Genetic and genomic approaches to assess adaptive genetic variation in plants: Forest trees as a model

Physiologia Plantarum

Volumn 137, Issue 4, 2009, Pages 509-519

  Gailing, Oliver ^a,b   Vornam, Barbara ^a   Leinemann, Ludger ^a   Finkeldey, Reiner ^a  

^a UNIVERSITY OF GÖTTINGEN   (Germany)

^b MICHIGAN TECHNOLOGICAL UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADAPTATION; BIOLOGICAL MODEL; GENETIC VARIABILITY; GENETICS; GENOMICS; METHODOLOGY; PLANT GENOME; QUANTITATIVE TRAIT LOCUS; REVIEW; TREE;

ADAPTATION, PHYSIOLOGICAL; GENETIC VARIATION; GENOME, PLANT; GENOMICS; MODELS, GENETIC; QUANTITATIVE TRAIT LOCI; TREES;

QUERCUS;

EID: 70450265626     PISSN: 00319317     EISSN: 13993054     Source Type: Journal    
DOI: 10.1111/j.1399-3054.2009.01263.x     Document Type: Review

References (80)

1. Arnholdt-Schmitt B, Costa JH, de Melo DF (2006) AOX -a functional marker for efficient cell reprogramming under stress? Trends Plant Sci 11 : 281 287
2. Austerlitz F, Mariette S, Machon N, Gouyon P-H, Godelle B (2000) Effects of colonization processes on genetic diversity: differences between annual plants and tree species. Genetics 154 : 1309 1321
3. Barreneche T, Bodenes C, Lexer C, Trontin J-F, Fluch S, Streiff R, Plomion C, Roussel G, Steinkellner H, Burg K, Favre J-M, Glossl J, Kremer A (1998) A genetic linkage map of Quercus robur L. (pedunculate oak) based on RAPD, SCAR, microsatellite, minisatellite, isozyme and 5S rDNA markers. Theor Appl Genet 97 : 1090 1103
4. Barreneche T, Casasoli M, Russell K, Akkak A, Meddour H, Plomion C, Villani F, Kremer A (2004) Comparative mapping between Quercus and Castanea using simple-sequence repeats (SSRs). Theor Appl Genet 108 : 558 566
5. Beavis WD (1998) QTL analysis: power, precision, and accuracy. In: Paterson AH (ed) Molecular Dissection of Complex Traits, CRC press, Boca Raton, pp 145 162
6. Benedict C, Skinner JS, Meng R, Chang YJ, Bhalerao R, Huner NPA, Finn CE, Chen THH, Hurry V (2006) The CBF1-dependent low temperature signalling pathway, regulon and increase in freeze tolerance are conserved in Populus spp. Plant Cell Environ 29 : 1259 1272
7. Bodenes C, Joandet S, Laigret F, Kremer A (1997) Detection of genomic regions differentiating two closely related oak species Quercus petraea (Matt.) Liebl. and Quercus robur L. Heredity 78 : 433 444
8. Brendel O, Le Thiec D, Scotti-Saintagne C, Bodenes C, Kremer A, Guehl J-M (2008) Quantitative trait loci controlling water use efficiency and related traits in Quercus robur L. Tree Genet Genomes 4 : 263 278
9. Brunner AM, Busov VB, Strauss SH (2004) Poplar genome sequence: functional genomics in an ecologically dominant plant species. Trends Plant Sci 9 : 49 56
10. Cardon LR, Bell JI (2001) Association study designs for complex diseases. Nat Rev Genet 2 : 91 99
11. Casasoli M, Derory J, Morera-Dutrey C, Brendel O, Porth I, Guehl JM, Villani F, Kremer A (2006) Comparison of quantitative trait loci for adaptive traits between oak and chestnut based on an expressed sequence tag consensus map. Genetics 172 : 533 546
12. Casasoli M, Mattioni C, Cherubini M, Villani F (2001) A genetic linkage map of European chestnut (Castanea sativa Mill) based on RAPD, ISSR and isozyme markers. Theor Appl Genet 102 : 1190 1199
13. Casasoli M, Pot D, Plomion C, Monteverdi MC, Barreneche T, Lauteri M, Villani F (2004) Identification of QTLs affecting adaptive traits in Castanea sativa Mill. Plant Cell Environ 27 : 1088 1101
