Genomics of trees

Tree Biotechnology

Volumn , Issue , 2014, Pages 514-557

  Aravanopoulos, Filippos A Phil ^a,b  

^a ARISTOTLE UNIVERSITY OF THESSALONIKI   (Greece)

^b INFORMATION TECHNOLOGIES INSTITUTE   (Greece)

Author keywords

Association; Comparative; Conservation; Functional; Genomics: structural; GWS; Landscape; Mapping: genetic; MAS; Population; QTL; Trees

Indexed keywords

ASSOCIATION REACTIONS; CONSERVATION; FORESTRY; MAPPING; STRUCTURAL ANALYSIS;

COMPARATIVE; FUNCTIONAL; GENOMICS; LANDSCAPE; POPULATION; TREES;

GENES;

EID: 84941369886     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1201/b16714     Document Type: Chapter

References (160)

1. Abbott, A. 2012. The genomes of the giants: a walk through the forest of tree genomes. Tree Genet. Genomes 8: 443.
2. Abril, N., J.M. Gion, R. Kerner, G. Müller-Starck, R.M. Cerrillo, C. Plomion, J. Renaut, L. Valledor and J.V. Jorrin-Novo. 2011. Proteomics research on forest trees, the most recalcitrant and orphan plant species. Phytochemistry 72: 1219-1242.
3. Achere, V., P. Faivre-Rampant, S. Jeandroz, G. Besnard, T. Markussen, A. Aragones, M. Fladung, E. Ritter and J.M. Favre. 2004. A full saturated linkage map of Picea abies including AFLP, SSR, ESTP, 5S rDNA and morphological markers. Theor. Appl. Genet. 108: 1602-1613.
4. Aravanopoulos, F.A. 2011. Genetic monitoring in natural perennial plant populations. Botany 89: 75-81.
5. Aravanopoulos, F.A. 2010. The importance of the biodiversity of Hellenic forest and land-based ecosystems for Europe and the Mediterranean. pp. 1-11. In: M. Ananiadou-Tzimopoulou (ed.). Proc. Conf. Environmental Council, Aristotle University of Thessaloniki, Aristotle University Press.
6. Aravanopoulos, F.A., G. Bucci, A. Akkak, R. Blanco-Silva, R. Botta, E. Buck, M. Cherubini, A.D. Drouzas, J. Fernandez-Lopez, C. Mattioni, D. Marinoni, A. Papadima, K. Russell, R. Zas and F. Villani. 2005. Molecular population genetics and dynamics of chestnut (Castanea sativa) in Europe: inferences for gene conservation and tree improvement. Acta Hort. 693: 403-412.
7. Aravanopoulos, F.A. 2001a. Analysis of genetic linkage and genome mapping. pp. 9-26. In: A.S. Tsaftaris and A.N. Polidoros (eds.). Genome Sequencing and Comparative Analysis, University Studio Press, Thessaloniki.
8. Aravanopoulos, F.A. 2001b. On the suitability of the application of the Kosambi mapping function in linkage data sets, when parental phase is unknown. Scientific Bull. Faculty of Forestry and Natural Environment, Aristotle University of Thessalonki 44: 737-748.
9. Aravanopoulos, F.A. 2001c. Genetic linkage analysis in Salix eriocephala suggests linkage conservation above the species level. Forest Genetics 8: 145-149.
10. Aravanopoulos, F.A. 1998. On the estimation of genome length in perennial woody angiosperms. pp. 457-460. In: I. Tsekos and M. Moustakas (eds.). Progress in Botanical Research. Kluwer Acad. Publ., Dordrecht.
11. Aravanopoulos, F.A., L. Zsuffa and K.X. Chong. 1993. The genetic basis of electrophoretic variation in Salix exigua Nutt. Hereditas 119: 77-88.
12. Austerlitz, F., S. Mariette, N. Machon, P.H. Gouyon and B. Godelle. 2000. Effects of colonization processes on genetic diversity: differences between annual plants and tree species. Genetics 154: 1309-1321.
13. Bailey, N.T.J. 1961. Introduction to the mathematical theory of genetic linkage. Clarendon Press, Oxford.
14. Barreneche, T., M. Casasoli, K. Russell, A. Akkak, H. Meddour, C. Plomion, F. Villani and A. Kremer. 2004. Comparative mapping between Quercus and Castanea using simplesequence repeats (SSRs). Theor. Appl. Genet. 108: 558-566.
15. Beavis, W.D. 1998. QTL analyses: power, precision, and accuracy. pp. 145-162. In: A.H. Patterson (ed.). Molecular Dissection of Complex Traits. CRC Publishing, Boca Raton.
16. Bernardo, R. 2008. Molecular markers and selection for complex traits in plants: learning from the last 20 years. Crop Sci. 48: 1649-1664.
17. Biswas, S. and J.M. Akey. 2006. Genomic insights into positive selection. Trends Genet. 22: 437-446.
18. Brereton, N.J.B., F.E. Pitre, A. Karp and R.J. Murphy. 2010. QTL mapping of enzymatic saccharification in short rotation coppice willow and its independence from biomass yield. Bioen. Res. 3: 251-261.
