The energy spectrum of all-particle cosmic rays around the knee region observed with the Tibet-III air-shower array

We have already reported the first result on the all-particle spectrum around the knee region based on data from 2000 November to 2001 October observed by the Tibet-III air-shower array. In this paper, we present an updated result using data set collected in the period from 2000 November through 2004 October in a wide range over 3 decades between $10^{14}$ eV and $10^{17}$ eV, in which the position of the knee is clearly seen at around 4 PeV. The spectral index is -2.68 $\pm$ 0.02(stat.) below 1PeV, while it is -3.12 $\pm$ 0.01(stat.) above 4 PeV in the case of QGSJET+HD model, and various systematic errors are under study now.Comment: 12 pages, 7 figures, accepted by Advances in space researc

Moon Shadow by Cosmic Rays under the Influence of Geomagnetic Field and Search for Antiprotons at Multi-TeV Energies

We have observed the shadowing of galactic cosmic ray flux in the direction of the moon, the so-called moon shadow, using the Tibet-III air shower array operating at Yangbajing (4300 m a.s.l.) in Tibet since 1999. Almost all cosmic rays are positively charged; for that reason, they are bent by the geomagnetic field, thereby shifting the moon shadow westward. The cosmic rays will also produce an additional shadow in the eastward direction of the moon if cosmic rays contain negatively charged particles, such as antiprotons, with some fraction. We selected 1.5 x10^{10} air shower events with energy beyond about 3 TeV from the dataset observed by the Tibet-III air shower array and detected the moon shadow at $\sim 40 \sigma$ level. The center of the moon was detected in the direction away from the apparent center of the moon by 0.23$^\circ$ to the west. Based on these data and a full Monte Carlo simulation, we searched for the existence of the shadow produced by antiprotons at the multi-TeV energy region. No evidence of the existence of antiprotons was found in this energy region. We obtained the 90% confidence level upper limit of the flux ratio of antiprotons to protons as 7% at multi-TeV energies.Comment: 13pages,4figures; Accepted for publication in Astroparticle Physic

Building The Sugarcane Genome For Biotechnology And Identifying Evolutionary Trends

Background: Sugarcane is the source of sugar in all tropical and subtropical countries and is becoming increasingly important for bio-based fuels. However, its large (10 Gb), polyploid, complex genome has hindered genome based breeding efforts. Here we release the largest and most diverse set of sugarcane genome sequences to date, as part of an on-going initiative to provide a sugarcane genomic information resource, with the ultimate goal of producing a gold standard genome.Results: Three hundred and seventeen chiefly euchromatic BACs were sequenced. A reference set of one thousand four hundred manually-annotated protein-coding genes was generated. A small RNA collection and a RNA-seq library were used to explore expression patterns and the sRNA landscape. In the sucrose and starch metabolism pathway, 16 non-redundant enzyme-encoding genes were identified. One of the sucrose pathway genes, sucrose-6-phosphate phosphohydrolase, is duplicated in sugarcane and sorghum, but not in rice and maize. A diversity analysis of the s6pp duplication region revealed haplotype-structured sequence composition. Examination of hom(e)ologous loci indicate both sequence structural and sRNA landscape variation. A synteny analysis shows that the sugarcane genome has expanded relative to the sorghum genome, largely due to the presence of transposable elements and uncharacterized intergenic and intronic sequences.Conclusion: This release of sugarcane genomic sequences will advance our understanding of sugarcane genetics and contribute to the development of molecular tools for breeding purposes and gene discovery. © 2014 de Setta et al.; licensee BioMed Central Ltd.151European Commission: Agriculture and Rural Development: Sugar http://ec.europa.eu/agriculture/sugar/index_en.htmKellogg, E.A., Evolutionary history of the grasses (2001) Plant Physiol, 125, pp. 1198-1205Grivet, L., Arruda, P., Sugarcane genomics: depicting the complex genome of an important tropical crop (2001) Curr Opin Plant Biol, 5, pp. 122-127Piperidis, G., Piperidis, N., D'Hont, A., Molecular cytogenetic investigation of chromosome composition and transmission in sugarcane (2010) Mol Genet Genomics, 284, pp. 65-73D'Hont, A., Unraveling the genome structure of polyploids using FISH and GISHexamples of sugarcane and banana (2005) Cytogenet Genome Res, 109, pp. 27-33D'Hont, A., Glaszmann, J.C., Sugarcane genome analysis with molecular markers: a first decade of research (2001) Int Soc Sugar Cane Technol Proc XXIV Congr, pp. 556-559Tomkins, J., Yu, Y., Miller-Smith, H., Frisch, D., Woo, S., Wing, R., A bacterial artificial chromosome library for sugarcane (1999) Theor Appl Genet, 99, pp. 419-424Vettore, L., Silva, F.R., Kemper, E.L., Souza, G.M., Silva, A.M., Ferro, M., Henrique-Silva, F., Monteiro-Vitorello, C.B., Analysis and functional annotation of an expressed sequence tag collection for tropical crop sugarcane (2003) Genome Res, 13, pp. 2725-2735Repbase http://www.girinst.org/repbase/Domingues, D.S., Cruz, G.M.Q., Metcalfe, C.J., Nogueira, F.T.S., Vicentini, R., Alves, C.S., Van Sluys, M.