Survey of Genomics Approaches to Improve Bioenergy Traits in Maize, Sorghum and Sugarcane

Journal of Integrative Plant Biology

Volumn 53, Issue 2, 2011, Pages 105-119

  Vermerris, Wilfred ^a  

^a UNIVERSITY OF FLORIDA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALTERNATIVE ENERGY; BIOENERGY; BIOMASS; CROP PRODUCTION; DEVELOPING WORLD; GENOMICS; MAIZE; SORGHUM;

GENETICS; GENOMICS; MAIZE; METHODOLOGY; REVIEW; SORGHUM; SUGARCANE;

GENOMICS; SACCHARUM; SORGHUM; ZEA MAYS;

POACEAE; ZEA MAYS;

EID: 79251512321     PISSN: 16729072     EISSN: 17447909     Source Type: Journal    
DOI: 10.1111/j.1744-7909.2010.01020.x     Document Type: Review

References (134)

1. Alwala S, Kimbeng CA, Veremis JC, Gravois KA (2009) Identification of molecular markers associated with sugar-related traits in a Saccharum interspecific cross. Euphytica 167, 127-142.
2. Angelini LG, Ceccarini L, Nassi o Di Nasso N, Bonari E (2009) Comparison of Arundo donax L. and Miscanthus x giganteus in a long-term field experiment in Central Italy: analysis of productive characteristics and energy balance. Biomass Bioenerg. 33, 635-643.
3. Arencibia AD, Carmona ER, Téllez P, Chan M-T, Yu S-M, Trujillo LE, Oramas P (1998) An efficient protocol for sugarcane (Saccharum spp. L.) transformation mediated by Agrobacterium tumefaciens. Transgenic Res. 7, 213-222.
4. Bai L, Singh M, Pitt L, Sweeney M, Brutnell TP (2007). Generating novel allelic variation through Activator insertional mutagenesis in maize. Genetics 175, 981-992.
5. Bernardo R, Yu J (2007) Prospects for genomewide selection for quantitative traits in maize. Crop Sci. 47, 1082-1090.
6. Bout S, Vermerris W (2003) A candidate gene-approach to clone the sorghum Brown midrib gene encoding caffeic acid O-methyltransferase. Mol. Genet. Genomics 269, 205-214.
7. Bouton (2007) Molecular breeding of switchgrass as a biofuel crop. Curr. Opin. Genet. Develop. 17, 553-558.
8. Bouton J (2008) Improvement of switchgrass as a bioenergy crop. In: Vermerris W, ed. Genetic Improvement of Bioenergy Crops. Springer, New York, NY pp. 295-308.
9. Bower R, Birch RG (1992) Transgenic sugarcane plants via microprojectile bombardment. Plant J. 2, 409-416.
10. Brenner S, Johnson M, Bridgham J, Golda G, Lioyd DH, Johnson D, Luo S, McCurdy S, Foy M, Ewan M, Roth R, George D, Eletr S, Albrecht G, Vermaas E, Williams SR, Moon K, Burcham T, Pallas M, DuBridge RB, Fearon K, Mao J, Corcoran K (2000) Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat. Biotechnol. 18, 630-634.
11. Burr B, Burr FA, Thompson KH, Albertson MC, Stuber CW (1988) Gene mapping with recombinant inbreds in maize. Genetics 118, 519-526.
12. Burton RA, Wilson SM, Hrmova M, Harvey AJ, Shirley NJ, Medhurst A, Stone BA, Newbigin EJ, Bacic A, Fincher GB (2006) Cellulose synthase-like CsIF genes mediate the synthesis of cell wall (1, 3;1, 4)-β-D-glucans. Science 311, 1940-1942.
13. Calvińo M, Bruggman R, Messing J (2008) Screen of genes linked to high sugar content in stems by comparative genomics. Rice 1, 166-176.