19. Brown, G.R., G.P. Gill, R.J. Kuntz, C.H. Langley and D.B. Neale. 2004. Nucleotide variation and linkage disequilibrium in loblolly pine. Proc. Natl. Acad. Sci. USA 101: 15255-15260.
20. Brown, G.R., D.L. Bassoni, G.P. Gill, J.R. Fontana, N.C. Wheeler, R.A. Megraw, M.F. Davis, M.M. Sewell, G.A. Tuskan and D.B. Neale. 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.
21. Buckler, E.S., J.B. Holland, P.J. Bradbury, C.B. Acharya, P.J. Brown, C. Browne, E. Ersoz, S. Flint-Garcia, A. Garcia, J.C. Glaubitz, M.M. Goodman, C. Harjes, K. Guill, D.E. Kroon, S. Larsson, N.K. Lepak, H.H. Li, S.E. Mitchell, G. Pressoir, J.A. Peiffer, M.O. Rosas, T.R. Rocheford, M.C. Romay, S. Romero, S. Salvo, H.S. Villeda, H.S. da Silva, Q. Sun, F. Tian, N. Upadyayula, D. Ware, H. Yates, J.M. Yu, Z.W. Zhang, S. Kresovich and M.D. McMullen. 2009. The genetic architecture of maize flowering time. Science 325: 714-718.
22. Carter, T.C. and D.S. Falconer. 1951. Stocks for detecting linkage in the mouse and the theory of their design. J. Genet. 50: 307-323.
23. Casasoli, M., D. Pot, C. Plomion, M.C. Monteverdi, T. Barreneche, M. Lauteri and F. Villani. 2004. Identification of QTLs affecting adaptive traits in Castanea sativa Mill. Plant Cell Envir. 27: 1088-1101.
24. Chakravarti, A., L.K. Lasher and J.E. Reefer. 1991. A maximum likelihood method for estimating genome length using genetic linkage data. Genetics 128: 175-182.
25. Chancerel, E., C. Lepoittevin, G. Le Provost, Y.C. Lin, J.P. Jaramillo-Correa, A.J. Eckert, J.L Wegrzyn, D. Zelenika, A. Boland, J.-M. Frigerio, P. Chaumeil, P. Garnier-Géré, C. Boury, D. Grivet, S.C. González-Martínez, P.Rouzé, Y. van de Peer, D.B. Neale, M.T. Cervera, A. Kremer and C. Plomion. 2011. Development and implementation of a highly- multiplexed SNP array for genetic mapping in maritime pine and comparative mapping with loblolly pine. BMC Gen. 12: 368.
26. Chen, J., X.M. Kallman, N. Gyllenstrand, G. Zaina, M. Morgante, J. Bousquet, A. Eckert, J. Wegrzyn, D. Neale, U. Lagercrantz and M. Lascoux. 2012. Disentangling the roles of history and local selection in shaping clinal variation of allele frequencies and gene expression in Norway spruce (Picea abies). Genetics 191: 865-881.
27. Clauss, M.J. and T. Mitchell-Olds. 2006. Population genetic structure of Arabidopsis lyrata in Europe. Mol. Ecol. 15: 2753-2766.
28. Conifer Comparative Genomics Project 2014. (2014, January 12). Retrieved from http:// dendrome.ucdavis.edu/ccgp.
29. Conkle, M.T. 1979. Isozyme variation and linkage in six conifer species. pp. 11-18. In: Proc. Symp. Isozymes of North American Forest Trees, USDA For. Serv. Gen. Techn. Rep.
30. Cornelius, J. 1994. The effectiveness of plus-tree selection for yield. Forest Ecol. Manag. 67: 23-34.
31. Dekkers, J.C.M. 2004. Commercial application of marker- and gene-assisted selection in livestock: strategies and lessons. J. Anim. Sci. 82: E313-E328.
32. Devey, M.E., S.D. Carson, M.F. Nolan, A.C. Matheson, C. Te Riini and J. Hohepa. 2004. QTL associations for density and diameter in Pinus radiata and the potential for marker-aided selection. Theor. Appl. Genet. 108: 516-524.
33. Druart, N., A. Johansson, K. Baba, J. Schrader, A. Sjodin, R.R. Bhalerao, L. Resman, J. Trygg, T. Moritz and R.P. Bhalerao. 2007. Environmental and hormonal regulation of the activity dormancy cycle in the cambial meristem involves stage specific modulation of transcriptional and metabolic networks. Plant J. 50: 557-573.
34. Dvornyk, V., A. Sirvio, M. Mikkonen and O. Savolainen. 2002. Low nucleotide diversity at the pal1 locus in the widely distributed Pinus sylvestris. Mol. Biol. Evol. 19: 179-188.
