From RNA-seq to large-scale genotyping - genomics resources for rye (Secale cereale L.)

BMC Plant Biology

Volumn 11, Issue , 2011, Pages

  Haseneyer, Grit ^a   Schmutzer, Thomas ^b   Seidel, Michael ^c   Zhou, Ruonan ^b   Mascher, Martin ^b   Schön, Chris Carolin ^a   Taudien, Stefan ^d   Scholz, Uwe ^b   Stein, Nils ^b   Mayer, Klaus F X ^c   Bauer, Eva ^a  

^a TECHNICAL UNIVERSITY OF MUNICH   (Germany)

^b LEIBNIZ INSTITUTE OF PLANT GENETICS AND CROP PLANT RESEARCH IPK   (Germany)

^c INSTITUTE OF EPIDEMIOLOGY   (Germany)

^d FRITZ LIPMANN INSTITUTE   (Germany)

Author keywords

Est resource; Next generation sequencing; Rye5k snp array; Secale cereale l.; Single nucleotide polymorphisms

Indexed keywords

HORDEUM; SECALE CEREALE; TRITICOSECALE; TRITICUM AESTIVUM;

PLANT RNA; TRANSCRIPTOME;

ARTICLE; BREEDING; DNA SEQUENCE; EXPRESSED SEQUENCE TAG; GENE FREQUENCY; GENETICS; GENOMICS; GENOTYPING TECHNIQUE; HIGH THROUGHPUT SEQUENCING; METHODOLOGY; MOLECULAR GENETICS; PLANT GENOME; RYE; SINGLE NUCLEOTIDE POLYMORPHISM;

BREEDING; EXPRESSED SEQUENCE TAGS; GENE FREQUENCY; GENOME, PLANT; GENOMICS; GENOTYPING TECHNIQUES; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MOLECULAR SEQUENCE ANNOTATION; POLYMORPHISM, SINGLE NUCLEOTIDE; RNA, PLANT; SECALE CEREALE; SEQUENCE ANALYSIS, DNA; TRANSCRIPTOME;

EID: 80053354042     PISSN: None     EISSN: 14712229     Source Type: Journal    
DOI: 10.1186/1471-2229-11-131     Document Type: Article

References (64)