14. Coart E, Lamote V, De Loose M, Van Bockstaele E, Lootens P, Roldan-Ruiz I (2002) AFLP markers demonstrate local genetic differentiation between two indigenous oak species Quercus robur L. and Quercus petraea (Matt.) Liebl in Flemish populations. Theor Appl Genet 105 : 431 439
15. Curtu A-L (2006) Patterns of Genetic Variation and Hybridization in a Mixed Oak (Quercus spp.) forest. Cuvillier Verlag, Gottingen, pp 159
16. Curtu AL, Gailing O, Leinemann L, Finkeldey R (2007) Genetic variation and differentiation within a natural community of five oak species (Quercus spp.). Plant Biol 9 : 116 126
17. Derory J, Leger P, Garcia V, Schaeffer J, Hauser M-T, Salin F, Luschnig C, Plomion C, Glossl J, Kremer A (2006) Transcriptome analysis of bud burst in sessile oak (Quercus petraea). New Phytol 170 : 723 738
18. Devey ME, Delfinomix A, Kinloch BB, Neale DB (1995) Random amplified polymorphic DNA markers linked to a gene for resistance to white-pine blister rust in sugar pine. Proc Natl Acad Sci USA 92 : 2066 2070
19. Ducousso A, Guyon JP, Kremer A (1996) Latitudinal and altitudinal variation of bud burst in western populations of sessile oak (Quercus petraea (Matt)Liebl)). Ann Sci For 53 : 775 782
20. Eriksson G, Ekberg I (2001) An Introduction to Forest Genetics, Uppsala, Sweden
21. Finkeldey R (2001) Genetic variation of oaks (Quercus spp.) in Switzerland. 1. Allelic diversity and differentiation at isozyme gene loci. For Genet 8 : 185 195
22. Finkeldey R, Hattemer HH (2007) Tropical Forest Genetics. Springer, Berlin
23. Finkeldey R, Ziehe M (2004) Genetic implications of silvicultural regimes. For Ecol Manage 197 : 231 244
24. Flint-Garcia SA, Thornsberry JM, Buckler ES (2003) Structure of linkage disequilibrium in plants. Annu Rev Plant Biol 54 : 357 374
25. Gailing O (2008) QTL analysis of leaf morphological characters in a Quercus robur full-sib family (Q. robur x Q. robur subsp. slavonica). Plant Biol 10 : 624 634
26. Gailing O, Kremer A, Steiner W, Hattemer HH, Finkeldey R (2005) Results on quantitative trait loci for flushing date in oaks can be transferred to different segregating progenies. Plant Biol 7 : 516 525
27. Gailing O, Langenfeld-Heyser R, Polle A, Finkeldey R (2008) QTL loci affecting stomatal density and growth in a Quercus robur progeny: implications for the adaptation to changing environments. Global Chang Biol 14 : 1934 1946
28. Gailing O, Wachter H, Heyder J, Schmitt H-P, Finkeldey R (2007) Chloroplast DNA analysis in oak stands (Quercus robur L.) in North Rhine-Westphalia with presumably Slavonian origin: is there an association between geographic origin and bud phenology? J Appl Bot Food Qual 81 : 165 171
29. Gailing O, Wachter H, Leinemann L, Hosius B, Finkeldey R, Schmitt H-P, Heyder J (2003) Characterisation of different provenances of late flushing pedunculate oak (Quercus robur L.) with chloroplast markers. Allg Forst- u J-Ztg 174 : 227 231
30. Geldermann H (1975) Investigations on inheritance of quantitative characters in animals by gene markers I. Methods. Theor Appl Genet 46 : 319 330
31. Gomory D (2000) A gene encoding for a non-specific NAD-dependent dehydrogenase shows a strong differentiation between Quercus robur and Quercus petraea. For Genet 7 : 167 170
