Development and evaluation of a high-throughput, low-cost genotyping platform based on oligonucleotide microarrays in rice

Plant Methods

Volumn 4, Issue 1, 2008, Pages

  Edwards, Jeremy D ^a   Janda, Jaroslav ^b   Sweeney, Megan T ^b   Gaikwad, Ambika B ^c   Liu, Bin ^d   Leung, Hei ^e   Galbraith, David W ^b  

^a UNIVERSITY OF FLORIDA   (United States)

^b UNIVERSITY OF ARIZONA   (United States)

^c NATIONAL BUREAU OF PLANT GENETIC RESOURCES   (India)

^d INSTITUTE OF ANIMAL SCIENCE   (China)

^e INTERNATIONAL RICE RESEARCH INSTITUTE   (Philippines)

Author keywords

[No Author keywords available]

Indexed keywords

JAPONICA; MAGNAPORTHE GRISEA;

EID: 45749141263     PISSN: None     EISSN: 17464811     Source Type: Journal    
DOI: 10.1186/1746-4811-4-13     Document Type: Article

References (62)

1. Advances in sequencing technology. EY Chan, Mutat Res 2005 573 13 40 15829235
2. DNA markers in plant improvement: an overview. LS Kumar, Biotechnol Adv 1999 17 143 182 14538138
3. Analyzing and comparing nucleic acid sequences by hybridization to arrays of oligonucleotides: evaluation using experimental models. EM Southern U Maskos JK Elder, Genomics 1992 13 1008 1017 1380482
4. Direct Allelic Variation Scanning of the Yeast Genome. EA Winzeler DR Richards AR Conway AL Goldstein S Kalman MJ McCullough JH McCusker DA Stevens L Wodicka DJ Lockhart RW Davis, Science 1998 281 1194 1197 9712584
5. Genome-wide expression monitoring in Saccharomyces cerevisiae. L Wodicka H Dong M Mittmann MH Ho DJ Lockhart, Nat Biotechnol 1997 15 1359 1367 9415887
6. Large-scale identification of single-feature polymorphisms in complex genomes. JO Borevitz D Liang D Plouffe HS Chang T Zhu D Weigel CC Berry E Winzeler J Chory, Genome Res 2003 13 513 523 12618383
7. Rapid array mapping of circadian clock and developmental mutations in Arabidopsis. SP Hazen JO Borevitz FG Harmon JL Pruneda-Paz TF Schultz MJ Yanovsky SJ Liljegren JR Ecker SA Kay, Plant Physiol 2005 138 990 997 15908595
8. A haplotype map of the human genome. The International HapMap Consortium, Nature 2005 437 1299 1320 16255080
9. Prospects for whole-genome linkage disequilibrium mapping of common disease genes. L Kruglyak, Nat Genet 1999 22 139 144 10369254
10. Human genome sequence variation and the influence of gene history, mutation and recombination. DE Reich SF Schaffner MJ Daly G McVean JC Mullikin JM Higgins DJ Richter ES Lander D Altshuler, Nat Genet 2002 32 135 142 12161752
11. Toward genome-wide SNP genotyping. AC Syvanen, Nat Genet 2005 37 5 10
12. Rapid mapping of zebrafish mutations with SNPs and oligonucleotide microarrays. HL Stickney J Schmutz IG Woods CC Holtzer MC Dickson PD Kelly RM Myers WS Talbot, Genome Res 2002 12 1929 1934 12466297
13. Spotted long oligonucleotide arrays for human gene expression analysis. A Barczak MW Rodriguez K Hanspers LL Koth YC Tai BM Bolstad TP Speed DJ Erle, Genome Res 2003 13 1775 1785 12805270
14. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. M Schena D Shalon RW Davis PO Brown, Science 1995 270 467 470 7569999
15. Assessment of the sensitivity and specificity of oligonucleotide (50 mer) microarrays. MD Kane TA Jatkoe CR Stumpf J Lu JD Thomas SJ Madore, Nucleic Acids Res 2000 28 4552 4557 11071945
16. Diversity arrays: a solid state technology for sequence information independent genotyping. D Jaccoud K Peng D Feinstein A Kilian, Nucleic Acids Res 2001 29 E25 11160945
17. Diversity Arrays Technology (DArT) for whole-genome profiling of barley. P Wenzl J Carling D Kudrna D Jaccoud E Huttner A Kleinhofs A Kilian, Proc Natl Acad Sci USA 2004 101 9915 9920 15192146
18. A high-throughput genomic tool: Diversity array technology complementary for rice genotyping. Y Xie K McNally CY Li H Leung YY Zhu, J Integr Plant Biol 2006 48 1069 1076
