Exome sequencing and advances in crop improvement

Advances in Genetics

Volumn 79, Issue , 2012, Pages 87-121

  Singh, Devi ^a   Singh, Pankaj K ^b   Chaudhary, Sarika ^c   Mehla, Kamiya ^b   Kumar, Shashi ^d  

^a SARDAR VALLABHBHAI PATEL UNIVERSITY OF AGRICULTURE AND TECHNOLOGY   (India)

^b UNIVERSITY OF NEBRASKA MEDICAL CENTER   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d INTERNATIONAL CENTRE FOR GENETIC ENGINEERING AND BIOTECHNOLOGY ICGEB   (India)

Author keywords

Crop improvement; DNA nanoball Sequencing; Exome; Metabolomics; MiRNA; Molecular Plant Breeding; Nanopore Sequencing; Next Generation Sequencing; Next Next Generation Sequencing; Proteomics; Pyrosequencing; Reversible Terminator Based Sequencing; RNA Seq; Sequencing by Ligation; Single Molecule Real Time Sequencing; Single Molecule RNAP Motion Based Real Time Sequencing; Transcriptomics; True Single Molecule Sequencing (TSMS); UTR; Whole Genome Sequencing

Indexed keywords

EID: 84866409523     PISSN: 00652660     EISSN: None     Source Type: Book Series    
DOI: 10.1016/B978-0-12-394395-8.00003-7     Document Type: Chapter

References (106)

1. Ashikari M., Sakakibara H., Lin S., Yamamoto T., Takashi T., Nishimura A., Angeles E.R., Qian Q., Kitano H., Matsuoka M. Cytokinin oxidase regulates rice grain production. Science 2005, 309:741-745.
2. Brooks S.A., Yan W., Jackson A.K., Deren C.W. A natural mutation in rc reverts white-rice-pericarp to red and results in a new, dominant, wild-type allele: Rc-g. Theor. Appl. Genet. 2008, 117:575-580.
3. Burke J.M., Burger J.C., Chapman M.A. Crop evolution: from genetics to genomics. Curr. Opin. Genet. Dev. 2007, 17:525-532.
4. Calvitti M., Moretti R., Lampazzi E., Bellini R., Dobson S.L. Characterization of a new Aedes albopictus (Diptera: Culicidae)-Wolbachia pipientis (Rickettsiales: Rickettsiaceae) symbiotic association generated by artificial transfer of the wPip strain from Culex pipiens (Diptera: Culicidae). J. Med. Entomol. 2010, 47:179-187.
5. Carpentier S.C., Witters E., Laukens K., Van Onckelen H., Swennen R., Panis B. Banana (Musa spp.) as a model to study the meristem proteome: acclimation to osmotic stress. Proteomics 2007, 7:92-105.
6. Carroll R.K., Shelburne S.A., Olsen R.J., Suber B., Sahasrabhojane P., Kumaraswami M., Beres S.B., Shea P.R., Flores A.R., Musser J.M. Naturally occurring single amino acid replacements in a regulatory protein alter streptococcal gene expression and virulence in mice. J. Clin. Invest. 2011, 121:1956-1968.
7. Clark R.M., Linton E., Messing J., Doebley J.F. Pattern of diversity in the genomic region near the maize domestication gene tb1. Proc. Natl. Acad. Sci. USA 2004, 101:700-707.
8. Cong B., Barrero L.S., Tanksley S.D. Regulatory change in YABBY-like transcription factor led to evolution of extreme fruit size during tomato domestication. Nat. Genet. 2008, 40:800-804.
9. Dai X., You C., Wang L., Chen G., Zhang Q., Wu C. Molecular characterization, expression pattern, and function analysis of the OsBC1L family in rice. Plant Mol. Biol. 2009, 71:469-481.
