Association genetics of wood physical traits in the conifer white spruce and relationships with gene expression

Genetics

Volumn 188, Issue 1, 2011, Pages 197-214

  Beaulieu, Jean ^a,b   Doerksen, Trevor ^a,b   Boyle, Brian ^b   Clément, Sébastien ^a   Deslauriers, Marie ^a   Beauseigle, Stéphanie ^b   Blais, Sylvie ^b   Poulin, Pier Luc ^b   Lenz, Patrick ^b   Caron, Sébastien ^b   Rigault, Philippe ^c   Bicho, Paul ^d   Bousquet, Jean ^b   Mackay, John ^b  

^a NATURAL RESOURCES CANADA   (Canada)

^b UNIVERSITÉ LAVAL   (Canada)

^c Gydle Inc   (Canada)

^d FPINNOVATIONS   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

1 AMINOCYCLOPROPANE 1 CARBOXYLATE OXIDASE; CARBOXYLIC ACID DERIVATIVE; LONG CHAIN ACYL COA SYNTHETASE 9; LONG CHAIN FATTY ACID COENZYME A LIGASE; UNCLASSIFIED DRUG;

ARTICLE; BREEDING; DOMINANT GENE; GENE EXPRESSION; GENETIC ASSOCIATION; GENETIC TRAIT; GENOTYPE; KIN SELECTION; MARKER GENE; MULTIGENE FAMILY; NONHUMAN; PHENOTYPIC VARIATION; PLANT DEVELOPMENT; POPULATION STRUCTURE; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; SPECIES DIFFERENCE; WHITE SPRUCE;

CLUSTER ANALYSIS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENES, PLANT; GENETIC ASSOCIATION STUDIES; GENOTYPE; LINKAGE DISEQUILIBRIUM; PICEA; POLYMORPHISM, SINGLE NUCLEOTIDE; POPULATION DYNAMICS; QUANTITATIVE TRAIT, HERITABLE; RNA, MESSENGER; WOOD;

CONIFEROPHYTA; PICEA GLAUCA;

EID: 79955930975     PISSN: 00166731     EISSN: 00166731     Source Type: Journal    
DOI: 10.1534/genetics.110.125781     Document Type: Article

References (135)

1. Alden, J., and C. Loopstra, 1987 Genetic diversity and population structure of Picea glauca on an altitudinal gradient in interior Alaska. Can. J. For. Res. 17: 1519-1526.
2. Andersson-Gunneras, S., E. J. Mellerowicz, J. Love, B. Segerman, Y. Ohmiya et al., 2006 Biosynthesis of cellulose-enriched tension wood in Populus: global analysis of transcripts and metabolites identifies biochemical and developmental regulators in secondary wall biosynthesis. Plant J. 45: 144-165.
3. Aspeborg, H., J. Schrader, P. M. Countinho, M. Stam, A. Kallas et al., 2005 Carbohydrate-active enzymes involved in the secondary cell wall biogenesis in hybrid aspen. Plant Physiol. 137: 983-997.
4. Beaulieu, J., 2003 Genetic variation in tracheid length and relationships with growth and wood traits in eastern white spruce (Picea glauca). Wood Fib. Sci. 35: 609-616.
5. Bedon, F., J. Grima-Pettenati and J. Mackay, 2007 Conifer R2R3-MYB transcription factors: sequence analyses and gene expression in wood-forming tissues of white spruce (Picea glauca). BMC Plant Biol. 7: 17.
6. Benjamini, Y., and Y. Hochberg, 1995 Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. B 57: 289-300.
7. Bomal, C., F. Bedon, S. Caron, S. D. Mansfield, C. Levasseur et al., 2008 Involvement of Pinus taeda MYB1 and MYB8 in phenyl-propanoid metabolism and secondary cell wall biogenesis: a comparative in planta analysis. J. Exp. Bot. 59: 3925-3939.