1. Limin AE, Fowler DB. Cold hardiness of forage grasses grown on the canadian prairies. Can J Plant Sci 1987, 67(4):1111-1115.
2. Ko JM, Seo BB, Suh DY, Do GS, Park DS, Kwack YH. Production of a new wheat line possessing the 1BL.1RS wheat-rye translocation derived from Korean rye cultivar Paldanghomil. Theor Appl Genet 2002, 104(2-3):171-176. 10.1007/s00122-001-0783-2, 12582683.
3. Goff SA, Ricke D, Lan TH, Presting G, Wang R, Dunn M, Glazebrook J, Sessions A, Oeller P, Varma H, et al. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 2002, 296(5565):92-100. 10.1126/science.1068275, 11935018.
4. Yu J, Hu S, Wang J, Wong GK, Li S, Liu B, Deng Y, Dai L, Zhou Y, Zhang X, et al. A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 2002, 296(5565):79-92. 10.1126/science.1068037, 11935017.
5. Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, Mitros T, Poliakov A, et al. The Sorghum bicolor genome and the diversification of grasses. Nature 2009, 457(7229):551-556. 10.1038/nature07723, 19189423.
6. The International Brachypodium Initiative Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 2010, 463(7282):763-768. 10.1038/nature08747, 20148030, The International Brachypodium Initiative.
7. Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA, et al. The B73 maize genome: complexity, diversity, and dynamics. Science 2009, 326(5956):1112-1115. 10.1126/science.1178534, 19965430.
8. Doležel J, Greilhuber J, Lucretti S, Meister A, Lysák MA, Nardi L, Obermayer R. Plant genome size estimation by flow cytometry: Inter-laboratory comparison. Ann Bot 1998, 82(suppl 1):17-26.
9. Flavell RB, Bennett MD, Smith JB, Smith DB. Genome size and the proportion of repeated nucleotide sequence DNA in plants. Biochemical Genetics 1974, 12(4):257-269. 10.1007/BF00485947, 4441361.
10. Shi B, Collins N-C, Langridge P, Gustafson J. Construction of a rye cv. Blanco BAC library, and progress towards cloning the rye Alt3 aluminium tolerance gene. Vortr Pflanzenzuchtg 2007, 71:205-209.
11. Hackauf B, Rudd S, van der Voort JR, Miedaner T, Wehling P. Comparative mapping of DNA sequences in rye (Secale cereale L.) in relation to the rice genome. Theor Appl Genet 2009, 118(2):371-384. 10.1007/s00122-008-0906-0, 18953524.
12. Khlestkina EK, Than MH, Pestsova EG, Roder MS, Malyshev SV, Korzun V, Borner A. Mapping of 99 new microsatellite-derived loci in rye (Secale cereale L.) including 39 expressed sequence tags. Theor Appl Genet 2004, 109(4):725-732. 10.1007/s00122-004-1659-z, 15300380.
13. Korzun V, Malyshev S, Voylokov AV, Börner A. A genetic map of rye (Secale cereale L.) combining RFLP, isozyme, protein, microsatellite and gene loci. Theor Appl Genet 2001, 102(5):709-717.
14. Ma XF, Wanous MK, Houchins K, Milla MAR, Goicoechea PG, Wang Z, Xie M, Gustafson JP. Molecular linkage mapping in rye (Secale cereale L.). Theor Appl Genet 2001, 102(4):517-523.
15. Senft P, Wricke G. An extended genetic map of rye (Secale cereale L.). Plant Breeding 1996, 115(6):508-510.
16. Metzker ML. Sequencing technologies - the next generation. Nat Rev Genet 2010, 11(1):31-46. 10.1038/nrg2626, 19997069.
17. Meyer E, Aglyamova GV, Wang S, Buchanan-Carter J, Abrego D, Colbourne JK, Willis BL, Matz MV. Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx. BMC Genomics 2009, 10:219. 10.1186/1471-2164-10-219, 2689275, 19435504.
18. Sun C, Li Y, Wu Q, Luo H, Sun Y, Song J, Lui EM, Chen S. De novo sequencing and analysis of the American ginseng root transcriptome using a GS FLX Titanium platform to discover putative genes involved in ginsenoside biosynthesis. BMC Genomics 2010, 11:262. 10.1186/1471-2164-11-262, 2873478, 20416102.
19. Hillier LW, Marth GT, Quinlan AR, Dooling D, Fewell G, Barnett D, Fox P, Glasscock JI, Hickenbotham M, Huang W, et al. Whole-genome sequencing and variant discovery in C. elegans. Nat Methods 2008, 5(2):183-188. 10.1038/nmeth.1179, 18204455.
20. Torres TT, Metta M, Ottenwalder B, Schlotterer C. Gene expression profiling by massively parallel sequencing. Genome Res 2008, 18(1):172-177. 2134766, 18032722.
21. Wicker T, Taudien S, Houben A, Keller B, Graner A, Platzer M, Stein N. A whole-genome snapshot of 454 sequences exposes the composition of the barley genome and provides evidence for parallel evolution of genome size in wheat and barley. Plant J 2009,
