Biofuel and energy crops: High-yield Saccharinae take center stage in the post-genomics era

Genome Biology

Volumn 14, Issue 6, 2013, Pages

  de Siqueira Ferreira, Savio ^a   Nishiyama, Milton Yutaka ^a   Paterson, Andrew H ^b   Souza, Glaucia Mendes ^a  

^a UNIVERSITY OF SÃO PAULO   (Brazil)

^b UNIVERSITY OF GEORGIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOFUEL; CARBON DIOXIDE; TRANSCRIPTOME;

BIOFUEL PRODUCTION; BIOTECHNOLOGICAL PROCEDURES; BIOTECHNOLOGICAL PRODUCTION; ENERGY CROP; ENERGY YIELD; EXPRESSED SEQUENCE TAG; GENETIC TRANSCRIPTION; GENOTYPE; HIGH THROUGHPUT SEQUENCING; MICROARRAY ANALYSIS; MISCANTHUS; NONHUMAN; PLANT BREEDING; PLANT DEVELOPMENT; PLANT GENETICS; PLANT PARAMETERS; PLANT YIELD; REVIEW; SINGLE NUCLEOTIDE POLYMORPHISM; SORGHUM; SUGARCANE; SUSTAINABLE DEVELOPMENT; BIOMASS; CROP; GENE EXPRESSION REGULATION; GENETICS; GENOMICS; GROWTH, DEVELOPMENT AND AGING; METABOLIC ENGINEERING; METABOLISM; PHOTOSYNTHESIS;

BIOFUELS; BIOMASS; CROPS, AGRICULTURAL; GENE EXPRESSION REGULATION, PLANT; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; METABOLIC ENGINEERING; METABOLIC NETWORKS AND PATHWAYS; PHOTOSYNTHESIS; SACCHARUM; SORGHUM; TRANSCRIPTOME;

EID: 84911957392     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2013-14-6-210     Document Type: Review

References (121)

1. Macedo IC, Seabra JEA, Silva JEAR: Green house gases emissions in the production and use of ethanol from sugarcane in Brazil: The 2005/2006 averages and a prediction for 2020. Biomass Bioenerg. 2008, 32: 582-595. 10.1016/j.biombioe.2007.12.006.
2. Waclawovsky AJ, Sato PM, Lembke CG, Moore PH, Souza GM: Sugarcane for bioenergy production: an assessment of yield and regulation of sucrose content. Plant Biotechnol J. 2010, 8: 263-276. 10.1111/j.1467-7652.2009.00491.x.
3. Kellogg EA: Phylogenetic relationships of Saccharinae and Sorghinae. Genomics of the Saccharinae. Edited by: Paterson AH. 2013, New York, Berlin: Springer, 11: 3-22.
4. Daniels J, Roach BT: Taxonomy and evolution. Sugarcane Improvement Through Breeding. Edited by: Heinz DJ. 1987, Amsterdam: Elsevier, 7-84.
5. Ming R, Moore PH, Wu K, D'Hont A, Glaszmann JC, Tew TL, Mirkov E, Silva J, Jifon J, Rai M, Schnell RJ, Brumbley SM, Lakshmanan P, Comstock JC, Paterson AH: Sugarcane improvement through breeding and biotechnology. Plant Breeding Rev. 2006, 27: 15-118.
6. Moore PM: Temporal and spatial regulation of sucrose accumulation in the sugarcane stem. Aust J Plant Physiol. 1995, 22: 661-679. 10.1071/PP9950661.
7. Irvine JE: Sugarcane [physiological characteristics, yield potential and climatic and environment factors]. Symposium on Potential Productivity of Field Crops Under Different Environments: 1983; Los Baños, Laguna (Philippines). 1983, Los Baños: International Rice Research Institute, 361-281.
8. Heaton EA, Dohleman FG, Long SP: Meeting US biofuel goals with less land: the potential of Miscanthus. Glob Change Biol. 2008, 14: 2000-2014. 10.1111/j.1365-2486.2008.01662.x.
9. Roach BT: Utilisation of Saccharum spontaneum in sugarcane breeding. Proc Int Soc Sugar Cane Technol. 1977, 16: 43-58.
10. Hodkinson TR, Renvoize SS, Chase MW: Systematics of Miscanthus. Aspects Appl Biol. 1997, 49: 189-198.
11. Lewandowski I, Clifton-Brown JC, Scurlock JMO, Huisman W: Miscanthus: European experience with a novel energy crop. Biomass Bioenerg. 2000, 19: 209-227. 10.1016/S0961-9534(00)00032-5.