-A., Analysis of plant LTR-retrotransposons at the fine-scale family level reveals individual molecular patterns (2012) BMC Genomics, 13, p. 137National Center for Biotechnology Information (NCBI) http://www.ncbi.nlm.nih.gov/Meyer, F., Paarmann, D., D'Souza, M., Olson, R., Glass, E.M., Kubal, M., Paczian, T., Edwards, R.A., The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes (2008) BMC Bioinformatics, 9, p. 386Keeling, P.L., Myers, A.M., Biochemistry and genetics of starch synthesis (2010) Annu Rev Food Sci Technol, 1, pp. 271-303Phytozome v9.1: Home http://www.phytozome.net/Dias, E.S., Carareto, C.M.A., Ancestral polymorphism and recent invasion of transposable elements in Drosophila species (2012) BMC Evol Biol, 12, p. 119Posada, D., Crandall, K., Intraspecific gene genealogies: trees grafting into networks (2001) Trends Ecol Evol, 16, pp. 37-45Swaminathan, K., Alabady, M.S., Varala, K., De Paoli, E., Ho, I., Rokhsar, D.S., Arumuganathan, A.K., Hudson, M.E., Genomic and small RNA sequencing of Miscanthus x giganteus shows the utility of sorghum as a reference genome sequence for Andropogoneae grasses (2010) Genome Biol, 11, pp. R12Zanca, A.S., Vicentini, R., Ortiz-Morea, F.A., Del Bem, L.E., da Silva, M.J., Vincentz, M., Nogueira, F.T., Identification and expression analysis of microRNAs and targets in the biofuel crop sugarcane (2010) BMC Plant Biol, 10, p. 260Piriyapongsa, J., Jordan, I.K., A family of human microRNA genes from miniature inverted-repeat transposable elements (2007) PLoS ONE, 2, pp. e203Barrera-Figueroa, B.E., Gao, L., Wu, Z., Zhou, X., Zhu, J., Jin, H., Liu, R., Zhu, J.-K., High throughput sequencing reveals novel and abiotic stress-regulated microRNAs in the inflorescences of rice (2012) BMC Plant Biol, 12, p. 132Nagaki, K., Tsujimoto, H., Sasakuma, T., A novel repetitive sequence of sugar cane, SCEN family, locating on centromeric regions (1998) Chromosom Res, 6, pp. 295-302Nagaki, K., Neumann, P., Zhang, D., Ouyang, S., Buell, C.R., Cheng, Z., Jiang, J., Structure, divergence, and distribution of the CRR centromeric retrotransposon family in rice (2005) Mol Biol Evol, 22, pp. 845-855Vicentini, R., Del Bem, L.E., Van Sluys, M.-A., Nogueira, F., Vincentz, M., Gene content analysis of sugarcane public ESTs reveals thousands of missing coding-genes and an unexpected pool of grasses conserved ncRNAs (2012) Trop Plant Biol, 5, pp. 199-205Kim, C., Lee, T.-H., Compton, R.O., Robertson, J.S., Pierce, G.J., Paterson, A.H., A genome-wide BAC end-sequence survey of sugarcane elucidates genome composition, and identifies BACs covering much of the euchromatin (2013) Plant Mol Biol, 81, pp. 139-147Paterson, A.H., Bowers, J.E., Bruggmann, R., Dubchak, I., Grimwood, J., Gundlach, H., Haberer, G., Carpita, N.C., The Sorghum bicolor genome and the diversification of grasses (2009) Nature, 457, pp. 551-556Chang, Y., Gong, L., Yuan, W., Li, X., Chen, G., Li, X., Zhang, Q., Wu, C., Replication protein A (RPA1a) is required for meiotic and somatic DNA repair but is dispensable for DNA replication and homologous recombination in rice (2009) Plant Physiol, 151, pp. 2162-2173Feschotte, C., Transposable elements and the evolution of regulatory networks (2008) Nat Rev Genet, 9, pp. 397-405Wang, J., Roe, B., Macmil, S., Yu, Q., Murray, J.E., Tang, H., Chen, C., Ming, R., Microcollinearity between autopolyploid sugarcane and diploid sorghum genomes (2010) BMC Genomics, 11, p. 261Garsmeur, O., Charron, C., Bocs, S., Jouffe, V., Samain, S., Couloux, A., Droc, G., D'Hont, A., High homologous gene conservation despite extreme autopolyploid redundancy in sugarcane (2011) New Phytol, 189, pp. 629-642Jannoo, N., Grivet, L., Chantret, N., Garsmeur, O., Glaszmann, J.C., Arruda, P., D'Hont, A., Orthologous comparison in a gene-rich region among grasses reveals stability in the sugarcane polyploid genome (2007) Plant J, 50, pp. 574-585Figueira, T.R.E.S., Okura, V., da Silva, F.R., da Silva, M.J., Kudrna, D., Ammiraju, J.S.S., Talag, J., Arruda, P., A BAC library of the SP80-3280 sugarcane variety (saccharum sp.) and its inferred microsynteny with the sorghum genome (2012) BMC Res Notes, 5, p. 185Schnable, P.S., Ware, D., Fulton, R.S., Stein, J.C., Wei, F., Pasternak, S., Liang, C., Gillam, B., The B73 maize genome: complexity, diversity, and dynamics (2009) Science, 326, pp. 1112-1115Tenaillon, M.I., Hufford, M.B., Gaut, B.S., Ross-Ibarra, J., Genome size and transposable element content as determined by high-throughput sequencing in maize and Zea luxurians (2011) Genome Biol Evol, 3, pp. 219-229Zhang, J., Yu, C., Krishnaswamy, L., Peterson, T., Transposable Elements as Catalysts for Chromosome Rearrangements (2011) Methods Mol Biol, pp. 315-326. , Totowa, NJ: Humana Press, Birchler JAMa, J., Wing, R.A., Bennetzen, J.L., Jackson, S.A., Plant centromere organization: a dynamic structure with conserved functions (2007) Trends Genet, 23, pp. 134-139D'Hont, A., Grivet, L., Feldmann, P., Rao, S., Berding, N., Glaszmann, J.C., Characterisation of the double genome structure of modern sugarcane cultivars (Saccharum spp.) by molecular cytogenetics (1996) Mol Gen Genet, 250, pp. 405-413Bao, Y., Wendel, J.F., Ge, S., Multiple patterns of rDNA evolution following polyploidy in Oryza (2010) Mol Phylogenet Evol, 55, pp. 136-142Lynch, M., (2007) The Origins of Genome Architecture, , Sunderland, Massachussetts, USA: Sinauer Associates IncThe map-based sequence of the rice genome (2005) Nature, 436, pp. 793-800. , International Rice Genome Sequencing ProjectLiu, B., Xu, C., Zhao, N., Qi, B., Kimatu, J.N., Pang, J., Han, F., Rapid genomic changes in polyploid wheat and related species: implications for genome evolution and genetic improvement (2009) J Genet Genomics, 36, pp. 519-528Lisch, D., How important are transposons for plant evolution? (2012) Nat Rev Genet, 14, pp. 49-61Udall, J.A., Wendel, J.F., Polyploidy and crop improvement (2006) Crop Sci, 46, pp. S3-S14Varshney, R.K., Graner, A., Sorrells, M.E., Genomics-assisted breeding for crop improvement (2005) Trends Plant Sci, 10, pp. 621-630Menossi, M., Silva-Filho, M.C., Vincentz, M., Van-Sluys, M.