Coordinated genetic regulation of growth and lignin revealed by quantitative trait locus analysis of cDNA microarray data in an interspecific backcross of eucalyptus

Plant Physiology

Volumn 135, Issue 4, 2004, Pages 2368-2378

  Kirst, Matias ^a   Myburg, Alexander A ^b   De León, José P G ^c   Kirst, Mariana E ^a   Scott, Jay ^a   Sederoff, Ronald ^a  

^a NORTH CAROLINA STATE UNIVERSITY   (United States)

^b UNIVERSITY OF PRETORIA   (South Africa)

^c Cía Forestal Oriental S A   (Uruguay)

Author keywords

[No Author keywords available]

Indexed keywords

ENZYMES; GENETIC ENGINEERING; GROWTH KINETICS; LIGNIN; METABOLISM;

GENETIC REGULATION; QUANTITATIVE TRAIT LOCI (QTL); TRANSCRIPTION;

PLANTS (BOTANY);

ENZYMES; EUCALYPTUS; GENETIC ENGINEERING; GROWTH RATE; LIGNINASE; METABOLISM; PLANTS;

EMBRYOPHYTA; EUCALYPTUS; EUCALYPTUS GLOBULUS; EUCALYPTUS GRANDIS;

EID: 4444335600     PISSN: 00320889     EISSN: None     Source Type: Journal    
DOI: 10.1104/pp.103.037960     Document Type: Article

References (68)