35. Eckert, A.J. and R.J. Dyer. 2012. Defining the landscape of adaptive genetic diversity. Mol. Ecol. 21: 2836-2838.
36. Eckert, A. 2011. Population and conservation genomics of forest trees: seeing the forest for the trees. BMC Proc. 5(Suppl. 7): I2, http://www.biomedcentral.com/1753-6561/5/S7/I2.
37. Eckert, A.J., A.D. Bower, S.C. Gonzalez-Martinez, J.L. Wegrzyn, G. Coop and D.B. Neale. 2010. Back to nature: ecological genomics of loblolly pine (Pinus taeda, Pinaceae). Mol. Ecol. 19: 3789-3805.
38. Eckert, A.J., A.D. Bower, J.L. Wegrzyn, B. Pande, K.D. Jermstad, K.V. Krutovsky, J.B.S. Clair and D.B. Neale. 2009. Association genetics of coastal Douglas fir (Pseudotsuga menziesii var. menziesii, Pinaceae). I. Cold-hardiness related traits. Genetics 182: 1289-1302.
39. Eveno, E., C. Collada, M.A. Guevara, V. Leger, A. Soto, L. Diaz, P. Leger, S.C. Gonzalez-Martinez, M.T. Cervera, C. Plomion and P.H. Garnier-Gere. 2008. Contrasting patterns of selection at Pinus pinaster Ait. Drought stress candidate genes as revealed by genetic differentiation analyses. Mol. Biol. Evol. 25: 417-437.
40. Fabbrini, F., M. Gaudet, C. Bastien, G. Zaina, A. Harfouche, I. Beritognolo, N. Marron, M. Morgante, G. Scarascia-Mugnozza and M. Sabatti. 2012. Phenotypic plasticity, QTL mapping and genomic characterization of bud set in black poplar. BMC Plant Biol. 12: 47.
41. Fagaceae Genomics Web 2014 (2014, January 12). Retrieved from http://www.fagaceae. org/.
42. Farjon, A. 2008. A natural history of conifers. Timber Press, Portland.
43. Fjellstrom, G. and D.E. Parfitt. 1994. RFLP inheritance and linkage in walnut. Theor. Appl. Genet. 89: 665-670.
44. Frank, S.A. 2004. Genetic predisposition to cancer-insights from population genetics. Nat. Rev. Genet. 5: 764-772.
45. Ganopoulos, I.V., F.A. Aravanopoulos and A. Tsaftaris. 2013. Genetic differentiation and gene flow between wild and cultivated Prunus avium: an analysis of molecular genetic evidence at a regional scale. Plant Biosyst. DOI:10.1080/11263504.2012.751065, pp. 1-8.
46. Ganopoulos, I.V., F.A. Aravanopoulos, A. Argiriou, A. Kalivas and A. Tsaftaris. 2012. Genome and population dynamics under selection and neutrality: an example of S-allele diversity in wild cherry (Prunus avium L.). Tree Genet. Genomes 8: 1181-1190.
47. Ganopoulos, I., F.A. Aravanopoulos, A. Argiriou, A. Kalivas and A. Tsaftaris. 2011. Is the genetic diversity of small scattered forest tree populations at the southern limits of their range more prone to stochastic events? A wild cherry case study by microsatellite-based markers. Tree Genet. Genomes 7: 1299-1313.
48. Gailing, O. 2008. QTL analysis of leaf morphological characters in a Quercus robur full-sib family (Q. robur x Q. robur ssp. slavonica). Plant Biol. 10: 624-634.
49. Gailing, O., B. Vornam, L. Leinemann and R. Finkeldey. 2009. Genetic and genomic approaches to assess adaptive genetic variation in plants: forest trees as a model. Physiol. Plantar. 137: 509-519.
50. Gebhardt, C. 2013. Bridging the gap between genome analysis and precision breeding in potato Trends Genet. 29: 248-256.
51. GenBank (2014, January 12). Retrieved from http://www.ncbi.nlm.nih.gov/dbEST/dbEST_ summary.html.
52. Gene Index Project 2014. Computational Biology and Functional Genomics Laboratory, Harvard University. (2014, January 12). Retrieved from http://compbio.dfci.harvard. edu/tgi/plant.html.
53. 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.
54. Gomez, A., F.A. Aravanopoulos, M.A. Bueno and R. Alia. 2003. Linkage of random amplified polymorphic DNA markers in Pinus halepensis. Mill. Silv. Genet. 51: 196-201.
55. Gonzalez-Martinez, S.C., E. Ersoz, G.R. Brown, N.C. Wheeler and D.B. Neale. 2006a. DNA sequence variation and selection of tag single nucleotide polymorphisms at candidate genes for drought-stress response in Pinus taeda L. Genetics 172: 1915-1926.
56. Gonzalez-Martinez, S.C., K.V. Krutovsky and D.B. Neale. 2006b. Forest-tree population genomics and adaptive evolution. New Phytol 170: 227-238.
57. Gonzalez-Martinez, 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.
58. Gonzalez-Martinez, S.C., D. Huber, E. Ersoz, J.M. Davis and D.B. Neale. 2008. Association genetics in Pinus taeda L. II. Carbon isotope discrimination. Heredity 101: 19-26.