-A., Souza, G.M., Sugarcane functional genomics: gene discovery for agronomic trait development (2008) Int J Plant Genomics, 2008, p. 458732. , doi:10.1155/2008/458732Palhares, A.C., Rodrigues-Morais, T.B., Van Sluys, M.-A., Domingues, D.S., Maccheroni, W., Jordão, H., Souza, A.P., Vieira, M.L.C., A novel linkage map of sugarcane with evidence for clustering of retrotransposon-based markers (2012) BMC Genet, 13, p. 51Andersen, J.R., Lübberstedt, T., Functional markers in plants (2003) Trends Plant Sci, 8, pp. 554-560Kalendar, R., Flavell, A.J., Ellis, T.H.N., Sjakste, T., Moisy, C., Schulman, A., Analysis of plant diversity with retrotransposon-based molecular markers (2011) Heredity (Edinb), 106, pp. 520-530PGML BACMan On The Web: Grasses http://www.plantgenome.uga.edu/bacman/BACManwww.phpRice Genome Annotation Project http://rice.plantbiology.msu.edu/Bowers, J.E., Arias, M.A., Asher, R., Avise, J.A., Ball, R.T., Brewer, G.A., Buss, R.W., Soderlund, C.A., Comparative physical mapping links conservation of microsynteny to chromosome structure and recombination in grasses (2005) Proc Natl Acad Sci U S A, 102, pp. 13206-13211Adam-Blondon, A.-F., Bernole, A., Faes, G., Lamoureux, D., Pateyron, S., Grando, M.S., Caboche, M., Chalhoub, B., Construction and characterization of BAC libraries from major grapevine cultivars (2005) Theor Appl Genet, 110, pp. 1363-1371Manetti, M.E., Rossi, M., Cruz, G.M.Q., Saccaro, N.L., Nakabashi, M., Altebarmakian, V., Rodier-Goud, M., Van Sluys, M.A., Mutator system derivatives isolated from sugarcane genome sequence (2012) Trop Plant Biol, 5, pp. 233-243Phrap http://www.phrap.org/RepeatMasker http://www.repeatmasker.org/Jurka, J., Kapitonov, V.V., Pavlicek, A., Klonowski, P., Kohany, O., Repbase update, a database of eukaryotic repetitive elements (2005) Cytogenet Genome Res, 110, pp. 462-467Han, Y., Wessler, S.R., MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences (2010) Nucleic Acids Res, 38 (22), pp. e199. , doi: 10.1093/nar/gkq862. Epub 2010 Sep 29Frickey, T., Lupas, A., CLANS: a Java application for visualizing protein families based on pairwise similarity (2004) Bioinformatics, 20, pp. 3702-3704Han, Y., Qin, S., Wessler, S.R., Comparison of class 2 transposable elements at superfamily resolution reveals conserved and distinct features in cereal grass genomes (2013) BMC Genomics, 14, p. 71Keller, O., Kollmar, M., Stanke, M., Waack, S., A novel hybrid gene prediction method employing protein multiple sequence alignments (2011) Bioinformatics, 27, pp. 757-763Majoros, W.H., Pertea, M., Salzberg, S.L., TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders (2004) Bioinformatics, 20, pp. 2878-2879Haas, B.J., Delcher, A.L., Mount, S.M., Wortman, J.R., Smith, R.K., Hannick, L.I., Maiti, R., White, O., Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies (2003) Nucleic Acids Res, 31, pp. 5654-5666Haas, B.J., Salzberg, S.L., Zhu, W., Pertea, M., Allen, J.E., Orvis, J., White, O., Wortman, J.R., Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to assemble spliced alignments (2008) Genome Biol, 9, pp. R7Petersen, T.N., Brunak, S., von Heijne, G., Nielsen, H., SignalP 4.0: discriminating signal peptides from transmembrane regions (2011) Nat Methods, 8, pp. 785-786TMHMM Server v. 2.0 http://www.cbs.dtu.dk/services/TMHMM-2.0/Rutherford, K., Parkhill, J., Crook, J., Horsnell, T., Rice, P., Rajandream, M.A., Barrell, B., Artemis: sequence visualization and annotation (2000) Bioinformatics, 16, pp. 944-945UniProt http://www.uniprot.org/InterPro: Protein sequence analysis and classification http://www.ebi.ac.uk/interpro/Conesa, A., Götz, S., Blast2GO: a comprehensive suite for functional analysis in plant genomics (2008) Int J Plant Genomics, 2008, pp. 1-12SUCEST-FUN Project http://sucest-fun.org/MG-RAST: metagenomics analysis server http://metagenomics.anl.gov/KAAS - KEGG automatic annotation server http://www.genome.jp/kegg/kaas/Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., Kumar, S., MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods (2011) Mol Biol Evol, 28, pp. 2731-2739Lyons, E., Freeling, M., How to usefully compare homologous plant genes and chromosomes as DNA sequences (2008) Plant J, 53, pp. 661-673Hall, T.A., BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT (1999) Nucleic Acids Symp Ser, 41, pp. 95-98Geneious - Homepage http://www.geneious.com/Heslop-Harrison, P., Schwarzacher, T., (2000) Practical In Situ Hybridization, , Oxford, UK: BIOS Scientific Publishers LtdAljanabi, S., Forget, L., Dookun, A., An improved and rapid protocol for the isolation of polysaccharide-and polyphenol-free sugarcane DNA (1999) Plant Mol Biol Report, 17, pp. 1-8Maq: Mapping and assembly with qualities http://maq.sourceforge.net/SeqMonk http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/Gasic, K., Hernandez, A., Korban, S.S., RNA extraction from different apple tissues rich in polyphenols and polysaccharides for cDNA (2004) Plant Mol Biol Report, 22 (DECEMBER), pp. 437a-437gLi, H., Durbin, R., Fast and accurate short read alignment with Burrows-Wheeler transform (2009) Bioinformatics, 25, pp. 1754-1760Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Durbin, R., The sequence Alignment/Map format and SAMtools (2009) Bioinformatics, 25, pp. 2078-2079Thompson, J.D., Higgins, D.G., Gibson, T.J., CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice (1994) Nucleic Acids Res, 22, pp. 4673-4680Bandelt, H.J., Forster, P., Röhl, A., Median-joining networks for inferring intraspecific phylogenies (1999) Mol Biol Evol, 16, pp. 37-48Paterson, A.H., Freeling, M., Tang, H., Wang, X., Insights from the comparison of plant genome sequences (2010) Annu Rev Plant Biol, 61, pp. 349-37

Are protons still dominant at the knee of the cosmic-ray energy spectrum?