14. Calvińo M, Miclaus M, Bruggmann R, Messing J (2009) Molecular markers for sweet sorghum based on microarray expression data. Rice 2, 129-142.
15. Carpita NC (1996) Structure and biogenesis of the cell walls of grasses. Annu. Rev. Plant Physiol. Plant Mol. Biol. 47, 445-476.
16. Carpita NC, Gibeaut DM (1993) Structural models of the primary cell walls in flowering plants: consistency of molecular structure with the physical properties of the wall during growth. Plant J. 3, 1-30.
17. Carpita NC, McCann MC (2008) Maize and sorghum: genetic resources for bioenergy grasses. Trends Plant Sci. 11, 314-320.
18. Casa AM, Pressoir G, Brown PJ, Mitchell SE, Rooney WL, Tuinstra MR, Franks CD, Kresovich S (2008) Community resources and strategies for association mapping in sorghum. Crop Sci. 48, 30-40.
19. Casas AM, Kononowicz AK, Zehr UB, Tomes DT, Axtell JD, Butler LG, Bressan RA, Hasegawa PM (1993) Transgenic sorghum plants via microprojectile bombardment. Proc. Natl. Acad. Sci. USA 90, 11212-11216.
20. Casu RE, Jarmey JM, Bonnett G, Manners JM (2007) Identification of transcripts associated with cell wall metabolism and development of the stem in sugarcane by Affymetrix GeneChip Sugarcane Genome Array expression profiling. Funct. Integr. Genomics 7, 153-167.
21. Chen L, Carpita NC, Reiter W-D, Wislon RH, Jeffries C, McCann MC (1998) A rapid method to screen for cell-wall mutants using discriminant analysis of Fourier transform infrared spectra. Plant J. 16, 385-392.
22. Chen SL, Renvoize SA (2006) Miscanthus. Flora of China 22, 581-583.
23. Christi Y (2007) Biodiesel from microalgae. Biotechnol. Adv. 25, 294-306.
24. Clifton-Brown J, Chiang Y-C, Hodkinson TR (2008) Miscanthus: Genetic resources and breeding potential to enhance bioenergy production. In: Vermerris W, ed. Genetic Improvement of Bioenergy Crops. Springer, New York, NY pp. 273-294.
25. Czernik S, Bridgwater AV (2004) Overview of applications of biomass fast pyrolysis oil. Energ. Fuels 18, 590-598.
26. D'Hont A, Souza GM, Menossi M, Vincentz M, Van Sluys MA, Glaszmann JC, Ulian E (2008) Sugarcane: A major source of sweetness, alcohol, and bio-energy. In: Moore PH, Ming R, eds. Genomics of Tropical Crop Plants. Springer, New York, NY pp. 483-513.
27. Dale BE (2007) Thinking clearly about biofuels: ending the irrelevant 'net energy' debate and developing better performance metrics for alternative fuels. Biofuels Bioprod. Bioref. 1, 14-17.
28. Dale BE, Lynd L (2010) Global sustainable bioenergy project offers a new approach to key bioenergy issues. Biofuels Bioprod. Bioref. 4, 8-11.
29. Davison BH, Keller M, Fowler VS (2009) The goals and research of the BioEnergy Sciences Center (BESC): developing cost-effective and sustainable means of producing biofuels by overcoming biomass recalcitrance. Bioenerg. Res. 2, 177-178.
30. Decker SR, Brunecky R, Tucker MP, Himmel ME, Selig MJ (2009) High-throughput screening techniques for biomass conversion. Bioenerg. Res. 2, 179-192.
31. Delmer DP (1999) Cellulose biosynthesis: Exciting times for a difficult field of study. Ann. Rev. Plant Physiol. Plant Mol. Biol. 50, 245-276.