12. Lewandowski I, Scurlock JMO, Lindvall E, Christou M: The development and current status of perennial rhizomatous grasses as energy crops in the US and Europe. Biomass Bioenerg. 2003, 25: 335-361. 10.1016/S0961-9534(03)00030-8.
13. Sacks EJ, Juvik JA, Lin Q, Stewart JR, Yamada T: The gene pool of Miscanthus species and its improvement. Genomics of the Saccharinae. Edited by: Paterson AH. 2013, New York, Berlin: Springer, 11: 73-104.
14. Hodkinson TR, Chase MW, Takahashi C, Leitch IJ, Bennett MD, Renvoize SA: The use of dna sequencing (ITS and trnL-F), AFLP, and fluorescent in situ hybridization to study allopolyploid Miscanthus (Poaceae). Am J Bot. 2002, 89: 279-286. 10.3732/ajb.89.2.279.
15. Dohleman FG, Long SP: More productive than maize in the Midwest: How does Miscanthus do it?. Plant Physiol. 2009, 150: 2104-2115. 10.1104/pp.109.139162.
16. Hodkinson TR, Chase MW, Lledo MD, Salamin N, Renvoize SA: Phylogenetics of Miscanthus, Saccharum and related genera (Saccharinae, Andropogoneae, Poaceae) based on DNA sequences from ITS nuclear ribosomal DNA and plastid trnLintron and trnL-F intergenic spacers. J Plant Res. 2002, 115: 381-392. 10.1007/s10265-002-0049-3.
17. Chen YH, Lo CC: Disease resistance and sugar content in Saccharum-Miscanthus hybrids. Rep Taiwan Sugar Res Inst. 1989, 1-7.
18. Sobral BWS, Braga DPV, LaHood ES, Keim P: Phylogenetic analysis of chloroplast restriction enzyme site mutations in the Saccharinae Griseb. subtribe of the Andropogoneae Dumort. tribe. Theoret Appl Genetics. 1994, 87: 843-853.
19. Burner DM, Tew TL, Harvey JJ, Belesky DP: Dry matter partitioning and quality of Miscanthus, Panicum, and Saccharum genotypes in Arkansas, USA. Biomass Bioenerg. 2009, 33: 610-619. 10.1016/j.biombioe.2008.10.002.
20. Kimber CT, Dahlberg JA, Kresovich S: The gene pool of Sorghum bicolor and its improvement. Genomics of the Saccharinae. Edited by: Paterson AH. 2013, New York, Berlin: Springer, 11: 23-42.
21. Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, Mitros T, Poliakov A, Schmutz J, Spannagl M, Tang H, Wang X, Wicker T, Bharti AK, Chapman J, Feltus FA, Gowik U, Grigoriev IV, Lyons E, Maher CA, Martis M, Narechania A, Otillar RP, Penning BW, Salamov AA, Wang Y, Zhang L, Carpita NC, et al: The Sorghum bicolor genome and the diversification of grasses. Nature. 2009, 457: 551-556. 10.1038/nature07723.
22. Carpita NC, McCann MC: Maize and sorghum: genetic resources for bioenergy grasses. Trends Plant Sci. 2008, 13: 415-420. 10.1016/j.tplants.2008.06.002.
23. Saballos A: Development and utilization of sorghum as a bioenergy crop. Genetic Improvement of Bioenergy Crops. Edited by: Vermerris W. 2008, New York: Springer, 211-248.
24. Zhu XG, Long SP, Ort DR: What is the maximum efficiency with which photosynthesis can convert solar energy into biomass?. Curr Opin Biotechnol. 2008, 19: 153-159. 10.1016/j.copbio.2008.02.004.
25. Vu JC, Allen LH: Growth at elevated CO(2) delays the adverse effects of drought stress on leaf photosynthesis of the C(4) sugarcane. J Plant Physiol. 2009, 166: 107-116. 10.1016/j.jplph.2008.02.009.
26. 2 increases water use efficiency by sustaining photosynthesis of water-limited maize and sorghum. J Plant Physiol. 2011, 168: 1909-1918. 10.1016/j.jplph.2011.05.005.
27. Hu FY, Tao DY, Sacks E, Fu BY, Xu P, Li J, Yang Y, McNally K, Khush GS, Paterson AH, Li ZK: Convergent evolution of perenniality in rice and sorghum. Proc Natl Acad Sci USA. 2003, 100: 4050-4054. 10.1073/pnas.0630531100.
