Search for nucleotide diversity patterns of local adaptation in dehydrins and other cold-related candidate genes in Scots pine (Pinus sylvestris L.)

Tree Genetics and Genomes

Volumn 5, Issue 1, 2009, Pages 117-132

  Wachowiak, Witold ^a,b   Balk, Peter A ^c   Savolainen, Outi ^a  

^a UNIVERSITY OF OULU   (Finland)

^b INSTITUTE OF DENDROLOGY   (Poland)

^c NSure   (Netherlands)

Author keywords

Cold tolerance; Gene families; Linkage disequilibrium; Nucleotide diversity; Pinus sylvestris; Plant adaptation; SNPs

Indexed keywords

CONIFEROPHYTA; PINUS SYLVESTRIS;

EID: 57349197887     PISSN: 16142942     EISSN: 16142950     Source Type: Journal    
DOI: 10.1007/s11295-008-0188-3     Document Type: Article

References (98)

1. ML Aho 1994 Autumn frost hardening of one-year-old Pinus sylvestris (L) seedlings-effect of origin and parent trees Scand J For Res 9 17 24
2. MR Ahuja DB Neale 2005 Evolution of genome size in conifers Silvae Genet 54 126 137
3. NH Barton 1999 Clines in polygenic traits Genet Res 74 223 236
4. ST tell us Trends Ecol Evol 20 435 440
5. MA Beaumont RA Nichols 1996 Evaluating loci for use in the genetic analysis of population structure Proc R Soc Lond B 263 1619 1626
6. MA Beaumont DJ Balding 2004 Identifying adaptive genetic divergence among populations from genome scans Mol Ecol 13 969 980
7. S Biswas JM Akey 2006 Genomic insights into positive selection Trends Genet 22 437 446
8. M Bouille J Bousquet 2005 Trans-species shared polymorphisms at orthologous nuclear gene loci among distant species in the conifer Picea (Pinaceae): implications for the long-term maintenance of genetic diversity in trees Am J Bot 92 63 73
9. GR Brown GP Gill RJ Kuntz CH Langley DB Neale 2004 Nucleotide diversity and linkage disequilibrium in loblolly pine Proc Natl Acad Sci U S A 101 15255 15260
10. D Charlesworth 2006 Balancing selection and its effects on sequences in nearby genome regions Plos Genetics 2 379 384
11. B Charlesworth M Nordborg D Charlesworth 1997 The effects of local selection, balanced polymorphism and background selection on equilibrium patterns of genetic diversity in subdivided populations Genet Res 70 155 174
12. R Cheddadi GG Vendramin T Litt L Francois M Kageyama S Lorentz JM Laurent JL de Beaulieu L Sadori A Jost D Lunt 2006 Imprints of glacial refugia in the modern genetic diversity of Pinus sylvestris Global Ecol Biogeogr 15 271 282
13. DW Choi B Zhu TJ Close 1999 The barley (Hordeum vulgare L.) dehydrin multigene family: sequences, allele types, chromosome assignments, and expression characteristics of 11 Dhn genes of cv Dicktoo Theor Appl Genet 98 1234 1247
14. TJ Close 1997 Dehydrins: a commonality in the response of plants to dehydration and low temperature Physiol Plantarum 100 291 296
15. CC Cockerham BS Weir 1993 Estimation of gene flow from F-statistics Evolution 47 855 863
16. Critchfield WB, Little ELJ (1966) Geographic distribution of the pines of the World. Miscellaneous Publication 991 edn. USDA Forest Service, pp 97
17. IS Day VS Reddy GS Ali ASN Reddy 2002 Analysis of EF-hand-containing proteins in Arabidopsis Genome Biol 3 research0056.1 research0056.24
18. V Dvornyk A Sirvio M Mikkonen O Savolainen 2002 Low nucleotide diversity at the pal1 locus in the widely distributed Pinus sylvestris Mol Biol Evol 19 179 188
19. G Eriksson S Andersson V Eiche J Ifver A Persson 1980 Severity index and transfer effects on survival and volume production of Pinus sylvestris in Northern Sweden Stud For Suec 156 1 36
20. E Eveno C Collada MA Guevara V Léger A Soto L Díaz P Léger SC González-Martínez MT Cervera C Plomion PH Garnier-Géré 2008 Contrasting patterns of selection at Pinus pinaster Ait. drought stress candidate genes as revealed by genetic differentiation analyses Mol Biol Evol 25 2 417 437
21. A Eyre-Walker PD Keightley NG Smith D Gaffney 2002 Quantifying the slightly deleterious mutation model of molecular evolution Mol Biol Evol 19 12 2142 2149
22. JC Fay CI Wu 2000 Hitchhiking under positive Darwinian selection Genetics 155 1405 1413
23. RR Finkelstein SSL Gampala CD Rock 2002 Abscisic acid signaling in seeds and seedlings Plant Cell 14 S15 S45
24. MR García-Gil M Mikkonen O Savolainen 2003 Nucleotide diversity at two phytochrome loci along a latitudinal cline in Pinus sylvestris Mol Ecol 12 1195 1206
25. BS Gaut SI Wright C Rizzon J Dvorak LK Anderson 2007 Opinion- Recombination: an underappreciated factor in the evolution of plant genomes Nat Rev, Genet 8 77 84
26. SC González-Martínez E Ersoz GR Brown NC Wheeler DB Neale 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
27. SC González-Martínez KV Krutovsky DB Neale 2006 Forest-tree population genomics and adaptive evolution New Phytol 170 227 238
28. SC González-Martínez NC Wheeler E Ersoz CD Nelson DB Neale 2007 Association genetics in Pinus taeda L. I. Wood property traits Genetics 175 399 409