8. Boyle, B., N. Dallaire and J. MacKay, 2009 Evaluation of the impact of single nucleotide polymorphisms and primer mismatches on quantitative PCR. BMC Biotechnol. 9: 75.
9. Bousquet, J., N. Isabel, B. Pelgas, J. Cottrell, D. Rungis et al., 2007 Spruce, pp. 93-114 in Forest Trees (Genome Mapping and Molecular Breeding in Plants, Vol. 7), edited by C. Kole. Springer-Verlag, Berlin.
10. Bradshaw, H. D., and R. F. Stettler, 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.
11. Breseghello, F., and M. E. Sorrells, 2006 Association analysis as a strategy for improvement of quantitative traits in plants. Crop Sci. 46: 1323-1330.
12. Brown, G. R., D. L. Bassoni, G. P. Gill, J. R. Fontana, N. C. Wheeler et al., 2003 Identification of quantitative trait loci influencing wood property traits in loblolly pine (Pinus taeda L.). III. QTL verification and candidate gene mapping. Genetics 164: 1537-1546.
13. Calus, M. P. L., T. H. E. Meuwissen, A. P. W. de Roos and R. F. Veerkamp, 2008 Accuracy of genomic selection using different methods to define haplotypes. Genetics 178: 553-561.
14. Cato, S., L. McMillan, L. Donaldson, T. Richardson, C. Echt et al., 2006 Wood formation from the base to the crown in Pinus radiata: gradients of tracheid wall thickness, wood density, radial growth rate and gene expression. Plant Mol. Biol. 60: 565-581.
15. Cavalier, D. M., O. Lerouxel, L. Neumetzler, K. Yamauchi, A. Reinecke et al., 2008 Disrupting two Arabidopsis thaliana xylosyl-transferase genes results in plants deficient in xyloglucan, a major primary cell wall component. Plant Cell 20: 1519-1537.
16. Chamary, J. V., and L. D. Hurst, 2009 The price of silent mutations. Sci. Am. 300(6): 46-53.
17. Chang, S., J. Puryear and J. Cairney, 1993 Simple and efficient method for isolating RNA from pine trees. Plant Mol. Biol. Rep. 11: 113-116.
18. Cheung, V. G., R. S. Spielman, K. G. Ewens, T. M. Weber, M. Morley et al., 2005 Mapping determinants of human gene expression by regional and genome-wide association. Nature 437: 1365-1369.
19. Corriveau, A., J. Beaulieu and G. Daoust, 1991 Heritability and genetic correlations of wood characters of Upper Ottawa Valley white spruce populations grown in Quebec. For. Chron. 67: 698-705.
20. Dillon, S. K., M. Nolan, W. Li, C. Bell, H. X. Wu et al., 2010 Allelic variation in cell wall candidate genes affecting solid wood properties in natural populations and land races of Pinus radiata. Genetics 185: 1477-1487.
21. Eckardt, N. A., 2008 Role of xyloglucan in primary cell walls. Plant Cell 20: 1421-1422.
22. Eckert, A. J., A. D. Bower, J. L. Wegrzyn, B. Pande, K. D. Jermstad et al., 2009 Association genetics of coastal Douglas fir (Pseudot-suga menziesii var. menziesii, Pinaceae). I. Cold-hardiness related traits. Genetics 182: 1289-1302.
23. Egertsdotter, U., L. Van Zyl, J. Mackay, R. Whetten, G. Peter et al., 2004 Gene expression profiling during formation of ear-lywood and latewood in loblolly pine: expression profiles of 350 genes. Plant Biol. 6: 654-663.
24. Evans, R., and J. Ilic, 2001 Rapid prediction of wood stiffness from microfibril angle and density. For. Prod. J. 51: 53-57.
25. Falush, D., M. Stephens and J. K. Pritchard, 2003 Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164: 1567-1587.
26. Fan, J.-B., A. Oliphant, R. Shen, B. G. Kermani, F. Garcia et al., 2003 Highly parallel SNP genotyping. Cold Spring Harbor Symp. Quant. Biol. 68: 69-78.