19. A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. indica). J Yu S Hu J Wang GK Wong S Li B Liu Y Deng L Dai Y Zhou X Zhang M Cao J Liu J Sun J Tang Y Chen X Huang W Lin C Ye W Tong L Cong J Geng Y Han L Li W Li G Hu X Huang W Li J Li Z Liu L Li J Liu Q Qi J Liu L Li T Li X Wang H Lu T Wu M Zhu P Ni H Han W Dong X Ren X Feng P Cui X Li H Wang X Xu W Zhai Z Xu J Zhang S He J Zhang J Xu K Zhang X Zheng J Dong W Zeng L Tao J Ye J Tan X Ren X Chen J He D Liu W Tian C Tian H Xia Q Bao G Li H Gao T Cao J Wang W Zhao P Li W Chen X Wang Y Zhang J Hu J Wang S Liu J Yang G Zhang Y Xiong Z Li L Mao C Zhou Z Zhu R Chen B Hao W Zheng S Chen W Guo G Li S Liu M Tao J Wang L Zhu L Yuan H Yang, Science 2002 296 79 92 11935017
20. Productivity improvements in rice. G Khush, Nutr Rev 2003 61 S114 116 12908742
21. Alignment of whole genomes. AL Delcher S Kasif RD Fleischmann J Peterson O White SL Salzberg, Nucleic Acids Res 27 2369 2376 10325427
22. Fast algorithms for large-scale genome alignment and comparison. AL Delcher A Phillippy J Carlton SL Salzberg, Nucleic Acids Res 2002 30 2478 2483 12034836
23. Versatile and open software for comparing large genomes. S Kurtz A Phillippy AL Delcher M Smoot M Shumway C Antonescu SL Salzberg, Genome Biol 2004 5 R12 14759262
24. The TIGR Plant Repeat Databases: a collective resource for the identification of repetitive sequences in plants. S Ouyang CR Buell, Nucleic Acids Res 2004 32 360 363
25. Functional rice centromeres are marked by a satellite repeat and a centromere-specific retrotransposon. Z Cheng F Dong T Langdon S Ouyang CR Buell M Gu FR Blattner J Jiang, Plant Cell 2002 14 1691 1704 12172016
26. Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. D Falush M Stephens JK Pritchard, Genetics 2003 164 1567 1587 12930761
27. Genetic structure and diversity in Oryza sativa L. AJ Garris TH Tai J Coburn S Kresovich S McCouch, Genetics 2005 169 1631 1638 15654106
28. Origin of the Genic Diversity of Cultivated Rice (Oryza-Spp) - Study of the Polymorphism Scored at 40 Isoenzyme Loci. G Second, Jpn J Genet 1982 57 25 57
29. Isozymes and Classification of Asian Rice Varieties. JC Glaszmann, Theor Appl Genet 1987 74 21 30
30. Genetic analysis of Indian aromatic and quality rice (Oryza sativa L.) germplasm using panels of fluorescently-labeled microsatellite markers. S Jain RK Jain SR McCouch, Theor Appl Genet 2004 109 965 977 15309297
31. Identification of markers linked to disease-resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations. RW Michelmore I Paran RV Kesseli, Proc Natl Acad Sci USA 1991 88 9828 9832 1682921
32. Controlling the false discovery rate: a practical and powerful approach to multiple testing. Y Benjamini Y Hochberg, Journal of the Royal Statistical Society Series B 1995 57 289 300
33. Candidate defense genes as predictors of quantitative blast resistance in rice. B Liu S Zhang X Zhu Q Yang S Wu M Mei R Mauleon J Leach T Mew H Leung, Mol Plant Microbe Interact 2004 17 1146 1152 15497407
34. Sequencing multiple and diverse rice varieties. Connecting whole-genome variation with phenotypes. KL McNally R Bruskiewich D Mackill CR Buell JE Leach H Leung, Plant Physiol 2006 141 26 31 16684934
35. Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana. RM Clark G Schweikert C Toomajian S Ossowski G Zeller P Shinn N Warthmann TT Hu G Fu DA Hinds H Chen KA Frazer DH Huson B Scholkopf M Nordborg G Ratsch JR Ecker D Weigel, Science 2007 317 338 342 17641193
36. Size of donor chromosome segments around introgressed loci and reduction of linkage drag in marker-assisted backcross programs. F Hospital, Genetics 2001 158 1363 1379 11454782
37. Lessons from applying genomics to wheat and barley improvement. P Langridge, 5th International Rice Genetics Symposium: 19-23 November 2005; Manila, Philippines Singapore: International Rice Research Institute, Brar DS, Mackill DJ, Hardy B, 2007 267 283
38. Advanced backcross QTL analysis: A method for the simultaneous discovery and transfer of valuable QTLs from unadapted germplasm into elite breeding lines. SD Tanksley JC Nelson, Theor Appl Genet 1996 92 191 203