28. Kong W, Jin H, Franks CD, Kim C, Bandopadhyay R, Rana MK, Auckland SA, Goff VH, Rainville LK, Burow GB, Woodfin C, Burke JJ, Paterson AH: Genetic analysis of recombinant inbred lines for Sorghum bicolor × Sorghum propinquum. G3 (Bethesda). 2013, 3: 101-108. 2013.
29. Paterson AH, Schertz KF, Lin YR, Liu SC, Chang YL: The weediness of wild plants: molecular analysis of genes influencing dispersal and persistence of Johnsongrass, Sorghum halepense (L) Pers. Proc Natl Acad Sci USA. 1995, 92: 6127-6131. 10.1073/pnas.92.13.6127.
30. Paterson AH, Moore PH, Tew TL: The gene pool of Saccharum species and their improvement. Genomics of the Saccharinae. Edited by: Paterson AH. 2013, New York, Berlin: Springer, 11: 43-72.
31. Somerville C, Youngs H, Taylor C, Davis SC, Long SP: Feedstocks for lignocellulosic biofuels. Science. 2010, 329: 790-792. 10.1126/science.1189268.
32. Wang D, Portis AR, Moose SP, Long SP: Cool C4 photosynthesis: pyruvate Pi dikinase expression and activity corresponds to the exceptional cold tolerance of carbon assimilation in Miscanthus × giganteus. Plant Physiol. 2008, 148: 557-567. 10.1104/pp.108.120709.
33. 2 increases photosynthesis, biomass and productivity, and modifies gene expression in sugarcane. Plant Cell Environ. 2008, 31: 1116-1127. 10.1111/j.1365-3040.2008.01822.x.
34. 2 concentration in the absence of drought. Plant Physiol. 2006, 140: 779-790. 10.1104/pp.105.073957.
35. Long SP, Ort DR: More than taking the heat: crops and global change. Curr Opin Plant Biol. 2010, 13: 241-248.
36. Souza AP, Arundale RA, Dohleman FG, Long SP, Buckeridge MS: Will the exceptional productivity of Miscanthus × giganteus increase further under rising atmospheric CO2?. Agr Forest Meteorol. 2013, 171-172. 82-92
37. Carpita NC: Structure and biogenesis of the cell walls of grasses. Annu Rev Plant Physiol Plant Mol Biol. 1996, 47: 445-476. 10.1146/annurev.arplant.47.1.445.
38. Sarkar P, Bosneaga E, Auer M: Plant cell walls throughout evolution: towards a molecular understanding of their design principles. J Exp Bot. 2009, 60: 3615-3635. 10.1093/jxb/erp245.
39. Souza A, Leite DC, Pattathil S, Hahn M, Buckeridge M: Composition and structure of sugarcane cell wall polysaccharides: implications for second-generation bioethanol production. Bioenerg Res. 2012, 1-16.
40. Hotta CT, Lembke CG, Domingues D, Ochoa E, Cruz GQ, Melotto-Passarin D, Marconi T, Santos M, Mollinari M, Margarido GA, Crivellari AC, dos Santos WD, de Souza AP, Hoshino AA, Carrer H, Souza AP, Garcia AAF, Buckeridge MS, Menossi M, Van Sluys MA, Souza GM: The biotechnology roadmap for sugarcane improvement. Tropical Plant Biol. 2010, 3: 75-87. 10.1007/s12042-010-9050-5.
41. Dal-Bianco M, Carneiro MS, Hotta CT, Chapola RG, Hoffmann HP, Garcia AA, Souza GM: Sugarcane improvement: how far can we go?. Curr Opin Biotechnol. 2012, 23: 265-270. 10.1016/j.copbio.2011.09.002.
42. USDA Germplasm Resources Information Network. [http://www.ars-grin.gov/]
43. Sugarcane Breeding Institute. [http://www.sugarcane.res.in]
44. van der Merwe MJ, Groenewald JH, Stitt M, Kossmann J, Botha FC: Downregulation of pyrophosphate: D-fructose-6-phosphate 1-phosphotransferase activity in sugarcane culms enhances sucrose accumulation due to elevated hexose-phosphate levels. Planta. 2010, 231: 595-608. 10.1007/s00425-009-1069-1.
45. Basnayake SW, Morgan TC, Wu L, Birch RG: Field performance of transgenic sugarcane expressing isomaltulose synthase. Plant Biotechnol J. 2012, 10: 217-225. 10.1111/j.1467-7652.2011.00655.x.
