Model SNP development for complex genomes based on hexaploid oat using high-throughput 454 sequencing technology

BMC Genomics

Volumn 12, Issue , 2011, Pages

  Oliver, Rebekah E ^a   Lazo, Gerard R ^b   Lutz, Joseph D ^c   Rubenfield, Marc J ^c,d   Tinker, Nicholas A ^e   Anderson, Joseph M ^f   Wisniewski Morehead, Nicole H ^a   Adhikary, Dinesh ^g   Jellen, Eric N ^g   Maughan, P Jeffrey ^g   Brown Guedira, Gina L ^h   Chao, Shiaoman ^a   Beattie, Aaron D ⁱ   Carson, Martin L ^j   Rines, Howard W ^k,l   Obert, Donald E ^a   Bonman, J Michael ^a   Jackson, Eric W ^a  

^a AGRICULTURAL RESEARCH SERVICE   (United States)

^b WESTERN REGIONAL RESEARCH CENTER   (United States)

^c GENERAL MILLS INC   (United States)

^d Beckman Coulter Genomics   (United States)

^e AGRICULTURE AND AGRI FOOD CANADA   (Canada)

^f PURDUE UNIVERSITY   (United States)

^g BRIGHAM YOUNG UNIVERSITY   (United States)

^h NORTH CAROLINA STATE UNIVERSITY   (United States)

ⁱ UNIVERSITY OF SASKATCHEWAN   (Canada)

^j USDA Agricultural Research Service Cereal Disease Laboratory   (United States)

^k UNIVERSITY OF MINNESOTA   (United States)

^l Knome Inc   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA;

ARTICLE; CONTROLLED STUDY; DNA LIBRARY; EXPRESSED SEQUENCE TAG; GENE FREQUENCY; GENE LOCUS; GENE SEQUENCE; GENETIC VARIABILITY; GENOME ANALYSIS; GENOTYPE; GERMPLASM; HETEROZYGOTE; HEXAPLOIDY; HIGH RESOLUTION MELTING; HIGH THROUGHPUT SCREENING; NONHUMAN; OAT; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; BIOLOGY; DNA SEQUENCE; GENETICS; METHODOLOGY; PLANT GENOME;

AVENA SATIVA;

AVENA SATIVA; COMPUTATIONAL BIOLOGY; EXPRESSED SEQUENCE TAGS; GENOME, PLANT; GENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA;

EID: 79251590266     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-12-77     Document Type: Article

References (54)