10. Deyholos M.K. Making the most of drought and salinity transcriptomics. Plant Cell Environ. 2010, 33:648-654.
11. DiGuistini S., Wang Y., Liao N.Y., Taylor G., Tanguay P., Feau N., Henrissat B., Chan S.K., Hesse-Orce U., Alamouti S.M., Tsui C.K., Docking R.T., Levasseur A., Haridas S., Robertson G., Birol I., Holt R.A., Marra M.A., Hamelin R.C., Hirst M., Jones S.J., Bohlmann J., Breuil C. Genome and transcriptome analyses of the mountain pine beetle-fungal symbiont Grosmannia clavigera, a lodgepole pine pathogen. Proc. Natl. Acad. Sci. USA 2011, 108:2504-2509.
12. Doebley J.F., Gaut B.S., Smith B.D. The molecular genetics of crop domestication. Cell 2006, 127:1309-1321.
13. Drmanac R., Sparks A.B., Callow M.J., Halpern A.L., Burns N.L., Kermani B.G., Carnevali P., Nazarenko I., Nilsen G.B., Yeung G., Dahl F., Fernandez A., Staker B., Pant K.P., Baccash J., Borcherding A.P., Brownley A., Cedeno R., Chen L., Chernikoff D., Cheung A., Chirita R., Curson B., Ebert J.C., Hacker C.R., Hartlage R., Hauser B., Huang S., Jiang Y., Karpinchyk V., Koenig M., Kong C., Landers T., Le C., Liu J., McBride C.E., Morenzoni M., Morey R.E., Mutch K., Perazich H., Perry K., Peters B.A., Peterson J., Pethiyagoda C.L., Pothuraju K., Richter C., Rosenbaum A.M., Roy S., Shafto J., Sharanhovich U., Shannon K.W., Sheppy C.G., Sun M., Thakuria J.V., Tran A., Vu D., Zaranek A.W., Wu X., Drmanac S., Oliphant A.R., Banyai W.C., Martin B., Ballinger D.G., Church G.M., Reid C.A. Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays. Science 2010, 327:78-81.
14. Du C.X., Fan H.F., Guo S.R., Tezuka T., Li J. Proteomic analysis of cucumber seedling roots subjected to salt stress. Phytochemistry 2010, 71:1450-1459.
15. Ebert M.S., Sharp P.A. Emerging roles for natural microRNA sponges. Curr. Biol. 2010, 20:R858-R861.
16. Edwards A., Voss H., Rice P., Civitello A., Stegemann J., Schwager C., Zimmermann J., Erfle H., Caskey C.T., Ansorge W. Automated DNA sequencing of the human HPRT locus. Genomics 1990, 6:593-608.
17. Eid J., Fehr A., Gray J., Luong K., Lyle J., Otto G., Peluso P., Rank D., Baybayan P., Bettman B., Bibillo A., Bjornson K., Chaudhuri B., Christians F., Cicero R., Clark S., Dalal R., Dewinter A., Dixon J., Foquet M., Gaertner A., Hardenbol P., Heiner C., Hester K., Holden D., Kearns G., Kong X., Kuse R., Lacroix Y., Lin S., Lundquist P., Ma C., Marks P., Maxham M., Murphy D., Park I., Pham T., Phillips M., Roy J., Sebra R., Shen G., Sorenson J., Tomaney A., Travers K., Trulson M., Vieceli J., Wegener J., Wu D., Yang A., Zaccarin D., Zhao P., Zhong F., Korlach J., Turner S. Real-time DNA sequencing from single polymerase molecules. Science 2009, 323:133-138.
18. Fan C., Xing Y., Mao H., Lu T., Han B., Xu C., Li X., Zhang Q. GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, encodes a putative transmembrane protein. Theor. Appl. Genet. 2006, 112:1164-1171.
19. Faris J.D., Gill B.S. Genomic targeting and high-resolution mapping of the domestication gene Q in wheat. Genome 2002, 45:706-718.
20. Flusberg B.A., Webster D.R., Lee J.H., Travers K.J., Olivares E.C., Clark T.A., Korlach J., Turner S.W. Direct detection of DNA methylation during single-molecule, real-time sequencing. Nat. Methods 2010, 7:461-465.