32. Devos KM (2010) Grass genome organization and evolution. Curr. Opin. Plant Biol. 13, 139-145.
33. Dien BS, Sarath G, Pedersen JF, Satler SE, Chen H, Funnell-Harris DL, Nichols NN, Cotta MA (2009) Improved sugar conversion and ethanol yield for forage sorghum (Sorghum bicolor (L.) Moench) lines with reduced lignin contents. Bioenerg. Res. 2, 153-164.
34. Doblin MS, Pettolino FA, Wilson SM, Campbell R, Burton RA, Fincher GB, Newbigin E, Bacic A (2009) A barley cellulose synthase-like CSLH gene mediates (1, 3;1, 4)-β-D-glucan synthesis is transgenic Arabidopsis. Proc. Natl. Acad. Sci. USA 106, 5996-6001.
35. Doust AN, Kellogg EA, Devos KM, Bennetzen JL (2009) Foxtail millet: A sequence-driven grass model system. Plant Physiol. 149, 137-141.
36. Dudley J (1993) Molecular markers in plant improvement: manipulation of genes affecting quantitative traits. Crop Sci. 33, 660-668.
37. Eveland AL, McCarty DR, Koch KE (2008) Trancript profiling by 3'-untranslated region sequencing resolves expression of gene families. Plant Physiol. 146, 31-44.
38. Fargione J, Hill J, Tilman D, Polasky S, Hawthorne P (2008). Land clearing and the biofuel carbon debt. Science 319, 1235-1238.
39. Fiedler F (2004) The state of the art of small-scale pellet-based heating systems and relevant regulations in Sweden, Austria and Germany. Renew. Sustain. Energ. Rev. 8, 201-221.
40. Fincher GB (2009) Revolutionary times in our understanding of cell wall biosynthesis and remodeling in the grasses. Plant Physiol. 149, 27-37.
41. Firbank L (2008) Assessing the ecological impacts of bioenergy. Bioenerg. Res. 1, 12-19.
42. Frame BR, Shou H, Chikwamba RK, Zhang Z, Xiang C, Fonger TM, Pegg SEK, Nettleton DS, Pei D, Wang K (2002) Agrobacterium tumefaciencs-mediated transformation of maize embryos using a standard binary vector system. Plant Physiol. 129, 13-22.
43. Goff SA, Ricke D, Lan TH, Presting G, Wang R, Dunn M, Glazebrook J, Sessions A, Oeller P, Varma H et al (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296, 92-100.
44. Goyal HB, Seal D, Saxena RC (2008) Bio-fuels from thermochemical conversion of renewable resources: A review. Renew. Sustain. Energy Rev. 12, 504-517.
45. Guillaumie S, Pichon M, Martinant JP, Bosio M, Goffner D, Barrière Y (2007a) Differential expression of phenylpropanoid and related genes in brown-midrib bm1, bm2, bm3, and bm4 young near-isogenic maize plants. Planta 226, 235-250.
46. Guillaumie S, San-Clemente H, Deswarte C, Martinez Y, Lapierre C, Murgneux A, Barrière Y, Pichon M, Goffner D (2007b) MAIZEWALL. Database and developmental gene expression profiling of cell wall biosynthesis and assembly in maize. Plant Physiol. 143, 339-363.
47. Hall DO (1982) Solar energy through biology: fuels from biomass. Cell. Mol. Life Sci. 38, 3-10.
48. Han F, Ullrich SE, Chirat S, Menteur S, Jestin L, Sarrafi A, Hayes PM, Jones BL, Blake TK, Wesenberg DM, Kleinhofs A, Kilian A (1995) Mapping of β-glucan content and β-glucanase activity loci in barley grain and malt. Theor. Appl. Genet. 91, 921-927.
49. Hazen SP, Scott-Craig JS, Walton JD (2002) Cellulose synthase-like genes of rice. Plant Physiol. 128, 336-340.
50. Hodkinson TR, Renvoize S (2001) Nomenclature of Miscanthus x giganteus (Poaceae). Kew Bull. 56, 759-760.
51. Hoffmann-Thoma G, Hikel K, Nicolay P, Willenbrink J (1996) Sucrose accumulation in sweet sorghum stem internodes in relation to growth. Physiol. Plant. 97, 277-284.