22. Lister R, Ecker JR. Finding the fifth base: genome-wide sequencing of cytosine methylation. Genome Res 2009, 19(6):959-966. 10.1101/gr.083451.108, 19273618.
23. Novaes E, Drost D, Farmerie W, Pappas G, Grattapaglia D, Sederoff R, Kirst M. High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome. BMC Genomics 2008, 9(1):312. 10.1186/1471-2164-9-312, 2483731, 18590545.
24. Korzun V, Malyshev S, Kartel N, Westermann T, Weber WE, Börner A. A genetic linkage map of rye (Secale cereale L.). Theor Appl Genet 1998, 96(2):203-208.
25. Oztur ZN, Talame V, Deyholos M, Michalowski CB, Galbraith DW, Gozukirmizi N, Tuberosa R, Bohnert HJ. Monitoring large-scale changes in transcript abundance in drought- and salt-stressed barley. Plant Mol Biol 2002, 48(5-6):551-573.
26. Kumar S, Blaxter ML. Comparing de novo assemblers for 454 transcriptome data. BMC Genomics 2010, 11:571. 10.1186/1471-2164-11-571, 3091720, 20950480.
27. Chevreux B, Pfisterer T, Drescher B, Driesel AJ, Muller WE, Wetter T, Suhai S. Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs. Genome Res 2004, 14(6):1147-1159. 10.1101/gr.1917404, 419793, 15140833.
28. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005, 437(7057):376-380. 1464427, 16056220.
29. Huang X, Madan A. CAP3: A DNA sequence assembly program. Genome Res 1999, 9(9):868-877. 10.1101/gr.9.9.868, 310812, 10508846.
30. Riano-Pachón DM, Nagel A, Neigenfind J, Wagner R, Basekow R, Weber E, Mueller-Roeber B, Diehl S, Kersten B. GabiPD: the GABI primary database - a plant integrative 'omics' database. Nucleic Acids Res 2009, (37 Database):D954-959.
31. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990, 215(3):403-410.
32. Rice Annotation Project The Rice Annotation Project Database (RAP-DB): 2008 update. Nucleic Acids Res 2008, 36(suppl_1):D1028-1033. 2238920, 18089549, Rice Annotation Project.
33. Matsumoto T, Tanaka T, Sakai H, Amano N, Kanamori H, Kurita K, Kikuta A, Kamiya K, Yamamoto M, Ikawa H, et al. Comprehensive sequence analysis of 24,783 barley full-length cDNAs derived from 12 clone libraries. Plant Physiology 2011, 156(1):20-28. 10.1104/pp.110.171579, 3091036, 21415278.
34. Mochida K, Yoshida T, Sakurai T, Ogihara Y, Shinozaki K. TriFLDB: a database of clustered full-length coding sequences from Triticeae with applications to comparative grass genomics. Plant Physiology 2009, 150(3):1135-1146. 10.1104/pp.109.138214, 2705016, 19448038.
35. Jurka J. Repeats in genomic DNA: mining and meaning. Curr Opin Struct Biol 1998, 8(3):333-337. 10.1016/S0959-440X(98)80067-5, 9666329.
36. Spannagl M, Noubibou O, Haase D, Yang L, Gundlach H, Hindemitt T, Klee K, Haberer G, Schoof H, Mayer KF. MIPSPlantsDB--plant database resource for integrative and comparative plant genome research. Nucleic Acids Res 2007, (35 Database):D834-840.
37. Hunter JD. Matplotlib: A 2D Graphics Environment. Comput Sci Eng 2007, 9(3):90-95.
38. Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 2005, 21(18):3674-3676. 10.1093/bioinformatics/bti610, 16081474.
39. Thiel T, Michalek W, Varshney RK, Graner A. Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor Appl Genet 2003, 106(3):411-422.
40. Rozen S, Skaletsky H. Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 2000, 132:365-386.
41. Marth GT, Korf I, Yandell MD, Yeh RT, Gu Z, Zakeri H, Stitziel NO, Hillier L, Kwok PY, Gish WR. A general approach to single-nucleotide polymorphism discovery. Nat Genet 1999, 23(4):452-456. 10.1038/70570, 10581034.
42. Huang W, Marth G. EagleView: a genome assembly viewer for next-generation sequencing technologies. Genome Res 2008, 18(9):1538-1543. 10.1101/gr.076067.108, 2527701, 18550804.
43. R Development Core Team R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria 2004, ISBN 3-900051-07-0, R Development Core Team., http://www.R-project.org
44. Zagrobelny M, Scheibye-Alsing K, Jensen NB, Moller BL, Gorodkin J, Bak S. 454 pyrosequencing based transcriptome analysis of Zygaena filipendulae with focus on genes involved in biosynthesis of cyanogenic glucosides. BMC Genomics 2009, 10:574. 10.1186/1471-2164-10-574, 2791780, 19954531.