46. Mudge SR, Basnayake SWV, Moyle RL, Osabe K, Graham MW, Morgan TE, Birch RG: Mature-stem expression of a silencing-resistant sucrose isomerase gene drives isomaltulose accumulation to high levels in sugarcane. Plant Biotechnol J. 2013, 11: 502-509. 10.1111/pbi.12038.
47. Khan MS, Ali S, Iqbal J: Developmental and photosynthetic regulation of delta-endotoxin reveals that engineered sugarcane conferring resistance to 'dead heart' contains no toxins in cane juice. Mol Biol Rep. 2011, 38: 2359-2369. 10.1007/s11033-010-0369-7.
48. Zhu YJ, McCafferty H, Osterman G, Lim S, Agbayani R, Lehrer A, Schenck S, Komor E: Genetic transformation with untranslatable coat protein gene of sugarcane yellow leaf virus reduces virus titers in sugarcane. Transgenic Res. 2011, 20: 503-512. 10.1007/s11248-010-9432-3.
49. Barros GOF, Ballen MAT, Woodard SL, Wilken LR, White SG, Damaj MB, Mirkov TE, Nikolov ZL: Recovery of bovine lysozyme from transgenic sugarcane stalks: extraction, membrane filtration, and purification. Bioprocess Biosyst Eng.
50. Petrasovits LA, Zhao L, McQualter RB, Snell KD, Somleva MN, Patterson NA, Nielsen LK, Brumbley SM: Enhanced polyhydroxybutyrate production in transgenic sugarcane. Plant Biotechnol J. 2012, 10: 569-578. 10.1111/j.1467-7652.2012.00686.x.
51. Jung JH, Fouad WM, Vermerris W, Gallo M, Altpeter F: RNAi suppression of lignin biosynthesis in sugarcane reduces recalcitrance for biofuel production from lignocellulosic biomass. Plant Biotechnol J. 2012, 10: 1067-1076. 10.1111/j.1467-7652.2012.00734.x.
52. Harrison MD, Geijskes J, Coleman HD, Shand K, Kinkema M, Palupe A, Hassall R, Sainz M, Lloyd R, Miles S, Dale JL: Accumulation of recombinant cellobiohydrolase and endoglucanase in the leaves of mature transgenic sugar cane. Plant Biotechnol J. 2011, 9: 884-896. 10.1111/j.1467-7652.2011.00597.x.
53. Prabu G, Prasad DT: Functional characterization of sugarcane MYB transcription factor gene promoter (PScMYBAS1) in response to abiotic stresses and hormones. Plant Cell Rep. 2012, 31: 661-669. 10.1007/s00299-011-1183-y.
54. Mudge SR, Osabe K, Casu RE, Bonnett GD, Manners JM, Birch RG: Efficient silencing of reporter transgenes coupled to known functional promoters in sugarcane, a highly polyploid crop species. Planta. 2009, 229: 549-558. 10.1007/s00425-008-0852-8.
55. Howe A, Sato S, Dweikat I, Fromm M, Clemente T: Rapid and reproducible Agrobacterium-mediated transformation of sorghum. Plant Cell Rep. 2006, 25: 784-791. 10.1007/s00299-005-0081-6.
56. Jakob K, Zhou F, Paterson A: Genetic improvement of C4 grasses as cellulosic biofuel feedstocks. Biofuels. Edited by: Tomes D, Lakshmanan P, Songstad D. 2011, New York: Springer, 113-138.
57. Manners J, Casu R: Transcriptome analysis and functional genomics of sugarcane. Tropical Plant Biol. 2011, 4: 9-21. 10.1007/s12042-011-9066-5.
58. Mendes Souza G, Berges H, Bocs S, Casu R, D'Hont A, Ferreira J, Henry R, Ming R, Potier B, Van Sluys MA, Vincentz M, Paterson AH: The sugarcane genome challenge: strategies for sequencing a highly complex genome. Tropical Plant Biol. 2011, 4: 145-156. 10.1007/s12042-011-9079-0.
59. Tomkins JP, Yu Y, Miller-Smith H, Frisch DA, Woo SS, Wing RA: A bacterial artificial chromosome library for sugarcane. Theor Appl Genet. 1999, 99: 419-424. 10.1007/s001220051252.
60. Le Cunff L, Garsmeur O, Raboin LM, Pauquet J, Telismart H, Selvi A, Grivet L, Philippe R, Begum D, Deu M, Costet L, Wing R, Glaszmann JC, D'Hont A: Diploid/polyploid syntenic shuttle mapping and haplotype-specific chromosome walking toward a rust resistance gene (Bru1) in highly polyploid sugarcane (2n approximately 12x approximately 115). Genetics. 2008, 180: 649-660. 10.1534/genetics.108.091355.