52. Holland JH (1925) Sources of industrial alcohol. Bull. Miscell. Inform. 5, 193-216.
53. Holt RA, Jones SJM (2008) The new paradigm of flow cell sequencing. Genome Res.18, 839-846.
54. Ishida Y, Saito H, Ohta S, Hiei Y, Komari T, Kumashiro T (1996) High efficiency transformation of maize (Zea mays L.) mediated by Agrobacterum tumefaciens. Nat. Biotechnol. 14, 747-750.
55. Jannoo N, Grivet L, Chantret N, Garsmeur O, Glaszmann JC, Arrudo P, D'Hont A (2007) Orthologous comparison in a gene-rich region among grasses reveals stability in the sugarcane polyploid genome. Plant J. 50, 574-585.
56. Johansson LS, Leckner B, Gustavsson L, Cooper D, Tullin C, Potter A (2004) Emission characteristics of modern and old-type residential boilers fired with wood logs and wood pellets. Atmosph. Environ. 38, 4183-4195.
57. Lee, SK, Chou H, Ham TS, Lee TS, Keasling JD (2008) Metabolic engineering of microorganisms for biofuels production: from bugs to synthetic biology to fuels. Curr. Opin. Biotechnol. 19, 556-563.
58. Lee M, Sharopova N, Beavis WD, Grant D, Katt M, Blair D, Hallauer A (2002) Expanding the genetic map of maize with the intermated B73 x Mo17 (IBM) population. Plant Mol. Biol. 48, 453-461.
59. Lewis MF, Lorenzana RE, Jung H-JG, Bernardo R (2010) Potential for simultaneous improvement of corn grain yield and stover quality for cellulosic ethanol. Crop Sci. 50, 516-523.
60. Lipinski ES, Kresovich S (1982) Sugar crops as a solar energy converter. Cell. Mol. Life Sci. 38, 13-18.
61. Lorenz AJ, Anex RP, Isci A, Coors JG, de Leon N, Weimer PJ (2009) Forage quality and composition measurements as predictors of ethanol yield from maize (Zea mays L.) stover. Biotechnol. Biofuels 2, 5.
62. Lorenzana RE, Friskop Lewis M, Jung H-HG, Bernardo R (2010) Quantitative trait loci and trait correlations for maize stover cell wall composition and glucose release for cellulosic ethanol. Crop Sci. 50, 541-555.
63. Maranca G (1940) La utilizzazione chimica del legno (Chemical utilization of wood). Italia Agric. 77, 128-130.
64. Martel E, De Nay S, Siljak-Yakovlev S, Brown S, Sarr A (1997) Genome size variation and basic chromosome number in pearl millet and fourteen related Pennisetum species. J. Hered. 88, 139-143.
65. Matsuoka S, Ferro J, Arruda P (2009) The Brazilian experience of sugarcane ethanol industry. In Vitro Cell Dev. Biol. 45, 372-381.
66. McCarty DR, Settles AM, Suzuki M, Tan BC, Latshaw S, Porch T, Robin K, Baier J, Avigne W, Lai J (2005). Steady-state transposon mutagenesis in inbred maize. Plant J. 44, 52-61.
67. McMullen MD, Kresovich S, Villeda HS, Bradbury P, Li H, Sun Q, Flint-Garcia S, Thornsberry J, Acharya C, Bottoms C, Brown P, Browne C, Eller M, Guill K, Harjes C, Kroon D, Lepak N, Mitchell SE, Peterson B, Pressoir G, Romero S, Oropeza Rosas M, Salvo S, Yates H, Hanson M, Jones E, Smith S, Glaubitz JC, Goodman M, Ware D, Holland JB, Buckler ES (2009) Genetic properties of the maize nested association mapping population. Science 325, 737-740.
