Unlocking triticeae genomics to sustainably feed the future

Plant and Cell Physiology

Volumn 54, Issue 12, 2013, Pages 1931-1950

  Mochida, Keiichi ^a,b   Shinozaki, Kazuo ^a  

^a RIKEN Center for Sustainable Resource Science   (Japan)

^b YOKOHAMA CITY UNIVERSITY   (Japan)

Author keywords

Barley; Brachypodium; Crop improvement; Next generation sequencing; Triticeae; Wheat

Indexed keywords

BARLEY; BRACHYPODIUM; CROP IMPROVEMENT; GENETICS; GENOMICS; HORDEUM; METHODOLOGY; NEXT-GENERATION SEQUENCING; PLANT GENOME; REVIEW; THEORETICAL MODEL; TRITICEAE; WHEAT;

BARLEY; BRACHYPODIUM; CROP IMPROVEMENT; NEXT-GENERATION SEQUENCING; TRITICEAE; WHEAT;

BRACHYPODIUM; GENOME, PLANT; GENOMICS; HORDEUM; MODELS, THEORETICAL; TRITICUM;

EID: 84890456707     PISSN: 00320781     EISSN: 14719053     Source Type: Journal    
DOI: 10.1093/pcp/pct163     Document Type: Review

References (198)

1. Aikawa, S., Kobayashi, M.J., Satake, A., Shimizu, K.K. and Kudoh, H. (2010) Robust control of the seasonal expression of the Arabidopsis FLC gene in a fluctuating environment. Proc. Natl Acad. Sci. USA 107: 11632-11637.
2. Alexandratos, N. and Bruinsma, J. (2012) World Agriculture Towards 2030/2050: The 2012 Revision. ESA Working paper No. 12.03.
3. Arai-Kichise, Y., Shiwa, Y., Nagasaki, H., Ebana, K., Yoshikawa, H., Yano, M. et al. (2011) Discovery of genome-wide DNA polymorphisms in a landrace cultivar of Japonica rice by whole-genome sequencing. Plant Cell Physiol. 52: 274-282.
4. Araki, R., Murata, J. and Murata, Y. (2011) A novel barley yellow stripe 1-like transporter (HvYSL2) localized to the root endodermis transports metal-phytosiderophore complexes. Plant Cell Physiol. 52: 1931-1940.
5. Ashelford, K., Eriksson, M.E., Allen, C.M., D'Amore, R., Johansson, M., Gould, P. et al. (2011) Full genome re-sequencing reveals a novel circadian clock mutation in Arabidopsis. Genome Biol. 12: R28.
6. Bai, S., Saito, T., Sakamoto, D., Ito, A., Fujii, H. and Moriguchi, T. (2013) Transcriptome analysis of Japanese pear (Pyrus pyrifolia Nakai) flower buds transitioning through endodormancy. Plant Cell Physiol. 54: 1132-1151.
7. Baker, J.M.,Hawkins, N.D.,Ward, J.L., Lovegrove,A., Napier, J.A., Shewry, P.R. et al. (2006) A metabolomic study of substantial equivalence of fieldgrown genetically modified wheat. Plant Biotechnol. J. 4: 381-392. (Pubitemid 43886811)
8. Bevan, M.W., Garvin, D.F. and Vogel, J.P. (2010) Brachypodium distachyon genomics for sustainable food and fuel production. Curr. Opin. Biotechnol. 21: 211-217.
9. Boden, S.A., Kavanova, M., Finnegan, E.J. and Wigge, P.A. (2013) Thermal stress effects on grain yield in Brachypodium distachyon occur via H2A.Z-nucleosomes. Genome Biol. 14: R65.
10. Bowne, J.B., Erwin, T.A., Juttner, J., Schnurbusch, T., Langridge, P., Bacic, A. et al. (2012) Drought responses of leaf tissues from wheat cultivars of differing drought tolerance at the metabolite level. Mol. Plant 5: 418-429.
11. Bragg, J.N., Wu, J., Gordon, S.P., Guttman, M.E., Thilmony, R., Lazo, G.R. et al. (2012) Generation and characterization of the Western Regional Research Center Brachypodium T-DNA insertional mutant collection. PLoS One 7: e41916.
12. Brenchley, R., Spannagl, M., Pfeifer, M., Barker, G.L., D'Amore, R., Allen, A.M. et al. (2012) Analysis of the bread wheat genome using whole-genome shotgun sequencing. Nature 491: 705-710.
13. Brini, F., Yamamoto, A., Jlaiel, L., Takeda, S., Hobo, T., Dinh, H.Q. et al. (2011) Pleiotropic effects of the wheat dehydrin DHN-5 on stress responses in Arabidopsis. Plant Cell Physiol. 52: 676-688.
14. Brkljacic, J., Grotewold, E., Scholl, R., Mockler, T., Garvin, D.F., Vain, P. et al. (2011) Brachypodium as a model for the grasses: today and the future. Plant Physiol. 157: 3-13.
15. Carninci, P., Kvam, C., Kitamura, A., Ohsumi, T., Okazaki, Y., Itoh, M. et al. (1996) High-efficiency full-length cDNA cloning by biotinylated CAP trapper. Genomics 37: 327-336. (Pubitemid 26386957)
16. Cavanagh, C., Morell, M., Mackay, I. and Powell, W. (2008) From mutations to MAGIC: resources for gene discovery, validation and delivery in crop plants. Curr. Opin. Plant Biol. 11: 215-221.
17. Cavanagh, C.R., Chao, S., Wang, S., Huang, B.E., Stephen, S., Kiani, S. et al. (2013) Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars. Proc. Natl Acad. Sci. USA 110: 8057-8062.
18. Chang, Y.Y., Chu, Y.W., Chen, C.W., Leu, W.M., Hsu, H.F. and Yang, C.H. (2011) Characterization of Oncidium 'Gower Ramsey' transcriptomes using 454 GS-FLX pyrosequencing and their application to the identification of genes associated with flowering time. Plant Cell Physiol. 52: 1532-1545.
19. Chen, H., He, H., Zhou, F., Yu, H. and Deng, X.W. (2013) Development of genomics-based genotyping platforms and their applications in rice breeding. Curr. Opin. Plant Biol. 16: 247-254.
20. Chochois, V., Vogel, J.P. and Watt, M. (2012) Application of Brachypodium to the genetic improvement of wheat roots. J. Exp. Bot. 63: 3467-3474.