27. Fisher, K., and S. Turner, 2007 PXY, a receptor-like kinase essential for maintaining polarity during plant vascular-tissue development. Curr. Biol. 17: 1061-1066.
28. Frontier, S., 1976 Study of the decrease of eigenvalues in a principal component analysis: comparison with the broken stick model. J. Exp. Mar. Biol. Ecol. 25: 67-75 (in French).
29. Fulda, M., E. Heinz and F. P. Wolter, 1997 Brassica napus cDNAs encoding fatty acyl-CoA synthetase. Plant Mol. Biol. 33: 911-922.
30. Furnier, G. R., and M. Stine, 1995 Interpopulation differentiation of nuclear and chloroplast loci in white spruce. Can. J. For. Res. 25: 736-742.
31. Gallo De Carvalho, M. C. D. C., D. G. G. Caldas, R. T. Carneiro, D. H. Moon, G. R. Salvatierra et al., 2008 SAGE transcript profiling of the juvenile cambial region of Eucalyptus grandis. Tree Physiol. 28: 905-919.
32. Geisler-Lee, J., M. Geisler, P. M. Countinho, B. Segerman, N. Nishikubo et al., 2006 Poplar carbohydrate-active enzymes. Gene identification and expression analyses. Plant Physiol. 140: 946-962.
33. Girke, T., J. Lauricha, H. Tran, K. Keegstra and N. Raikhel, 2004 The cell wall navigator database. A systems-based ap proach to organism-unrestricted mining of protein families in volved in cell wall metabolism. Plant Physiol. 136: 3003-3008.
34. Goddard, M. E., and B. J. Hayes, 2009 Mapping genes for complex traits in domestic animals and their use in breeding programmes. Nat. Rev. Genet. 10: 381-391.
35. Goicoechea, M., E. Lacombe, S. Legay, S. Mihaljevic, P. Rech et al., 2005 EgMYB2, a new transcriptional activator from Eucalyptus xylem, regulates secondary cell wall formation and lignin biosynthesis. Plant J. 43: 553-567.
36. González-Martínez, S. C., N. C. Wheeler, E. Ersoz, C. D. Nelson and D. B. Neale, 2007 Association genetics in Pinus taeda L. I. Wood property traits. Genetics 175: 399-409.
37. Grattapaglia, D., and M. V. D. Resende, 2011 Genomic selection in forest tree breeding. Tree Genet. Genomes 7: 241-255.
38. Grattapaglia, D., F. L. G. Bertolucci, R. Penchel and R. R. Sederoff, 1996 Genetic mapping of qunatitative trait loci controlling growth and wood quality traits in Eucalyptus grandis using a maternal half-sib family and RAPD markers. Genetics 144: 1205-1214.
39. Grattapaglia, D., C. Plomion, M. Kirst and R. R. Sederoff, 2009 Genomics of growth traits in forest trees. Curr. Opin. Plant Biol. 12: 148-156.
40. Groover, A., 2005 What genes make a tree a tree? Trends Plant Sci. 10: 210-214.
41. Groover, A., M. Devey, T. Fiddler, J. Lee, R. Megraw et al., 1994 Identification of quantitative trait loci influencing wood specific gravity in an outbred pedigree of loblolly pine. Genetics 138: 1293-1300.
42. Guglielmino, N., M. Libermann, A. M. Catesson, A. Mareck, R. Prat et al., 1996 Pectin methylesterases from poplar cambium and inner bark: localization, properties and seasonal changes. Planta 202: 70-75.
43. Hardy, O. J., and X. Vekemans, 2002 SPAGeDi: a versatile computer program to analyse spatial genetic structure at the individual or population levels. Mol. Ecol. Notes 2: 618-620.
44. Haussmann, B. I. G., H. K. Parzies, T. Presterl, Z. Sušić and T. Miedaner, 2004 Plant genetic resources in crop improvement. Plant Genet. Resour. 2: 3-21.