32. Gonzalez-Martinez SC, Ersoz E, Brown GR, Wheeler NC, Neale DB (2006) 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
33. Gonzalez-Martinez SC, Huber D, Ersoz E, Davis JM, Neale DB (2008) Association genetics in Pinus taeda L. II. Carbon isotope discrimination. Heredity 101 : 19 26
34. Gonzalez-Martinez SC, Wheeler NC, Ersoz E, Nelson CD, Neale DB (2007) Association genetics in Pinus taeda L. I. Wood property traits. Genetics 175 : 399 409
35. Grattapaglia D, Sederoff R (1994) Genetic linkage maps of Eucalyptus grandis and Eucalyptus urophylla using a pseudo-testcross mapping strategy and RAPD markers. Genetics 137 : 1121 1137
36. Hamrick JL (2004) Response of forest trees to global environmental changes. For Ecol Manage 197 : 323 335
37. Hamrick JL, Godt MJW, Sherman-Broyles SL (1992) Factors influencing levels of genetic diversity in woody plant species. New For 6 : 95 124
38. Hertel H, Degen B (1998) Stieleiche von Traubeneiche mit Hilfe von Isoenzymanalysen sicher unterscheiden. Allg Forstz 53 : 246 247
39. Ingvarsson PK (2005) Nucleotide polymorphism and linkage disequilbrium within and among natural populations of European Aspen (Populus tremula L., Salicaceae). Genetics 169 : 945 953
40. Jermstad KD, Bassoni DL, Jech KS, Wheeler NC, Neale DB (2001) Mapping of quantitative trait loci controlling adaptive traits in coastal Douglas-fir. I. Timing of vegetative bud flush. Theor Appl Genet 102 : 1142 1151
41. Kremer A (1994) Programme d'ameloration genetique du chene rouge en France. In: Timbal J, Kremer A, Le Goff N and Nepveu G (eds) Le chene rouge d' Amerique. INRA Editions, Paris, pp 425 446
42. Kremer A, Casasoli M, Barreneche T, Bodenes C, Sisco P, Kubisiak T, Scalfi M, Leonardi E, Bakker E, Buiteveldt J, Romero-Severson J, Arumuganathan K, Derory J, Scotti-Saintagne C, Roussel G, Bertocchi E, Lexer C, Porth I, Hebard F, Clark C, Carlson J, Plomion C, Koelewijn H-P and Villani F (2007) Fagaceae Trees. In: Kole C (ed) Genome Mapping and Molecular Breeding in Plants Forest Trees. Springer, Berlin, pp 161 187
43. Kremer A, Dupouey JL, Deans JD, Cottrell J, Csaikl U, Finkeldey R, Espinel S, Jensen J, Kleinschmit J, Van Dam B, Ducousso A, Forrest I, Lopez de Heredia U, Lowe AJ, Tutkova M, Munro RC, Steinhoff S, Badeau V (2002) Leaf morphological differentiation between Quercus robur and Quercus petraea is stable across western European mixed oak stands. Ann For Sci 59 : 777 778
44. Krutovsky KV, Elsik CG, Matvienko M, Kozik A, Neale DB (2007) Conserved ortholog sets in forest trees. Tree Genet Genomes 3 : 61 70
45. Krutovsky KV, Neale D (2005a) Nucleotide diversity and linkage disequilibrium in cold-hardiness- and wood quality-related candidate genes in douglas fir. Genetics 171 : 2029 2041
46. Krutovsky KV, Neale DB (2005b) Forest genomics and new molecular genetic approaches to measuring and conserving adaptive genetic diversity in forest trees. In: Geburek T, Turok J (eds) Conservation and Management of Forest Genetic Resources in Europe. Arbora Publishers, Zvolen, pp 369 390
47. Lexer C, Rosenthal DM, Raymond O, Donovan LA, Rieseberg LH (2005) Genetics of species differences in the wild annual sunflowers, Helianthus annuus and H. petiolaris. Genetics 169 : 2225 2239
48. Liewlaksaneeyanawin C, Zhuang J, Tang M, Farzaneh N, Lueng GL, Cullis C, Findlay S, Ritland CE, Bohlmann J, Ritland K (2009) Identification of COS markers in the Pinaceae. Tree Genet Genomes 5 : 247 255