21. Franco-Zorrilla J.M., Valli A., Todesco M., Mateos I., Puga M.I., Rubio-Somoza I., Leyva A., Weigel D., Garcia J.A., Paz-Ares J. Target mimicry provides a new mechanism for regulation of microRNA activity. Nat. Genet. 2007, 39:1033-1037.
22. Frary A., Nesbitt T.C., Grandillo S., Knaap E., Cong B., Liu J., Meller J., Elber R., Alpert K.B., Tanksley S.D. fw2.2: a quantitative trait locus key to the evolution of tomato fruit size. Science 2000, 289:85-88.
23. Fukushima A., Kusano M., Redestig H., Arita M., Saito K. Metabolomic correlation-network modules in Arabidopsis based on a graph-clustering approach. BMC Syst. Biol. 2011, 5:1.
24. Gonzalez-Fernandez R., Prats E., Jorrin-Novo J.V. Proteomics of plant pathogenic fungi. J. Biomed. Biotechnol. 2010, 2010:932527.
25. Green R.E., Krause J., Briggs A.W., Maricic T., Stenzel U., Kircher M., Patterson N., Li H., Zhai W., Fritz M.H., Hansen N.F., Durand E.Y., Malaspinas A.S., Jensen J.D., Marques-Bonet T., Alkan C., Prufer K., Meyer M., Burbano H.A., Good J.M., Schultz R., Aximu-Petri A., Butthof A., Hober B., Hoffner B., Siegemund M., Weihmann A., Nusbaum C., Lander E.S., Russ C., Novod N., Affourtit J., Egholm M., Verna C., Rudan P., Brajkovic D., Kucan Z., Gusic I., Doronichev V.B., Golovanova L.V., Lalueza-Fox C., de la Rasilla M., Fortea J., Rosas A., Schmitz R.W., Johnson P.L., Eichler E.E., Falush D., Birney E., Mullikin J.C., Slatkin M., Nielsen R., Kelso J., Lachmann M., Reich D., Paabo S. A draft sequence of the Neandertal genome. Science 2010, 328:710-722.
26. Greenleaf W.J., Block S.M. Single-molecule, motion-based DNA sequencing using RNA polymerase. Science 2006, 313:801.
27. Guo Y., Song Y. Differential proteomic analysis of apoplastic proteins during initial phase of salt stress in rice. Plant Signal Behav. 2009, 4:121-122.
28. Hayashi M., Takahashi H., Tamura K., Huang J., Yu L.H., Kawai-Yamada M., Tezuka T., Uchimiya H. Enhanced dihydroflavonol-4-reductase activity and NAD homeostasis leading to cell death tolerance in transgenic rice. Proc. Natl. Acad. Sci. USA 2005, 102:7020-7025.
29. Hebert P.D., Ratnasingham S., deWaard J.R. Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proc. Biol. Sci. 2003, 270(Suppl. 1):S96-S99.
30. Heuberger A.L., Lewis M.R., Chen M.H., Brick M.A., Leach J.E., Ryan E.P. Metabolomic and functional genomic analyses reveal varietal differences in bioactive compounds of cooked rice. PLoS One 2011, 5:e12915.
31. Hirano H.Y., Eiguchi M., Sano Y. A single base change altered the regulation of the Waxy gene at the posttranscriptional level during the domestication of rice. Mol. Biol. Evol. 1998, 15:978-987.
32. Hu B., Du J., Zou R.Y., Yuan Y.J. An environment-sensitive synthetic microbial ecosystem. PLoS One 2010, 5:e10619.
33. Huang X., Feng Q., Qian Q., Zhao Q., Wang L., Wang A., Guan J., Fan D., Weng Q., Huang T., Dong G., Sang T., Han B. High-throughput genotyping by whole-genome resequencing. Genome Res. 2009, 19:1068-1076.