21. Close, T.J., Bhat, P.R., Lonardi, S., Wu, Y., Rostoks, N., Ramsay, L. et al. (2009) Development and implementation of high-throughput SNP genotyping in barley. BMC Genomics 10: 582.
22. Conde, A., Chaves, M.M. and Geros, H. (2011) Membrane transport, sensing and signaling in plant adaptation to environmental stress. Plant Cell Physiol. 52: 1583-1602.
23. Cui, Y., Lee, M.Y., Huo, N., Bragg, J., Yan, L., Yuan, C. et al. (2012) Fine mapping of the Bsr1 barley stripe mosaic virus resistance gene in the model grass Brachypodium distachyon. PLoS One 7: e38333.
24. Dal Santo, S., Tornielli, G.B., Zenoni, S., Fasoli, M., Farina, L., Anesi, A. et al. (2013) The plasticity of the grapevine berry transcriptome. Genome Biol. 14: r54.
25. Dalmais, M., Antelme, S., Ho-Yue-Kuang, S., Wang, Y., Darracq, O., d'Yvoire, M.B. et al. (2013) A TILLING platform for functional genomics in Brachypodium distachyon. PLoS One 8: e65503.
26. Davidson, R.M., Gowda, M., Moghe, G., Lin, H., Vaillancourt, B., Shiu, S.H. et al. (2012) Comparative transcriptomics of three Poaceae species reveals patterns of gene expression evolution. Plant J. 71: 492-502.
27. De Vos, D., Dzhurakhalov, A., Draelants, D., Bogaerts, I., Kalve, S., Prinsen, E. et al. (2012) Towards mechanistic models of plant organ growth. J. Exp. Bot. 63: 3325-3337.
28. Draper, J., Mur, L.A., Jenkins, G., Ghosh-Biswas, G.C., Bablak, P., Hasterok, R. et al. (2001) Brachypodium distachyon. A new model system for functional genomics in grasses. Plant Physiol. 127: 1539-1555. (Pubitemid 34050024)
29. Dubcovsky, J. and Dvorak, J. (2007) Genome plasticity a key factor in the success of polyploid wheat under domestication. Science 316: 1862-1866. (Pubitemid 47025777)
30. Endo, A., Tatematsu, K., Hanada, K., Duermeyer, L., Okamoto, M., Yonekura-Sakakibara, K. et al. (2012) Tissue-specific transcriptome analysis reveals cell wall metabolism, flavonol biosynthesis and defense responses are activated in the endosperm of germinating Arabidopsis thaliana seeds. Plant Cell Physiol. 53: 16-27.
31. Figueroa, M., Alderman, S., Garvin, D.F. and Pfender, W.F. (2013) Infection of Brachypodium distachyon by formae speciales of Puccinia graminis: early infection events and host-pathogen incompatibility. PLoS One 8: e56857.
32. Filichkin, S.A., Priest, H.D., Givan, S.A., Shen, R., Bryant, D.W., Fox, S.E. et al. (2010) Genome-wide mapping of alternative splicing in Arabidopsis thaliana. Genome Res. 20: 45-58.
33. Fu, C.H., Chen, Y.W., Hsiao, Y.Y., Pan, Z.J., Liu, Z.J., Huang, Y.M. et al. (2011) OrchidBase: a collection of sequences of the transcriptome derived from orchids. Plant Cell Physiol. 52: 238-243.
34. Fukushima, A. and Kusano, M. (2013) Recent progress in the development of metabolome databases for plant systems biology. Front. Plant Sci. 4: 73.
35. Fukushima, E.O., Seki, H., Sawai, S., Suzuki, M., Ohyama, K., Saito, K. et al. (2013) Combinatorial biosynthesis of legume natural and rare triterpenoids in engineered yeast. Plant Cell Physiol. 54: 740-749.
36. Gaj, T., Gersbach, C.A. and Barbas, C.F. 3rd (2013) ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering. Trends Biotechnol. 31: 397-405.
37. Garvin, D.F., McKenzie, N., Vogel, J.P., Mockler, T.C., Blankenheim, Z.J., Wright, J. et al. (2010) An SSR-based genetic linkage map of the model grass Brachypodium distachyon. Genome 53: 1-13.
38. Gil-Amado, J.A. and Gomez-Jimenez, M.C. (2013) Transcriptome analysis of mature fruit abscission control in olive. Plant Cell Physiol. 54: 244-269.
39. Goodstein, D.M., Shu, S., Howson, R., Neupane, R., Hayes, R.D., Fazo, J. et al. (2012) Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res. 40: D1178-D1186.
40. Griffiths, S., Sharp, R., Foote, T.N., Bertin, I., Wanous, M., Reader, S. et al. (2006) Molecular characterization of Ph1 as a major chromosome pairing locus in polyploid wheat. Nature 439: 749-752. (Pubitemid 43237624)
41. Hamada, K., Hongo, K., Suwabe, K., Shimizu, A., Nagayama, T., Abe, R. et al. (2011) OryzaExpress: an integrated database of gene expression networks and omics annotations in rice. Plant Cell Physiol. 52: 220-229.
42. Heigwer, F., Kerr, G., Walther, N., Glaeser, K., Pelz, O., Breinig, M. et al. (2013) E-TALEN: a web tool to design TALENs for genome engineering. Nucleic Acids Res. 41: e190.
43. Hernandez, P., Martis, M., Dorado, G., Pfeifer, M., Galvez, S., Schaaf, S. et al. (2012) Next-generation sequencing and syntenic integration of flow-sorted arms of wheat chromosome 4A exposes the chromosome structure and gene content. Plant J. 69: 377-386.
44. Higashi, Y. and Saito, K. (2013) Network analysis for gene discovery in plant-specialized metabolism. Plant Cell Environ. 36: 1597-1606.
45. Hirano, K., Aya, K., Morinaka, Y., Nagamatsu, S., Sato, Y., Antonio, B.A. et al. (2013a) Survey of genes involved in rice secondary cell wall formation through a co-expression network. Plant Cell Physiol. 54: 1803-1821.
46. Hirano, K., Kondo, M., Aya, K., Miyao, A., Sato, Y., Antonio, B.A. et al. (2013b) Identification of transcription factors involved in rice secondary cell wall formation. Plant Cell Physiol. 54: 1791-1802.