1. Brooks AJ. The essence of SNPs. Gene 1999, 234:177-186. 10.1016/S0378-1119(99)00219-X, 10395891.
2. Kanazin V, Talbert H, See D, DeCamp P, Nevo E, Blake T. Discovery and assay of single-nucleotide polymorphism in barley (Hordeum vulgare). Plant Mol Biol 2002, 48:529-537. 10.1023/A:1014859031781, 11999833.
3. Rostoks N, Mudie S, Cardle L, Russell J, Ramsay L, Booth A, Svensson JT, Wanamaker SI, Walia H, Rodriguez EM, Hedley PE, Liu H, Morris J, Close TJ, Marshall DF, Waugh R. Genome-wide SNP discovery and linkage analysis in barley based on genes responsive to abiotic stress. Mol Gen Genom 2005, 274:515-527.
4. Nasu S, Suzuki J, Ohta R, Hasegawa K, Yui R, Kitazawa N, Monna L, Minobe Y. Search for and analysis of single nucleotide polymorphisms (SNPs) in rice (Oryza sativa, Oryza rufipogon) and establishment of SNP markers. DNA Res 2002, 9:613-171.
5. Wright SI, Bi IV, Schroeder SG, Yamasaki M, Doebley JF, McMullen MD, Gaut BS. The effects of artificial selection on the maize genome. Science 2005, 308:1310-1314. 10.1126/science.1107891, 15919994.
6. Zhu YL, Song QJ, Hyten DL, Van Tassell CP, Matukumalli LK, Grimm DR, Hyatt SM, Fickus EW, Young ND, Cregan PB. Single-nucleotide polymorphisms in soybean. Genetics 2003, 163:1123-1134. 1462490, 12663549.
7. Choi I-Y, Hyten DL, Matukumalli LK, Song Q, Chaky JM, Quigley CV, Chase K, Lark KG, Reiter RS, Yoon M-S, Hwang E-Y, Yi S-I, Young ND, Shoemaker RC, van Tassell CP, Specht JE, Cregan PB. A soybean transcript map: Gene distribution, haplotype and single-nucleotide polymorphism analysis. Genetics 2007, 176:685-696. 10.1534/genetics.107.070821, 1893076, 17339218.
8. McNally KL, Bruskiewich R, Mackill D, Buell CR, Leach JE, Leung H. Sequencing multiple and diverse rice varieties. Connecting whole-genome variation with phenotypes. Plant Phys 2006, 141:26-31.
9. Marcel TC, Varshney RK, Barbieri M, Jafary H, de Kock MJD, Graner A, Niks RE. A high-density consensus map of barley to compare the distribution of QTLs for partial resistance to Puccinia hordei and of defence gene homologues. Theor Appl Genet 2007, 114:487-500. 10.1007/s00122-006-0448-2, 17115126.
10. Stein N, Prasad M, Scholz U, Thiel T, Zhang H, Wolf M, Kota R, Varshney RV, Perovic D, Grosse I, Graner A. A 1,000-loci transcript map of the barley genome: new anchoring points for integrative grass genomics. Theor Appl Genet 2007, 114:1432-2242.
11. Hyten DL, Song Q, Choi I-Y, Yoon M-S, Specht JE, Matukumalli LK, Nelson RL, Shoemaker RC, Young ND, Cregan PB. High-throughput genotyping with the GoldenGate assay in the complex genome of soybean. Theor Appl Genet 2008, 116:945-952. 10.1007/s00122-008-0726-2, 18278477.
12. Storm B, Darnhofer-Patel B, van den Boom D, Rodi CP. MALDI-TOF mass spectrometry-based SNP genotyping. Methods Mol Biol 2003, 212:241-262.
13. Syvänen A-C. Toward genome-wide SNP genotyping. Nat Genet 2005, 37:S5-S10.
14. Giancola S, McKhann HI, Bérard A, Camilleri C, Durand S, Libeau P, Roux F, Reboud X, Gut IG, Brunel D. Utilization of the three high-throughput SNP genotyping methods, the GOOD assay, Ampifluor and Taqman, in diploid and polyploidy plants. Theor Appl Genet 2006, 112:1115-1124. 10.1007/s00122-006-0213-6, 16453133.
15. Oliphant A, Barker DL, Stuelpnagel JR, Chee MS. BeadArray technology: Enabling an accurate, cost-effective approach to high-throughput genotyping. BioTechniques 2002, 32:C56-S61.
16. Fan J-B, 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, Wickam E, Doucet D, Chang W, Campbell D, Zhang B, Kruglyak S, Bentley D, Haas J, Rigault P, Zhou L, Stuelpnagel J, Chee MS. Highly parallel SNP genotyping. Cold Spring Harbor Symp Quant Biol 2003, 68:69-78. 10.1101/sqb.2003.68.69, 15338605.
17. Wittner CT, Reed G, Gundry CN, Vandersteen JG, Pryor RJ. High-resolution genotyping by amplicons melting analysis using LCGreen. Clin Chem 2003, 49:853-860. 10.1373/49.6.853, 12765979.
18. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Memben LA, Berka J, Braverman MS, Chen Y-J, Chen Z, Dewell SB, Lei D, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer MLI, Jarvie TP, Jirage KB, Kim J-B, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005, 437:376-380. 1464427, 16056220.
19. Huse SM, Huber JA, Morrison HG, Sogin ML, Welch DM. Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biol 2007, 8:R143. 10.1186/gb-2007-8-7-r143, 2323236, 17659080.
20. Novaes E, Drost DR, Farmerie WG, Pappas GJ, Grattapaglia D, Sederoff RR, Kirst M. High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome. BMC Genomics 2008, 9:312. 10.1186/1471-2164-9-312, 2483731, 18590545.
21. Wegrzyn JL, Lee JM, Liechty J, Neale DB. PineSAP - Pine alignment and SNP identification pipeline. Bioinformatics 2009, 25:2609-2610. 10.1093/bioinformatics/btp477, 2752621, 19667082.
22. Akhunov E, Nicolet C, Dvorak J. Single nucleotide polymorphism genotyping in polyploidy wheat with the Illumina GoldenGate assay. Theor Appl Genet 2009, 119:507-517. 10.1007/s00122-009-1059-5, 2715469, 19449174.
23. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, Gocayne JD, Amanatides P, Ballew RM, Huson DH, Russo J, Zhang Q, Kodira CD, Zheng XH, Chen L, Skupski M, Subramanian G, Thomas PD, Zhang J, Gabor GL, Nelson C, Broder S, Clark AG, Nadeau J, McKusick VA, Zinder N, et al. The sequence of the human genome. Science 2001, 291:1304-1351. 10.1126/science.1058040, 11181995.
24. Yu J, Hu S, Wang J, Wong GK, Li S, Liu B, Deng Y, Dai L, Zhou Y, Zhang X, Cao M, Liu J, Sun J, Tang J, Chen Y, Huang X, Lin W, Ye C, Tong W, Cong L, Geng J, Han Y, Li L, Li W, Hu G, Huang X, Li W, Li J, Liu Z, Li L, et al. A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 2002, 296:79-92. 10.1126/science.1068037, 11935017.
25. Rickert AM, Premstaller A, Gebhardt C, Oefner PJ. Genotyping of SNPs in a polyploidy genome by pyrosequencing. BioTechniques 2002, 32:592-603.
26. Mochida K, Yamazaki Y, Ogihara Y. Discrimination of homoeologous gene expression in hexaploid wheat by SNP analysis of contigs grouped from a large number of expressed sequence tags. Mol Gen Genom 2003, 270:371-377.
27. Adams KL, Cronn R, Percifield R, Wendel JF. Genes duplicated by polyploidy show unequal contributions to the transcriptome and organ-specific reciprocal silencing. Proc Natl Acad Sci 2003, 100:4649-4654. 10.1073/pnas.0630618100, 153610, 12665616.
28. Rines HW, Phillips RL, Anderson OD, Vance CP, Crossman CC, Lazo GR, Miller SS, Taller JM. ESTs, cytogenetic stocks and other tools for oat genomics. Proc 7th Int. Oat Conf 2004, 69. Helsinki, Finland, Peltonen-Saino P, Topi-Hulmi M.
29. Li CD, Rossnagel BG, Scoles GJ. The development of oat microsatellite markers and their use in identifying relationships among Avena species and oat cultivars. Theor Appl Genet 2000, 101:1259-1268.
30. Holland JB, Helland SJ, Sharapova N, Rhyne DC. Polymorphism of PCR-based markers targeting exons, introns, promoter regions, and SSRs in maize and introns and repeat sequences in oat. Genome 2001, 44:1065-1076. 10.1139/gen-44-6-1065, 11768210.
31. Jannink J-L, Gardner SW. Expanding the pool of PCR-based markers in oat. Crop Sci 2005, 45:2383-2387.
32. Becher R. EST-derived microsatellites as a rich source of molecular markers for oats. Plant Breed 2007, 126:274-278.
33. Maloney PV, Lyerly JH, Wooten DR, Anderson JM, Livingston DP, Brown GL, Marshall DS, Murphy JP. Marker development and quantitative trait loci for a fall-sown oat recombinant inbred population. Crop Sci 2011,
34. Wight CP, Yan W, Mitchell J, Deyl J, Tinker NA. A set of new simple sequence repeat and avenin DNA markers suitable for mapping and fingerprinting studies in oat (Avena spp.). Crop Sci 2010, 50:1207-1218.