59. Gosselin, I., Y. Zhou, J. Bousquet and N. Isabel. 2002. Megagametophyte-derived linkage maps of white spruce (Picea glauca) based on RAPD, SCAR and ESTP markers. Theor. Appl. Genet. 104: 987-997.
60. Grattapaglia, D. 2004. Integrating genomics into Eucalyptus breeding. Genetics and Molecular Research 3: 369-379.
61. Grattapaglia, D. and M.D.V. Resende. 2011. Genomic selection in forest tree breeding. Tree Genet. Genomes 7: 241-255.
62. Grattapaglia, D., C. Plomion, M. Kirst and R.R. Sederoff. 2009. Current genomics of growth traits in forest trees. Opinion Plant Biol. 12: 148-156.
63. Grattapaglia, D. and M. Kirst. 2008. Eucalyptus applied genomics: from gene sequences to breeding tools. New Phytol. 179: 911-929.
64. Grattapaglia, D. 2007. Marker-assisted selection in Eucalyptus. pp. 251-282. In: E.P. Guimaraes, J. Ruane, B.D. Scherf, A. Sonnino and J.D. Dargie (eds.). Marker-Assisted Selection: Current Status and Future Perspectives in Crops, Livestock, Forestry and Fish, FAO, Rome.
65. Grattapaglia, D. and R. Sederoff. 1994: Genetic linkage maps of Eucalyptus grandis and E. urophylla using a pseudotestcross: mapping strategy and RAPD markers. Genetics 137: 1121-1137.
66. Grivet, D., V.L. Sork, R.D. Westfall and F.W. Davis. 2008. Conserving the evolutionary potential of California valley oak (Quercus lobata Nee): a multivariate genetic approach to conservation planning. Mol. Ecol. 17: 139-156.
67. Grivet, D., F. Sebastiani, S.C. Gonzalez-Martinez and G.G. Vendramin. 2009. Patterns of polymorphism resulting from long-range colonization in the Mediterranean conifer Aleppo pine. New Phytol. 184: 1016-1028.
68. Groover, A.T. 2007. Will genomics guide a greener forest biotech? Trends Plant Sci. 12: 234-238.
69. Gyllenstrand, N., D. Clapham, T. Kallman and U. Lagercrantz. 2007. A Norway spruce FLOWERING LOCUS T homolog is implicated in control of growth rhythm in conifers. Plant Physiol. 144: 248-257.
70. Haldane, J.B.S. 1919. The combination of linkage values and the calculation of distance between the loci of linked factors. J. Genet. 8: 299-309.
71. Hall, D., V. Luquez, V.M. Garcia, K.R. St. Onge, S. Jansson and P.K. Ingvarsson. 2007. Adaptive population differentiation in phenology across a latitudinal gradient in European aspen (Populus tremula L.): a comparison of neutral markers, candidate genes and phenotypic traits. Evolution 61: 2849-2860.
72. Hamberger, B., D. Hall, M. Yuen, C. Oddy, B. Hamberger, C.I. Keeling, C. Ritland, K. Ritland and J. Bohlmann. 2009. Targeted isolation, sequence assembly and characterization of two white spruce (Picea glauca) BAC clones for terpenoid synthase and cytochrome P450 genes involved in conifer defense reveal insights into a conifer genome. BMC Plant Biol. 9: 106.
73. Hamrick, J.L., M. Jo, W. Godt and S.L. Sherman-Broyles. 1992. Factors influencing levels of genetic diversity in woody plant species. New Forests 6: 95-124.
74. Hanley, S.J., M.D. Mallott and A. Karp. 2006. Alignment of a Salix linkage map to the Populus genomic sequence reveals macrosynteny between willow and poplar genomes. Tree Genet Genomes 3: 35-48.
75. Harfouche, A., F.A. Aravanopoulos, A.G Doulis and S. Xenopoulos. 2000. Identification of RAPD markers associated with crown form in Cupressus sempervirens by bulked segregant analysis. Forest Genetics 7: 169-176.
76. Hayes, B.J., P.J. Bowman, A.J. Chamberlain and M.E. Goddard. 2009. Invited review: genomic selection in dairy cattle: progress and challenges. J. Dairy Sci. 92: 433-443.
77. Hertzberg, M., H. Aspeborg, J. Schrader, A. Andersson, R. Erlandsson, K. Blomqvist, R. Bhalerao, M. Uhlen, T.T. Teeri, J. Lundeberg, B. Sundberg, P. Nilsson and G. Sandberg. 2001. A transcriptional roadmap to wood formation. Proc. Natl. Acad. Sci. USA 98: 14732-14737.
78. Heuertz, M., E. De Paoli, T. Kallman, H. Larsson, I. Jurman, M. Morgante, M. Lascoux and N. Gyllenstrand. 2006. Multilocus patterns of nucleotide diversity, linkage disequilibrium and demographic history of Norway spruce (Picea abies (L.) Karst). Genetics 174: 2095-2105.
