, Hurwitz BL, Peiffer JA, McMullen MD, Grills GS, Ross-Ibarra J, Ware DH, Buckler ES (2009a) A first-generation haplotype map of maize. Science 326: 1115.
13. Gore MA, Wright MH, Ersoz ES, Bouffard P, Szekeres ES, Jarvie TP, Hurwitz BL, Narechania A, Harkins TT, Grills GS, Ware DH, Buckler ES (2009b) Large-scale discovery of gene-enriched SNPs. Plant Genome 2: 121-133.
14. Gupta PK, Rustgi S, Mir RR (2008) Array-based high-throughput DNA markers for crop improvement. Heredity 101: 5-18.
15. Jones E, Chu WC, Ayele M, Ho J, Bruggeman E, Yourstone K, Rafalksi A, Smith OS, McMullen MD, Bezawada C, Warren L, Babayev J, Basu S, Smith S (2009) Development of single nucleotide polymorphism (SNP) markers for use in commercial maize (Zea mais L.) germplasm. Mol Breed 24: 165-176.
16. Keller I, Bensasson D, Nichols RA (2007) Transition-transversion bias is not universal: a counter example from grasshopper pseudogenes. PLoS zgenet 3: e22. doi: 10. 1371/journal. pgen0030022.
17. Lai J, Li R, Xu X, Jin W, Xu M, Zhao H, Xiang Z, Song W, Ying K, Zhang M, Jiao Y, Ni P, Zhang J, Li D, Guo X, Ye K, Jian M, Wang B, Zheng H, Liang H, Zhang X, Wang S, Chen A, Li J, Fu Y, Springer NM, Yang H, Wang J, Dai J, Schnable PS, Wang J (2010) Genome-wide patterns of genetic variation among elite maize inbred lines. Nature Genet 42: 1027-1030.
18. Livak KJ, Flood SJ, Marmaro J, Giusti W, Deetz K (1995) Oligonucleotide with fluorescent dyes at opposite ends provide a quenched probe system useful for detecting PCR product and nucleic acid hybridization. Genome Res 4: 357-362.
19. Mammadov JA, Chen W, Ren R, Pai R, Marchione W, Yalçin F, Witsenboer H, Greene TW, Thomspon SA, Kumpatla SP (2010) Development of highly polymorphic SNP markers from the complexity reduced portion of maize (Zea mays L.) genome for use in marker-assisted breeding. Theor Appl Genet 121: 577-588.
20. Mazumder B, Seshadri V, Fox PL (2003) Translation control by the 3′-UTR: the ends specify the means. Trends Biochem Sci 28: 91-98.
21. McMullen MD, Kresovich S, Villeda HS, Bradbury P, Li H, Sun Q, Flint-Garcia S, Thornsberry J, Acharya C, Bottoms C, Brown P, Browne C, Eller M, Guill K, Harjes C, Kroon D, Lepak N, Mitchell SE, Peterson B, Pressoir G, Romero S, Rosas MO, Salvo S, Yates H, Hanson M, Jones E, Smith S, Glaubitz JC, Goodman M, Ware D, Holland JB, Buckler ES (2009) Genetic properties of the maize nested association mapping population. Science 325: 737-740.
22. Morton BR, Bi IV, McMullen MD, Gaut BS (2006) Variation in mutation dynamics across the maize genome as a function of region and flanking base composition. Genetics 172: 569-577.
23. Nijman IJ, Kuipers S, Verheul M, Guryev V, Cuppen E (2008) A genome-wide SNP panel for mapping and association studies in the rat. BMC Genomics 9: 95.
24. Pickering BM, Willis AE (2005) The implications of structured 5′ untranslated regions on translation and disease. Semin Cell Dev Biol 16: 39-47.
25. SNP Line XL (2010) http://www.kbioscience.co.uk/instrumentation/SNPline/snp%20line%20XL.html. Accessed 23 Dec 2010.
26. Steermers FJ, Gunderson KL (2007) Whole genome genotyping technologies on the BeadArrayTM platform. Biotechnol J 2: 41-49.
27. ® Genotyping instrument platform https://products. appliedbiosystems. com/ab/en/US/adirect/ab?cmd=catNavigate2& catID=605780& tab=DetailInfo. Accessed 23 Dec 2010.
28. van Orsouw N, Hogers RC, Janssen A, Yalcin F, Snoeijers S, Verstege E, Scheiders H, van der Poel H, van Oeveren J, Verstegen H, van Eijk MJT (2007) Complexity reduction of polymorphic sequences (CRoPS™): a novel approach for large-scale polymorphism discovery in complex genomes. PLoS One 11: 1-10.
29. Varshney R (2010) Gene-based marker systems in plants: high throughput approaches for marker discovery and genotyping. In: Mohan Jain S, Brar DS (eds) Molecular techniques in crop improvement, 2nd edn. Springer Science + Business Media B. V., Dordrecht, pp 119-142.
30. Varshney R, Mahendar T, Aggarwal RK, Bo{double acute}rner A (2007) Genic molecular markers in plants: development and applications. In: Varshney RK, Tuberosa R (eds) Genomics-assisted crop improvement, Vol 1 Genomics approaches and platforms. Springer, Dordrecht, pp 13-29.
31. Wright WT, Heggarty SV, Young IS, Nicholls DP, Whittall R, Humphries SE, Graham CA (2008) Multiplex MassARRAY spectrometry (iPLEX) produces a fast and economical test for 56 familial hypercholesterolaemia-causing mutations. Clin Genet 74: 463-468.
32. Zhang Z, Gerstein M (2003) Patterns of nucleotide substitution, insertion and deletion in the human genome inferred from pseudogenes. Nucleic Acids Res 31: 5338-5348.
33. Zhao Z, Boerwinkle E (2002) Neighboring-nucleotide effects on single nucleotide polymorphisms: A study of 2. 6 million polymorphisms across the human genome. Genome Res 12: 1679-1686.
34. Zhao Z, Fu YX, Hewett-Emmett D, Boerwinkle E (2003) Investigating single nucleotide polymorphism (SNP) density in the human genome and its implications for molecular evolution. Gene 312: 207-213.
35. Zhao W, Canaran P, Jurkuta R, Fulton T, Glaubitz J, Buckler E, Doebley J, Gaut B, Goodman M, Holland J, Kresovich S, McMullen M, Stein L, Ware D (2006) Panzea: a database and resource for molecular and functional diversity in the maize genome. Nucleic Acids Res 34: D752-D757.