68. Meuwissen THE, Hayes BJ, Goddard ME (2001) Prediction of total genetic value using genome-wide dense marker maps. Genetics 157, 1819-1829.
69. Ming R, Liu S, Moore PH, Irvine JE, Paterson AH (2001) QTL analysis in a complex autopolyploid: Genetic control of sugar content in sugarcane. Genome Res. 11, 2075-2084.
70. Moura JCMS, Bonine CAV, Viana JOF, Dornelas MC, Mazzafera P (2010) Abiotic and biotic stresses and changes in the lignin content and composition in plants. J. Integr. Plant Biol. 52, 360-376.
71. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods. 5, 621-628.
72. Murray SC, Sharma A, Roone WL, Klein PE, Mullet JE, Mitchell SE, Kresovich S (2008a) Genetic improvement of sorghum as a biofuel feedstock I: quantitative loci for stem sugar and grain nonstructural carbohydrates. Crop Sci. 48, 2165-2179.
73. Murray SC, Sharma A, Roone WL, Klein PE, Mullet JE, Mitchell SE, Kresovich S (2008b). Genetic improvement of sorghum as a biofuel feedstock II: quantitative loci for stem and leaf structural carbohydrates. Crop Sci. 48, 2180-2193.
74. Murugesan A, Umarani C, Chinnusamy TR, Krishnan M, Subramanian R, Neduzchezhain N (2009) Production and analysis of bio-diesel from non-edible oils - A review. Renew. Sustain. Energ. Rev. 13, 825-834.
75. Nemeth C, Freeman J, Jones HD, Sparks C, Pellny MD, Wilkinson MD, Dunwell J, Andersson AAM, Åman P, Guillon F, Saulnier L, Mitchell RAC, Shewry PR (2010) Down-regulation of the CSLF6 gene results in decreased (1, 3;1, 4)-β-D-glucan in endosperm of wheat. Plant Physiol. 152, 1209-1218.
76. Papini-Terzi F, Rocha FR, Vêncio RZN, Felix JM, Branco DS, Waclawovsky AJ, Del Bem LEV, Lembke CG, Costa MDL, Nishiyama Jr MY, Vicentini R, Vincentz MGA, Ulian EC, Menossi M, Souza GM (2009) Sugarcane genes associated with sucrose content. BMC Genomics 10, 120-141.
77. Papini-Terzi FS, Rocha FR, Vencio RZN, Oliveira KC, Felix J, Vicentini R, Rocha Cde S, Simões AC, Ulian EC, di Mauro SM, da Silva AM, Pereira CA, Menossi M, Souza GM (2005) Transcription profiling of signal transduction-related genes in sugarcane tissues. DNA Res. 12, 27-38.
78. Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, Mitros T, Poliakov A, et al (2009a) The Sorghum bicolor genome and the diversification of grasses. Nature 457, 551-556.
79. Paterson AH, Bowers JE, Chapman BA (2004) Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics. Proc. Natl. Acad. Sci. USA 101, 9903-9908.
80. Paterson AH, Bowers JE, Feltus FA, Tang H, Lin L, Wang X (2009b) Comparative genomics of grasses promises a bountiful harvest. Plant Physiol. 149, 125-131.
81. Penning B, Tayengwa R, Hunter III CT, Eveland A, Vermerris W, Olek A, Koch KE, McCarty DR, Davis M, Thomas SR, McCann M, Carpita N (2009). Genetic resources for functional genomics of maize cell wall biology. Plant Physiol. 151, 1703-1728.
82. Perlack RD, Wright LL, Turhollow A, Graham R, Stokes B, Erbach D (2005) Biomass as feedstock for a bioenergy and bioproducts industry: The technical feasibility of a billion-ton annual supply. Tech. Rep. ORNL/TM-2006/66, Oak Ridge National Laboratory, Oak Ridge, TN .