79. Hill, W.G. 1981. Estimation of effective population-size from data on linkage disequilibrium. Genet. Res. 38: 209-216.
80. Hulbert, S.H., T.W. Illot, E.J. Legg, S.E. Linkloln, E.S. Lander and R.W. Michelmore. 1988. Genetic analysis of the fungus Bremia lactucae using RFLPs. Genetics 120: 947-958.
81. Ingvarsson, P.K. 2005. Nucleotide polymorphism and linkage disequilibrium within and among natural populations of European aspen (Populus tremula L., Salicaceae). Genetics 169: 945-953.
82. Ingvarsson, P.K., M.V. Garcia, D. Hall, V. Luquez and S. Jansson. 2006. Clinal variation in PhyB2, a candidate gene for day-length-induced growth cessation and bud set, across a latitudinal gradient in European Aspen (Populus tremula). Genetics 172: 1845-53.
83. Intenational Genome Poplar Consortium 2014 (2014, January 12). Retrieved from http:// www.ornl.gov/sci/ipgc/.
84. Jansson, S. and C.J. Douglas. 2007. Populus: a model system for plant biology. Ann. Rev. Plant Biol. 58: 435-458.
85. Kenrick, P. 1999. The family tree flowers. Nature 402: 358-359.
86. Komulainen, P., G.R. Brown, M. Mikkonen, A. Karhu., M.R. Garcia-Gil, D. O’Malley, B. Lee, D.B. Neale and O. Savolainen. 2003. Comparing EST-based genetic maps between Pinus sylvestris and Pinus taeda. Theor. Appl. Genet. 107: 667-678.
87. Kosambi, D.D. 1944. The estimation of map distances from recombination values. Ann. Eugen. London 12: 172-175.
88. Kovach, A., J.L. Wegrzyn, G. Parra, C. Holt, G.E. Bruening, C.A. Loopstra, J. Hartigan, M. Yandell, C.H. Langley, I. Korf and D.B. Neale. 2010. The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences. BMC Genomics 11: 420.
89. Kremer, A. and V. Le Corre. 2012. Decoupling of differentiation between traits and their underlying genes in response to divergent selection. Heredity 108: 375-385.
90. Krutovsky, K.V. 2006. From population genetics to population genomics of forest trees: integrated population genomics approach. Russian J. Genet. 42: 1088-1100.
91. Krutovsky, K.V. and D.B. Neale. 2005. Nucleotide diversity and linkage disequilibrium in cold hardiness and wood quality related candidate genes in Douglas-fir. Genetics 171: 2029-2041.
92. Lande, R. and R. Thompson. 1990. Efficiency of marker-assisted selection in the Improvement of quantitative traits. Genetics 124: 743-756.
93. Le Corre, V. and A. Kremer. 2003. Genetic variability at neutral markers, quantitative trait loci and trait in a subdivided population under selection. Genetics 164: 1205-1219.
94. Lerceteau, E., C. Plomion and B. Anderson. 2000. AFLP mapping and detection of quantitative trait loci (QTLs) for economically important traits in Pinus sylvestris: a preliminary study. Mol. Breed. 6: 451-458.
95. Lima, B.L., J.E.C. Teixeira, R. Gazaffi, A.F. Garcia, D. Grattapaglia, R.K.D. Valle and L.E.A. Camargo. 2011. Identification of a novel QTL contributing to rust resistance in Eucalyptus. BMC Proc. 5(Suppl. 7): P32, http://www.biomedcentral.com/1753-6561/5/S7/P32.
96. Long, A.D. and C.H. Langley. 1999. The power of association studies to detect the contribution of candidate genetic loci to variation in complex traits. Genome Res. 9: 720-731.
97. Lorenz, W.W., F. Sun, C. Liang, D. Kolychev, H. Wang, X. Zhao, M.M. Cordonnier-Pratt, L.H. Pratt and J.F. Dean. 2006. Water stress-responsive genes in loblolly pine (Pinus taeda) roots identified by analyses of expressed sequence tag libraries. Tree Physiol. 26: 1-16.
98. Luikart, G., P. England, D. Tallmon, S. Jordan and P. Taberlet. 2003. The power and promise of population genomics: from genotyping to genome typing. Nat. Rev. Genet. 4: 981-994.
99. Mackay, J., J.F.D. Dean, C. Plomion, D.G. Peterson, F.M. Canovas, N. Pavy, P.K. Ingvarsson, O. Savolainen, M.A. Guevara, S. Fluch, B. Vinceti, D. Abarca, C. Diaz-Sala and M.T. Cervera. 2012. Towards decoding the conifer giga-genome. Plant Mol. Biol. 80: 555-569.
100. Magallo, S.A. and M.J. Sanderson. 2005. Angiosperm divergence times: the effect of genes, codon positions and time constrains. Evolution 59: 1653-1670.
101. Malliarou, E. and F.A. Aravanopoulos. 2012. A comparative analysis of genetic diversity of tree species in Greece and Europe. pp. 413-418. In: Proc. 14th. Pan-Hellenic Conf., Hellenic Sci. Soc. Plant Genet. Breeding, Thessaloniki.