61. Figueira TR, Okura V, Rodrigues da Silva F, Jose da Silva M, Kudrna D, Ammiraju JS, Talag J, Wing R, Arruda P: A BAC library of the SP80-3280 sugarcane variety (saccharum sp.) and its inferred microsynteny with the sorghum genome. BMC Res Notes. 2012, 5: 185-10.1186/1756-0500-5-185.
62. Wang J, Roe B, Macmil S, Yu Q, Murray JE, Tang H, Chen C, Najar F, Wiley G, Bowers J, Van Sluys MA, Rokhsar DS, Hudson ME, Moose SP, Paterson AH, Ming R: Microcollinearity between autopolyploid sugarcane and diploid sorghum genomes. BMC Genomics. 2010, 11: 261-10.1186/1471-2164-11-261.
63. Kim C, Lee TH, Compton RO, Robertson JS, Pierce GJ, Paterson AH: A genome-wide BAC end-sequence survey of sugarcane elucidates genome composition, and identifies BACs covering much of the euchromatin. Plant Mol Biol. 2013, 81: 139-147. 10.1007/s11103-012-9987-x.
64. Garsmeur O, Charron C, Bocs S, Jouffe V, Samain S, Couloux A, Droc G, Zini C, Glaszmann JC, Van Sluys MA, D'Hont A: High homologous gene conservation despite extreme autopolyploid redundancy in sugarcane. New Phytologist. 2011, 189: 629-642. 10.1111/j.1469-8137.2010.03497.x.
65. Sugarcane Genome Project. [http://sugarcanegenome.org]
66. Garcia AA, Mollinari M, Marconi TG, Mancini MC, Costa EA, Henry R, Bundock PC, Pinto LR, Souza AP: Bulding a SNP-based multipoint sugarcane linkage map using loci with all possible dosages [abstract]. International Plant and Animal Genome Conference XX: (conference program). 2012, [https://pag.confex.com/pag/xx/webprogram/Paper1490.html]
67. Vettore AL, da Silva FR, Kemper EL, Souza GM, da Silva AM, Ferro MI, Henrique-Silva F, Giglioti EA, Lemos MV, Coutinho LL, Nobrega MP, Carrer H, França SC, Bacci Júnior M, Goldman MH, Gomes SL, Nunes LR, Camargo LE, Siqueira WJ, Van Sluys MA, Thiemann OH, Kuramae EE, Santelli RV, Marino CL, Targon ML, Ferro JA, Silveira HC, Marini DC, Lemos EG, Monteiro-Vitorello CB, et al: Analysis and functional annotation of an expressed sequence tag collection for tropical crop sugarcane. Genome Res. 2003, 13: 2725-2735. 10.1101/gr.1532103.
68. Nishiyama MY, Vicente F, Sato PM, Ferreira SS, Feltus FA, Souza GM: Transcriptome analysis in the Saccharinae. Genomics of the Saccharinae. Edited by: Paterson AH. 2013, New York, Berlin: Springer, 11: 121-140.
69. Pastina MM, Malosetti M, Gazaffi R, Mollinari M, Margarido GR, Oliveira KM, Pinto LR, Souza AP, van Eeuwijk FA, Garcia AA: A mixed model QTL analysis for sugarcane multiple-harvest-location trial data. Theor Appl Genet. 2012, 124: 835-849. 10.1007/s00122-011-1748-8.
70. Wu KK, Burnquist W, Sorrells ME, Tew TL, Moore PH, Tanksley SD: The detection and estimation of linkage in polyploids using single-dose restriction fragments. Theoret Appl Genet. 1992, 83: 294-300.
71. Pastina MM, Pinto LR, Oliveira KM, Souza AP, Garcia AA: Molecular mapping of complex traits. Genetics, Genomics and Breeding of Sugarcane. Edited by: Henry R, Kole C. 2010, Enfield, NH: Science Publishers, 117-148.
72. Palhares AC, Rodrigues-Morais TB, Van Sluys MA, Domingues DS, Maccheroni W, Jordao H, Souza AP, Marconi TG, Mollinari M, Gazaffi R, Garcia AA, Vieira ML: A novel linkage map of sugarcane with evidence for clustering of retrotransposon-based markers. BMC Genet. 2012, 13: 51-
73. Margarido GRA, Souza AP, Garcia AAF: OneMap: software for genetic mapping in outcrossing species. Hereditas. 2007, 144: 78-79. 10.1111/j.2007.0018-0661.02000.x.