47. Hirayama, T. and Shinozaki, K. (2010) Research on plant abiotic stress responses in the post-genome era: past, present and future. Plant J. 61: 1041-1052.
48. Hirsch, C.N. and Buell, C.R. (2013) Tapping the promise of genomics in species with complex, nonmodel genomes. Annu. Rev. Plant Biol. 64: 89-110.
49. Hong, J.P., Takeshi, Y., Kondou, Y., Schachtman, D.P., Matsui, M. and Shin, R. (2013) Identification and characterization of transcription factors regulating Arabidopsis HAK5. Plant Cell Physiol. 54: 1478-1490.
50. Horie, T., Kaneko, T., Sugimoto, G., Sasano, S., Panda, S.K., Shibasaka, M. et al. (2011) Mechanisms of water transport mediated by PIP aquaporins and their regulation via phosphorylation events under salinity stress in barley roots. Plant Cell Physiol. 52: 663-675.
51. Hu, W., Yuan, Q., Wang, Y., Cai, R., Deng, X., Wang, J. et al. (2012) Overexpression of a wheat aquaporin gene, TaAQP8, enhances salt stress tolerance in transgenic tobacco. Plant Cell Physiol. 53: 2127-2141.
52. Huang, B.E., George, A.W., Forrest, K.L., Kilian, A., Hayden, M.J., Morell, M.K. et al. (2012) A multiparent advanced generation inter-cross population for genetic analysis in wheat. Plant Biotechnol. J. 10: 826-839.
53. Huang, M.D., Hsing, Y.I. and Huang, A.H. (2011) Transcriptomes of the anther sporophyte: availability and uses. Plant Cell Physiol. 52: 1459-1466.
54. Huang, X., Wei, X., Sang, T., Zhao, Q., Feng, Q., Zhao, Y. et al. (2010) Genome-wide association studies of 14 agronomic traits in rice landraces. Nat. Genet. 42: 961-967.
55. Huo, N., Garvin, D.F., You, F.M., McMahon, S., Luo, M.C., Gu, Y.Q. et al. (2011) Comparison of a high-density genetic linkage map to genome features in the model grass Brachypodium distachyon. Theor. Appl. Genet. 123: 455-464.
56. Iida, K., Kawaguchi, S., Kobayashi, N., Yoshida, Y., Ishii, M., Harada, E. et al. (2011) ARTADE2DB: improved statistical inferences for Arabidopsis gene functions and structure predictions by dynamic structure-based dynamic expression (DSDE) analyses. Plant Cell Physiol. 52: 254-264.
57. Ikeda, Y. (2012) Plant imprinted genes identified by genome-wide approaches and their regulatory mechanisms. Plant Cell Physiol. 53: 809-816.
58. Imanishi, T., Itoh, T., Suzuki, Y., O'Donovan, C., Fukuchi, S., Koyanagi, K.O. et al. (2004) Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol. 2: e162.
59. International Barley Genome Sequencing Consortium. (2012) A physical, genetic and functional sequence assembly of the barley genome. Nature 491: 711-716.
60. International Brachypodium Initiative. (2010) Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 463: 763-768.
61. Ishikawa, T., Takahara, K., Hirabayashi, T., Matsumura, H., Fujisawa, S., Terauchi, R. et al. (2010) Metabolome analysis of response to oxidative stress in rice suspension cells overexpressing cell death suppressor Bax inhibitor-1. Plant Cell Physiol. 51: 9-20.
62. Izawa, T., Mihara, M., Suzuki, Y., Gupta, M., Itoh, H., Nagano, A.J. et al. (2011) Os-GIGANTEA confers robust diurnal rhythms on the global transcriptome of rice in the field. Plant Cell 23: 1741-1755.
63. James, G.V., Patel, V., Nordstrom, K.J., Klasen, J.R., Salome, P.A., Weigel, D. et al. (2013) User guide for mapping-by-sequencing in Arabidopsis. Genome Biol. 14: R61.
64. Jia, J., Zhao, S., Kong, X., Li, Y., Zhao, G., He, W. et al. (2013) Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation. Nature 496: 91-95.
65. Kamada-Nobusada, T., Makita, N., Kojima, M. and Sakakibara, H. (2013) Nitrogen-dependent regulation of de novo cytokinin biosynthesis in rice: the role of glutamine metabolism as an additional signal. Plant Cell Physiol. 54: 1881-1893.
66. Kanno, Y., Jikumaru, Y., Hanada, A., Nambara, E., Abrams, S.R., Kamiya, Y. et al. (2010) Comprehensive hormone profiling in developing Arabidopsis seeds: examination of the site of ABA biosynthesis, ABA transport and hormone interactions. Plant Cell Physiol. 51: 1988-2001.
67. Katsuragi, T., Ono, N., Yasumoto, K., Altaf-Ul-Amin, M., Hirai, M.Y., Sriyudthsak, K. et al. (2013) SS-mPMG and SS-GA: tools for finding pathways and dynamic simulation of metabolic networks. Plant Cell Physiol. 54: 728-739.
68. Kawaura, K., Mochida, K., Enju, A., Totoki, Y., Toyoda, A., Sakaki, Y. et al. (2009) Assessment of adaptive evolution between wheat and rice as deduced from full-length common wheat cDNA sequence data and expression patterns. BMC Genomics 10: 271.
69. Kawaura, K., Mochida, K., Yamazaki, Y. and Ogihara, Y. (2006) Transcriptome analysis of salinity stress responses in common wheat using a 22k oligo-DNA microarray. Funct. Integr. Genomics 6: 132-142.
70. Kim, J.M., To, T.K., Ishida, J., Matsui, A., Kimura, H. and Seki, M. (2012a) Transition of chromatin status during the process of recovery from drought stress in Arabidopsis thaliana. Plant Cell Physiol. 53: 847-856.
71. Kim, J.M., To, T.K. and Seki, M. (2012b) An epigenetic integrator: new insights into genome regulation, environmental stress responses and developmental controls by histone deacetylase 6. Plant Cell Physiol. 53: 794-800.
72. Kinoshita, T. and Jacobsen, S.E. (2012) Opening the door to epigenetics in PCP. Plant Cell Physiol. 53: 763-765.
73. Kogel, K.H., Voll, L.M., Schafer, P., Jansen, C., Wu, Y., Langen, G. et al. (2010) Transcriptome and metabolome profiling of field-grown transgenic barley lack induced differences but show cultivar-specific variances. Proc. Natl Acad. Sci. USA 107: 6198-6203.