A hybrid experiment consisting of emulsion chambers, burst detectors and the Tibet II air-shower array was carried out at Yangbajing (4,300 m a.s.l., 606 g/cm$^2$) in Tibet to obtain the energy spectra of primary protons and heliums. From three-year operation, these energy spectra are deduced between $10^{15}$ and $10^{16}$ eV by triggering the air showers associated with a high energy core and using a neural network method in the primary mass separation. The proton spectrum can be expressed by a single power-law function with a differential index of $-3.01 \pm 0.11$ and $-3.05 \pm 0.12$ based on the QGSJET+HD and SIBYLL+HD models, respectively, which are steeper than that extrapolated from the direct observations of $-2.74 \pm 0.01$ in the energy range below $10^{14}$ eV. The absolute fluxes of protons and heliums are derived within 30% systematic errors depending on the hadronic interaction models used in Monte Carlo simulation. The result of our experiment suggests that the main component responsible for the change of the power index of the all-particle spectrum around $3 \times 10^{15}$ eV, so-called ``knee'', is composed of nuclei heavier than helium. This is the first measurement of the differential energy spectra of primary protons and heliums by selecting them event by event at the knee energy region.Comment: This paper has been accepted for publication Physics Letters B on October 19th, 2005. This paper has been accepted for publication Physics Letters B on October 19th, 200

The Biotechnology Roadmap For Sugarcane Improvement

Due to the strategic importance of sugarcane to Brazil, FAPESP, the main São Paulo state research funding agency, launched in 2008 the FAPESP Bioenergy Research Program (BIOEN, http://bioenfapesp.org). BIOEN aims to generate new knowledge and human resources for the improvement of the sugarcane and ethanol industry. As part of the BIOEN program, a Workshop on Sugarcane Improvement was held on March 18th and 19th 2009 in São Paulo, Brazil. The aim of the workshop was to explore present and future challenges for sugarcane improvement and its use as a sustainable bioenergy and biomaterial feedstock. The workshop was divided in four sections that represent important challenges for sugarcane improvement: a) gene discovery and sugarcane genomics, b) transgenics and controlled transgene expression, c) sugarcane physiology (photosynthesis, sucrose metabolism, and drought) and d) breeding and statistical genetics. This report summarizes the roadmap for the improvement of sugarcane. © 2010 Springer Science+Business Media, LLC.327587Aitken, K.S., Jackson, P.A., McIntyre, C.L., A combination of AFLP and SSR markers provides extensive map coverage and identification of homo(eo)logous linkage groups in a sugarcane cultivar (2005) TAG. Theor Appl Genet. Theoretische Und Angewandte Genetik, 110, pp. 789-801Aitken, K.S., Jackson, P.A., McIntyre, C.L., Construction of a genetic linkage map for Saccharum officinarum incorporating both simplex and duplex markers to increase genome coverage (2007) Genome, 50 (8), pp. 742-756Aitken, K.S., Hermann, S., Karno, K., Bonnett, G.D., McIntyre, L.C., Jackson, P.A., Genetic control of yield related stalk traits in sugarcane (2008) TAG Theor Appl Genet. Theoretische Und Angewandte Genetik, 117 (7), pp. 1191-1203Al-Janabi, S.M., Parmessur, Y., Kross, H., Dhayan, S., Saumtally, S., Ramdoyal, K., Autrey, L.J.C., Dookun-Saumtally, A., Identification of a major quantitative trait locus (QTL) for yellow spot (Mycovellosiella koepkei) disease resistance in sugarcane (2007) Mol Breed, 19, pp. 1-14Araújo, P.G., Rossi, M., de Jesus, E.M., Saccaro Jr., N.L., Kajihara, D., Massa, R., de Felix, J.M., van Sluys, M.A., Transcriptionally active transposable elements in recent hybrid sugarcane (2005) Plant J, 44, pp. 707-717Arencibia, A., Molina, P., de la Riva, G., Selman-Houssein, G., Production of transgenic sugarcane (Saccharum officinarum L.) plants by intact cell electroporation (1995) Plant Cell Rep, 14, pp. 305-309Arencibia, A., Carmona, E., Tellez, P., Chan, M.T., Yu, S.M., Trujillo, L., Oramas, P., An efficient protocol for sugarcane (Saccharum spp.) transformation mediated by Agrobacterium tumefaciens (1998) Transgenic Res, 7, pp. 213-222Arencibia, A., Carmona, E., Cornide, M.T., Castiglione, S., O'Relly, J., Cinea, A., Oramas, P., Sala, F., Somaclonal variation in insect-resistant transgenic sugarcane (Saccharum hybrid) plants produced by cell electroporation (1999) Transgenic Res, 8, pp. 349-360Asnaghi, C., D'Hont, A., Glaszmann, J.C., Rott, P., Resistance of sugarcane cultivar R 570 to Puccinia melanocephala isolates from different geographic