1. Anterola AM, Jeon JH, Davin LB, Lewis NG (2002) Transcriptional control of monolignol biosynthesis in Pinus taeda: factors affecting monolignol ratios and carbon allocation in phenylpropanoid metabolism. J Biol Chem 277: 18272-18280
2. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25: 25-29
3. Bassam BJ, Caetano-Anolles G, Gresshoff PM (1991) Fast and sensitive silver staining of DNA in polyacrylamide gels. Anal Biochem 196: 80-83
4. Basten CJ, Weir BS, Zeng Z-B (2000) QTL Cartographer, Version 1.15. A Reference Manual and Tutorial for QTL Mapping. Department of Statistics, North Carolina State University, Raleigh, NC
5. Blount JW, Korth KL, Masoud SA, Rasmussen S, Lamb C, Dixon RA (2000) Altering expression of cinnamic acid 4-hydroxylase in transgenic plants provides evidence for a feedback loop at the entry point into the phenylpropanoid pathway. Plant Physiol 122: 107-116
6. Borevitz JO, Xia YJ, Blount J, Dixon RA, Lamb C (2000) Activation tagging identifies a conserved MYB regulator of phenylpropanoid biosynthesis. Plant Cell 12: 2383-2393
7. Bourquin V, Nishikubo N, Abe H, Brumer H, Denman S, Eklund M, Christiernin M, Teeri TT, Sundberg B, Mellerowicz EJ (2002) Xyloglucan endotransglycosylases have a function during the formation of secondary cell walls of vascular tissues. Plant Cell 14: 3073-3088
8. Bradshaw HD, Stettler RF (1995) Molecular genetics of growth and development in Populus. 4. Mapping QTLs with large effects on growth, form, and phenology traits in a forest tree. Genetics 139: 963-973
9. Brem RB, Yvert G, Clinton R, Kruglyak L (2002) Genetic dissection of transcriptional regulation in budding yeast. Science 296: 752-755
10. Buchanan BB, Gruissem W, Jones RL, editors (2000) Biochemistry and Molecular Biology of Plants. American Society of Plant Physiologists, Rockville, MD
11. Byrne M, Murrell JC, Owen JV, Kriedemann P, Williams ER, Moran GF (1997) Identification and mode of action of quantitative trait loci affecting seedling height and leaf area in Eucalyptus nitens. Theor Appl Genet 94: 674-681
12. Chang S, Puryear J, Cairney J (1993) A simple and efficient method for isolating RNA from pine trees. Plant Mol Biol Rep 11: 117-121
13. Churchill GA (2002) Fundamentals of experimental design for cDNA microarrays. Nat Genet (Suppl) 32: 490-495
14. Churchill GA, Doerge RW (1994) Empirical threshold values for quantitative trait mapping. Genetics 138: 963-971
15. Darley CP, Forrester AM, McQueen-Mason SJ (2001) The molecular basis of plant cell wall extension. Plant Mol Biol 47: 179-195
16. Doerge RW, Churchill GA (1996) Permutation tests for multiple loci affecting a quantitative character. Genetics 142: 285-294
17. Eaves IA, Wicker LS, Ghandour G, Lyons PA, Peterson LB, Todd JA, Glynne RJ (2002) Combining mouse congenic strains and microarray gene expression analyses to study a complex trait: the NOD model of type 1 diabetes. Genome Res 12: 232-243
18. Eisen MB, Spellman PT, Brown PO, Botstein D (1998) Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 95: 14863-14868
19. Emebiri LC, Devey ME, Matheson AC, Slee MU (1998) Interval mapping of quantitative trait loci affecting NESTUR, a stem growth efficiency index of radiata pine seedlings. Theor Appl Genet 97: 1062-1068
20. Flint J, Mott R (2001) Finding the molecular basis of quantitative traits: successes and pitfalls. Nat Rev Genet 2: 437-445
21. Franke R, McMichael CM, Meyer K, Shirley AM, Cusumano JC, Chapple C (2000) Modified lignin in tobacco and poplar plants overexpressing the Arabidopsis gene encoding ferulate 5-hydroxylase. Plant J 22: 223-234
22. Fukuda H (1996) Xylogenesis: initiation, progression, and cell death. Annu Rev Plant Physiol Plant Mol Biol 47: 299-325
23. Glazier AM, Nadeau JH, Aitman TJ (2002) Finding genes that underlie complex traits. Science 298: 2345-2349
24. Grattapaglia D, Bertolucci FLG, Penchel R, Sederoff RR (1996) Genetic mapping of quantitative trait loci controlling growth and wood quality traits in Eucalyptus grandis using a maternal half-sib family and RAPD markers. Genetics 144: 1205-1214
25. Gregory RA, Wilson BF (1968) A comparison of cambial activity of white spruce in Alaska and New England. Can J Bot 46: 733-734
26. Guillet G, Poupart J, Basurco J, De Luca V (2000) Expression of tryptophan decarboxylase and tyrosine decarboxylase genes in tobacco results in altered biochemical and physiological phenotypes. Plant Physiol 122: 933-943
27. Harmer SL, Hogenesch LB, Straume M, Chang HS, Han B, Zhu T, Wang X, Kreps JA, Kay SA (2000) Orchestrated transcription of key pathways in Arabidopsis by the circadian clock. Science 290: 2110-2113
28. Hegde P, Qi R, Abernathy K, Gay C, Dharap S, Gaspard R, Hughes JE, Snesrud E, Lee N, Quackenbush J (2000) A concise guide to cDNA microarray analysis. Biotechniques 29: 548-550
29. Hu WJ, Harding SA, Lung J, Popko JL, Ralph J, Stokke DD, Tsai CJ, Chiang VL (1999) Repression of lignin biosynthesis promotes cellulose accumulation and growth in transgenic trees. Nat Biotechnol 17: 808-812
30. Jin W, Riley RM, Wolfinger RD, White KP, Passador-Gurgel G, Gibson G (2001) The contributions of sex, genotype and age to transcriptional variance in Drosophila melanogaster. Nat Genet 29: 389-395
31. Kaar WE, Brink DL (1991) Simplified analysis of acid-soluble lignin. J Wood Chem Technol 11: 465-477
32. Kao CH, Zeng ZB, Teasdale RD (1999) Multiple interval mapping for quantitative trait loci. Genetics 152: 1203-1216
33. Karp CL, Grupe A, Schadt E, Ewart SL, Keane-Moore M, Cuomo PJ, Kohl J, Wahl L, Kuperman D, Germer S, et al (2000) Identification of complement factor 5 as a susceptibility locus for experimental allergic asthma. Nat Immunol 1: 221-226
34. Kaya Z, Sewell MM, Neale DB (1999) Identification of quantitative trait loci influencing annual height- and diameter-increment growth in loblolly pine (Pinus taeda L.). Theor Appl Genet 98: 586-592