45. Hayashi, T., and R. Kaida, 2011 Functions of xyloglucan in plant cells. Mol. Plant 4: 17-24.
46. Hill, W. G., and B. S. Weir, 1988 Variances and covariances of squared linkage disequilibria in finite populations. Theor. Popul. Biol. 22: 54-78.
47. Hirschhorn, J. N., K. Lohmueller, B. Edwards and K. Hirschhorn, 2002 A comprehensive review of genetic association studies. Genet. Med. 4: 45-61.
48. Holliday, J. A., K. Ritland and S. N. Aitken, 2010 Widespread, ecologically relevant genetic markers developed from association mapping of climate-related traits in Sitka spruce (Picea sitchensis). New Phytol. 188: 501-514.
49. Huertz, M., E. De Paoli, T. Källman, H. Larsson, I. Jurman et al., 2006 Multilocus patterns of nucleotide diversity, linkage disequilibrium and demographic history of Norway Spruce [Picea abies (L.) Karst]. Genetics 174: 2095-2105.
50. Ichinose, H., N. Nishikubo, T. Demura and S. Kanako, 2010 Characterization of a-L-arabinofuranosidase related to the secondary cell walls formation in Arabidopsis thaliana. Plant Biotechnol. 27: 259-266.
51. Ingvarsson, P., M. V. Garcia, V. Luquez, D. Hall and S. Jansson, 2008 Nucleotide polymorphism and phenotypic associations within and around the phytochrome B2 locus in European aspen (Populus tremula, Salicaceae). Genetics 178: 2217-2226.
52. Jakobsson, M., and N. A. Rosenberg, 2007 CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioin-formatics 23: 1801-1806.
53. Jaramillo-Correa, J. P., J. Beaulieu and J. Bousquet, 2001 Contrasting evolutionary forces driving population structure at expressed sequence tag polymorphisms, allozymes and quantitative traits in white spruce. Mol. Ecol. 10: 2729-2740.
54. Johanson, U., M. Karlsson, I. Johansson, S. Gustavsson, S. Sjovall et al., 2001 The complete set of genes encoding major intrinsic proteins in Arabidopsis provides a framework for a new nomenclature for major intrinsic proteins in plants. Plant Physiol. 126: 1358-1369.
55. Kennedy, B. W., M. Quinton and J. A. van Arendonk, 1992 Estimation of effects of single genes on quantitative traits. J. Anim. Sci. 70: 2000-2012.
56. Kimchi-Sarfati, C., J. M. Oh, I.-W. Kim, Z. E. Sauna, A. M. Calcagno et al., 2007 A "silent" polymorphism in the MDR1 gene changes substrate specificity. Science 315: 525-528.
57. Kirst, M., A. A. Myburg, J. P. G. De León, M. E. Kirst, J. Scott et al., 2004 Coordinated genetic regulation of growth and lignin revealed by quantitative trait locus analysis of cDNA microarray data in an interspecific backcross of Eucalyptus. Plant Physiol. 135: 2368-2378.
58. Kubo, M., M. Udagawa, N. Nishikubo, G. Horiguchi, M. Yamaguchi et al., 2005 Transcription switches for protoxylem and metaxylem vessel formation. Genes Dev. 19: 1855-1860.
59. Legendre, P., and L. Legendre, 1998 Numerical Ecology, Second English Edition. Elsevier, New York.
60. Lenz, P., A. Cloutier, J. MacKay and J. Beaulieu, 2010 Genetic control of wood properties in Picea glauca-an analysis of trends with cambial age. Can. J. For. Res. 40: 703-715.
61. Li, P., J. Beaulieu, A. Corriveau and J. Bousquet, 1993 Genetic variation in juvenile growth and phenology in a white spruce provenance-progeny test. Silvae Genet. 42: 52-60.
62. Li, P., J. Beaulieu and J. Bousquet, 1997 Genetic structure and patterns of genetic variation among populations in eastern white spruce (Picea glauca). Can. J. For. Res. 27: 189-198.