74. Kojima, M., Kamada-Nobusada, T., Komatsu, H., Takei, K., Kuroha, T., Mizutani, M. et al. (2009) Highly sensitive and high-throughput analysis of plant hormones using MS-probe modification and liquid chromatography-tandem mass spectrometry: an application for hormone profiling in Oryza sativa. Plant Cell Physiol. 50: 1201-1214.
75. Kondou, Y., Higuchi, M., Takahashi, S., Sakurai, T., Ichikawa, T., Kuroda, H. et al. (2009) Systematic approaches to using the FOX hunting system to identify useful rice genes. Plant J. 57: 883-894.
76. Kover, P.X., Valdar, W., Trakalo, J., Scarcelli, N., Ehrenreich, I.M., Purugganan, M.D. et al. (2009) A multiparent advanced generation inter-cross to fine-map quantitative traits in Arabidopsis thaliana. PLoS Genet. 5: e1000551.
77. Krasileva, K.V., Buffalo, V., Bailey, P., Pearce, S., Ayling, S., Tabbita, F. et al. (2013) Separating homeologs by phasing in the tetraploid wheat transcriptome. Genome Biol. 14: R66.
78. Kubo, T., Fujita, M., Takahashi, H., Nakazono, M., Tsutsumi, N. and Kurata, N. (2013) Transcriptome analysis of developing ovules in rice isolated by laser microdissection. Plant Cell Physiol. 54: 750-765.
79. Kudo, T., Akiyama, K., Kojima, M., Makita, N., Sakurai, T. and Sakakibara, H. (2013) UniVIO: a multiple omics database with hormonome and transcriptome data from rice. Plant Cell Physiol. 54: e9.
80. Kump, K.L., Bradbury, P.J., Wisser, R.J., Buckler, E.S., Belcher, A.R., Oropeza-Rosas, M.A. et al. (2011) Genome-wide association study of quantitative resistance to southern leaf blight in the maize nested association mapping population. Nat. Genet. 43: 163-168.
81. Lai, K., Berkman, P.J., Lorenc, M.T., Duran, C., Smits, L., Manoli, S. et al. (2012) WheatGenome.info: an integrated database and portal for wheat genome information. Plant Cell Physiol. 53: e2.
82. Leaungthitikanchana, S., Fujibe, T., Tanaka, M., Wang, S., Sotta, N., Takano, J. et al. (2013) Differential expression of three BOR1 genes corresponding to different genomes in response to boron conditions in hexaploid wheat (Triticum aestivum L.). Plant Cell Physiol. 54: 1056-1063.
83. Lee, Y.J., Perdian, D.C., Song, Z., Yeung, E.S. and Nikolau, B.J. (2012) Use of mass spectrometry for imaging metabolites in plants. Plant J. 70: 81-95.
84. Li, C., Rudi, H., Stockinger, E.J., Cheng, H., Cao, M., Fox, S.E. et al. (2012) Comparative analyses reveal potential uses of Brachypodium distachyon as a model for cold stress responses in temperate grasses. BMC Plant Biol. 12: 65.
85. Li, L., Stoeckert, C.J. Jr. and Roos, D.S. (2003) OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 13: 2178-2189. (Pubitemid 37161775)
86. Ling, H.Q., Zhao, S., Liu, D., Wang, J., Sun, H., Zhang, C. et al. (2013) Draft genome of the wheat A-genome progenitor Triticum urartu. Nature 496: 87-90.
87. Liu, S., Sehgal, S.K., Li, J., Lin, M., Trick, H.N., Yu, J. et al. (2013) Cloning and characterization of a critical regulator for preharvest sprouting in wheat. Genetics 195: 263-273.
88. Loraine, A.E., McCormick, S., Estrada, A., Patel, K. and Qin, P. (2013) RNA-seq of Arabidopsis pollen uncovers novel transcription and alternative splicing. Plant Physiol. 162: 1092-1109.
89. Lucas, S.J., Akpinar, B.A., Kantar, M., Weinstein, Z., Aydinoglu, F., Safar, J. et al. (2013) Physical mapping integrated with syntenic analysis to characterize the gene space of the long arm of wheat chromosome 1A. PLoS One 8: e59542.
90. Maeda, N., Kasukawa, T., Oyama, R., Gough, J., Frith, M., Engstrom, P.G. et al. (2006) Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs. PLoS Genet. 2: e62.
91. Mandadi, K.K. and Scholthof, K.B. (2012) Characterization of a viral synergism in the monocot Brachypodium distachyon reveals distinctly altered host molecular processes associated with disease. Plant Physiol. 160: 1432-1452.
92. Mandadi, K.K. and Scholthof, K.B. (2013) Plant immune responses against viruses: how does a virus cause disease? Plant Cell 25: 1489-1505.
93. Martis, M.M., Klemme, S., Banaei-Moghaddam, A.M., Blattner, F.R., Macas, J., Schmutzer, T. et al. (2012) Selfish supernumerary chromosome reveals its origin as a mosaic of host genome and organellar sequences. Proc. Natl Acad. Sci. USA 109: 13343-13346.
94. Mascher, M., Richmond, T.A., Gerhardt, D.J., Himmelbach, A., Clissold, L., Sampath, D. et al. (2013a) Barley whole exome capture: a tool for genomic research in the genus Hordeum and beyond. Plant J. 76: 494-505.
95. Mascher, M., Wu, S., Amand, P.S., Stein, N. and Poland, J. (2013b) Application of genotyping-by-sequencing on semiconductor sequencing platforms: a comparison of genetic and referencebased marker ordering in barley. PLoS One 8: e76925.
96. Matsui, A., Ishida, J., Morosawa, T., Mochizuki, Y., Kaminuma, E., Endo, T.A. et al. (2008) Arabidopsis transcriptome analysis under drought, cold, high-salinity and ABA treatment conditions using a tiling array. Plant Cell Physiol. 49: 1135-1149.
97. Matsumoto, T., Tanaka, T., Sakai, H., Amano, N., Kanamori, H., Kurita, K. et al. (2011) Comprehensive sequence analysis of 24,783 barley full-length cDNAs derived from 12 clone libraries. Plant Physiol. 156: 20-28.