34. Hwang H., Cho M.H., Hahn B.S., Lim H., Kwon Y.K., Hahn T.R., Bhoo S.H. Proteomic identification of rhythmic proteins in rice seedlings. Biochim. Biophys. Acta 2011, 1814:470-479.
35. Ishikawa R., Thanh P.T., Nimura N., Htun T.M., Yamasaki M., Ishii T. Allelic interaction at seed-shattering loci in the genetic backgrounds of wild and cultivated rice species. Genes Genet. Syst. 2010, 85:265-271.
36. Jin J., Huang W., Gao J.P., Yang J., Shi M., Zhu M.Z., Luo D., Lin H.X. Genetic control of rice plant architecture under domestication. Nat. Genet. 2008, 40:1365-1369.
37. Kambam P.K., Henson M.A., Sun L. Design and mathematical modelling of a synthetic symbiotic ecosystem. IET Syst. Biol. 2008, 2:33-38.
38. Konishi S., Ebana K., Izawa T. Inference of the japonica rice domestication process from the distribution of six functional nucleotide polymorphisms of domestication-related genes in various landraces and modern cultivars. Plant Cell Physiol. 2008, 49:1283-1293.
39. Konishi S., Izawa T., Lin S.Y., Ebana K., Fukuta Y., Sasaki T., Yano M. An SNP caused loss of seed shattering during rice domestication. Science 2006, 312:1392-1396.
40. Korlach J., Bjornson K.P., Chaudhuri B.P., Cicero R.L., Flusberg B.A., Gray J.J., Holden D., Saxena R., Wegener J., Turner S.W. Real-time DNA sequencing from single polymerase molecules. Methods Enzymol. 2010, 472:431-455.
41. Kusano M., Tohge T., Fukushima A., Kobayashi M., Hayashi N., Otsuki H., Kondou Y., Goto H., Kawashima M., Matsuda F., Niida R., Matsui M., Saito K., Fernie A.R. Metabolomics reveals comprehensive reprogramming involving two independent metabolic responses of Arabidopsis to UV-B light. Plant J. 2011, 67:354-369.
42. Li C., Zhou A., Sang T. Rice domestication by reducing shattering. Science 2006, 311:1936-1939.
43. Li W., Wu J., Weng S., Zhang D., Zhang Y., Shi C. Characterization and fine mapping of the glabrous leaf and hull mutants (gl1) in rice (Oryza sativa L.). Plant Cell Rep. 2010, 29:617-627.
44. Li X., Qian Q., Fu Z., Wang Y., Xiong G., Zeng D., Wang X., Liu X., Teng S., Hiroshi F., Yuan M., Luo D., Han B., Li J. Control of tillering in rice. Nature 2003, 422:618-621.
45. Li X.J., Yang M.F., Chen H., Qu L.Q., Chen F., Shen S.H. Abscisic acid pretreatment enhances salt tolerance of rice seedlings: proteomic evidence. Biochim. Biophys. Acta 2010, 1804:929-940.
46. Lim C.W., Park J.Y., Lee S.H., Hwang C.H. Comparative proteomic analysis of soybean nodulation using a supernodulation mutant, SS2-2. Biosci. Biotechnol. Biochem. 2010, 74:2396-2404.
47. Lindeberg M., Myers C.R., Collmer A., Schneider D.J. Roadmap to new virulence determinants in Pseudomonas syringae: insights from comparative genomics and genome organization. Mol. Plant Microbe. Interact. 2008, 21:685-700.
48. Liu A., Burke J.M. Patterns of nucleotide diversity in wild and cultivated sunflower. Genetics 2006, 173:321-330.
49. Liu W.X., Liu H.L., Chai Z.J., Xu X.P., Song Y.R., Qu le Q. Evaluation of seed storage-protein gene 5' untranslated regions in enhancing gene expression in transgenic rice seed. Theor. Appl. Genet. 2010, 121:1267-1274.