63. Littell, R. C., G. A. Milliken, W. W. Stroup, R. D. Wolfinger and O. Schabenberger, 2006 SAS for Mixed Models, Ed. 2. SAS Institute, Cary, NC.
64. Loiselle, B. A., V. L. Sork, J. Nason and C. Graham, 1995 Spatial genetic structure of a tropical understory shrub, Psychotria offici-nalis (Rubiaceae). Am. J. Bot. 82: 1420-1425.
65. Lorenz, W. W., and J. F. D. Dean, 2002 SAGE profiling and demonstration of differential gene expression along the axial developmental gradient of lignifying xylem in loblolly pine (Pinus taeda). Tree Physiol. 22: 301-310.
66. Mackay, T. F. C., 2001 The genetic architecture of quantitative traits. Annu. Rev. Genet. 35: 303-339.
67. MacKay, J., and J. Dean, 2011 Transcriptomics, in Genetics, Genomics and Breeding of Conifers, edited by C. Plomion, J. Bousquet and C. Kole. CRC Press, New York(in press).
68. Malosetti, M., C. G. van der Linden, B. Vosman and F. van Eeuwijk, 2007 A mixed-model approach to association mapping using pedigree information with an illustration of resistance to Phytophthora infestans in potato. Genetics 175: 879-889.
69. Marchini, J., L. R. Cardon, M. S. Phillips and P. Donnelly, 2004 The effects of human population structure on large genetic association studies. Nat. Genet. 36: 512-517.
70. Marth, G. T., I. Korf, M. D. Yandell, R. T. Yeh, Z. Gu et al., 1999 A general approach to single-nucleotide polymorphism discovery. Nat. Genet. 23: 452-456.
71. Micheli, F., 2001 Pectin methylesterases: cell wall enzymes with important roles in plant physiology. Trends Plant Sci. 6: 414-419.
72. Miller, A. R., W. L. Pengelly and L. W. Roberts, 1984 Introduction of xylem differentiation in Lactuca by ethylene. Plant Physiol. 75: 1165-1166.
73. Murray, B. G., 1998 Nuclear DNA amounts in gymnosperms. Ann. Bot. 82: 3-15.
74. Myles, S., J. Peiffer, P. J. Brown, E. S. Ersoz, Z. Zhang et al., 2009 Association mapping: critical considerations shift from genotyping to experimental design. Plant Cell 21: 2194-2202.
75. Namroud, M.-C., J. Beaulieu, N. Juge, J. Laroche and J. Bousquet, 2008 Scanning the genome for gene single nucleotide polymorphisms involved in adaptive population differentiation in white spruce. Mol. Ecol. 17: 3599-3613.
76. Namroud, M.-C., C. Guillet-Claude, J. Mackay, N. Isabel and J. Bousquet, 2010 Molecular evolution of regulatory genes in spruces from different species and continent: heterogeneous patterns of linkage disequilibrium and selection but correlated recent demographic changes. J. Mol. Evol. 70: 371-386.
77. Neale, D. B., and A. Kremer, 2011 Forest tree genomics: growing resources and applications. Nat. Rev. Genet. 12: 111-122.
78. Neale, D. B., and O. Savolainen, 2004 Association genetics of complex traits in conifers. Trends Plant Sci. 9: 325-330.
79. Nienstaedt, H., and A. H. Teich, 1972 The Genetics of White Spruce (Research Paper WO-15). USDA Forest Service, Washington, DC.
80. Nienstaedt, H., and J. C. Zasada, 1990 Picea glauca (Moench) Voss white spruce, pp. 204-226 in Conifers. Agriculture Handbook No. 654 (Silvics of North America, Vol. 1), coordinated by R. M. Burns and B. H. Honkala. USDA Forest Service, Washington, DC.
81. Nilsson, J., A. Karlberg, H. Antti, M. Lopez-Vernaza, E. Mellerowicz et al., 2008 Dissecting the molecular basis of the regulation of wood formation by auxin in hybrid aspen. Plant Cell 20: 843-855.