98. Matsuoka, Y. (2011) Evolution of polyploid triticum wheats under cultivation: the role of domestication, natural hybridization and allopolyploid speciation in their diversification. Plant Cell Physiol. 52: 750-764.
99. Matsuoka, Y., Yamazaki, Y., Ogihara, Y. and Tsunewaki, K. (2002) Whole chloroplast genome comparison of rice, maize, and wheat: implications for chloroplast gene diversification and phylogeny of cereals. Mol. Biol. Evol. 19: 2084-2091. (Pubitemid 35440444)
100. Mayer, K.F., Martis, M., Hedley, P.E., Simkova, H., Liu, H., Morris, J.A. et al. (2011) Unlocking the barley genome by chromosomal and comparative genomics. Plant Cell 23: 1249-1263.
101. Mayer, K.F., Taudien, S., Martis, M., Simkova, H., Suchankova, P., Gundlach, H. et al. (2009) Gene content and virtual gene order of barley chromosome 1H. Plant Physiol. 151: 496-505.
102. Mirouze, M. and Paszkowski, J. (2011) Epigenetic contribution to stress adaptation in plants. Curr. Opin. Plant Biol. 14: 267-274.
103. Miyao, A., Nakagome, M., Ohnuma, T., Yamagata, H., Kanamori, H., Katayose, Y. et al. (2012) Molecular spectrum of somaclonal variation in regenerated rice revealed by whole-genome sequencing. Plant Cell Physiol. 53: 256-264.
104. Mochida, K., Kawaura, K., Shimosaka, E., Kawakami, N., Shin, I.T., Kohara, Y. et al. (2006) Tissue expression map of a large number of expressed sequence tags and its application to in silico screening of stress response genes in common wheat. Mol. Genet. Genomics 276: 304-312. (Pubitemid 44268040)
105. Mochida, K., Saisho, D., Yoshida, T., Sakurai, T. and Shinozaki, K. (2008) TriMEDB: a database to integrate transcribed markers and facilitate genetic studies of the tribe Triticeae. BMC Plant Biol. 8: 72.
106. Mochida, K. and Shinozaki, K. (2010) Genomics and bioinformatics resources for crop improvement. Plant Cell Physiol. 51: 497-523.
107. Mochida, K. and Shinozaki, K. (2011) Advances in omics and bioinformatics tools for systems analyses of plant functions. Plant Cell Physiol. 52: 2017-2038.
108. Mochida, K., Uehara-Yamaguchi, Y., Takahashi, F., Yoshida, T., Sakurai, T. and Shinozaki, K. (2013a) Large-scale collection and analysis of full-length cDNAs from Brachypodium distachyon and integration with Pooideae sequence resources. PLoS One 8: e75265.
109. Mochida, K., Uehara-Yamaguchi, Y., Yoshida, T., Sakurai, T. and Shinozaki, K. (2011a) Global landscape of a co-expressed gene network in barley and its application to gene discovery in Triticeae crops. Plant Cell Physiol. 52: 785-803.
110. Mochida, K., Yamazaki, Y. and Ogihara, Y. (2003) Discrimination of homoeologous gene expression in hexaploid wheat by SNP analysis of contigs grouped from a large number of expressed sequence tags. Mol. Genet. Genomics 270: 371-377. (Pubitemid 38085121)
111. Mochida, K., Yoshida, T., Sakurai, T., Ogihara, Y. and Shinozaki, K. (2009a) TriFLDB: a database of clustered full-length coding sequences from Triticeae with applications to comparative grass genomics. Plant Physiol. 150: 1135-1146.
112. Mochida, K., Yoshida, T., Sakurai, T., Yamaguchi-Shinozaki, K., Shinozaki, K. and Tran, L.S. (2009b) In silico analysis of transcription factor repertoire and prediction of stress responsive transcription factors in soybean. DNA Res. 16: 353-369.
113. Mochida, K., Yoshida, T., Sakurai, T., Yamaguchi-Shinozaki, K., Shinozaki, K. and Tran, L.S. (2010) LegumeTFDB: an integrative database of Glycine max, Lotus japonicus and Medicago truncatula transcription factors. Bioinformatics 26: 290-291.
114. Mochida, K., Yoshida, T., Sakurai, T., Yamaguchi-Shinozaki, K., Shinozaki, K. and Tran, L.S. (2011b) In silico analysis of transcription factor repertoires and prediction of stress-responsive transcription factors from six major gramineae plants. DNA Res. 18: 321-332.
115. Mochida, K., Yoshida, T., Sakurai, T., Yamaguchi-Shinozaki, K., Shinozaki, K. and Tran, L.S. (2013b) TreeTFDB: an integrative database of the transcription factors from six economically important tree crops for functional predictions and comparative and functional genomics. DNA Res. 20: 151-162.
116. Morrell, P.L., Buckler, E.S. and Ross-Ibarra, J. (2011) Crop genomics: advances and applications. Nat. Rev. Genet. 13: 85-96.
117. Morris, G.P., Ramu, P., Deshpande, S.P., Hash, C.T., Shah, T., Upadhyaya, H.D. et al. (2013) Population genomic and genomewide association studies of agroclimatic traits in sorghum. Proc. Natl Acad. Sci. USA 110: 453-458.
118. Moussaieff, A., Rogachev, I., Brodsky, L., Malitsky, S., Toal, T.W., Belcher, H. et al. (2013) High-resolution metabolic mapping of cell types in plant roots. Proc. Natl Acad. Sci. USA 110: E1232-E1241.
119. Mueller, A.H., Dockter, C., Gough, S.P., Lundqvist, U., von Wettstein, D. and Hansson, M. (2012) Characterization of mutations in barley fch2 encoding chlorophyllide a oxygenase. Plant Cell Physiol. 53: 1232-1246.
120. Mur, L.A., Allainguillaume, J., Catalan, P., Hasterok, R., Jenkins, G., Lesniewska, K. et al. (2011) Exploiting the Brachypodium Tool Box in cereal and grass research. New Phytol. 191: 334-347.
121. Mutwil, M., Klie, S., Tohge, T., Giorgi, F.M., Wilkins, O., Campbell, M.M. et al. (2011) PlaNet: combined sequence and expression comparisons across plant networks derived from seven species. Plant Cell 23: 895-910.
122. Nagano, A.J., Sato, Y., Mihara, M., Antonio, B.A., Motoyama, R., Itoh, H. et al. (2012) Deciphering and prediction of transcriptome dynamics under fluctuating field conditions. Cell 151: 1358-1369.