102. Manescu, C., C. Maios, N. Hamamouch, A. Harfouche, A. Doulis and F.A. Aravanopoulos. 2011. Linkage mapping in Cupressus sempervirens L. based on molecular and morphological markers. Genetics and Molecular Research 10: 1891-1909.
103. Mardis, E.R. 2008. The impact of next-generation sequencing technology on genetics. Trends Genet. 24: 133-41.
104. Meuwissen, T.H., B.J. Hayes and M.E. Goddard. 2001. Prediction of total genetic value using genome-wide dense marker maps. Genetics 157: 1819-1829.
105. Michelmore, R.W., I. Paran and R.V. Kesseli. 1991. Identification of markers linked to disease resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions using segregating populations. Proc. Natl. Acad. Sci. USA 88: 9828-9832.
106. Miguel, de M.M., N.N. de Maria, M.A. Guevara, L. Diaz, E. Saez-Laguna, D. Sanchez-Gomez, E. Chancerel, I. Aranda, C. Collada, C. Plomion, J.A. Cabezas and M.T. Cervera. 2012. Annotated genetic linkage maps of Pinus pinaster Ait. from a Central Spain population using microsatellite and gene based markers. BMC Genomics PMID 23036012.
107. Morgan, T.H. 1928. The Theory of Genes. Yale University Press, New Haven.
108. Myburg, A., D. Grattapaglia, G. Tuskan, J. Jenkins, J. Schmutz, E. Mizrachi, C. Hefer, G. Pappas, L. Sterck, Y. van de Peer, R. Hayes and D. Rokhsar. 2011. The Eucalyptus grandis genome project: genome and transcriptome resources for comparative analysis of woody plant biology. BMC Proc. 5(Suppl. 7): I20.
109. 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.
110. Neale, D.B. and A. Kremer. 2011. Forest tree genomics: growing resources and applications. Nat. Rev. Genet. 12: 111-122.
111. Neale, D.B. and P.K. Ingvarsson. 2008. Population, quantitative and comparative genomics of adaptation in forest trees. Curr. Opinion Plant Biol. 11: 149-155.
112. Neale, D.B. 2007. Genomics to tree breeding and forest health. Curr. Opinion Genet. Devel. 17: 1-6.
113. Neale, D.B. and O. Savolainen. 2004. Association genetics of complex traits in conifers. Trends Plant Sci. 9: 325-330.
114. Nelson, C.D., W.L. Nanee and R.L Doudriek. 2008. A partial genetic linkage map of slash pine (Pinus elliottii Engelm. var. elliottii) based on random amplified polymorphic DNAs. Theor. Appl. Genet. 87: 145-151.
115. Nordborg, M., T.T. Hu, Y. Ishino, J. Jhaveri, C. Toomajian, H. Zheng, E. Bakker, P. Calabrese, J. Gladstone, R. Goyal, M. Jakobsson, S. Kim, Y. Morozov, B. Padhukasahasram, V. Plagnol, N.A. Rosenberg, C. Shah, J.D. Wall, J. Wang, K. Zhao, T. Kalbfleisch, V. Schulz, M. Kreitman and J. Bergelson. 2005. The pattern of polymorphism in Arabidopsis thaliana. PLoS Biol. 3: e196.
116. Owen, A.R.G. 1950. The theory of genetic recombination. Adv. Genet. 3: 117-157.
117. Paiva, J.A., P.H. Garnier-Gere, J.C. Rodrigues, A. Alves, S. Santos, J. Graca, G. Le Provost, P. Chaumeil, D. Da Silva-Perez, A. Bosc. 2009. Plasticity of maritime pine (Pinus pinaster) wood-forming tissues during a growing season. New Phytol. 179: 1180-1194.
118. Palme, A.E., M. Wright and O. Savolainen. 2008. Patterns of divergence among conifer ESTs and polymorphism in Pinus sylvestris identify putative selective sweeps. Mol. Biol. Evol. 25: 2567-2577.
119. Parchman, T.L., Z. Gompert, J. Mudge, F.D. Schilkey, C.W. Benkman and C.A. Buerkle. 2012. Genome-wide association genetics of an adaptive trait in lodgepole pine. Mol. Ecol. 21: 2991-3005.
120. Pelgas, B., S. Beauseigle, V. Achere, S. Jeandroz, J. Bousquet and N. Isabel. 2006. Comparative genome mapping among Picea glauca, P. mariana x P. rubens and P. abies, and correspondence with other Pinaceae. Theor. Appl. Genet. 113: 1371-1393.
121. 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.
122. Pyhajarvi, T., M. Rosario Garcia-Gil, T. Knur, M. Mikkonen, W. Wachowiak and O. Savolainen. 2007. Demographic history has influenced nucleotide diversity in European Pinus sylvestris populations. Genetics 177: 1713-1724.