82. Oakley, R. V., Y.-S. Wang, W. Ramakrishna, S. A. Harding and C.-J. Tsai, 2007 Differential expansion and expression of a- and b-tubulin gene families in Populus. Plant Physiol. 145: 961-973.
83. Paiva, J., 2006 Phenotypic and molecular plasticity of wood forming tissues in maritime pine (Pinus pinaster Ait.). Ph.D. Thesis, Bordeaux University, Cestas, France and New University of Lisbon, Oeiras, Portugal.
84. Patzlaff, A., S. McInnis, A. Courtenay, C. Surman, L. J. Newman et al., 2003a Characterisation of a pine MYB that regulates lig-nification. Plant J. 36: 743-754.
85. Patzlaff, A., L. J. Newman, C. Dubos, R. W. Whetten, C. Smith et al., 2003b Characterisation of PtMYB1, an R2R3-MYB from pine xylem. Plant Mol. Biol. 53: 597-608.
86. Paux, E., M. Tamasloukht, N. Ladouce, P. Sivadon and J. Grima-Pettenati, 2004 Identification of genes preferentially expressed during wood formation in Eucalyptus. Plant Mol. Biol. 55: 263-280.
87. Pavy, N., C. Paule, L. Parsons, J. A. Crow, M.-J. Morency et al., 2005a Generation, annotation, analysis and database integration of 16,500 white spruce EST clusters. BMC Genomics 6: 144.
88. Pavy, N., J. Laroche, J. Bousquet and J. Mackay, 2005b Large-scale statistical analysis of secondary xylem ESTs in pine. Plant Mol. Biol. 57: 203-224.
89. Pavy, N., L. S. Parsons, C. Paule, J. MacKay and J. Bousquet, 2006 Automated SNP detection from a large collection of white spruce expressed sequences: contributing factors and approaches for the categorization of SNPs. BMC Genomics 7: 174.
90. Pavy, N., B. Boyle, C. Nelson, C. Paule, I. Giguére et al., 2008a Identification of conserved core xylem gene sets: conifer cDNA microarray development, transcript profiling and computational analyses. New Phytol. 180: 766-786.
91. Pavy, N., B. Pelgas, S. Beauseigle, S. Blais, F. Gagnon et al., 2008b Enhancing genetic mapping of complex genomes through the design of highly-multiplexed SNP arrays: application to the large and unsequenced genomes of white spruce and black spruce. BMC Genomics 9: 21.
92. Pelgas, B., N. Isabel and J. Bousquet, 2004 Efficient screening for expressed sequence tag polymorphisms (ESTPs) by DNA pool sequencing and denaturing gradient gel electrophoresis (DGGE) in spruces. Mol. Breed. 13: 263-279.
93. Pelgas, B., S. Beauseigle, V. Acheré, S. Jeandroz, J. Bousquet et al., 2006 Comparative genome mapping among Picea glauca, P. mariana x P. rubens and P. abies, and correspondance with other Pinaceae. Theor. Appl. Genet. 113: 1371-1393.
94. Pelgas, B., J. Bousquet, P. G. Meirmans, K. Ritland and N. Isabel, 2011 QTL mapping in white spruce: gene maps and genomic regions underlying adaptive traits across pedigrees, years and environments. BMC Genomics 12: 145.
95. Pilate, G., A. Déjardin, F. Laurans and J.-C. Leplé, 2004 Tension wood as a model for functional genomics of wood formation. New Phytol. 164: 63-72.
96. Plomion, C., C. E. Durell and D. M. O'Malley, 1996 Genetic dissection of height in maritime pine seedlings raised under accelerated growth conditions. Theor. Appl. Genet. 93: 849-858.
97. Plomion, C., C. Pionneau, J. Brach, P. Costa and H. Bailléres, 2000 Compression wood-responsive proteins in developing xylem of maritime pine (Pinus pinaster Ait.). Plant Physiol. 123: 959-970.
98. Pongdontri, P., and M. Hills, 2001 Characterization of a novel plant acyl-CoA synthetase that is expressed in lipogenic tissues of Brassica napus L. Plant Mol. Biol. 47: 717-726.