123. Naika, M., Shameer, K., Mathew, O.K., Gowda, R. and Sowdhamini, R. (2013) STIFDB2: an updated version of plant stress-responsive transcription factor database with additional stress signals, stressresponsive transcription factor binding sites and stress-responsive genes in Arabidopsis and rice. Plant Cell Physiol. 54: e8.
124. Nomoto, Y., Kubozono, S., Yamashino, T., Nakamichi, N. and Mizuno, T. (2012) Circadian clock-and PIF4-controlled plant growth: a coincidence mechanism directly integrates a hormone signaling network into the photoperiodic control of plant architectures in Arabidopsis thaliana. Plant Cell Physiol. 53: 1950-1964.
125. Obayashi, T., Nishida, K., Kasahara, K. and Kinoshita, K. (2011) ATTED-II updates: condition-specific gene coexpression to extend coexpression analyses and applications to a broad range of flowering plants. Plant Cell Physiol. 52: 213-219.
126. Ogihara, Y., Isono, K., Kojima, T., Endo, A., Hanaoka, M., Shiina, T. et al. (2002) Structural features of a wheat plastome as revealed by complete sequencing of chloroplast DNA. Mol. Genet. Genomics 266: 740-746. (Pubitemid 34045296)
127. Ogihara, Y., Mochida, K., Nemoto, Y., Murai, K., Yamazaki, Y., Shin, I.T. et al. (2003) Correlated clustering and virtual display of gene expression patterns in the wheat life cycle by large-scale statistical analyses of expressed sequence tags. Plant J. 33: 1001-1011. (Pubitemid 36400282)
128. Ogihara, Y., Yamazaki, Y., Murai, K., Kanno, A., Terachi, T., Shiina, T. et al. (2005) Structural dynamics of cereal mitochondrial genomes as revealed by complete nucleotide sequencing of the wheat mitochondrial genome. Nucleic Acids Res. 33: 6235-6250. (Pubitemid 41742561)
129. Ohyanagi, H., Tanaka, T., Sakai, H., Shigemoto, Y., Yamaguchi, K., Habara, T. et al. (2006) The Rice Annotation Project Database (RAP-DB): hub for Oryza sativa ssp. japonica genome information. Nucleic Acids Res. 34: D741-D744.
130. Okazaki, Y., Kamide, Y., Hirai, M.Y. and Saito, K. (2013) Plant lipidomics based on hydrophilic interaction chromatography coupled to ion trap time-of-flight mass spectrometry. Metabolomics 9: 121-131.
131. Okazaki, Y. and Saito, K. (2012) Recent advances of metabolomics in plant biotechnology. Plant Biotechnol. Rep. 6: 1-15.
132. Osaka, M., Matsuda, T., Sakazono, S., Masuko-Suzuki, H., Maeda, S., Sewaki, M. et al. (2013) Cell type-specific transcriptome of Brassicaceae stigmatic papilla cells from a combination of laser microdissection and RNA sequencing. Plant Cell Physiol. 54: 1894-1906.
133. Pasam, R.K., Sharma, R., Malosetti, M., van Eeuwijk, F.A., Haseneyer, G., Kilian, B. et al. (2012) Genome-wide association studies for agronomical traits in a world wide spring barley collection. BMC Plant Biol. 12: 16.
134. Paux, E., Sourdille, P., Salse, J., Saintenac, C., Choulet, F., Leroy, P. et al. (2008) A physical map of the 1-gigabase bread wheat chromosome 3B. Science 322: 101-104.
135. Peraldi, A., Beccari, G., Steed, A. and Nicholson, P. (2011) Brachypodium distachyon: a new pathosystem to study Fusarium head blight and other Fusarium diseases of wheat. BMC Plant Biol. 11: 100.
136. Pfeifer, M., Martis, M., Asp, T., Mayer, K.F., Lubberstedt, T., Byrne, S. et al. (2013) The perennial ryegrass GenomeZipper: targeted use of genome resources for comparative grass genomics. Plant Physiol. 161: 571-582.
137. Philippe, R., Paux, E., Bertin, I., Sourdille, P., Choulet, F., Laugier, C. et al. (2013) A high density physical map of chromosome 1BL supports evolutionary studies, map-based cloning and sequencing in wheat. Genome Biol. 14: R64.
138. Plocik, A.M. and Graveley, B.R. (2013) New insights from existing sequence data: generating breakthroughs without a pipette. Mol. Cell 49: 605-617.
139. Poland, J.A., Brown, P.J., Sorrells, M.E. and Jannink, J.L. (2012) Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach. PLoS One 7: e32253.
140. Postnikova, O.A., Shao, J. and Nemchinov, L.G. (2013) Analysis of the alfalfa root transcriptome in response to salinity stress. Plant Cell Physiol. 54: 1041-1055.
141. Putri, S.P., Nakayama, Y., Matsuda, F., Uchikata, T., Kobayashi, S., Matsubara, A. et al. (2013) Current metabolomics: practical applications. J. Biosci. Bioeng. 115: 579-589.
142. Qin, F., Shinozaki, K. and Yamaguchi-Shinozaki, K. (2011) Achievements and challenges in understanding plant abiotic stress responses and tolerance. Plant Cell Physiol. 52: 1569-1582.
143. Ramilowski, J.A., Sawai, S., Seki, H., Mochida, K., Yoshida, T., Sakurai, T. et al. (2013) Glycyrrhiza uralensis transcriptome landscape and study of phytochemicals. Plant Cell Physiol. 54: 697-710.
144. Rancour, D.M., Marita, J.M. and Hatfield, R.D. (2012) Cell wall composition throughout development for the model grass Brachypodium distachyon. Front. Plant Sci. 3: 266.
145. Richards, C.L., Rosas, U., Banta, J., Bhambhra, N. and Purugganan, M.D. (2012) Genome-wide patterns of Arabidopsis gene expression in nature. PLoS Genet. 8: e1002662.
146. Riedelsheimer, C., Lisec, J., Czedik-Eysenberg, A., Sulpice, R., Flis, A., Grieder, C. et al. (2012) Genome-wide association mapping of leaf metabolic profiles for dissecting complex traits in maize. Proc. Natl Acad. Sci. USA 109: 8872-8877.