50. Lu J., Sivamani E., Li X., Qu R. Activity of the 5' regulatory regions of the rice polyubiquitin rubi3 gene in transgenic rice plants as analyzed by both GUS and GFP reporter genes. Plant Cell Rep. 2008, 27:1587-1600.
51. Lu T., Lu G., Fan D., Zhu C., Li W., Zhao Q., Feng Q., Zhao Y., Guo Y., Huang X., Han B. Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq. Genome Res. 2010, 20:1238-1249.
52. Ma H., Zhao J. Genome-wide identification, classification, and expression analysis of the arabinogalactan protein gene family in rice (Oryza sativa L.). J. Exp. Bot. 2010, 61:2647-2668.
53. Margulies M., Egholm M., Altman W.E., Attiya S., Bader J.S., Bemben L.A., Berka J., Braverman M.S., Chen Y.J., Chen Z., Dewell S.B., Du L., Fierro J.M., Gomes X.V., Godwin B.C., He W., Helgesen S., Ho C.H., Irzyk G.P., Jando S.C., Alenquer M.L., Jarvie T.P., Jirage K.B., Kim J.B., Knight J.R., Lanza J.R., Leamon J.H., Lefkowitz S.M., Lei M., Li J., Lohman K.L., Lu H., Makhijani V.B., McDade K.E., McKenna M.P., Myers E.W., Nickerson E., Nobile J.R., Plant R., Puc B.P., Ronan M.T., Roth G.T., Sarkis G.J., Simons J.F., Simpson J.W., Srinivasan M., Tartaro K.R., Tomasz A., Vogt K.A., Volkmer G.A., Wang S.H., Wang Y., Weiner M.P., Yu P., Begley R.F., Rothberg J.M. Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005, 437:376-380.
54. Martinez-Esteso M.J., Selles-Marchart S., Vera-Urbina J.C., Pedreno M.A., Bru-Martinez R. DIGE analysis of proteome changes accompanying large resveratrol production by grapevine (Vitis vinifera cv. Gamay) cell cultures in response to methyl-beta-cyclodextrin and methyl jasmonate elicitors. J. Proteomics 2011, 74:1421-1436.
55. Maxam A.M., Gilbert W. A new method for sequencing DNA. Proc. Natl. Acad. Sci. USA 1977, 74:560-564.
56. Mitsui J., Fukuda Y., Azuma K., Tozaki H., Ishiura H., Takahashi Y., Goto J., Tsuji S. Multiplexed resequencing analysis to identify rare variants in pooled DNA with barcode indexing using next-generation sequencer. J. Hum. Genet. 2010, 55:448-455.
57. Murphy K.M., Berg K.D., Eshleman J.R. Sequencing of genomic DNA by combined amplification and cycle sequencing reaction. Clin. Chem. 2005, 51:35-39.
58. Nagy P.D., Pogany J. Global genomics and proteomics approaches to identify host factors as targets to induce resistance against Tomato bushy stunt virus. Adv. Virus Res. 2010, 76:123-177.
59. Nesbitt T.C., Tanksley S.D. Comparative sequencing in the genus Lycopersicon. Implications for the evolution of fruit size in the domestication of cultivated tomatoes. Genetics 2002, 162:365-379.
60. O'Brien H.E., Thakur S., Guttman D.S. Evolution of plant pathogenesis in Pseudomonas syringae: a genomics perspective. Annu. Rev. Phytopathol. 2010, 49:269-289.
61. Olsen K.M., Caicedo A.L., Polato N., McClung A., McCouch S., Purugganan M.D. Selection under domestication: evidence for a sweep in the rice waxy genomic region. Genetics 2006, 173:975-983.
62. Ouyang Y., Chen J., Xie W., Wang L., Zhang Q. Comprehensive sequence and expression profile analysis of Hsp20 gene family in rice. Plant Mol. Biol. 2009, 70:341-357.
