Bioinformatics-based identification of candidate genes from QTLs associated with cell wall traits in Populus

Bioenergy Research

Volumn 3, Issue 2, 2010, Pages 172-182

  Ranjan, Priya ^a,b   Yin, Tongming ^a,b   Zhang, Xinye ^a,b   Kalluri, Udaya C ^a,b   Yang, Xiaohan ^a,b   Jawdy, Sara ^a,b   Tuskan, Gerald A ^a,b  

^a OAK RIDGE NATIONAL LABORATORY   (United States)

^b OAK RIDGE NATIONAL LABORATORY   (United States)

Author keywords

Biofuels; Guaiacyl lignin; Populus; Quantitative trait loci; Syringyl lignin; Whole genome duplication; Wood chemistry

Indexed keywords

GENOME DUPLICATION; GUAIACYL; GUAIACYL LIGNIN; POPULUS; QUANTITATIVE TRAIT LOCUS; WOOD CHEMISTRY;

BIOFUELS; BIOINFORMATICS; CELLULOSE; LIGNIN; PLANTS (BOTANY); STEM CELLS; TECHNOLOGICAL FORECASTING;

GENE EXPRESSION;

CELLS; CELLULOSE; CHEMISTRY; LIGNINS; PLANTS; POPULUS; WOOD;

POPULUS;

EID: 77952426659     PISSN: 19391234     EISSN: 19391242     Source Type: Journal    
DOI: 10.1007/s12155-009-9060-z     Document Type: Article

References (43)