147. Rustenholz, C., Choulet, F., Laugier, C., Safar, J., Simkova, H., Dolezel, J. et al. (2011) A 3,000-loci transcription map of chromosome 3B unravels the structural and functional features of gene islands in hexaploid wheat. Plant Physiol. 157: 1596-1608.
148. Safar, J., Bartos, J., Janda, J., Bellec, A., Kubalakova, M., Valarik, M. et al. (2004) Dissecting large and complex genomes: flow sorting and BAC cloning of individual chromosomes from bread wheat. Plant J. 39: 960-968. (Pubitemid 39320567)
149. Saisho, D., Ishii, M., Hori, K. and Sato, K. (2011) Natural variation of barley vernalization requirements: implication of quantitative variation of winter growth habit as an adaptive trait in East Asia. Plant Cell Physiol. 52: 775-784.
150. Saisho, D. and Takeda, K. (2011) Barley: emergence as a new research material of crop science. Plant Cell Physiol. 52: 724-727.
151. Saito, T., Ariizumi, T., Okabe, Y., Asamizu, E., Hiwasa-Tanase, K., Fukuda, N. et al. (2011) TOMATOMA: a novel tomato mutant database distributing Micro-Tom mutant collections. Plant Cell Physiol. 52: 283-296.
152. Sakai, H., Lee, S.S., Tanaka, T., Numa, H., Kim, J., Kawahara, Y. et al. (2013) Rice Annotation Project Database (RAP-DB): an integrative and interactive database for rice genomics. Plant Cell Physiol. 54: e6.
153. Sakurai, T., Kondou, Y., Akiyama, K., Kurotani, A., Higuchi, M., Ichikawa, T. et al. (2011) RiceFOX: a database of Arabidopsis mutant lines overexpressing rice full-length cDNA that contains a wide range of trait information to facilitate analysis of gene function. Plant Cell Physiol. 52: 265-273.
154. Sakurai, T., Yamada, Y., Sawada, Y., Matsuda, F., Akiyama, K., Shinozaki, K. et al. (2013) PRIMe Update: innovative content for plant metabolomics and integration of gene expression and metabolite accumulation. Plant Cell Physiol. 54: e5.
155. Sasaki, E., Takahashi, C., Asami, T. and Shimada, Y. (2011) AtCAST, a
156. Sato, K., Close, T.J., Bhat, P., Munoz-Amatriain, M. and Muehlbauer, G.J. (2011) Single nucleotide polymorphism mapping and alignment of recombinant chromosome substitution lines in barley. Plant Cell Physiol. 52: 728-737.
157. Sato, K., Nankaku, N. and Takeda, K. (2009a) A high-density transcript linkage map of barley derived from a single population. Heredity 103: 110-117.
158. Sato, K., Shin, I.T., Seki, M., Shinozaki, K., Yoshida, H., Takeda, K. et al. (2009b) Development of 5006 full-length cDNAs in barley: a tool for accessing cereal genomics resources. DNA Res. 16: 81-89.
159. Sato, K. and Takeda, K. (2009) An application of high-throughput SNP genotyping for barley genome mapping and characterization of recombinant chromosome substitution lines. Theor. Appl. Genet. 119: 613-619.
160. Schmitz, R.J., Schultz, M.D., Urich, M.A., Nery, J.R., Pelizzola, M., Libiger, O. et al. (2013) Patterns of population epigenomic diversity. Nature 495: 193-198.
161. Schulte, D., Close, T.J., Graner, A., Langridge, P., Matsumoto, T., Muehlbauer, G. et al. (2009) The International Barley Sequencing Consortium-at the threshold of efficient access to the barley genome. Plant Physiol. 149: 142-147.
162. Shan, Q., Wang, Y., Chen, K., Liang, Z., Li, J., Zhang, Y. et al. (2013) Rapid and efficient gene modification in rice and brachypodium using TALENs. Mol. Plant 6: 1365-1368.
163. Smith, D.B. and Flavell, R.B. (1975) Characterization of wheat genome by renaturation kinetics. Chromosoma 50: 223-242.
164. Spannagl, M., Martis, M.M., Pfeifer, M., Nussbaumer, T. and Mayer, K.F. (2013) Analysing complex Triticeae genomes-concepts and strategies. Plant Methods 9: 35.
165. Sreenivasulu, N., Graner, A. and Wobus, U. (2008) Barley genomics: an overview. Int. J. Plant Genomics 2008: 486258.
166. Stein, N., Prasad, M., Scholz, U., Thiel, T., Zhang, H., Wolf, M. et al. (2007) A 1,000-loci transcript map of the barley genome: new anchoring points for integrative grass genomics. Theor. Appl. Genet. 114: 823-839. (Pubitemid 46339689)
167. Su, C.L., Chao, Y.T., Alex Chang, Y.C., Chen, W.C., Chen, C.Y., Lee, A.Y. et al. (2011) De novo assembly of expressed transcripts and global analysis of the Phalaenopsis aphrodite transcriptome. Plant Cell Physiol. 52: 1501-1514.
168. Swarbreck, S.M., Lindquist, E.A., Ackerly, D.D. and Andersen, G.L. (2011) Analysis of leaf and root transcriptomes of soil-grown Avena barbata plants. Plant Cell Physiol. 52: 317-332.
169. Szczesniak, M.W., Kabza, M., Pokrzywa, R., Gudys, A. and Makalowska, I. (2013) ERISdb: a database of plant splice sites and splicing signals. Plant Cell Physiol. 54: e10.
170. Takehisa, H., Sato, Y., Igarashi, M., Abiko, T., Antonio, B.A., Kamatsuki, K. et al. (2012) Genome-wide transcriptome dissection of the rice root system: implications for developmental and physiological functions. Plant J. 69: 126-140.
171. Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M. and Kumar, S. (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28: 2731-2739.
172. Thiel, J., Riewe, D., Rutten, T., Melzer, M., Friedel, S., Bollenbeck, F. et al. (2012) Differentiation of endosperm transfer cells of barley: a comprehensive analysis at the micro-scale. Plant J. 71: 639-655.
173. Thole, V., Worland, B., Wright, J., Bevan, M.W. and Vain, P. (2010) Distribution and characterization of more than 1000 T-DNA tags in the genome of Brachypodium distachyon community standard line Bd21. Plant Biotechnol. J. 8: 734-747.
174. Tian, F., Bradbury, P.J., Brown, P.J., Hung, H., Sun, Q., Flint-Garcia, S. et al. (2011) Genome-wide association study of leaf architecture in the maize nested association mapping population. Nat. Genet. 43: 159-162.