49. Mariette S, Cottrell J, Csaikl UM, Goikoechea P, Konig AO, Lowe AJ, Van Dam BC, Barreneche T, Bodenes C, Streiff R, Burg K, Groppe K, Munro RC, Tabbener H, Kremer A (2002) Comparison of levels of genetic diversity detected with AFLP and microsatellite markers within and among mixed Q. petraea (Matt.) Liebl. and Q. robur L. stands. Silvae Genet 51 : 72 79
50. Muir G and Schlotterer C (2005) Evidence for shared ancestral polymorphism rather than recurrent gene flow at microsatellite loci differentiating two hybridising oaks (Quercus spp.). Mol Ecol 14 : 549 561
51. Muller-Starck G, Herzog S, Hattemer HH (1993) Intra- and interpopulational genetic variation in juvenile populations of Quercus robur L. and Qercus petraea Liebl Ann Sci For 50 (Suppl 1 233s 244s
52. Neale DB (2007) Genomics to tree breeding and forest health. Curr Opin Genet Dev 17 : 539 544
53. Neale DB, Savolainen O (2004) Association genetics of complex traits in conifers. Trends Plant Sci 9 : 325 330
54. Orr HA (1998) The population genetics of adaptation: the distribution of factors fixed during adaptive evolution. Evolution 52 : 935 949
55. Papageorgiou AC, Vidalis A, Gailing O, Tsiripidis I, Hatziskakis S, Boukos S, Alatsidas S, Finkeldey R (2008) Genetic variation of beech (Fagus sylvatica L.) in Rodopi (N.E. Greece). Eur J For Res 127 : 81 88
56. Parelle J, Zapater M, Scotti-Saintagne C, Kremer A, Jolivet Y, Dreyer E, Brendel O (2007) Quantitative trait loci of tolerance to waterlogging in a European oak (Quercus robur L.): physiological relevance and temporal effect patterns. Plant Cell Environ 30 : 422 434
57. Petit R, Brewer S, Bordacs S, Burg K, Cheddadi R, Coart E, Cottrell J, Csaikl U, van Dam B, Deans D, Espinel S, Fineschi S, Finkeldey R, Glaz I, Goicoechea PG, Jensen JS, Konig AO, Lowe AJ, Madsen SF, Matyas G, Munro RC, Popescu F, Slade D, Tabbener H, de Vries SGM, Ziegenhagen B, de Beaulieu J-L, Kremer A (2002a) Identification of refugia and post-glacial colonisation routes of European white oaks based on chloroplast DNA and fossil pollen evidence. For Ecol Manage 156 : 49 74
58. Petit R, Csaikl U, Bordacs S, Burg K, Coart E, Cottrell J, van Dam B, Deans D, Dumolin-Lapegue S, Fineschi S, Finkeldey R, Gillies A, Glaz I, Goicoechea PG, Jensen JS, Konig AO, Lowe AJ, Madsen SF, Matyas G, Munro RC, Olalde M, Pemonge M-H, Popescu F, Slade D, Tabbener H, Taurchini D, de Vries SGM, Ziegenhagen B, Kremer A (2002b) Chloroplast DNA variation in European white oaks. Phylogeography and patterns of diversity based on data from over 2600 populations. For Ecol Manage 156 : 5 26
59. Petit R, Pineau E, Demesure B, Bacilieri R, Ducousso A, Kremer A (1997) Chloroplast DNA footprints of postglacial recolonization by oaks. Proc Natl Acad Sci USA 94 : 9996 10001
60. Petit RJ, Bodenes C, Ducousso A, Roussel G, Kremer A (2003) Hybridization as a mechanism of invasion in oaks. New Phytol 161 : 151 164
61. Plomion C, Chagne D, Pot D, Kumar S, Wilcox PL, Burdon RD, Prat D, Peterson DG, Paiva J, Chaumeil P, Vendramin GG, Sebastiani F, Nelson CD, Echt CS, Savolainen O, Kubisiak TL, Cervera MT, de Maria N and Islam-Faridi MN (2007) Pines. In: Kole C (ed) Genome Mapping and Molecular Breeding in Plants, Forest Trees. Springer, New York, pp 29 92
