Seasonal reorganization of the xylem transcriptome at different tree ages reveals novel insights into wood formation in Pinus radiata

New Phytologist

Volumn 187, Issue 3, 2010, Pages 764-776

  Li, Xinguo ^a   Wu, Harry X ^a   Southerton, Simon G ^a  

^a CSIRO   (Australia)

Author keywords

Earlywood; Latewood; Microarrays; Pinus radiata; Seasonal change; SilviScan; Transcriptome profiling; Wood development

Indexed keywords

MESSENGER RNA;

AGE; CONIFEROUS TREE; GENETIC ANALYSIS; MATURATION; PHYSIOLOGICAL RESPONSE; RNA; SEASONAL VARIATION; WOOD; XYLEM;

ARTICLE; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; GROWTH, DEVELOPMENT AND AGING; METABOLISM; PINE; PLANT GENE; SEASON; TREE; WOOD; XYLEM;

GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENE EXPRESSION REGULATION, PLANT; GENES, PLANT; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PINUS; RNA, MESSENGER; SEASONS; TREES; WOOD; XYLEM;

PINUS RADIATA;

EID: 77954887058     PISSN: 0028646X     EISSN: 14698137     Source Type: Journal    
DOI: 10.1111/j.1469-8137.2010.03333.x     Document Type: Article

References (54)