74. Jiang S-Y, Ma Z, Vanitha J, Ramachandran S: Genetic variation and expression diversity between grain and sweet sorghum lines. BMC Genomics. 2013, 14: 18-10.1186/1471-2164-14-18.
75. Dugas DV, Monaco MK, Olsen A, Klein RR, Kumari S, Ware D, Klein PE: Functional annotation of the transcriptome of Sorghum bicolor in response to osmotic stress and abscisic acid. BMC Genomics. 2011, 12: 514-10.1186/1471-2164-12-514.
76. Mizuno H, Kawahigashi H, Kawahara Y, Kanamori H, Ogata J, Minami H, Itoh T, Matsumoto T: Global transcriptome analysis reveals distinct expression among duplicated genes during sorghum-Bipolaris sorghicola interaction. BMC Plant Biol. 2012, 12: 121-10.1186/1471-2229-12-121.
77. Casu R: Role of bioinformatics as a tool for sugarcane research. Genetics, Genomics and Breeding of Sugarcane. Edited by: Henry R, Kole C. 2010, Enfield, NH: Science Publishers, 229-248.
78. Menossi M, Silva-Filho MC, Vincentz M, Van Sluys MA, Souza GM: Sugarcane functional genomics: gene discovery for agronomic trait development. Int J Plant Genomics. 2008, 2008: 458732-
79. Nishiyama MY, Vicente F, Lembke CG, Sato PM, Dal-Bianco ML, Fandino RA, Hotta CT, Souza GM: The SUCEST-FUN Regulatory Network Database: designing and energy grass. Int Sugar J. 2012, 114: 821-826.
80. Computational Biology and Functional Genomics Laboratory: DFCI Sugarcane Gene Index. [http://compbio.dfci.harvard.edu/cgi-bin/tgi/gimain.pl?gudb=s_officinarum]
81. Vicentini R, Bem LEV, Sluys MA, Nogueira FTS, Vincentz M: Gene content analysis of sugarcane public ESTs reveals thousands of missing coding-genes and an unexpected pool of grasses conserved ncRNAs. Tropical Plant Biol. 2012, 5: 199-205. 10.1007/s12042-012-9103-z.
82. Iseli C, Jongeneel CV, Bucher P: ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. Proc Int Conf Intell Syst Mol Biol. 1999, 138-148.
83. Ostlund G, Schmitt T, Forslund K, Kostler T, Messina DN, Roopra S, Frings O, Sonnhammer EL: InParanoid 7: new algorithms and tools for eukaryotic orthology analysis. Nucleic Acids Res. 2010, 38 (Database): D196-203. 10.1093/nar/gkp931.
84. Alexeyenko A, Tamas I, Liu G, Sonnhammer EL: Automatic clustering of orthologs and inparalogs shared by multiple proteomes. Bioinformatics. 2006, 22: e9-15. 10.1093/bioinformatics/btl213.
85. Casu R, Hotta CT, Souza GM: Functional genomics: transcriptomics of sugarcane - current status and future prospects. Genetics, Genomics and Breeding of Sugarcane. Edited by: Henry R, Kole C. 2010, Enfield, NH: Science Publishers, 167-191.
86. Lembke CG, Nishiyama MY, Sato PM, de Andrade RF, Souza GM: Identification of sense and antisense transcripts regulated by drought in sugarcane. Plant Mol Biol. 2012, 79: 461-477. 10.1007/s11103-012-9922-1.
87. Calsa T, Figueira A: Serial analysis of gene expression in sugarcane (Saccharum spp.) leaves revealed alternative C4 metabolism and putative antisense transcripts. Plant Mol Biol. 2007, 63: 745-762. 10.1007/s11103-006-9121-z.
88. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A: Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 2011, 29: 644-652. 10.1038/nbt.1883.
89. Bundock PC, Eliott FG, Ablett G, Benson AD, Casu RE, Aitken KS, Henry RJ: Targeted single nucleotide polymorphism (SNP) discovery in a highly polyploid plant species using 454 sequencing. Plant Biotechnol J. 2009, 7: 347-354. 10.1111/j.1467-7652.2009.00401.x.
90. Ferreira TH, Gentile A, Vilela RD, Costa GG, Dias LI, Endres L, Menossi M: microRNAs associated with drought response in the bioenergy crop sugarcane (Saccharum spp.). PLoS One. 2012, 7: e46703-10.1371/journal.pone.0046703.