39. An introgression line population of Lycopersicon pennellii in the cultivated tomato enables the identification and fine mapping of yield-associated QTL. Y Eshed D Zamir, Genetics 1995 141 1147 1162 8582620
40. Seed banks and molecular maps: unlocking genetic potential from the wild. SD Tanksley SR McCouch, Science 1997 277 1063 1066 9262467
41. Dwarf8 polymorphisms associate with variation in flowering time. JM Thornsberry MM Goodman J Doebley S Kresovich D Nielsen ES Buckler, Nat Genet 2001 28 286 289 11431702
42. Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp. mays L.). MI Tenaillon MC Sawkins AD Long RL Gaut JF Doebley BS Gaut, Proc Natl Acad Sci USA 2001 98 9161 9166 11470895
43. Structure of linkage disequilibrium and phenotypic associations in the maize genome. DL Remington JM Thornsberry Y Matsuoka LM Wilson SR Whitt J Doebley S Kresovich MM Goodman ES Buckler, Proc Natl Acad Sci USA 2001 98 11479 11484 11562485
44. A mixed-model approach to association mapping using pedigree information with an illustration of resistance to Phytophthora infestans in potato. M Malosetti CG van der Linden B Vosman FA van Eeuwijk, Genetics 2007 175 879 889 17151263
45. Pack-MULE transposable elements mediate gene evolution in plants. N Jiang Z Bao X Zhang SR Eddy SR Wessler, Nature 2004 431 569 573 15457261
46. Gene movement by Helitron transposons contributes to the haplotype variability of maize. J Lai Y Li J Messing HK Dooner, Proc Natl Acad Sci USA 2005 102 9068 9073 15951422
47. Uneven chromosome contraction and expansion in the maize genome. R Bruggmann AK Bharti H Gundlach J Lai S Young AC Pontaroli F Wei G Haberer G Fuks C Du, Genome Res 2006 16 1241 16902087
48. Intraspecific violation of genetic colinearity and its implications in maize. H Fu HK Dooner, Proc Natl Acad Sci USA 2002 99 9573 9578 12060715
49. The Institute for Genomic Research Osa1 Rice Genome Annotation Database. Q Yuan S Ouyang A Wang W Zhu R Maiti H Lin J Hamilton B Haas R Sultana F Cheung, Plant Physiol 2005 138 18 15888674
50. Basic local alignment search tool. SF Altschul W Gish W Miller EW Myers DJ Lipman, J Mol Biol 1990 215 403 410 2231712
51. Optimization of probe length and the number of probes per gene for optimal microarray analysis of gene expression. CC Chou CH Chen TT Lee K Peck, Nucleic Acids Res 2004 32 e99 15243142
52. Hybridization of synthetic oligodeoxyribonucleotides to phi chi 174 DNA: the effect of single base pair mismatch. RB Wallace J Shaffer RF Murphy J Bonner T Hirose K Itakura, Nucleic Acids Res 1979 6 6353 6357
53. Microarray-based analysis of gene expression in very large gene families: the cytochrome P450 gene superfamily of Arabidopsis thaliana. W Xu S Bak A Decker SM Paquette R Feyereisen DW Galbraith, Gene 2001 272 61 74 11470511
54. A plant DNA minipreparation: Version II. SL Dellaporta J Wood JB Hicks, Plant Mol Biol Rep 1983 1 19 21
55. Limma: Linear Models for Microarray Data. GK Smyth, Bioinformatics and Computational Biology Solutions using R and Bioconductor New York: Springer, Gentleman RC, Dudoit S, Irizarry R, Huber W, 2005 397 420
56. Bioconductor: open software development for computational biology and bioinformatics. RC Gentleman VJ Carey DM Bates B Bolstad M Dettling S Dudoit B Ellis L Gautier Y Ge J Gentry, Genome Biol 2004 5 R80 15461798
57. Normalization of cDNA microarray data. GK Smyth T Speed, Methods 2003 31 265 273 14597310
58. Use of within-array replicate spots for assessing differential expression in microarray experiments. GK Smyth J Michaud HS Scott, Bioinformatics 2005 21 9 2067 2075 15657102
59. Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. GK Smyth, Statistical Applications in Genetics and Molecular Biology 2004 3 3
60. PowerMarker: an integrated analysis environment for genetic marker analysis. K Liu SV Muse, Bioinformatics 2005 21 2128 2129 15705655
61. TreeView: an application to display phylogenetic trees on personal computers. RD Page, Comput Appl Biosci 1996 12 357 358 8902363
62. Computer note. GGT: software for the display of graphical genotypes. R van Berloo, J Hered 1999 90 328 329