locations (2001) Plant Dis, 85, pp. 282-286Batley, J., Barker, G., Sullivan, H.O., Edwards, K.J., Edwards, D., Victoria, A., Mining for single nucleotide polymorphisms and insertions/deletions in maize expressed sequence tag data 1 (2003) Society, 132, pp. 84-91Beetham, P.R., Kipp, P.B., Sawycky, X.L., Arnzen, C.J., May, G.D., A tool for functional plant genomics: Chimeric RNA/DNA oligonucleotides cause in vivo gene-specific mutations (1999) Proc Natl Acad Sci USA, 96, pp. 8774-8778Birch, R.G., Plant transformation: Problems and strategies for practical application (1997) Annu Rev Plant Physiol Plant Mol Biol, 48, pp. 297-326Bock, R., Transgenic plastids in basic research and plant biotechnology (2001) J Mol Biol, 312, pp. 425-438Botha, F.C., Sawyer, B.J.B., Birch, R.G., Sucrose metabolism in the culm of transgenic sugarcane with reduced soluble acid invertase activity (2001) Proc Int Soc Sugar Cane Technol, 24, pp. 588-591. , Hogarth DM (ed), BrisbaneBower, R., Birch, R.G., Transgenic sugarcane plants via microprojectile bombardment (1992) Plant J, 2, pp. 409-416Braga, D.P.V., Arrigoni, E.D.B., Silva-Filho, M.C., Ulian, E.C., Expression of the Cry1Ab protein in genetically modified sugarcane for the control of Diatraea saccharalis (Lepidoptera: Crambidae) (2003) J New Seed, 5, pp. 209-222Brumbley, S.M., Petrasovits, L.A., Bonaventura, P.A., O'Shea, M.J., Purnell, M.P., Nielsen, L.K., Production of polyhydroxyalkanoates in sugarcane (2003) Proc Int Soc Sugar Cane Technol Mol Biol Workshop, 4, p. 31. , Montpellier, FranceBryan, G.T., Wu, K.S., Farrall, L., Jia, Y., Hershey, H.P., McAdams, S.A., Faulk, K.N., Valent, B., A single amino acid difference distinguishes resistant and susceptible alleles of the rice blast resistance gene Pi-ta (2000) Plant Cell, 12, pp. 2033-2045Bundock, P.C., Eliott, F.G., Ablett, G., Benson, A.D., Casu, R.E., Aitken, K.S., Targeted single nucleotide polymorphism (SNP) discovery in a highly polyploid plant species using 454 sequencing (2009) Plant Biotechnol J, 7 (4), pp. 347-354Calsa Jr., T., Figueira, A., Serial analysis of gene expression in sugarcane (Saccharum spp.) leaves revealed alternative C4 metabolism and putative antisense transcripts (2007) Plant Mol Biol, 63, pp. 745-762Camargo, S.R., Cançado, G.M.A., Ulian, E.C., Menossi, M., Identification of genes responsive to the application of ethanol on sugarcane leaves (2007) Plant Cell Rep, 26, pp. 2119-2128Carson, D.L., Botha, F.C., Preliminary analysis of expressed sequence tags for sugarcane (2000) Crop Sci, 40, pp. 1769-1779Casu, R.E., Grof, C.P.L., Rae, A.L., McIntyre, C.L., Dimmock, C.M., Manners, J.M., Identification of a novel sugar transporter homologue strongly expressed in maturing stem vascular tissues of sugarcane by expressed sequence tag and microarray analysis (2003) Plant Mol Biol, 52, pp. 371-386Casu, R.E., Dimmock, C.M., Chapman, S.C., Grof, C.P.L., McIntyre, C.L., Bonnett, G.D., Manners, J.M., Identification of differentially expressed transcripts from maturing stem of sugarcane by in silico analysis of stem expressed sequence tags and gene expression profiling (2004) Plant Mol Biol, 54, pp. 503-517Casu, R.E., Manners, J.M., Bonnett, G.D., Jackson, P.A., McIntyre, C.L., Dunne, R., Chapman, S.C., Grof, C.P.L., Genomics approaches for the identification of genes determining important traits in sugarcane (2005) Field Crops Res, 92, pp. 137-147Chen, Z.J., Ni, Z.F., Mechanisms of genomic rearrangements and gene expression changes in plant polyploids (2006) Bioessays, 28, pp. 240-252Christin, P.A., Salamin, N., Savolainen, V., Duvall, M.R., Besnard, G., C4 photosynthesis evolved in grasses via parallel adaptive genetic changes (2007) Curr Biol, 17, pp. 1241-1247da Silva, J., Sorrells, M.E., Linkage analysis in polyploids using molecular markers (1996) Methods of Genome Analysis in Plants: Their Merits and Pitfalls, , P. Jauhar (Ed.), Boca Raton: CRC PressDaniell, H., Environmentally friendly approaches to genetic engineering (1999) In Vitro Cell. De Biol. Plant, 35, pp. 361-368Daniell, H., Streatfield, S.J., Wycoff, K., Medical molecular farming: Production of antibodies, biopharmaceuticals and edible vaccines in plants (2001) Trend Plant Sci, 6, pp. 219-225Daugrois, J.H., Grivet, L., Roques, D., Hoarau, J.Y., Lombardi, H., Glaszmann, J.C., D'Hont, A., A putative major gene for rust resistence linked with a RFLP marker in Sugarcane cultivar 'R570 (1996) Theor Appl Genet, 92, pp. 1059-1064de Cosa, B., Moar, W., Lee, S.B., Miller, M., Daniell, H., Overexpression of the Bt cry2Aa2 operon in chloroplasts leads to formation of insecticidal crystals (2001) Nat Biotechnol, 19, pp. 71-74de Souza, A.P., Gaspar, M., da