1. Anderssen RS, Wu Y, Dolferus R, Saunders I. An a posteriori strategy for enhancing gene discovery in anonymous cDNA microarray experiments. Bioinformatics 2004, 20:1721-1727.
2. Aspeborg H, Schrader J, Coutinho PM, Stam M, Kallas A, Djerbi S, Nilsson P, Denman S, Amini B, Sterky F. Carbohydrate-active enzymes involved in the secondary cell wall biogenesis in hybrid aspen. Plant Physiology 2005, 137:983-997.
3. Baldi P, Long AD. A Bayesian framework for the analysis of microarray expression data: regularized t-test and statistical inferences of gene changes. Bioinformatics 2001, 17:509-519.
4. Bertaud F, Holmbom B. Chemical composition of earlywood and latewood in Norway spruce heartwood, sapwood and transition zone wood. Wood Science and Technology 2004, 38:245-256.
5. An automated EST sequence management and functional annotation system. http://bc02.iis.sinica.edu.tw/bio301/, In.
6. Cannon CH, Kua CS, Lobenhofer EK, Hurban P. Capturing genomic signatures of DNA sequence variation using a standard anonymous microarray platform. Nucleic Acids Research 2006, 34:e121.
7. Chang SJ, Puryear J, Cairney J. A simple and efficient method for isolating RNA from pine trees. Plant Molecular Biology Reporter 1993, 11:113-116.
8. Domec JC, Gartner BL. How do water transport and water storage differ in coniferous earlywood and latewood? Journal of Experimental Botany 2002, 53:2369-2379.
9. Donaldson L, Vuocolo T, Gray C, Strandberg Y, Reverter A, McWilliam S, Wang YH, Byrne K, Tellam R. Construction and validation of a bovine innate immune microarray. BMC Genomics 2005, 6:135.
10. Egertsdotter U, van Zyl LM, MacKay J, Peter G, Kirst M, Clark C, Whetten R, Sederoff R. Gene expression during formation of earlywood and latewood in loblolly pine: expression profiles of 350 genes. Plant Biology 2004, 6:654-663.
11. Evans R. Rapid measurement of the transverse dimensions of tracheids in radial wood sections from Pinus radiata. Holzforschung 1994, 48:168-172.
12. Evans R, Stringer S, Kibblewhite RP. Variation of microfibril angle, density and fibre orientation in twenty-nine Eucalyptus nitens trees. Appita Journal 2000, 53:450-457.
13. Gapare WJ, Wu HX, Abarquez A. Genetic control of the time of transition from juvenile to mature wood in Pinus radiata D. Don. Annals of Forest Science 2006, 63:871-878.
14. Gion JM, Lalanne C, Le Provost G, Ferry-Dumazet H, Paiva J, Chaumeil P, Frigerio JM, Brach J, Barre A, de Daruvar A. The proteome of maritime pine wood forming tissue. Proteomics 2005, 5:3731-3751.
15. Hayward RE, DeRisi JL, Alfadhli S, Kaslow DC, Brown PO, Rathod PK. Shotgun DNA microarrays and stage-specific gene expression in Plasmodium falciparum malaria. Molecular Microbiology 2000, 35:6-14.
16. Hegarty MJ, Jones JM, Wilson ID, Barker GL, Coghill JA, Sanchez-Baracaldo P, Liu GQ, Buggs RJA, Abbott RJ, Edwards KJ. Development of anonymous cDNA microarrays to study changes to the Senecio floral transcriptome during hybrid speciation. Molecular Ecology 2005, 14:2493-2510.
17. Hou HW, Zhou YT, Mwange KN, Li WF, He XQ, Cui KM. ABP1 expression regulated by IAA and ABA is associated with the cambium periodicity in Eucommia ulmoides Oliv. Journal of Experimental Botany 2006, 57:3857-3867.
18. Huang DW, Sherman BT, Tan Q, Collins JR, Alvord WG, Roayaei J, Stephens R, Baseler MW, Lane HC, Lempicki RA. The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists. Genome Biology 2007a, 8:R183.
19. Huang DW, Sherman BT, Tan Q, Kir J, Liu D, Bryant D, Guo Y, Stephens R, Baseler MW, Lane HC. DAVID bioinformatics resources: expanded annotation database and novel algorithms to better extract biology from large gene lists. Nucleic Acids Research 2007b, 35:W169-W175.
20. Israelsson M, Sundberg B, Moritz T. Tissue-specific localization of gibberellins and expression of gibberellin-biosynthetic and signaling genes in wood-forming tissues in aspen. Plant Journal 2005, 44:494-504.
21. Ivkovich M, Namkoong G, Koshy M. Genetic variation in wood properties of interior spruce. II. Tracheid characteristics. Canadian Journal of Forest Research 2002, 32:2128-2139.
22. Jorstad TS, Midelfart H, Bones AM. A mixture model approach to sample size estimation in two-sample comparative microarray experiments. BMC Bioinformatics 2008, 9:117.
23. Kammenga JE, Herman MA, Ouborg NJ, Johnson L, Breitling R. Microarray challenges in ecology. Trends in Ecology and Evolution 2007, 22:273-279.
24. Kapushesky M, Kemmeren P, Culhane AC, Durinck S, Ihmels J, Korner C, Kull M, Torrente A, Sarkans U, Vilo J. Expression Profiler: next generation-an online platform for analysis of microarray data. Nucleic Acids Research 2004, 32:W465-W470.
25. Koubaa A, Zhang SYT, Makni S. Defining the transition from earlywood to latewood in black spruce based on intra-ring wood density profiles from X-ray densitometry. Annals of Forest Science 2002, 59:511-518.
26. Larsson O, Wahlestedt C, Timmons JA. Considerations when using the significance analysis of microarrays (SAM) algorithm. BMC Bioinformatics 2005, 6:129.
27. Lehnert SA, Wang YH, Byrne KA. Development and application of a bovine cDNA microarray for expression profiling of muscle and adipose tissue. Australian Journal of Experimental Agriculture 2004, 44:1127-1133.
28. Li X, Wu HX, Dillon SK, Southerton SG. Generation and analysis of expressed sequence tags from six developing xylem libraries in Pinus radiata D. Don. BMC Genomics 2009, 10:41.