35. Kirst M (2004) Transcription Regulation and Plant Diversity. PhD thesis. North Carolina State University, Raleigh, NC (http://www.lib.ncsu. edu/theses/available/etd-01042004-175350/)
36. Korstanje R, Paigen B (2002) From QTL to gene: the harvest begins. Nat Genet 31: 235-236
37. Li L, Zhou YH, Cheng XF, Sun JY, Marita JM, Ralph J, Chiang VL (2003) Combinatorial modification of multiple lignin traits in trees through multigene cotransformation. Proc Natl Acad Sci USA 100: 4939-4944
38. Li LG, Popko JL, Umezawa T, Chiang VL (2000) 5-Hydroxyconiferyl aldehyde modulates enzymatic methylation for syringyl monolignol formation, a new view of monolignol biosynthesis in angiosperms. J Biol Chem 275: 6537-6545
39. Lu FC, Ralph J (1997) Derivatization followed by reductive cleavage (DFRC method), a new method for lignin analysis: protocol for analysis of DFRC monomers. J Agric Food Chem 45: 2590-2592
40. Maruya E, Saji H, Yokoyama S (1996) PCR-LIS-SSCP (low ionic strength single-stranded conformation polymorphism): a simple method for high-resolution allele typing of HLA-DRB1, -DQB1, and -DPB1. Genome Res 6: 51-57
41. Mellerowicz EJ, Baucher M, Sundberg B, Boerjan W (2001) Unravelling cell wall formation in the woody dicot stem. Plant Mol Biol 47: 239-274
42. Meyer K, Cusumano JC, Somerville C, Chapple CCS (1996) Ferulate-5-hydroxylase from Arabidopsis thaliana defines a new family of cytochrome P450-dependent monooxygenases. Proc Natl Acad Sci USA 93: 6869-6874
43. Mobley EM, Kunkel BN, Keith B (1999) Identification, characterization and comparative analysis of a novel chorismate mutase gene in Arabidopsis thaliana. Gene 240: 115-123
44. Morgante M, Salamini F (2003) From plant genomics to breeding practice. Curr Opin Biotechnol 14: 214-219
45. Myburg AA (2001) Genetic Architecture of Hybrid Fitness and Wood Quality Traits in a Wide Interspecific Cross of Eucalyptus Tree Species. PhD thesis. North Carolina State University, Raleigh, NC (http://www.lib.ncsu.edu/theses/ available/etd-20010723-175234/)
46. 1 hybrid based on a double pseudo-backcross mapping approach. Theor Appl Genet 107: 1028-1042
47. Neter J, Kunter MH, Nachtshein CJ, Wasserman W (1996) Applied Linear Statistical Models, Ed 4. WCB/McGraw-Hill, Chicago
48. Ogino T, Garner C, Markley JL, Herrmann KM (1982) Biosynthesis of aromatic compounds - C13 NMR spectroscopy of whole Escherichia coli cells. Proc Natl Acad Sci USA 79: 5828-5832
49. Patzlaff A, McInnis S, Courtenay A, Surman C, Newman LJ, Smith C, Bevan MW, Mansfield S, Whetten RW, Sederoff RR, et al (2003) Characterisation of a pine MYB that regulates lignification. Plant J 36: 743-754
50. Plomion C, Durel CE, O'Malley DM (1996) Genetic dissection of height in maritime pine seedlings raised under accelerated growth conditions. Theor Appl Genet 93: 849-858
51. Sarkanen KV, Chang H-M, Allan GG (1967) Species variation in lignins. 3. Hardwood lignins. Tappi 50: 587-590
52. Schadt EE, Monks SA, Drake TA, Lusis AJ, Che N, Colinayo V, Ruff TG, Milligan SB, Lamb JR, Cavet G, et al (2003) Genetics of gene expression surveyed in maize, mouse and man. Nature 422: 297-302
53. Schena M, Shalon D, Davis RW, Brown PO (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270: 467-470
54. Shen B, Li CJ, Tarczynski MC (2002) High free methionine and decreased lignin content result from a mutation in the Arabidopsis S-adenosyl-L-methionine synthetase 3 gene. Plant J 29: 371-380
55. Suzuki Y, Orita M, Shiraishi M, Hayashi K, Sekiya T (1990) Detection of Ras gene mutations in human lung cancers by single-strand conformation polymorphism analysis of polymerase chain reaction products. Oncogene 5: 1037-1043
56. Uggla C, Mellerowicz EJ, Sundberg B (1998) Indole-3-acetic acid controls cambial growth in Scots pine by positional signaling. Plant Physiol 117: 113-121
57. Verhaegen D, Plomion C, Gion JM, Poitel M, Costa P, Kremer A (1997) Quantitative trait dissection analysis in Eucalyptus using RAPD markers. 1. Detection of QTL in interspecific hybrid progeny, stability of QTL expression across different ages. Theor Appl Genet 95: 597-608
58. Wayne ML, McIntyre LM (2002) Combining mapping and arraying: an approach to candidate gene identification. Proc Natl Acad Sci USA 99: 14903-14906
59. Weng C, Kubisiak TL, Nelson CD, Stine M (2002) Mapping quantitative trait loci controlling early growth in a (longleaf pine x slash pine) x slash pine BC1 family. Theor Appl Genet 104: 852-859
60. Wilson BF, Howard RA (1968) A computer model for cambial activity. Forest Sci 14: 77-90
61. Wolfinger RD, Gibson G, Wolfinger ED, Bennett L, Hamadeh H, Bushel P, Afshari C, Paules RS (2001) Assessing gene significance from cDNA microarray expression data via mixed models. J Comput Biol 8: 625-637
62. Wu RL (1998) Genetic mapping of QTLs affecting tree growth and architecture in Populus: implication for ideotype breeding. Theor Appl Genet 96: 447-457
63. Wu RL, Remington DL, MacKay JJ, McKeand SE, O'Malley DM (1999) Average effect of a mutation in lignin biosynthesis in loblolly pine. Theor Appl Genet 99: 705-710
64. Wullschleger SD, Difazio SP (2003) Emerging use of gene expression microarrays in plant physiology. Comp Funct Genom 4: 216-224
65. Yvert G, Brem RB, Whittle J, Akey JM, Foss E, Smith EN, Mackelprang R, Kruglyak L (2003) Trans-acting regulatory variation in Saccharomyces cerevisiae and the role of transcription factors. Nat Genet 35: 57-64
66. Zeng ZB (1993) Theoretical basis for separation of multiple linked gene effects in mapping quantitative trait loci. Proc Natl Acad Sci USA 90: 10972-10976
67. Zeng ZB (1994) Precision mapping of quantitative trait loci. Genetics 136: 1457-1468
68. Zobel BJ, van Buijtenen JP (1989) Wood variation. Springer-Verlag, Heidelberg