83. Pimentel D, Patzek TW (2005) Ethanol production using corn, switchgrass, and wood; biodiesel production using soybean and sunflower. Nat. Resour. Res. 14, 65-76.
84. Pinto LR, Garcia AAF, Pastina MM, Teixeira LHM, Bressiani JA, Ulian EC, Bidoia MAP, Souza AP (2010) Analysis of genomic and functional RFLP derived markers associated with sucrose content, fiber and yield QTLs in a sugarcane (Saccharum spp.) commercial cross. Euphytica 172, 313-327.
85. Porter KS, Axtell JD, Lechtenberg VL, Colenbrander VF (1978) Phenotype, fiber composition, and in vitro dry matter disappearance of chemically induced brown midrib (bmr) mutants of sorghum. Crop Sci. 18, 205-209.
86. Rafalski JA (2002) Novel genetic mapping tools in plants: SNPs and LD-based approaches. Plant Sci. 162, 329-333.
87. Ragauskas AJ, William CK, Davison BH, Britovsek G, Cairney J, Eckert CA, Frederick Jr WJ, Hallett JP, Leak DJ, Liotta CL, Mielenz JR, Murphy R, Templer R, Tschaplinski T (2006) The path forward for biofuels and biomaterials. Science 311, 484-489.
88. Ralph J, Lundquist K, Brunow G, Lu F, Kim H, Schatz PF, Marita JM, Hatfield RD, Ralph SA, Christensen JH, Boerjan W (2004) Lignins: Natural polymers from oxidative coupling of 4-hydroxyphenylpropanoids. Phytochem. Rev. 3, 29-60.
89. Rayburn AL, Crawford J, Rayburn CM, Juvik JA (2009) Genome size of three Miscanthus species. Plant Mol. Biol. Rep. 27, 184-188.
90. Richard TL (2010) Challenges in scaling up biofuels infrastructure. Science 329, 793-796.
91. Ritter KB, Jordan DR, Chapman SC, Goodwin ID, Mace ES, McIntyre CL (2008) Identification of QTL for sugar-related traits in a sweet x grain sorghum (Sorghum bicolor (L.) Moench) recombinant inbred population. Mol. Breed. 22, 367-384.
92. Rooney WL, Blumenthal J, Bean B, Mullet JE (2007) Designing sorghum as a dedicated bioenergy feedstock. Biofuels Bioprod. Bioref. 1, 147-157.
93. Saballos A (2008) Development and utilization of sorghum as a bioenergy crop. In: Vermerris W, ed. Genetic Improvement of Bioenergy Crops. Springer, New York, NY pp. 211-248.
94. Saballos A, Ejeta G, Kang CH, Vermerris W (2009) A genomewide analysis of the cinnamyl alcohol dehydrogenase family in sorghum [Sorghum bicolor (L.) Moench] identifies SbCAD2 as the Brown midrib6 gene. Genetics 181, 783-795.
95. Saballos A, Vermerris W, Rivera L, Ejeta G (2008) Allelic association, chemical characterization and saccharification properties of brown midrib mutants of sorghum (Sorghum bicolor (L.) Moench). Bioenerg. Res. 1, 93-204.
96. Salvi S, Sponza G, Morgante M, Tomes D, Niu X, Fengler KA, Meeley R, Ananiev EV, Svitashev S, Bruggemann E, Li B, Hainey CF, Radovic S, Zaina G, Rafalski JA, Tingey SV, Miao GH, Phillips RL, Tuberosa R (2007) Conserved non-coding genomic sequences associated with a flowering-time quantitative trait locus in maize. Proc. Natl. Acad. Sci. USA 104, 11376-11381.
97. Sang T (2011) Toward the domestication of lignocellulosic energy crops: Learning from food crop domestication. J. Integr. Plant Biol. 53, 96-104.
98. Santoro N, Cantu SL, Tornqvist C-E, Falbel TG, Bolivar JL, Patterson SE, Pauly M, Walton JD (2010) A high-throughput platform for screening milligram quantities of plant biomass for lignocellulosic digestibility. Bioenerg. Res. 3, 93-102.