Silva, E.A., Ulian, E.C., Waclawovsky, A.J., Nishiyama Jr., M.Y., dos Santos, R.T.M.M., Buckeridge, M.S., Elevated CO2 increases photosynthesis, biomass and productivity, and modifies gene expression in sugarcane (2008) Plant, Cell and Environment, 31, pp. 1116-1127D'Hont, A., Unraveling the genome structure of polyploids using FISH and GISH, examples of sugarcane and banana (2005) Cytogenet Genome Res, 109, pp. 27-33D'Hont, A., Glaszmann, J.C., Sugarcane genome analysis with molecular markers, a first decade of research (2001) Proc Int Soc Sugar Cane Technol, 24, pp. 556-559D'Hont, A., Grivet, L., Feldmann, P., Rao, S., Berding, N., Glaszmann, J.C., Characterisation of the double genome structure of modern sugarcane cultivars (Saccharum spp.) by molecular cytogenetics (1996) Mol Gen Genet, 250, pp. 405-413D'Hont, A., Ison, D., Alix, K., Roux, C., Glaszmann, J.C., Determination of basic chromosome numbers in the genus Saccharum by physical mapping of ribosomal RNA genes (1998) Genome, 41, pp. 221-225Elliott, A.R., Bretell, R.I.S., Grof, C.P.L., Agrobacterium-mediatd transformation of sugarcane using GFP as a screenable marker (1998) Aust J Plant Physiol, 25, pp. 739-743Elliott, A.R., Dugdale, B., Bretell, R.I.S., Grof, C.P.L., Green-fluorescent protein facilitates rapid in vivo detction of genetically transformed plant cells (1999) Plant Cell Rep, 18, pp. 707-714Enriquez, G.A., Trujillo, L.E., Menendez, C., Vazquez, R.I., Tiel, K., Arieta, J., Selman, G., Hernandez, L., Sugarcane (Saccharum hybrid) genetic transformation mediated by Agrobacterium tumefaciens: Production of transgenic plants expressing proteins with agronomic and industrial value (2000) Plant Genetic Engineering: Towards the Third Millennium, pp. 76-81. , A. D. Arencibia (Ed.), Amsterdam: Elsevier ScienceEnriquez-Obregon, G.A., Vázquez-Padrón, R.I., Prieto-Samsonov, D.L., de la Riva, G.A., Selman-Houssein, G., Herbicide resistant sugarcane (Saccharum officinarum) plants by Agrobacterium-mediated transformation (1998) Planta, 206, pp. 20-27Falco, M.C., Tulmann Neto, A.T., Ulian, E.C., Transformation and expression of a gene for herbicide resistance in a Brazilian sugarcane (2000) Plant Cell Rep, 19, pp. 1188-1194Falco, M.C., Silva-Filho, M.C., Expression of soybean proteinase inhibitors intransgenic sugarcane plants: Effects on natural defense against Diatrae saccharalis (2003) Plant Physiol Biochem, 41, pp. 761-766Finnegan, J., McElroy, D., Transgene inactivatin: Plants fight back! (1994) Nat Biotechnol, 12, pp. 883-888Francia, E., Tacconi, G., Crosatti, C., Barabaschi, D., Bulgarelli, D., Dall'Aglio, E., Val, G., Marker assisted selecion in crop plants (2005) Plant Cell Tissue Organ Cult, 82, pp. 317-342Gallo-Meagher, M., Irvine, J.E., Herbicide resistant transgenic sugarcane plants containing the bar gene (1996) Crop Sci, 36, pp. 1367-1374Garcia, A.A.F., Kido, E.A., Meza, A.N., Souza, H.M.B., Pinto, L.R., Pastina, M.M., Leite, C.S., Souza, A.P., Development of an integrated genetic map of a sugarcane (Saccharum spp.) commercial cross, based on a maximum-likelihood approach for estimation of linkage and linkage phases (2006) TAG. Theor Appl Genet, 112, pp. 298-314Gilbert, R.A., Gallo-Meagher, M., Comstock, J.C., Miller, J.D., Jain, M., Abouzid, A., Agronomic evaluation of sugarcane lines transformed for resistance to sugarcane mosaic virus strain E (2005) Crop Sci, 45, pp. 2060-2067Gilbert, R.A., Glynn, N.C., Comstock, J.C., Davis, M.J., Agronomic performance and genetic characterization of sugarcane transformed for resistance to sugarcane yellow leaf virus (2009) Field Crops Res, 111, pp. 39-46Grivet, L., Arruda, P., Sugarcane genomics: Depicting the complex genome of an important tropical crop (2002) Curr Opin Plant Biol, 5, pp. 122-127Groenewald, J.H., Groenewald, S., Whittaker, A., Huckett, B.I., Botha, F.C., Molecular agriculture: Prospects for production of alternative commodities in sugarcane through genetic engineering (1995) Proc South African Sugar Technol, 69, pp. 14-20Ha, S., Moore, P.H., Heinz, D., Kato, S., Ohmido, N., Fukui, K., Quantitative chromosome map of the polyploid Saccharum spontaneum by multicolor in situ hybridization and imaging methods (1999) Plant Mol Biol, 39, pp. 1165-1173Hemaprabha, G., Govindaraj, P., Balasundaram, N., Singh, N.K., Genetic diversity analysis of indian sugarcane breeding pool based on sugarcane specific STMS markers (2005) Sugar Tech, 7, pp. 9-14Hoarau, J.Y., Offman, B., D'Hont, A., Risterucci, A.M., Roques, D., Glaszmann, J.C., Grivet, L., Genetic dissection of a modern sugarcane cultivar (Saccharum spp.). I. Genome mapping with AFLP markers (2001) Theor Appl Genet, 