91. Gentile A, Ferreira TH, Mattos RS, Dias LI, Hoshino AA, Carneiro MS, Souza GM, Calsa T, Nogueira RM, Endres L, Menossi M: Effects of drought on the microtranscriptome of field-grown sugarcane plants. Planta. 2013, 237: 783-798. 10.1007/s00425-012-1795-7.
92. Thiebaut F, Grativol C, Carnavale-Bottino M, Rojas CA, Tanurdzic M, Farinelli L, Martienssen RA, Hemerly AS, Ferreira PC: Computational identification and analysis of novel sugarcane microRNAs. BMC Genomics. 2012, 13: 290-10.1186/1471-2164-13-290.
93. Domingues DS, Cruz GM, Metcalfe CJ, Nogueira FT, Vicentini R, Alves Cde S, Van Sluys MA: Analysis of plant LTR-retrotransposons at the fine-scale family level reveals individual molecular patterns. BMC Genomics. 2012, 13: 137-10.1186/1471-2164-13-137.
94. Swaminathan K, Alabady M, Varala K, De Paoli E, Ho I, Rokhsar D, Arumuganathan A, Ming R, Green P, Meyers B, Moose SP, Hudson ME: Genomic and small RNA sequencing of Miscanthus × giganteus shows the utility of sorghum as a reference genome sequence for Andropogoneae grasses. Genome Biol. 2010, 11: R12-10.1186/gb-2010-11-2-r12.
95. Kim C, Zhang D, Auckland S, Rainville L, Jakob K, Kronmiller B, Sacks E, Deuter M, Paterson A: SSR-based genetic maps of Miscanthus sinensis and M. sacchariflorus, and their comparison to sorghum. Theoret Appl Genet. 2012, 124: 1325-1338. 10.1007/s00122-012-1790-1.
96. Swaminathan K, Chae W, Mitros T, Varala K, Xie L, Barling A, Glowacka K, Hall M, Jezowski S, Ming R, Hudson M, Juvik JA, Rokhsar DS, Moose SP: A framework genetic map for Miscanthus sinensis from RNAseq-based markers shows recent tetraploidy. BMC Genomics. 2012, 13: 142-10.1186/1471-2164-13-142.
97. Wang X, Paterson AH: Comparative genomic analysis of C4 photosynthesis pathway evolution in grasses. Genomics of the Saccharinae. Edited by: Paterson AH. 2013, New York, Berlin: Springer, 11: 447-477.
98. Hatch MD, Slack CR: Photosynthesis by sugar-cane leaves. A new carboxylation reaction and the pathway of sugar formation. Biochem J. 1966, 101: 103-111.
99. Seemann JR, Sharkey TD, Wang J, Osmond CB: Environmental effects on photosynthesis, nitrogen-use efficiency, and metabolite pools in leaves of sun and shade plants. Plant Physiol. 1987, 84: 796-802. 10.1104/pp.84.3.796.
100. Hattersley PW: The distribution of C3 and C4 grasses in australia in relation to climate. Oecologia. 1983, 57: 113-128. 10.1007/BF00379569.
101. Ehleringer JR, Bjorkman O: A comparison of photosynthetic characteristics of encelia species possessing glabrous and pubescent leaves. Plant Physiol. 1978, 62: 185-190. 10.1104/pp.62.2.185.
102. Cerling TE, Harris JM, MacFadden BJ, Leakey MG, Quade J, Eisenmann V, Ehleringer JR: Global vegetation change through the Miocene/Pliocene boundary. Nature. 1997, 389: 153-158. 10.1038/38229.
103. Sage RF: The evolution of C4 photosynthesis. New Phytologist. 2004, 161: 341-370. 10.1111/j.1469-8137.2004.00974.x.
104. Muhaidat R, Sage RF, Dengler NG: Diversity of Kranz anatomy and biochemistry in C4 eudicots. Am J Bot. 2007, 94: 362-381. 10.3732/ajb.94.3.362.
105. Giussani LM, Cota-Sanchez JH, Zuloaga FO, Kellogg EA: A molecular phylogeny of the grass subfamily Panicoideae (Poaceae) shows multiple origins of C4 photosynthesis. Am J Bot. 2001, 88: 1993-2012. 10.2307/3558427.
106. Pyankov VI, Artyusheva EG, Edwards GE, Black CC, Soltis PS: Phylogenetic analysis of tribe Salsoleae (Chenopodiaceae) based on ribosomal ITS sequences: implications for the evolution of photosynthesis types. Am J Bot. 2001, 88: 1189-1198. 10.2307/3558329.