123. Plomion, C., D. Chagne, D. Pot, S. Kumar, P.L. Wilcox, R.D. Burdon, D. Prat, D.G. Peterson, J. Paiva, P. Chaumeil, G.G. Vendramin, F. Sebastiani, C.D. Nelson, C.S. Echt, O. Savolainen, T.L. Kubisiak, M.T. Cervera, N. de Maria and M.N. Islam-Faridi. 2007. Pines. pp. 29-92. In: C. Kole (ed.). Genome Mapping and Molecular Breeding in Plants, Forest Trees. Springer, New York.
124. Plomion, C., C.E. Durel 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.
125. Pot, D., J.C. Rodrigues, P. Rozenberg, G. Chantre, J. Tibbits, C. Cahalan, F. Pichavant and C. Plomion. 2006. QTLs and candidate genes for wood properties in maritime pine (Pinus pinaster Ait.). Tree Genet. Genomes 2: 10-24.
126. Prunier, J., J. Laroche, J. Beaulieu and J. Bousquet. 2011. Scanning the genome for gene SNPs related to climate adaptation and estimating selection at the molecular level in boreal black spruce. Mol. Ecol. 20: 1702-1716.
127. Rafalski, A. and M. Morgante. 2004. Corn and humans: recombination and linkage disequilibrium in two genomes of similar size. Trends Genet. 20: 103-111.
128. Remington, D.L. and D.M. O’Malley. 2000. Evaluation of major genetic loci contributing to inbreeding depression for survival and early growth in a selfed family of Pinus taeda. Evolution 54: 1580-1589.
129. Remington, D.L., R.W. Whetten, B.H. Liu and D.M. O’Malley. 1999. Construction of an AFLP genetic map with nearly complete genome coverage in Pinus taeda. Theor. Appl. Genet. 98: 1279-1292.
130. Risch, N.J. 2000. Searching for genetic determinants in the new millennium. Nature 405: 847-856.
131. Ruttink, T., M. Arend, K. Morreel, V. Storme, S. Rombauts, J. Fromm, R.P. Bhalerao, W. Boerjan and A. Rohde. 2007. A molecular timetable for apical bud formation and dormancy induction in poplar. Plant Cell 19: 2370-2390.
132. Savolainen, O., T. Pyhajarvi and T. Knurr. 2007. Gene flow and local adaptation in trees. Ann. Rev. Ecol. Evol. Syst. 38: 595-619.
133. Savolainen, O. and T. Pyhajarvi. 2007. Genomic diversity in forest trees. Curr. Opinion Plant Biol. 10: 162-167.
134. Scalfi, M., M. Troggio, P. Piovani, S. Leonardi, G. Magnaschi, G.G. Vendramin and P. Menozzi. 2004. A RAPD, AFLP and SSR linkage map, and QTL analysis in European beech (Fagus sylvatica L.). Theor. Appl. Genet. 108: 433-441.
135. Scotti-Saintagne, C., S. Mariette, I. Porth, P.G. Goicoechea, T. Barreneche, K. Bodenes, K. Burg and A. Kremer. 2004. Genome scanning for interspecific differentiation between two closely related oak species [Quercus robur L. and Q. petraea (Matt.) Liebl.]. Genetics 168: 1615-1626.
136. Shastry, B.S. 2002. SNP alleles in human disease and evolution. J. Hum. Genet. 47: 561-566.
137. Sillanpaa, M.J. and J. Corander. 2002. Model choice in gene mapping: what and why. Trends Genet. 18: 301-307.
138. Skov, E. and H. Wellendorf. 1998. RAPD-markers in haploid megagametophytes Silv. Genet. 47: 273-282.
139. Solberg, T.R., A.K. Sonesson, J.A. Woolliams and T.H. Meuwissen. 2008. Genomic selection using different marker types and densities. J. Anim. Sci. 86: 2447-2454.
140. Sork, V.L., S.N. Aitken, R.J. Dyer, A.J. Eckert, P. Legendre and D.B. Neale. 2013. Putting the landscape into the genomics of trees: approaches for understanding local adaptation and population responses to changing climate. Tree Genet. Genomes. DOI:10.1007/ s11295-013-0596-x.
141. Staszak, A.M. and T.A. Pawłowski. 2012. Forest tree research in post genomic era. Introduction to systems biology of broadleaves. Dendrobiology 68: 113-123.
142. Stuber, C.W., R.H. Moll, M.M. Goodman, H.E. Schaffer and B.S. Weir. 1980. Allozyme frequency changes associated with selection for increased grain yield in maize. Genetics 95: 225-236.
143. 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.
144. Tsumura, Y., T. Kado, T. Takahashi, N. Tani, T. Ujino-Ihara and H. Iwata. 2007. Genome scan to detect genetic structure and adaptive genes of natural populations of Cryptomeria japonica. Genetics 76: 2393-2403.