63. Pan Z., Liu Q., Yun Z., Guan R., Zeng W., Xu Q., Deng X. Comparative proteomics of a lycopene-accumulating mutant reveals the important role of oxidative stress on carotenogenesis in sweet orange (Citrus sinensis [L.] osbeck). Proteomics 2009, 9:5455-5470.
64. Pareek C.S., Smoczynski R., Tretyn A. Sequencing technologies and genome sequencing. J. Appl. Genet. 2011, 52:413-435.
65. Peng J., Richards D.E., Hartley N.M., Murphy G.P., Devos K.M., Flintham J.E., Beales J., Fish L.J., Worland A.J., Pelica F., Sudhakar D., Christou P., Snape J.W., Gale M.D., Harberd N.P. 'Green revolution' genes encode mutant gibberellin response modulators. Nature 1999, 400:256-261.
66. Porreca G.J. Genome sequencing on nanoballs. Nat. Biotechnol. 2010, 28:43-44.
67. Qiu X., Xie W., Lian X., Zhang Q. Molecular analyses of the rice glutamate dehydrogenase gene family and their response to nitrogen and phosphorous deprivation. Plant Cell Rep. 2009, 28:1115-1126.
68. Rothberg J.M., Hinz W., Rearick T.M., Schultz J., Mileski W., Davey M., Leamon J.H., Johnson K., Milgrew M.J., Edwards M., Hoon J., Simons J.F., Marran D., Myers J.W., Davidson J.F., Branting A., Nobile J.R., Puc B.P., Light D., Clark T.A., Huber M., Branciforte J.T., Stoner I.B., Cawley S.E., Lyons M., Fu Y., Homer N., Sedova M., Miao X., Reed B., Sabina J., Feierstein E., Schorn M., Alanjary M., Dimalanta E., Dressman D., Kasinskas R., Sokolsky T., Fidanza J.A., Namsaraev E., McKernan K.J., Williams A., Roth G.T., Bustillo J. An integrated semiconductor device enabling non-optical genome sequencing. Nature 2011, 475:348-352.
69. Ruiz-Ferrer V., Voinnet O. Roles of plant small RNAs in biotic stress responses. Annu. Rev. Plant Biol. 2009, 60:485-510.
70. Sanchez D.H., Pieckenstain F.L., Szymanski J., Erban A., Bromke M., Hannah M.A., Kraemer U., Kopka J., Udvardi M.K. Comparative functional genomics of salt stress in related model and cultivated plants identifies and overcomes limitations to translational genomics. PLoS One 2011, 6:e17094.
71. Sanger F., Coulson A.R. A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. J. Mol. Biol. 1975, 94:441-448.
72. Seidl M.F., Van den Ackerveken G., Govers F., Snel B. A domain-centric analysis of oomycete plant pathogen genomes reveals unique protein organization. Plant Physiol. 2011, 155:628-644.
73. SenGupta D.J., Cookson B.T. SeqSharp: a general approach for improving cycle-sequencing that facilitates a robust one-step combined amplification and sequencing method. J. Mol. Diagn. 2010, 12:272-277.
74. Severin A.J., Woody J.L., Bolon Y.T., Joseph B., Diers B.W., Farmer A.D., Muehlbauer G.J., Nelson R.T., Grant D., Specht J.E., Graham M.A., Cannon S.B., May G.D., Vance C.P., Shoemaker R.C. RNA-Seq Atlas of Glycine max: a guide to the soybean transcriptome. BMC Plant Biol. 2010, 10:160.
75. Shan X., Wang J., Chua L., Jiang D., Peng W., Xie D. The role of Arabidopsis Rubisco activase in jasmonate-induced leaf senescence. Plant Physiol. 2011, 155:751-764.
76. Shomura A., Izawa T., Ebana K., Ebitani T., Kanegae H., Konishi S., Yano M. Deletion in a gene associated with grain size increased yields during rice domestication. Nat. Genet. 2008, 40:1023-1028.
77. Simons K.J., Fellers J.P., Trick H.N., Zhang Z., Tai Y.S., Gill B.S., Faris J.D. Molecular characterization of the major wheat domestication gene Q. Genetics 2006, 172:547-555.