99. Pot, D., J.-C. Rodrigues, P. Rozenberg, G. Chantre, J. Tibbits et al., 2006 QTLs and candidate genes for wood properties in maritime pine (Pinus pinaster Ait.). Tree Genet. Genomes 2: 10-24.
100. Pritchard, J., X. Wen and D. Falush, 2007 Documentation for Structure Software: Version 2.2. Department of Human Genetics, University of Chicago, Chicago.
101. Pritchard, J. K., M. Stephens and P. Donnelly, 2000 Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
102. Qiu, D., I. W. Wilson, S. Gan, R. Washusen, G. F. Moran et al., 2008 Gene expression in Eucalyptus branch wood with marked variation in cellulose microfibril orientation and lacking G-layers. New Phytol. 179: 94-101.
103. R Development Core Team, 2010 R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna.
104. Rafalski, A., 2010 Association genetics in crop improvement. Curr. Opin. Plant Biol. 13: 174-180.
105. Ritland, K., K. Krutovsky, Y. Tsumura, B. Pelgas, N. Isabel et al., 2011 Genetic mapping in conifers, in Genetics, Genomics and Breeding of Conifers, edited by C. Plomion, J. Bousquet and C. Kole. CRC Press, New York (in press).
106. Rozen, S., and H. Skaletsky, 2000 Primer3 on the WWW for general users and for biologist programmers, pp. 365-386 in Bio-informatics Methods and Protocols: Methods in Molecular Biology, edited by S. Misener and S. A. Krawetz. Humana Press, Totowa, NJ.
107. Rutledge, R. G., and D. Stewart, 2008 A kinetic-based sigmoidal model for the polymerase chain reaction and its application to high-capacity absolute quantitative real-time PCR. BMC Biotech-nol. 8: 47.
108. SAS Institute, 2008 The SAS System for Windows, Version 9.1. SAS Institute, Cary, NC.
109. Savidge, R. A., G. M. C. Mutumba, J. K. Heald and P. F. Wareing, 1983 Gas chromatography-mass spectroscopy identification of 1-aminocyclopropane-1-carboxylic acid in compression wood vascular cambium of Pinus contorta Dougl. Plant Physiol. 71: 434-436.
110. Schnurr, J. A., J. M. Shockey, G.-J. de Boer and J. A. Browse, 2002 Fatty acid export from the chloroplast. Molecular characterization of a major plastidial acyl-coenzyme A synthetase from Arabidopsis. Plant Physiol. 129: 1700-1709.
111. Schrader, J., J. Nilsson, E. Mellerowicz, A. Berglund, P. Nilsson et al., 2004 A high-resolution transcript profile across the wood-forming meristem of poplar identifies potential regulators of cambial stem cell identity. Plant Cell 16: 2278-2292.
112. Sewell, M. M., D. L. Bassoni, R. A. Megraw, N. C. Wheeler and D. B. Neale, 2000 Identification of QTLs influencing wood property traits in loblolly pine (Pinus taeda L.). I. Physical wood properties. Theor. Appl. Genet. 101: 1273-1281.
113. Shen, R., J.-B. Fan, D. Campbell, W. Chang, J. Chen et al., 2005 High-throughput SNP genotyping on universal bead arrays. Mutat. Res. 573: 70-82.
114. Shiu, S.-H., and A. B. Bleecker, 2001 Plant receptor-like kinase gene family: diversity, function, and signaling. Sci. STKE 2001 (113): re22.
115. Shockey, J. M., M. S. Fulda and J. A. Browse, 2002 Arabidopsis contains nine long-chain acyl-coenzyme A synthetase genes that participate in fatty acid and glycerolipid metabolism. Plant Phys-iol. 129: 1710-1722.
116. Siedlecka, A., S. Wiklund, M.-A. Péronne, F. Micheli, J. Lesniewska et al., 2008 Pectin methyl esterase inhibits intrusive and symplastic cell growth in developing wood cells of Populus. Plant Physiol. 146: 554-565.