145. Tuskan, G.A., S. DiFazio, S. Jansson, J. Bohlmann, I. Grigoriev, U. Hellsten, N. Putnam, S. Ralph, S. Rombauts, A. Salamov, J. Schein, L. Sterck, A. Aerts, R.R. Bhalerao, R.P. Bhalerao, D. Blaudez,W. Boerjan, A. Brun, A. Brunner, V. Busov, M. Campbell, J. Carlson, M. Chalot, J. Chapman, G.L. Chen, D. Cooper, P.M. Coutinho, J. Couturier, S. Covert, Q. Cronk, R. Cunningham, J. Davis, S. Degroeve, A. Djardin, C. Depamphilis, J. Detter, B. Dirks, I. Dubchak, S. Duplessis, J. Ehlting, B. Ellis, K. Gendler, D. Goodstein, M. Gribskov, J. Grimwood, A. Groover, L. Gunter, B. Hamberger, B. Heinze, Y. Helariutta, B. Henrissat, D. Holligan, R. Holt, W. Huang, N. Islam-Faridi, S. Jones, M. Jones-Rhoades, R. Jorgensen, C. Joshi, J. Kangasjrvi, J. Karlsson, C. Kelleher, R. Kirkpatrick, M. Kirst, A. Kohler, U. Kalluri, F. Larimer, J. Leebens-Mack, J.C. Lepl, P. Locascio, Y. Lou, S. Lucas, F. Martin, B. Montanini, C. Napoli, D.R. Nelson, C. Nelson, K. Nieminen, O. Nilsson, V. Pereda, G. Peter, R. Philippe, G. Pilate, A. Poliakov, J. Razumovskaya, P. Richardson, C. Rinaldi, K. Ritland, P. Rouz, D. Ryaboy, J. Schmutz, J. Schrader, B. Segerman, H. Shin, A. Siddiqui, F. Sterky, A. Terry, C.J. Tsai, E. Uberbacher, P. Unneberg, J. Vahala, K. Wall, S. Wessler, G. Yang, T. Yin, C. Douglas, M. Marra, G. Sandberg, Y. van de Peer and D. Rokhsar. 2006. The genome of black cottonwood, Populus trichocarpa (Torr. and Gray). Science 313: 1596-1604.
146. Visscher, P.M. 2008. Sizing up human height variation. Nat. Genet. 40: 489-490.
147. Wachowiak, W., P.A. Balk and O. Savolainen. 2009. Search for nucleotide diversity patterns of local adaptation in dehydrins and other cold-related candidate genes in Scots pine (Pinus sylvestris L.). Tree Genet. Genomes 5: 117-132.
148. Walbot, V. 2013. Open questions: reflections on plant development and genetics. BMC Biol. 11: 25, http://www.biomedcentral.com/1741-7007/11/25.
149. Wang, R.L., A. Stec, J. Hey, L. Lukens and J. Doebley. 1999. The limits of selection during maize domestication. Nature 398: 236-239.
150. Wang, W.Y.S., B.J. Barratt, D.G. Clayton and J.A. Todd. 2005. Genome-wide association studies: theoretical and practical concerns. Nat. Rev. Genet. 6: 109-118.
151. Weng, C., L. Kubisiak, D. Nelson and M. Stine. 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.
152. Wheeler, N.C., K.D. Jermstad, K.V. Krutovsky, S.N. Aitken, G.T. Howe, J. Krakowski and D.B. Neale. 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.
153. White, T.L., W.T. Adams and D.B. Neale. 2007. Forest Genetics, CABI Publ., Wallinford.
154. Willyard, A., J. Syring, D.S. Gernandt, A. Liston and R. Cronn. 2007. Fossil calibration of molecular divergence infers a moderate mutation rate and recent radiations for Pinus. Mol. Biol. Evol. 24: 90-101.
155. Wright, S.I. and B.S. Gaut. 2005. Molecular population genetics and the search for adaptive evolution in plants. Mol. Biol. Evol. 22: 506-519.
156. Yang, J., B. Benyamin, B.P. McEvoy, S. Gordon, A.K. Henders, D.R. Nyholt et al. 2010. Common SNPs explain a large proportion of the heritability for human height. Nat. Genet. 42: 565-569.
157. Yazdani, R., J. Nilsson, C. Plomion and G. Mathur. 2003. Marker trait association for autumn cold acclimation and growth rhythm in Pinus sylvestris. Scand. J. For. Res. 18: 29-38.
158. Ye, X., V. Busov, N. Zhao, R. Meilan, L.M. McDonnell, H.D. Coleman, S.D. Mansfield, F. Chen, Y. Li and Z.M. Cheng. 2011. Transgenic Populus trees for forest products, bioenergy, and functional genomics. Crit. Rev. Plant Sci. 30: 415-434.
159. Yu, Q., B. Li, C. Nelson, S. McKeand, V. Batista and T. Mullin. 2006. Association of the cad-n1 allele with increased stem growth and wood density in full-sib families of loblolly pine. Tree Genet. Genomes 2: 98-108.
160. Zoldos, V., D. Papes, S.C. Brown, O. Panaud and S. Siljak-Yakovlev. 1998. Genome size and base composition of seven Quercus species: inter- and intra-population variation. Genome 41: 162-168.