78. Smith L.M., Sanders J.Z., Kaiser R.J., Hughes P., Dodd C., Connell C.R., Heiner C., Kent S.B., Hood L.E. Fluorescence detection in automated DNA sequence analysis. Nature 1986, 321:674-679.
79. Sudini H., Liles M.R., Arias C.R., Bowen K.L., Huettel R.N. Exploring soil bacterial communities in different peanut-cropping sequences using multiple molecular approaches. Phytopathology 2011, 101:819-827.
80. Sugio T., Satoh J., Matsuura H., Shinmyo A., Kato K. The 5'-untranslated region of the Oryza sativa alcohol dehydrogenase gene functions as a translational enhancer in monocotyledonous plant cells. J. Biosci. Bioeng. 2008, 105:300-302.
81. Sweeney M.T., Thomson M.J., Cho Y.G., Park Y.J., Williamson S.H., Bustamante C.D., McCouch S.R. Global dissemination of a single mutation conferring white pericarp in rice. PLoS Genet. 2007, 3:e133.
82. Takahashi H., Hayashi M., Goto F., Sato S., Soga T., Nishioka T., Tomita M., Kawai-Yamada M., Uchimiya H. Evaluation of metabolic alteration in transgenic rice overexpressing dihydroflavonol-4-reductase. Ann. Bot. 2006, 98:819-825.
83. Tan L., Li X., Liu F., Sun X., Li C., Zhu Z., Fu Y., Cai H., Wang X., Xie D., Sun C. Control of a key transition from prostrate to erect growth in rice domestication. Nat. Genet. 2008, 40:1360-1364.
84. Tang H., Sezen U., Paterson A.H. Domestication and plant genomes. Curr. Opin. Plant Biol. 2010, 13:160-166.
85. Thompson J.F., Steinmann K.E. Single molecule sequencing with a HeliScope genetic analysis system. Curr. Protoc. Mol. Biol. 2010, Chapter 7, Unit7 10.
86. Thurber C.S., Reagon M., Gross B.L., Olsen K.M., Jia Y., Caicedo A.L. Molecular evolution of shattering loci in U.S. weedy rice. Mol. Ecol. 2010, 19:3271-3284.
87. Venu R.C., Zhang Y., Weaver B., Carswell P., Mitchell T.K., Meyers B.C., Boehm M.J., Wang G.L. Large scale identification of genes involved in plant-fungal interactions using Illumina's sequencing-by-synthesis technology. Methods Mol. Biol. 2011, 722:167-178.
88. Wang E., Wang J., Zhu X., Hao W., Wang L., Li Q., Zhang L., He W., Lu B., Lin H., Ma H., Zhang G., He Z. Control of rice grain-filling and yield by a gene with a potential signature of domestication. Nat. Genet. 2008, 40:1370-1374.
89. Wang E., Xu X., Zhang L., Zhang H., Lin L., Wang Q., Li Q., Ge S., Lu B.R., Wang W., He Z. Duplication and independent selection of cell-wall invertase genes GIF1 and OsCIN1 during rice evolution and domestication. BMC Evol. Biol. 2010, 10:108.
90. Wang H., Nussbaum-Wagler T., Li B., Zhao Q., Vigouroux Y., Faller M., Bomblies K., Lukens L., Doebley J.F. The origin of the naked grains of maize. Nature 2005, 436:714-719.
91. Wang L., Guo K., Li Y., Tu Y., Hu H., Wang B., Cui X., Peng L. Expression profiling and integrative analysis of the CESA/CSL superfamily in rice. BMC Plant Biol. 2010, 10:282.
92. Wang Y., Shen D., Bo S., Chen H., Zheng J., Zhu Q.H., Cai D., Helliwell C., Fan L. Sequence variation and selection of small RNAs in domesticated rice. BMC Evol. Biol. 2010, 10:119.