45. Wu TD, Watanabe CK. GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics 2005, 21(9):1859-1875. 10.1093/bioinformatics/bti310, 15728110.
46. Li H, Ruan J, Durbin R. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 2008, 18(11):1851-1858. 10.1101/gr.078212.108, 2577856, 18714091.
47. Huang S, Li R, Zhang Z, Li L, Gu X, Fan W, Lucas WJ, Wang X, Xie B, Ni P, et al. The genome of the cucumber, Cucumis sativus L. Nat Genet 2009, 41(12):1275-1281. 10.1038/ng.475, 19881527.
48. Li R, Fan W, Tian G, Zhu H, He L, Cai J, Huang Q, Cai Q, Li B, Bai Y, et al. The sequence and de novo assembly of the giant panda genome. Nature 2010, 463(7279):311-317. 10.1038/nature08696, 20010809.
49. Mayer KF, Taudien S, Martis M, Simkova H, Suchankova P, Gundlach H, Wicker T, Petzold A, Felder M, Steuernagel B, et al. Gene content and virtual gene order of barley chromosome 1H. Plant Physiol 2009, 151(2):496-505. 10.1104/pp.109.142612, 2754631, 19692534.
50. Coche T, Dewez M. Reducing bias in cDNA sequence representation by molecular selection. Nucleic Acids Res 1994, 22(21):4545-4546. 10.1093/nar/22.21.4545, 308492, 7971286.
51. Emrich SJ, Barbazuk WB, Li L, Schnable PS. Gene discovery and annotation using LCM-454 transcriptome sequencing. Genome Res 2007, 17(1):69-73. 1716268, 17095711.
52. Patanjali SR, Parimoo S, Weissman SM. Construction of a uniform-abundance (normalized) cDNA library. Proc Natl Acad Sci USA 1991, 88(5):1943-1947. 10.1073/pnas.88.5.1943, 51142, 1705712.
53. Schafleitner R, Tincopa LR, Palomino O, Rossel G, Robles RF, Alagon R, Rivera C, Quispe C, Rojas L, Pacheco JA, et al. A sweet potato gene index established by de novo assembly of pyrosequencing and Sanger sequences and mining for gene-based microsatellite markers. BMC Genomics 2010, 11:604. 10.1186/1471-2164-11-604, 3017860, 20977749.
54. Bolot S, Abrouk M, Masood-Quraishi U, Stein N, Messing J, Feuillet C, Salse J. The 'inner circle' of the cereal genomes. Curr Opin Plant Biol 2009, 12(2):119-125. 10.1016/j.pbi.2008.10.011, 19095493.
55. Gaut BS. Evolutionary dynamics of grass genomes. New Phytologist 2002, 154(1):15-28.
56. Lu T, Lu G, Fan D, Zhu C, Li W, Zhao Q, Feng Q, Zhao Y, Guo Y, Huang X, et al. Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq. Genome Res 2010, 20(9):1238-1249. 10.1101/gr.106120.110, 2928502, 20627892.
57. Steuernagel B, Taudien S, Gundlach H, Seidel M, Ariyadasa R, Schulte D, Petzold A, Felder M, Graner A, Scholz U, et al. De novo 454 sequencing of barcoded BAC pools for comprehensive gene survey and genome analysis in the complex genome of barley. BMC Genomics 2009, 10:547. 10.1186/1471-2164-10-547, 2784808, 19930547.
58. Paux E, Sourdille P, Salse J, Saintenac C, Choulet F, Leroy P, Korol A, Michalak M, Kianian S, Spielmeyer W, et al. A physical map of the 1-gigabase bread wheat chromosome 3B. Science 2008, 322(5898):101-104. 10.1126/science.1161847, 18832645.
59. Bartos J, Paux E, Kofler R, Havrankova M, Kopecky D, Suchankova P, Safar J, Simkova H, Town C, Lelley T, et al. A first survey of the rye (Secale cereale) genome composition through BAC end sequencing of the short arm of chromosome 1R. BMC Plant Biol 2008, 8(1):95. 10.1186/1471-2229-8-95, 2565679, 18803819.
60. Korzun V. Molecular markers and their application in cereals breeding. Proceedings of the workshop "Marker assisted selection: A fast track to increase genetic gain in plant and animal breeding?": 17-18 October 2003; University of Turin, Italy 2003, 18-22. Lanteri S, Electronic forum on biotechnology in food and agriculture.
61. Gupta PK, Varshney RK, Sharma PC, Ramesh B. Molecular markers and their applications in wheat breeding. Plant Breeding 1999, 118(5):369-390.
62. Schulman AH. Molecular markers to assess genetic diversity. Euphytica 2007, 158(3):313-321.
63. Matukumalli LK, Lawley CT, Schnabel RD, Taylor JF, Allan MF, Heaton MP, O'Connell J, Moore SS, Smith TPL, Sonstegard TS, et al. Development and Characterization of a High Density SNP Genotyping Assay for Cattle. PLoS ONE 2009, 4(4):e5350. 10.1371/journal.pone.0005350, 2669730, 19390634.
64. Adams MW, Shank DB. The relationship of heterozygosity to homeostasis in maize hybrids. Genetics 1959, 44(5):777-786. 1209980, 17247856.