62. Porth I, Scotti-Saintagne C, Barreneche T, Kremer A, Burg K (2005) Linkage mapping of osmotic stress induced genes of oak. Tree Genet Genomes 1 : 31 40
63. Ritter E, Espinel S, Favre J-M, Fladung M (2004) High-density linkage maps of conifer species and their potential application. In: Kumar S, Fladung M (eds) Molecular Genetics and Breeding of Forest Trees. The Haworth Press, New York, pp 341 357
64. Saintagne C, Bodenes C, Barreneche T, Pot D, Plomion C, Kremer A (2004) Distribution of genomic regions differentiating oak species assessed by QTL detection. Heredity 92 : 20 30
65. Savolainen O, Pyhajarvi T (2007) Genomic diversity in forest trees. Curr Opin Plant Biol 10 : 162 167
66. Scalfi M, Troggio M, Piovani P, Leonardi S, Magnaschi G, Vendramin GG, Menozzi P (2004) A RAPD, AFLP and SSR linkage map, and QTL analysis in European beech (Fagus sylvatica L.). Theor Appl Genet 108 : 433 441
67. Scotti-Saintagne C, Bodenes C, Barreneche T, Bertocchi E, Plomion C, Kremer A (2004a) Detection of quantitative trait loci controlling bud burst and height growth in Quercus robur L. Theor Appl Genet 109 : 1648 1659
68. Scotti-Saintagne C, Mariette S, Porth I, Goicoechea PG, Barreneche T, Bodenes K, Burg K, Kremer A (2004b) Genome scanning of interspecific differentiation between two closely related oak species (Quercus robur L. and Q. petraea (Matt.) Liebl.). Genetics 168 : 1615 1626
69. Shinozaki K, Yamaguchi-Shinozaki K (2000) Molecular responses to dehydration and low temperature: differences and cross-talk between two stress signaling pathways. Curr Opin Plant Biol 3 : 217 223
70. Shinozaki K, Yamaguchi-Shinozaki K and Seki M (2003) Regulatory network of gene expression in the drought and cold stress responses. Curr Opin Plant Biol 6 : 410 417
71. Tanksley SD (1993) Mapping polygenes. Annu Rev Genet 27 : 205 233
72. Thumma BR, Nolan MR, Evans R, Moran GF (2005) Polymorphisms in cinnamoyl CoA reductase (CCR) are associated with variation in microfibril angle in Eucalyptus spp. Genetics 171 : 1257 1265
73. Vornam B, Gailing O, Finkeldey R, Collada C, Guevera M, Soto Á, de María N, González-Martínez S, Díaz L, Alia R, Aranda I, Climent J, Cervera M, Goicoechea P, Léger V, Eveno E, Derory J, Garnier-Géré P, Kremer A, Plomion C (2007) Naturally occurring nucleotide diversity in candidate genes for forest tree adaptation: magnitude, distribution and association with quantitative trait variation. GABI - The German Plant Genome Research Program Progress Report 2004-2007 : 116 120
74. Vos P, Hogers R, Bleeker M, Reijans M, van de Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabeau M (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23 : 4407 4414
75. Wachter H (2001) Untersuchungen zum Eichensterben in NRW. Schriftenreihe der Landesforstverwaltung NRW 13 : 1 112
76. Wright JW (1976) Introduction to Forest Genetics. Academic Press, London
77. Wu CI, Ting CT (2004) Genes and speciation. Nat Rev Genet 5 : 114 122
78. Wu HX (2002) Study of early selection in tree breeding. 4. Efficiency of marker-aided early selection (MAES). Silvae Genet 51 : 261 269
79. Zanetto A, Roussel G, Kremer A (1994) Geographic variation of inter-specific differentiation between Quercus robur L. and Quercus petraea (Matt.) Liebl. For Genet 1 : 111 123
80. Zanetto A, Kremer A, Muller-Starck G, Hattemer H (1996) Inheritance of isozymes in pedunculate oak (Quercus robur L.). J Heredity 87 : 364 370