107. Vicentini A, Barber JC, Aliscioni SS, Giussani LM, Kellogg EA: The age of the grasses and clusters of origins of C4 photosynthesis. Glob Change Biol. 2008, 14: 2963-2977. 10.1111/j.1365-2486.2008.01688.x.
108. 2 decline promoted C4 photosynthesis in grasses. Curr Biol. 2008, 18: 37-43. 10.1016/j.cub.2007.11.058.
109. Sheen J: C4 gene expression. Annu Rev Plant Physiol Plant Mol Biol. 1999, 50: 187-217. 10.1146/annurev.arplant.50.1.187.
110. Buckeridge MS, Cavalari AA, Silva GB: Parede celular. Fisiologia Vegetal. Edited by: Kerbauy GB. 2008, Rio de Janeiro: Guanabara Koogan, 165-181.
111. Rooney WL, Blumenthal J, Bean B, Mullet JE: Designing sorghum as a dedicated bioenergy feedstock. Biofuels Bioprod Bioref. 2007, 1: 147-157. 10.1002/bbb.15.
112. Nogueira FT, De Rosa VE, Menossi M, Ulian EC, Arruda P: RNA expression profiles and data mining of sugarcane response to low temperature. Plant Physiol. 2003, 132: 1811-1824. 10.1104/pp.102.017483.
113. Rocha FR, Papini-Terzi FS, Nishiyama MY, Vêncio RZ, Vicentini R, Duarte RD, de Rosa VE, Vinagre F, Barsalobres C, Medeiros AH, Rodrigues FA, Ulian EC, Zingaretti SM, Galbiatti JA, Almeida RS, Figueira AV, Hemerly AS, Silva-Filho MC, Menossi M, Souza GM: Signal transduction-related responses to phytohormones and environmental challenges in sugarcane. BMC Genomics. 2007, 8: 71-10.1186/1471-2164-8-71.
114. Papini-Terzi FS, Rocha FR, Vêncio RZ, Oliveira KC, Felix Jde M, Vicentini R, Rocha Cde S, Simões AC, Ulian EC, di Mauro SM, da Silva AM, Pereira CA, Menossi M, Souza GM: Transcription profiling of signal transduction-related genes in sugarcane tissues. DNA Res. 2005, 12: 27-38. 10.1093/dnares/12.1.27.
115. Casu RE, Jarmey JM, Bonnett GD, Manners JM: Identification of transcripts associated with cell wall metabolism and development in the stem of sugarcane by Affymetrix GeneChip Sugarcane Genome Array expression profiling. Funct Integr Genomics. 2007, 7: 153-167. 10.1007/s10142-006-0038-z.
116. McCormick AJ, Cramer MD, Watt DA: Regulation of photosynthesis by sugars in sugarcane leaves. J Plant Physiol. 2008, 165: 1817-1829. 10.1016/j.jplph.2008.01.008.
117. Buchanan CD, Lim S, Salzman RA, Kagiampakis I, Morishige DT, Weers BD, Klein RR, Pratt LH, Cordonnier-Pratt MM, Klein PE, Mullet JE: Sorghum bicolor's transcriptome response to dehydration, high salinity and ABA. Plant Mol Biol. 2005, 58: 699-720. 10.1007/s11103-005-7876-2.
118. Salzman RA, Brady JA, Finlayson SA, Buchanan CD, Summer EJ, Sun F, Klein PE, Klein RR, Pratt LH, Cordonnier-Pratt MM, Mullet JE: Transcriptional profiling of sorghum induced by methyl jasmonate, salicylic acid, and aminocyclopropane carboxylic acid reveals cooperative regulation and novel gene responses. Plant Physiol. 2005, 138: 352-368. 10.1104/pp.104.058206.
119. Zhu-Salzman K, Salzman RA, Ahn JE, Koiwa H: Transcriptional regulation of sorghum defense determinants against a phloem-feeding aphid. Plant Physiol. 2004, 134: 420-431. 10.1104/pp.103.028324.
120. Park SJ, Huang Y, Ayoubi P: Identification of expression profiles of sorghum genes in response to greenbug phloem-feeding using cDNA subtraction and microarray analysis. Planta. 2006, 223: 932-947. 10.1007/s00425-005-0148-1.
121. Zanca AS, Vicentini R, Ortiz-Morea FA, Del Bem LE, da Silva MJ, Vincentz M, Nogueira FT: Identification and expression analysis of microRNAs and targets in the biofuel crop sugarcane. BMC Plant Biol. 2010, 10: 260-10.1186/1471-2229-10-260.