175. Torada, A., Koike, M., Mochida, K. and Ogihara, Y. (2006) SSR-based linkage map with new markers using an intraspecific population of common wheat. Theor. Appl. Genet. 112: 1042-1051.
176. Tsai, W.C., Fu, C.H., Hsiao, Y.Y., Huang, Y.M., Chen, L.J., Wang, M. et al. (2013) OrchidBase 2.0: comprehensive collection of Orchidaceae floral transcriptomes. Plant Cell Physiol. 54: e7.
177. Uchida, N., Sakamoto, T., Kurata, T. and Tasaka, M. (2011) Identification of EMS-induced causal mutations in a non-reference Arabidopsis thaliana accession by whole genome sequencing. Plant Cell Physiol. 52: 716-722.
178. Van Moerkercke, A., Fabris, M., Pollier, J., Baart, G.J., Rombauts, S., Hasnain, G. et al. (2013) CathaCyc, a metabolic pathway database built from Catharanthus roseus RNA-Seq data. Plant Cell Physiol. 54: 673-685.
179. Verelst, W., Bertolini, E., De Bodt, S., Vandepoele, K., Demeulenaere, M., Pe, M.E. et al. (2013) Molecular and physiological analysis of growth-limiting drought stress in Brachypodium distachyon leaves. Mol. Plant 6: 311-322.
180. Wang, T.L., Uauy, C., Robson, F. and Till, B. (2012) TILLING in extremis. Plant Biotechnol. J. 10: 761-772.
181. Watanabe, C.K., Hachiya, T., Takahara, K., Kawai-Yamada, M., Uchimiya, H., Uesono, Y. et al. (2010) Effects of AOX1a deficiency on plant growth, gene expression of respiratory components and metabolic profile under low-nitrogen stress in Arabidopsis thaliana. Plant Cell Physiol. 51: 810-822.
182. Wheeler, T. and von Braun, J. (2013) Climate change impacts on global food security. Science 341: 508-513.
183. Wicker, T., Mayer, K.F., Gundlach, H., Martis, M., Steuernagel, B., Scholz, U. et al. (2011) Frequent gene movement and pseudogene evolution is common to the large and complex genomes of wheat, barley, and their relatives. Plant Cell 23: 1706-1718.
184. Wicker, T., Narechania, A., Sabot, F., Stein, J., Vu, G.T., Graner, A. et al. (2008) Low-pass shotgun sequencing of the barley genome facilitates rapid identification of genes, conserved non-coding sequences and novel repeats. BMC Genomics 9: 518.
185. Wicker, T., Schlagenhauf, E., Graner, A., Close, T.J., Keller, B. and Stein, N. (2006) 454 sequencing put to the test using the complex genome of barley. BMC Genomics 7: 275.
186. Wicker, T., Taudien, S., Houben, A., Keller, B., Graner, A., Platzer, M. et al. (2009) 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. 59: 712-722.
187. Widodo, Patterson, J.H., Newbigin, E., Tester, M., Bacic, A. and Roessner, U. (2009) Metabolic responses to salt stress of barley (Hordeum vulgare L.) cultivars, Sahara and Clipper, which differ in salinity tolerance. J. Exp. Bot. 60: 4089-4103.
188. Wu, D., Cai, S., Chen, M., Ye, L., Chen, Z., Zhang, H. et al. (2013a) Tissue metabolic responses to salt stress in wild and cultivated barley. PLoS One 8: e55431.
189. Wu, D., Shen, Q., Cai, S., Chen, Z.H., Dai, F. and Zhang, G. (2013b) Ionomic responses and correlations between elements and metabolites under salt stress in wild and cultivated barley. Plant Cell Physiol. 54: 1976-1988.
190. Yamakawa, H. and Hakata, M. (2010) Atlas of rice grain filling-related metabolism under high temperature: joint analysis of metabolome and transcriptome demonstrated inhibition of starch accumulation and induction of amino acid accumulation. Plant Cell Physiol. 51: 795-809.
191. Yamazaki, M., Mochida, K., Asano, T., Nakabayashi, R., Chiba, M., Udomson, N. et al. (2013) Coupling deep transcriptome analysis with untargeted metabolic profiling in Ophiorrhiza pumila to further the understanding of the biosynthesis of the anti-cancer alkaloid camptothecin and anthraquinones. Plant Cell Physiol. 54: 686-696.
192. Yokoyama, R. and Nishitani, K. (2004) Genomic basis for cell-wall diversity in plants. A comparative approach to gene families in rice and Arabidopsis. Plant Cell Physiol. 45: 1111-1121.
193. Yordem, B.K., Conte, S.S., Ma, J.F., Yokosho, K., Vasques, K.A., Gopalsamy, S.N. et al. (2011) Brachypodium distachyon as a new model system for understanding iron homeostasis in grasses: phylogenetic and expression analysis of Yellow Stripe-Like (YSL) transporters. Ann. Bot. 108: 821-833.
194. Yoshimura, K., Mori, T., Yokoyama, K., Koike, Y., Tanabe, N., Sato, N. et al. (2011) Identification of alternative splicing events regulated by an Arabidopsis serine/arginine-like protein, atSR45a, in response to high-light stress using a tiling array. Plant Cell Physiol. 52: 1786-1805.
195. Yura, K., Sulaiman, S., Hatta, Y., Shionyu, M. and Go, M. (2009) RESOPS: a database for analyzing the correspondence of RNA editing sites to protein three-dimensional structures. Plant Cell Physiol. 50: 1865-1873.
196. Zhang, H., Jin, J., Tang, L., Zhao, Y., Gu, X., Gao, G. et al. (2011) PlantTFDB 2.0: update and improvement of the comprehensive plant transcription factor database. Nucleic Acids Res. 39: D1114-D1117.
197. Zhang, H., Sreenivasulu, N., Weschke, W., Stein, N., Rudd, S., Radchuk, V. et al. (2004) Large-scale analysis of the barley transcriptome based on expressed sequence tags. Plant J. 40: 276-290. (Pubitemid 39404076)
198. Zheng, L., Fujii, M., Yamaji, N., Sasaki, A., Yamane, M., Sakurai, I. et al. (2011) Isolation and characterization of a barley yellow stripe-like gene, HvYSL5. Plant Cell Physiol. 52: 765-774.