99. Sattler SE, Funnell-Harris DL, Pedersen JF (2010) Brown midrib mutations and their importance to the utilization of maize, sorghum, and pearl millet lignocellulosic tissues. Plant Sci. 178, 229-238.
100. Sattler SE, Saathoff AJ, Haas EJ, Palmer NA, Funnell-Harris DL, Sarath G, Pedersen JF (2009) A nonsense mutation in a cinnamyl alcohol dehydrogenase gene is responsible for the sorghum brown midrib6 phenotype. Plant Physiol. 150, 584-595.
101. Scheller HV, Singh S, Blanch H, Keasling JD (2010) The Joint BioEnegy Institute(JBEI): Developing new biofuels by overcoming biomass recalcitrance. Bioenerg. Res. 3, 105-107.
102. Schena M, Shalon D, Davis RW, Brown PO (1995). Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270, 467-470.
103. Schmer MR, Vogel KP, Mitchell RB, Perrin RK (2008) Net energy of cellulosic ethanol from switchgrass. Proc. Natl. Acad. Sci. USA 105, 464-469.
104. Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Lucinda Fulton L, Graves TA, et al (2009) The B73 maize genome: Complexity, diversity, and dynamics. Science 326, 1112-1115.
105. Searchinger T, Heimlich R, Houghton RA, Dong F, Elobeid A, Fobiosa J, Tokgoz S, Hayes D, Yu TH (2008) Use of U.S. croplands for biofuels increases greenhouse gases through emissions from land use change. Science 319, 1238-1240.
106. Sewell MM, Davis MF, Tuskan GA, Wheeler NC, Elam CC, Bassoni DL, Neale DB (2002) Identification of QTLs influencing wood property traits in loblolly pine (Pinus taeda L.). Theor. Appl. Genet. 104, 214-222.
107. Shi C, Koch G, Ouzunova M, Wenzel G, Zein I, Lübberstedt T (2006) Comparison of maize brown-midrib isogenic lines by cellular UV-microspectrophotometry and comparative transcript profiling. Plant Mol. Biol. 62, 697-714.
108. Simon SA, Zhai J, Nandety RJ, McCormick KP, Zeng J, Meija D, Meyers BC (2009) Short-read sequencing technologies for transcriptional analyses. Annu. Rev. Plant Biol. 60, 305-333.
109. Slater S, Keegstra K, Donohue TJ (2010) The US Department of Energy Great Lakes Bioenergy Research Center: Midwestern biomass as a resource for renewable fuels. Bioenerg. Res. 3, 3-5.
110. Stuber CW, Polacco M, Senior ML (1999) Synergy of empirical breeding, marker-assisted selection and genomics to increase crop yield potential. Crop Sci. 39, 1571-1583.
111. Tenenbaum DJ (2008) Food vs. fuel: Diversion of crops could cause more hunger. Environ. Health Perspect. 116, A254-A257.
112. Tew TL, Cobill RM (2008) Genetic improvement of sugarcane (Saccharum spp.) as an energy crop. In: Vermerris W, ed. Genetic Improvement of Bioenergy Crops. Springer, New York, NY pp. 249-272.
113. Tew TL, Cobill RM, Richard JEP (2008). Evaluation of sweet sorghum and sorghum × sudangrass hybrids as feedstocks for ethanol production. Bioenerg. Res. 1, 147-152.
114. The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408, 796-815.
115. The International Brachypodium Initiative (2010) Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 463, 763-768.
116. USDA Economic Research Service (2010)
117. Vandenbrink JP, Delgado MP, Frederick JR, Feltus FA (2010) A sorghum diversity panel biofuel feedstock screen for genotypes with high hydrolysis yield potential. Ind. Crops Prod. 31, 444-448.