1. Adams KL, Wendel JF (2005) Polyploidy and genome evolution in plants. Curr Opin Plant Biol 8: 135-141.
2. Adams KL, Percifield R, Wendel JF (2004) Organ-specific silencing of duplicated genes in a newly synthesized cotton allotetraploid. Genetics 168: 2217-2226.
3. Bechtold N, Ellis J, Pelletier G (1993) In planta Agrobacterium-mediated gene transfer by infiltration of adult Arabidopsis thaliana plants. C R Acad Sci Ser III Sci Vie 316: 1194-1199.
4. Blanc G, Wolfe KH (2004) Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution. Plant Cell 16: 1679-1691.
5. Boerjan W, Ralph J, Baucher M (2003) Lignin biosynthesis. Annu Rev Plant Biol 54: 519-546.
6. Breitling R, Armengaud P, Amtmann A, Herzyk P (2004) Rank products: a simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments. FEBS Lett 573: 83-92.
7. Brodeur-Campbell SE, Vucetich JA, Richter DL, Waite TA, Rosemier JN, Tsai CJ (2006) Insect herbivory on low-lignin transgenic aspen. Environ Entomol 35: 1696-1701.
8. Byrne KP, Wolfe KH (2007) Consistent patterns of rate asymmetry and gene loss indicate widespread neofunctionalization of yeast genes after whole-genome duplication. Genetics 175: 1341-1350.
9. Chen F, Dixon RA (2007) Lignin modification improves fermentable sugar yields for biofuel production. Nat Biotechnol 25: 759-761.
10. Chiang VL (2006) Monolignol biosynthesis and genetic engineering of lignin in trees, a review. Environmental Chemistry Letters 4(3): 143-146.
11. Davis MF, Tuskan GA, Payne P, Tschaplinski TJ, Meilan R (2006) Assessment of Populus wood chemistry following the introduction of a Bt toxin gene. Tree Physiology 26: 557-564.
12. Davison BH, Drescher SR, Tuskan GA, Davis MF, Nghiem NP (2006) Variation of S/G ratio and lignin content in a Populus family influences the release of xylose by dilute acid hydrolysis. Appl Biochem Biotechnol 130(1-3): 427-435.
13. Dinus RJ, Payne P, Sewell NM, Chiang VL, Tuskan GA (2001) Genetic modification of short rotation poplar wood: properties for ethanol fuel and fiber productions. Crit Rev Plant Sci 20: 51-69.
14. Farrokhi N, Burton RA, Brownfield L, Hrmova M, Wilson SM, Bacic A, Fincher GB (2006) Plant cell wall biosynthesis: genetic, biochemical and functional genomics approaches to the identification of key genes. Plant Biotechnol J 4: 145-167.
15. Himmel ME, Ding SY, Johnson DK, Adney WS, Nimlos MR, Brady JW et al (2007) Biomass recalcitrance: engineering plants and enzymes for biofuels production. Science 315(5813): 804-807.
16. Hong F, Breitling R, McEntee CW, Wittner BS, Nemhauser JL, Chory J (2006) RankProd: a bioconductor package for detecting differentially expressed genes in meta-analysis. Bioinformatics 22: 2825-2827.
17. Ingvarsson PK, Garcia V, Luquez V, Hall D, Jansson S (2008) Nucleotide polymorphism and phenotypic associations within and around the phytochrome B2 locus in European aspen (Populus tremula, Salicaceae). Genetics 178: 2217-2226.
18. Jaillon O, Aury JM, Wincker P (2009) "Changing by doubling", the impact of whole genome duplications in the evolution of eukaryotes. Comptes Rendus Biologies 332: 241-253.
19. Kalluri UC, Joshi CP (2004) Differential expression patterns of two cellulose synthase genes are associated with primary and secondary cell wall development in aspen trees. Planta 220: 47-55.
20. Leple JC, Dauwe R, Morreel K, Storme V, Lapierre C, Pollet B et al (2007) Downregulation of cinnamoyl-coenzyme A reductase in poplar: multiple-level phenotyping reveals effects on cell wall polymer metabolism and structure. Plant Cell 19: 3669-3691.
21. Persson S, Wei H, Milne J, Page GP, Somerville CR (2005) Identification of genes required for cellulose synthesis by regression analysis of public microarray data sets. Proc Natl Acad Sci USA 102: 8633-8638.
22. Ragauskas AJ, Williams CK, Davison BH, Britovsek G, Cairney J, Eckert CA et al (2006) The path forward for biofuels and biomaterials. Science 311(5760): 484-489.
23. Ralph J, Akiyama T, Kim H, Lu FC, Schatz PF, Marita JM et al (2006) Effects of coumarate 3-hydroxylase down-regulation on lignin structure. J Biol Chem 281: 8843-8853.
24. Ranjan P, Kao YY, Jiang H, Joshi CP, Harding SA, Tsai CJ (2004) Suppression subtractive hybridization-mediated transcriptome analysis from multiple tissues of aspen (Populus tremuloides) altered in phenylpropanoid metabolism. Planta 219: 694-704.
25. Rikke BA, Johnson TE (1998) Towards the cloning of genes underlying murine QTLs. Mamm Genome 9: 963-968.
26. Roberts AW, Bushoven JT (2007) The cellulose synthase (CESA) gene superfamily of the moss Physcomitrella patens. Plant Mol Biol 63: 207-219.
27. Ron M, Weller JI (2007) From QTL to QTN identification in livestock-winning by points rather than knock-out: a review. Anim Genet 38: 429-439.
28. Roth C, Rastogi S, Arvestad L, Dittmar K, Light S, Ekman D et al (2007) Evolution after gene duplication: models, mechanisms, sequences, systems, and organisms. Journal of Experimental Zoology Part B-Molecular and Developmental Evolution 308B: 58-73.
29. Rubin EM (2008) Genomics of cellulosic biofuels. Nature 454(7206): 841-845.
30. Salvi S, Tuberosa R (2005) To clone or not to clone plant QTLs: present and future challenges. Trends Plant Sci 10: 297-304.
31. Semon M, Wolfe KH (2007) Consequences of genome duplication. Curr Opin Genet Dev 17: 505-512.
32. Sykes R, Kodrzycki B, Tuskan G, Foutz K, Davis M (2008) Within tree variability of lignin composition in Populus. Wood Sci Technol 42: 649-661.
33. Tuskan GA, West D, Bradshaw HD, Neale D, Sewell M, Wheeler N et al (1999) Two high-throughput techniques for determining wood properties as part of a molecular genetics analysis of loblolly pine and hybrid poplar. Appl Biochem Biotech 77-79: 1-11.
34. Tuskan GA, Gunter LE, Yang ZMK, Yin TM, Sewell MM, DiFazio SP (2004) Characterization of microsatellites revealed by genomic sequencing of Populus trichocarpa. Can J For Res 34: 85-93.
35. Tuskan GA, DiFazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U et al (2006) The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313: 1596-1604.
36. van de Peer Y (2004) Computational approaches to unveiling ancient genome duplications. Nat Rev, Genet 5: 752-763.
37. Vanholme R, Morreel K, Ralph J, Boerjan W (2008) Lignin engineering. Curr Opin Plant Biol 11: 278-285.
38. van Ooijen JW (2004) MapQTL 5, software for the mapping of quantitative trait loci in experimental populations. Kyazma B. V, Wageningen.
39. Yang XH, Jawdy S, Tschaplinski TJ, Tuskan GA (2009) Genome-wide identification of lineage-specific genes in Arabidopsis, Oryza and Populus. Genomics 93: 473-480.
40. Yin TM, DiFazio SP, Gunter LE, Riemenschneider D, Tuskan GA (2004) Large-scale heterospecific segregation distortion in Populus revealed by a dense genetic map. Theor Appl Genet 109: 451-463.
41. Yin TM, Zhang XY, Gunter LE, Li SX, Wullschleger SD, Huang MR et al (2009) Microsatellite primer resource for Populus developed from the mapped sequence scaffolds of the Nisqually-1 genome. New Phytol 181(2): 498-503.
42. Zhong R, Burk DH, Morrison WH, Ye ZH (2002) A kinesin-like protein is essential for oriented deposition of cellulose microfibrils and cell wall strength. Plant Cell 14: 3101-3117.
43. Zhong R, Demura T, Ye ZH (2006) SND1, a NAC domain transcription factor, is a key regulator of secondary wall synthesis in fibers of Arabidopsis. Plant Cell 18: 3158-3170.