103, pp. 84-97Imelfort, M., Duran, C., Batley, J., Edwards, D., Discovering genetic polymorphisms in next-generation sequencing data (2009) Plant Biotechnol J, 7, pp. 312-317Ingelbrecht, I.L., Irvine, J.E., Mirkov, T.E., Posttranscriptional gene silencing in transgenic sugarcane. Dissection Of homology-dependent virus resistance in a monocot that has a complex polyploid genome (1999) Plant Physiol, 119, pp. 1187-1198Inman-Bamber, N.G., Sugarcane water stress criteria for irrigation and drying off (2004) Field Crops Res, 89, pp. 107-122Inman-Bamber, N.G., Smith, D.M., Water relations in sugarcane and response to water deficits (2005) Field Crops Res, 92, pp. 185-202Inman-Bamber, N.G., Muchow, R.C., Robertson, M.J., Dry matter partitioning of sugarcane in Australia and South Africa (2002) Field Crops Res, 76, pp. 71-84Inman-Bamber, N.G., Bonnett, G.D., Spillman, M.F., Hewitt, M.L., Jackson, J., Increasing sucrose accumulation in sugarcane by manipulating leaf extension and photosynthesis with irrigation (2008) Aust J Agric Res, 59, pp. 13-26Inman-Bamber, N.G., Bonnett, G.D., Spillman, M.F., Hewitt, M.L., Xu, J., Source-sink differences in genotypes and water regimes influencing sucrose accumulation in sugarcane stalks (2009) Crop Pasture Sci, 60, pp. 316-327(2007) Fourth Assessment Report, , Intergovernmental Panel on Climate Change, Cambridge University PressJackson, P.A., Breeding for improved sugar content in sugarcane (2005) Field Crops Res, 92, pp. 277-290Jain, M., Chengalrayan, K., Abouzid, A., Gallo, M., Prospecting the utility of a PMI/mannose selection system for the recovery of transgenic sugarcane (Saccharum spp. hybrid) plants (2007) Plant Cell Rep, 26 (5), pp. 581-590Jannoo, N., Grivet, L., Chantret, N., Garsmeur, O., Glaszmann, J.C., Arruda, P., D'Hont, A., Orthologous comparison in a gene-rich region among grasses reveals stability in the sugarcane polyploid genome (2007) Plant J, 50, pp. 574-585Jansen, R.C., Nap, J.P., Genetical genomics: The added value from segregation (2001) Trends Genet, 17, pp. 388-391Joyce, A., McQualter, R.B., Bernard, M.J., Smith, G.R., Engineering for resistance to SCMV in sugarcane (1998) Acta Hortic, 461, pp. 385-391Joyce, A., McQualtert, R.B., Handley, J.A., Dale, J.L., Harding, R.M., Smith, G.R., Transgenic sugarcane resistant to sugarcane mosaic virus (1998) Proc Aust Soc Sugar Cane Technol, 20, pp. 204-210Kanazin, V., Talbert, H., See, D., Decamp, P., Nevo, E., Blake, T., Discovery and assay of single-nucleotide polymorphisms in barley (Hordeum (2002) Plant Mol Biol, 48, pp. 529-537Lakshmanan, P., Geijskes, R.J., Aitken, K.S., Grof, C.L.P., Bonnett, G.D., Smith, G.R., Sugarcane biotechnology: The challenges and opportunities (2005) In Vitro Cell Dev Biol, 41, pp. 345-363Legaspi, J.C., Mirkov, T.E., Evaluation of transgenic sugarcane against stalkborers (2000) Proc Int Soc Sugar Cane Technol, 4, pp. 68-71. , Allsopp PG, Suasa-Ard W (eds), Sugarcane Entomology Workshop, Khon KaenLeibbrandt, N.B., Snyman, S.J., Stability of gene expression and agronomic performance of a transgenic herbicide-resistant sugarcane line in South Africa (2003) Crop Sci, 43, pp. 671-677Lima, M.L., Garcia, A.A., Oliveira, K.M., Matsuoka, S., Arizono, H., de Souza Jr., C.L., de Souza, A.P., Analysis of genetic similarity detected by AFLP and coefficient of parentage among genotypes of sugar cane (Saccharum spp.) (2002) Theor Appl Genet, 104, pp. 30-38Ma, H., Albert, H.H., Paull, R., Moore, P.H., Metabolic engineering of invertase activities in different subcellular compartments affects sucrose accumulation in sugarcane cells (2000) Aust J Plant Physiol, 27, pp. 1021-1030Ma, H.M., Schulze, S., Lee, S., Yang, M., Mirkov, E., Irvine, J., Moore, Paterson, A., An EST survey of the sugarcane transcriptome (2004) Theor Appl Genet, 108, pp. 851-863Maliga, P., Plastid transformation in higher plants (2004) Annu Re Plant Biol, 55, pp. 289-313Manickavasagam, M., Ganapathi, A., Anbazhagan, R., Sudhakar, B., Selvaraj, N., Vasudevan, A., Kasthurirengan, S., Agrobacterium-mediated genetic transformation and development of herbicide-resistant sugarcane (Saccharum species hybrids) using axillary buds (2004) Plant Cell Rep, 23, pp. 134-143McCormick, A.J., Cramer, M.D., Watt, D.A., Sink strength regulates photosynthesis in sugarcane (2006) New Phytol, 171, pp. 759-770McCormick, A.J., Cramer, M.D., Watt, D.A., Regulation of photosynthesis by sugars in sugarcane leaves (2008) J Plant Physiol, 165, pp. 1817-1829McCormick, A.J., Cramer, M.D., Watt, D.A., Changes in photosynthetic rates and gene expression of leaves during a source-sink perturbation in sugarcane (2008) Ann Bot, 101, pp. 