118. Venuto B, Kindiger B (2008) Forage and biomass feedstock production from hybrid forage sorghum and sorghum-sudangrass. Grassl. Sci. 54, 189-196.
119. Vermerris W, Saballos A, Ejeta G, Mosier NS, Ladisch MR, Carpita NC (2007) Molecular breeding to enhance ethanol production from corn and sorghum stover. Crop Sci. 47, S145-S153.
120. Vettore AL, da Silva FR, Kemper EL, Souza CM, da Silva AM, Ferro MIT, Silva FH, Giglioti ÉA, Lemos MVF, Coutinho LL, Nobrega MP, Carrer H, França SC Jr, Bacci M, Goldman MHS, Gomes SL, Nunes LR, Camargo LEA, Siqueira WJ, Van Sluys MA, Thiemann OH, Kuramae EE, Santelli RV, Marino CL, Targon MLPN (2003) Analysis and functional annotation of an expressed sequence tag collection for tropical crop sugarcane. Genome Res. 13, 2725-2735.
121. Vogel J (2008) Unique aspects of the grass cell wall. Curr. Opin. Plant Biol. 301-307.
122. Waclawovsky AJ, Sato PM, Lembke CG, Moore PH, Souza GM (2010) Sugarcane for bioenergy production: an assessment of yield and regulation of sucrose content. Plant Biotechnol. J. 8, 263-276.
123. 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 (2010) Microcollinearity between autopolyploid sugarcane and diploid sorghum genomes. BMC Genomics 11, 261.
124. Weimer PJ, Dien BS, Springer TL, Vogel KP (2005) In vitro gas production as a surrogate measure of the fermentability of cellulosic biomass to ethanol. Appl. Microbiol. Biotechnol. 67, 52-58.
125. Wijffels RH, Barbosa MJ (2010) An outlook on microalgal fuels. Science 329, 796-799.
126. Wilhelm WW, Johnson JMF, Hatfield JL, Voorhees WB, Linden DR (2004) Crop and soil productivity response to corn residue removal: A literature review. Agron. J. 96, 1-17.
127. Wilhelm WW, Johnson JMF, Karlen DL, Lightle DT (2007) Corn stover to sustain soil organic carbon further constrains biomass supply. Agron. J. 99, 1665-1667.
128. Wolfrum EJ, Lorenz AJ, de Leon N (2009) Correlating detergent fiber analysis and dietary fiber analysis data for corn stover collected by NIRS. Cellulose 16, 577-585.
129. Xin Z, Wang ML, Barkley NA, Burow G, Franks C, Pederson G, Burke J (2008) Applying genotyping (TILLING) and phenotyping analyses to elucidate gene function in a chemically induced sorghum mutant population. BMC Plant Biol. 8, 108-140.
130. Xin Z, Wang ML, Burow G, Burke J (2009) An induced sorghum mutant population suitable for bioenergy research. Bioenerg. Res. 2, 10-16.
131. Yong W, Link B, O'Malley R, Tewari J, Hunter CT, Lu CA, Li X, Bleecker AB, Koch KE, McCann MC, McCarty DR, Staiger C, Thomas SR, Vermerris W, Carpita NC (2005) Genomics of plant cell wall biogenesis. Planta 221, 747-751.
132. Yu J, Buckler ES (2006) Genetic association mapping and genome organization of maize. Curr. Opin. Biotechnol. 17, 155-160.
133. Zhang SZ, Yang BP, Feng CL, Chen RK, Luo JP, Cai WW, Liu FH (2006). Expression of the Grifola frondosa trehalose synthase gene and improvement of drought-tolerance in sugarcane (Saccharum officinarum L.). J. Integr. Plant Biol. 48, 453-459.
134. Zhao Z, Cai T, Tagliani L, Miller M, Wang N, Pang H, Rudert M, Schroeder S, Hondred D, Seltzer J, Pierce D (2000) Agrobacterium-mediated sorghum transformation. Plant Mol. Biol. 44, 789-798.