117. Sokal, R. R., and F. J. Rohlf, 1981 Biometry, Ed. 2. W. H. Freeman, San Francisco.
118. Storey, J. D., 2002 A direct approach to false discovery rates. J. R. Stat. Soc. Ser. B 64: 479-498.
119. Storey, J. D., and R. Tibshirani, 2003 Statistical significance for genomewide studies. Proc. Natl. Acad. Sci. USA 100: 9440-9445.
120. Storey, J. D., J. E. Taylor and D. Siegmund, 2004 Strong control, conservative point estimation and simultaneous conservative consistency of false discovery rates: a unified approach. J. R. Stat. Soc. Ser. B 66: 187-205.
121. Swindell, S. R., and T. N. Plasterer, 1997 SEQMAN: contig assembly, pp. 75-89; in Sequence Data Analysis Guidebook, edited by S. R. Swindell. Humana Press, Totowa, NJ.
122. Takahashi-Schmidt, J., 2008 Functional studies of selected extracellular carbohydrate-active hydrolases in wood formation. Ph.D. Thesis, Faculty of Forest Sciences, Department of Forest Genetics and Plant Physiology, Umeå University, Umeå, Sweden.
123. Thumma, B. R., M. F. Nolan, R. Evans and G. F. Moran, 2005 Polymorphisms in Cinnamoyl CoA Reductase (CCR) are associated with variation in microfibril angle in Eucalyptus spp. Genetics 171: 1257-1265.
124. Thumma, B. R., B. A. Matheson, D. Zhang, C. Meeske, R. Meder et al., 2009 Identification of a cis-acting regulatory polymorphism in a eucalypt COBRA-like gene affecting cellulose content. Genetics 183: 1153-1164.
125. Ukrainetz, N. K., K. Ritland and S. D. Mansfield, 2008 Identification of quantitative trait loci for wood quality and growth across eight full-sib coastal Douglas-fir families. Tree Genet. Genomes 4: 159-170.
126. Vander Willigen, C., O. Postaire, C. Tournaire-Roux, Y. Boursiac and C. Maurel, 2006 Expression and inhibition of aquaporins in germinating Arabidopsis seeds. Plant Cell Physiol. 47: 1241-1250.
127. Vandesompele, J., K. De Preter, F. Pattyn, B. Poppe, N. Van Roy, et al., 2002 Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol. 3: research0034.1-0034.11.
128. Wheeler, N. C., K. D. Jermstad, K. Krutovsky, S. N. Aitken, G. T. Howe et al., 2005 Mapping of quantitative trait loci controlling adaptive traits in coastal Douglas-fir. IV. Cold-hardiness QTL verification and candidate gene mapping. Mol. Breed. 15: 145-156.
129. Whetten, R., Y. H. Sun, Y. Zhang and R. Sederoff, 2001 Functional genomics and cell wall biosynthesis in loblolly pine. Plant Mol. Biol. 47: 275-291.
130. Wong, C. K., and R. Bernardo, 2008 Genomewide selection in oil palm: increasing selection gain per unit time and cost with small populations. Theor. Appl. Genet. 116: 815-824.
131. Yang, S-H., L. van Zyl, E.-G. No and C. A. Loopstra, 2004 Microarray analysis of genes preferentially expressed in differentiating xylem of loblolly pine (Pinus taeda). Plant Sci. 166: 1185-1195.
132. Yu, J., G. Pressoir, W. H. Briggs, I. V. Bi, M. Yamasaki et al., 2006 A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat. Genet. 38: 203-208.
133. Zhu, C., M. Gore, E. S. Buckler and J. Yu, 2008 Status and prospects of association mapping in plants. Plant Genome 1: 5-20.
134. Zobel, B. J., and J. B. Jett, 1995 Genetics of Wood Production. Springer-Verlag, New York.
135. Zobel, B. J., and J. P. van Buijtenen, 1989 Wood Variation. Its Causes and Control. Springer-Verlag, New York.