89-102McIntyre, C.L., Jackson, P.A., Low level of selfing found in a sample of crosses in Australian sugarcane breeding programs (2001) Euphytica, 117, pp. 245-249McIntyre, C.L., Whan, A., Croft, B., Magarey, R., Smith, G.R., Identification and validation of molecular markers associated with Pachymetra root rot and brown rust resistance in sugarcane using map- and association-based approaches (2005) Mol Breed, 16, pp. 151-161McIntyre, C.L., Jackson, M., Cordeiro, G.M., Amouyal, O., Hermann, S., Aitken, K.S., Eliott, F., Bonnett, G.D., The identification and characterisation of alleles of sucrose phosphate synthase gene family III in sugarcane (2006) Mol Breed, 18, pp. 39-50McQualter, R.B., Dale, J.L., Harding, R.M., McMahon, J.A., Smith, G.R., Production and evaluation of transgenic sugarcane containing a Fiji disease virus (FDV) genome segment S9-derived synthetic resistance gene (2004) Aust J Agric Res, 55, pp. 139-145McQualter, R.B., Chong, B.F., Meyer, K., van Dyk, D.E., O'Shea, M.G., Walton, N.J., Viitanen, P.V., Brumbley, S.M., Initial evaluation of sugarcane as a production platform for a p-hydroxybenzoic acid (2004) Plant Biotechnol J, 2, pp. 1-13Messing, J., Synergy of two reference genomes for the grass family (2009) Plant Physiol, 149, pp. 117-124Molinari, H.B.C., Marur, C.J., Daros, E., Campos, M.K.F., Carvalho, J.F.R.P., Bespalhok Filho, J.C., Pereira, L.F.P., Vieira, L.G.E., Evaluation of the stress-inducible production of praline in transgenic sugarcane (Saccharum spp.): Osmotic adjustment, chlorophyll fluorescence and oxidative stress (2007) Physiol Plant, 130, pp. 218-229Moore, P.H., Progress and development in sugarcane biotechnology (1999) Proc Int Soc Sugar Cane Technol, 23, pp. 241-258Mudge, S.R., Osabe, K., Casu, R.E., Bonnet, G.D., Manners, J.M., Birch, R.G., Efficient silencing of reporter transgenes coupled to known function promoters in sugarcane, a highly polyploidy crop species (2009) Planta, 229, pp. 549-558Nogueira, F.T.S., Rosa Jr., E., Menossi, M., Ulian, E.C., Aruda, P., RNA expression profiles and data mining of sugarcane response to low temperature (2003) Plant Physiol, 132, pp. 1811-1824Nutt, K.A., Allsopp, P.G., McGhie, T.K., Shepherd, K.M., Joyce, P.A., Transgenic sugarcane with increased resistance to canegrubs (1999) Conference of the Australian Society of Sugar Cane Technologists, pp. 27-30. , 1999, Townsville. Proceedings... PK Editorial Services, TownsvilleOliveira, K.M., Pinto, L.R., Marconi, T.G., Margarido, G.R., Pastina, M.M., Teixeira, L.H.M., Figueira, A.V., Souza, A.P., Functional integrated genetic linkage map based on EST-markers for a sugarcane (Saccharum spp.) commercial cross (2007) Mol Breed, 20, pp. 189-208Papini-Terzi, F.S., Rocha, F.R., Vencio, R.Z., Oliveira, K.C., de Felix, J.M., Vicentini, R., Rocha, C., Souza, G.M., Transcription profiling of signal transduction-related genes in sugarcane tissues DNA (2005) Resistente, 12, pp. 27-38Papini-Terzi, F.S., Rocha, F.R., Vencio, R.Z., Felix, J.M., Branco, D.S., Waclawovsky, A.J., del Bem, L.E.V., Souza, G.M., Sugarcane genes associated with sucrose content (2009) BMC Genomics, 10, p. 120Paterson, A.H., The Sorghum bicolor genome and the diversification of grasses (2009) Nature, 457, pp. 551-556Petrasovits, L.A., Purnell, M.P., Nielsen, L.K., Brumbley, S.M., Production of polyhydroxybutyrate in sugarcane (2007) Plant Biotechnol J, 5, pp. 162-172Piperidis, N., Jackson, P.A., D'Hont, A., Besse, P., Hoarau, J.Y., Courtois, B., Aitken, K.S., McIntyre, C.L., Comparative genetics in sugarcane enables structured map enhancement and validation of marker-trait associations (2008) Mol Breed, 21, pp. 233-247Raboin, L., Oliveira, K.M., Lecunff, L., Telismart, H., Roques, D., Butterfield, M.K., Hoarau, J.Y., D'Hont, A., Genetic mapping in sugarcane, a high polyploid, using bi-parental progeny: Identification of a gene controlling stalk colour and a new rust resistance gene (2006) TAG. Theor Appl Genet, 112, pp. 1382-1391Raboin, L.M., Pauquet, J., Butterfield, M., D'Hont, A., Glaszmann, J.C., Analysis of genome-wide linkage disequilibrium in the highly polyploid sugarcane (2008) Theor Appl Genet, 116, pp. 701-714Ramdoyal, K., Badaloo, G.H., Prebreeding in sugarcane with an emphasis on the programme of the Mauritius Sugar Industry Research Institute (2002) Managing Plant Genetic Diversity, , J. M. M. Engels, R. Rao, A. H. D. Brown, and M. T. Jackson (Eds.), Oxford: CABI Publishing GroupRangel, P., Gomez, L., Victoria, J.I., Angel, F., Transgenic plants of CC 84-75 resistant to the virus associated with the sugarcane yellow leaf syndrome In: SILVER JUBILEE CONGRESS, Guatemala (2003) Proceedings of International Society of Su