35. Oliver RE, Obert DE, Hu G, Bonman JM, O'Leary-Jepsen E, Jackson EW. Development of oat-based markers from barley and wheat microsatellites. Genome 2010, 53:458-471. 10.1139/G10-021, 20555435.
36. Tinker NA, Kilian A, Wight CP, Heller-Uszynska K, Wenzyl P, Rines HW, Bjørnstad T, Howarth CJ, Jannink J-L, Anderson JM, Rossnagel BG, Stuthman DD, Sorrells ME, Jackson EW, Tuvesson S, Kolb FL, Olsson O, Federizzi LC, Carson ML, Ohm HW, Molnar SJ, Scoles GJ, Eckstein PE, Bonman MJ, Ceplitis A, Langdon T. New DArT markers for oat provide enhanced map coverage and global germplasm characterization. BMC Genomics 2009, 10:39. 10.1186/1471-2164-10-39, 2661094, 19159465.
37. You FM, Huo N, Gu YQ, Luo M-C, Ma Y, Hane D, Lazo GR, Dvorak J, Anderson OD. BatchPrimer3: A high throughput web application for PCR and sequencing primer design. BMC Bioinformatics 2008, 9:253. 10.1186/1471-2105-9-253, 2438325, 18510760.
38. Portyanko VA, Hoffman DL, Lee M, Holland JB. A linkage map of hexaploid oat based on grass anchor DNA clones and its relationship to other oat maps. Genome 2001, 44:249-265. 10.1139/gen-44-2-249, 11341736.
39. Ladizinsky G. Domestication via hybridization of the wild tetraploid oats Avena magna and A. murphyi. Theor Appl Genet 1995, 91:639-646.
40. Speksnijder AGCL, Kowalchuk GA, De Jong S, Kline E, Stephen JR, Laanbroek HJ. Microvariation artifacts introduced by PCR and cloning of closely related 16S rRNA gene sequences. Appl Environ Microbiol 2001, 67:469-472. 10.1128/AEM.67.1.469-472.2001, 92603, 11133483.
41. Fominaya A, Vega C, Ferrer E. C-banding and nucleolar activity of tetraploid Avena species. Genome 1988, 30:633-638.
42. Fominaya A, Vega C, Ferrer E. Giemsa C-banded karyotypes of Avena species. Genome 1988, 30:627-632.
43. Jellen EN, Phillips RL, Rines HW. C-banded karyotypes and polymorphism in hexaploid oat accessions (Avena spp.) using Wright's stain. Genome 1993, 36:1129-1137. 10.1139/g93-151, 18470055.
44. Jellen EN, Ladizinsky G. Giemsa C-banding in Avena insularis Ladizinsky. Gen Res Crop Evol 2000, 47:227-230.
45. Ladizinsky G. A new species of Avena from Sicily, possibly the tetraploid progenitor of hexaploid oats. Genet Res Crop Evol 1998, 45:263-269.
46. Wight CP, Tinker NA, Kianian SF, Sorrells ME, O'Donoughue LS, Hoffman DL, Groh S, Scoles GJ, Li CD, Webster FH, Phillips RL, Rines HW, Livingston SM, Armstrong KC, Fedak G, Molnar SJ. A molecular marker map in 'Kanota' × 'Ogle' hexaploid oat (Avena spp.) enhanced by additional markers and a robust framework. Genome 2003, 46:28-47. 10.1139/g02-099, 12669794.
47. Lin K-C, Bushnell WR, Szabo LJ, Smith AG. Isolation and expression of a host response gene family encoding thaumatin-like proteins in incompatible oat-stem rust fungus interactions. Mol Plant-Microbe Interact 1996, 9:511-522. 10.1094/MPMI-9-0511, 8755626.
48. Chevreux B, Wetter T, Suhai S. Genome sequence assembly using trace signals and additional sequence information. Comput Sci Biol Proc German Conf Bioinformatics 1999, 45-56.
49. The Gene Ontology Consortium Gene ontology: Tool for the unification of biology. Nature 2000, 25:25-29. The Gene Ontology Consortium.
50. Oliveros JC. VENNY. An interactive tool for comparing lists with Venn Diagrams. 2007, 2223552, 18039769., http://bioinfogp.cnb.csic.es/tools/venny/index.html
51. Manly KF, Cudmore RH, Meer JM. Map Manager QTX, cross-platform software for genetic mapping. Mammal Genome 2001, 12:930-932.
52. Dice LR. Measures of the amount of ecologic association between species. Ecology 1945, 126:297-302.
53. Rohlf FJ. NTSYS-pc: Numerical taxonomy and multivariate analysis system, Version 2.2. 2005, New York, Exeter Publishing Ltd.
54. Drummond AJ, Ashton B, Buxton S, Cheung M, Heled J, Kearse M, Moir R, Stones-Havas S, Thierer T, Wilson A. Geneious v4.8.3. 201.