29. MacMillan CP, Mansfield SD, Stachurski ZH, Evans R, Southerton SG. Fasciclin-like arabinogalactan proteins: specialization for stem biomechanics and cell wall architecture in Arabidopsis and eucalyptus. Plant Journal 2010, 62:689-703.
30. Montaner D, Tarraga J, Huerta-Cepas J, Burguet J, Vaquerizas JM, Conde L, Minguez P, Vera J, Mukherjee S, Valls J. Next station in microarray data analysis: GEPAS. Nucleic Acids Research 2006, 34:W486-W491.
31. Moyle R, Schrader J, Stenberg A, Olsson O, Saxena S, Sandberg G, Bhalerao RP. Environmental and auxin regulation of wood formation involves members of the Aux/IAA gene family in hybrid Aspen. Plant Journal 2002, 31:675-685.
32. Mwange KN, Hou HW, Wang YQ, He XQ, Cui KM. Opposite patterns in the annual distribution and time-course of endogenous abscisic acid and indole-3-acetic acid in relation to the periodicity of cambial activity in Eucommia ulmoides Oliv. Journal of Experimental Botany 2005, 56:1017-1028.
33. Nilsson J, Karlberg A, Antti H, Lopez-Vernaza M, Mellerowicz E, Perrot-Rechenmann C, Sandberg G, Bhalerao RP. Dissecting the molecular basis of the regulation of wood formation by auxin in hybrid aspen. Plant Cell 2008, 20:843-855.
34. Paiva JAP, Garnier-Gere PH, Rodrigues JC, Alves A, Santos S, Graca J, Le Provost G, Chaumeil P, Da Silva-Perez D, Bosc A. Plasticity of maritime pine (Pinus pinaster) wood-forming tissues during a growing season. New Phytologist 2008, 179:1080-1094.
35. Park S, Keathley DE, Han KH. Transcriptional profiles of the annual growth cycle in Populus deltoides. Tree Physiology 2008, 28:321-329.
36. Pawitan Y, Michiels S, Koscielny S, Gusnanto A, Ploner A. False discovery rate, sensitivity and sample size for microarray studies. Bioinformatics 2005, 21:3017-3024.
37. Provost Gl, Paiva J, Pot D, Brach J, Plomion C. Seasonal variation in transcript accumulation in wood-forming tissues of maritime pine (Pinus pinaster Ait.) with emphasis on a cell wall glycine-rich protein. Planta 2003, 217:820-830.
38. Qiu D, Wilson IW, Gan S, Washusen R, Moran GF, Southerton SG. Gene expression in Eucalyptus branch wood with marked variation in cellulose microfibril orientation and lacking G-layers. New Phytologist 2008, 179:94-103.
39. Robert HS, Friml J. Auxin and other signals on the move in plants. Nature Chemical Biology 2009, 5:325-332.
40. Schouten JP, McElgunn CJ, Waaijer R, Zwijnenburg D, Diepvens F, Pals G. Relative quantification of 40 nucleic acid sequences by multiplex ligation-dependent probe amplification. Nucleic Acids Research 2002, 30:e57.
41. Shamir R, Maron-Katz A, Tanay A, Linhart C, Steinfeld I, Sharan R, Shiloh Y, Elkon R. EXPANDER - An integrative program suite for microarray data analysis. BMC Bioinformatics 2005, 6:232.
42. Sharan R, Maron-Katz A, Shamir R. CLICK and EXPANDER: a system for clustering and visualizing gene expression data. Bioinformatics 2003, 19:1787-1799.
43. Skene DS. The period of time taken by cambial derivatives to grow and differentiate into tracheids in Pinus radiata D. Don. Annals of Botany 1969, 33:254-262.
44. Sundberg B, Little CHA, Cui K, Sandberg G. Level of endogenous indole-3-acetic-acid in the stem of Pinus sylvestris in relation to the seasonal variation of cambial activity. Plant, Cell & Environment 1991, 14:241-246.
45. Tarraga J, Medina I, Carbonell J, Huerta-Cepas J, Minguez P, Alloza E, Al-Shahrour F, Vegas-Azcarate S, Goetz S, Escobar P. GEPAS, a web-based tool for microarray data analysis and interpretation. Nucleic Acids Research 2008, 36:W308-W314.
46. Tusher VG, Tibshirani R, Chu G. Significance analysis of microarrays applied to the ionizing radiation response. Proceedings of the National Academy of Sciences, USA 2001, 98:5116-5121.
47. Uggla C, Magel E, Moritz T, Sundberg B. Function and dynamics of auxin and carbohydrates during earlywood/latewood transition in Scots pine. Plant Physiology 2001, 125:2029-2039.
48. Uggla C, Mellerowicz EJ, Sundberg B. Indole-3-acetic acid controls cambial growth in Scots pine by positional signaling. Plant Physiology 1998, 117:113-121.
49. Utsumi Y, Sano Y, Funada R, Ohtani J, Fujikawa S. Seasonal and perennial changes in the distribution of water in the sapwood of conifers in a sub-frigid zone. Plant Physiology 2003, 131:1826-1833.
50. Wintz H, Yoo LJ, Loguinov A, Wu YY, Steevens JA, Holland RD, Beger RD, Perkins EJ, Hughes O, Vulpe CD. Gene expression profiles in fathead minnow exposed to 2,4-DNT: correlation with toxicity in mammals. Toxicological Sciences 2006, 94:71-82.
51. Wu HX, Eldridge KG, Matheson AC, Powell MP, McRae TA. Achievement in forest tree improvement in Australia and New Zealand 8. Successful introduction and breeding of radiata pine to Australia. Australian Forestry 2007, 70:215-225.
52. Wu YG, Rozenfeld S, Defferrard A, Ruggiero K, Udall JA, Kim H, Llewellyn DJ, Dennis ES. Cycloheximide treatment of cotton ovules alters the abundance of specific classes of mRNAs and generates novel ESTs for microarray expression profiling. Molecular Genetics and Genomics 2005, 274:477-493.
53. Yang SH, Loopstra CA. Seasonal variation in gene expression for loblolly pines (Pinus taeda) from different geographical regions. Tree Physiology 2005, 25:1063-1073.
54. Yang SH, Wang HY, Sathyan P, Stasolla C, Loopstra CA. Real-time RT-PCR analysis of loblolly pine (Pinus taeda) arabinogalactan-protein and arabinogalactan-protein-like genes. Physiologia Plantarum 2005, 124:91-106.