93. Washida H., Kaneko S., Crofts N., Sugino A., Wang C., Okita T.W. Identification of cis-localization elements that target glutelin RNAs to a specific subdomain of the cortical endoplasmic reticulum in rice endosperm cells. Plant Cell Physiol. 2009, 50:1710-1714.
94. Wheeler D.A., Srinivasan M., Egholm M., Shen Y., Chen L., McGuire A., He W., Chen Y.J., Makhijani V., Roth G.T., Gomes X., Tartaro K., Niazi F., Turcotte C.L., Irzyk G.P., Lupski J.R., Chinault C., Song X.Z., Liu Y., Yuan Y., Nazareth L., Qin X., Muzny D.M., Margulies M., Weinstock G.M., Gibbs R.A., Rothberg J.M. The complete genome of an individual by massively parallel DNA sequencing. Nature 2008, 452:872-876.
95. Wienkoop S., Baginsky S., Weckwerth W. Arabidopsis thaliana as a model organism for plant proteome research. J. Proteomics 2010, 73:2239-2248.
96. Wu X.M., Liu M.Y., Ge X.X., Xu Q., Guo W.W. Stage and tissue-specific modulation of ten conserved miRNAs and their targets during somatic embryogenesis of Valencia sweet orange. Planta 2011, 233:495-505.
97. Xin M., Wang Y., Yao Y., Song N., Hu Z., Qin D., Xie C., Peng H., Ni Z., Sun Q. Identification and characterization of wheat long non-protein coding RNAs responsive to powdery mildew infection and heat stress by using microarray analysis and SBS sequencing. BMC Plant Biol. 2011, 11:61.
98. Xue W., Xing Y., Weng X., Zhao Y., Tang W., Wang L., Zhou H., Yu S., Xu C., Li X., Zhang Q. Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice. Nat. Genet. 2008, 40:761-767.
99. Yamanaka S., Nakamura I., Watanabe K.N., Sato Y. Identification of SNPs in the waxy gene among glutinous rice cultivars and their evolutionary significance during the domestication process of rice. Theor. Appl. Genet. 2004, 108:1200-1204.
100. Yang H., Huang Y., Zhi H., Yu D. Proteomics-based analysis of novel genes involved in response toward Soybean mosaic virus infection. Mol. Biol. Rep. 2010, 38:511-521.
101. Yang L., Wakasa Y., Kawakatsu T., Takaiwa F. The 3'-untranslated region of rice glutelin GluB-1 affects accumulation of heterologous protein in transgenic rice. Biotechnol. Lett. 2009, 31:1625-1631.
102. Zenoni S., Ferrarini A., Giacomelli E., Xumerle L., Fasoli M., Malerba G., Bellin D., Pezzotti M., Delledonne M. Characterization of transcriptional complexity during berry development in Vitis vinifera using RNA-Seq. Plant Physiol. 2010, 152:1787-1795.
103. Zhang G., Guo G., Hu X., Zhang Y., Li Q., Li R., Zhuang R., Lu Z., He Z., Fang X., Chen L., Tian W., Tao Y., Kristiansen K., Zhang X., Li S., Yang H., Wang J. Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome. Genome Res. 2010, 20:646-654.
104. Zhang X., Zou Z., Gong P., Zhang J., Ziaf K., Li H., Xiao F., Ye Z. Over-expression of microRNA169 confers enhanced drought tolerance to tomato. Biotechnol. Lett. 2011, 33:403-409.
105. Zhang X., Zou Z., Zhang J., Zhang Y., Han Q., Hu T., Xu X., Liu H., Li H., Ye Z. Over-expression of sly-miR156a in tomato results in multiple vegetative and reproductive trait alterations and partial phenocopy of the sft mutant. FEBS Lett. 2011, 585:435-439.
106. Zhao M., Ding H., Zhu J.K., Zhang F., Li W.X. Involvement of miR169 in the nitrogen-starvation responses in Arabidopsis. New Phytol. 2011, 190:906-915.