29. D Hall V Luquez VM Garcia KR Onge S Jansson PK 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 61-12 2849 2860
30. PW Hedrick 2007 Balancing selection Curr Biol 17 R230 R231
31. M Heuertz E De Paoli T Kallman H Larsson I Jurman M Morgante M Lascoux N Gyllenstrand 2006 Multilocus patterns of nucleotide diversity, linkage disequilibrium and demographic history of Norway spruce [Picea abies (L.) Karst] Genetics 174 2095 2105
32. WG Hill A Robertson 1968 Linkage disequilibrium in finite populations Theor Appl Genet 38 226 231
33. WG Hill BS Weir 1988 Variances and covariances of squared linkage disequilibria in finite populations Theor Popul Biol 33 54 78
34. FA Hoekstra EA Golovina J Buitink 2001 Mechanisms of plant desiccation tolerance Trends Plant Sci 6 431 438
35. GT Howe SN Aitken DB Neale KD Jermstad NC Wheeler THH Chen 2003 From genotype to phenotype: unravelling the complexities of cold adaptation in forest trees Can J Bot-Revue Canadienne De Botanique 81 1247 1266
36. RR Hudson 2000 A new statistic for detecting genetic differentiation Genetics 155 2011 2014
37. RR Hudson 2001 Two-locus sampling distributions and their application Genetics 159 1805 1817
38. RR Hudson M Kreitman M Aguade 1987 A test of neutral molecular evolution based on nucleotide data Genetics 116 153 159
39. RR Hudson DD Boos NL Kaplan 1992 A statistical test for detecting geographic subdivision Mol Biol Evol 9 138 151
40. AL Hughes M Nei 1988 Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection Nature 335 167 170
41. Huntley B, Birks HJB (1983) An atlas of past and present pollen map in Europe: 0-13000 years ago. Cambridge University Press, Cambridge
42. P Hurme T Repo O Savolainen T Paakkonen 1997 Climatic adaptation of bud set and frost hardiness in Scots pine (Pinus sylvestris) Can J Forest Res-Revue Canadienne De Recherche Forestiere 27 716 723
43. P Hurme MJ Sillanpaa E Arjas T Repo O Savolainen 2000 Genetic basis of climatic adaptation in Scots pine by Bayesian quantitative trait locus analysis Genetics 156 1309 1322
44. PK Ingvarsson 2005 Nucleotide polymorphism and linkage disequilibrium within and among natural populations of European aspen (Populus tremula L., Salicaceae) Genetics 169 945 953
45. AM Ismail AE Hall TJ Close 1999 Allelic variation of a dehydrin gene cosegregates with chilling tolerance during seedling emergence Proc Natl Acad Sci U S A 96 13566 13570
46. P Järvinen J Lemmetyinen O Savolainen T Sopanen 2003 DNA sequence variation in BpMADS2 gene in two populations of Betula pendula Mol Ecol 12 369 384
47. KD Jermstad DL Bassoni NC Wheeler TS Anekonda SN Aitken WT Adams DB Neale 2001 Mapping of quantitative trait loci controlling adaptive traits in coastal Douglas-fir. II. Spring and fall cold-hardiness Theor Appl Genet 102 1152 1158
48. RVL Joosen M Lammers PA Balk P Bronnum MCJM Konings M Perks E Stattin MF Van Wordragen AHM van der Geest 2006 Correlating gene expression to physiological parameters and environmental conditions during cold acclimation of Pinus sylvestris, identification of molecular markers using cDNA microarrays Tree Physiol 26 1297 1313
49. T Kado H Yoshimaru Y Tsumura H Tachida 2003 DNA variation in a conifer, Cryptomeria japonica (Cupressaceae sensu lato) Genetics 164 1547 1559
50. SR Kalberer M Wisniewski R Arora 2006 Deacclimation and reacclimation of cold-hardy plants: current understanding and emerging concepts Plant Science 171 3 16
51. A Karhu P Hurme M Karjalainen P Karvonen K Karkkainen D Neale O Savolainen 1996 Do molecular markers reflect patterns of differentiation in adaptive traits of conifers Theor Appl Genet 93 215 221
52. MC Koag RD Fenton S Wilkens TJ Close 2003 The binding of maize DHN1 to lipid vesicles. Gain of structure and lipid specificity Plant Physiol 131 309 316
53. HP Koelewijn V Koski O Savolainen 1999 Magnitude and timing of inbreeding depression in Scots pine (Pinus sylvestris L.) Evolution 53 758 768
54. S Kontunen-Soppela K Taulavuori E Taulavuori P Lahdesmaki K Laine 2000 Soluble proteins and dehydrins in nitrogen-fertilized Scots pine seedlings during deacclimation and the onset of growth Physiol Plantarum 109 404 409
55. KV Krutovsky DB Neale 2005 Nucleotide diversity and linkage disequilibrium in cold-hardiness and wood quality-related candidate genes in Douglas fir Genetics 171 2029 2041
56. RG Latta 1998 Differentiation of allelic frequencies at quantitative trait loci affecting locally adaptive traits Am Nat 151 283 292
57. RG Latta 2004 Gene flow, adaptive population divergence and comparative population structure across loci New Phytol 161 51 58
58. V Le Corre A Kremer 2003 Genetic variability at neutral markers, quantitative trait loci and trait in a subdivided population under selection Genetics 164 1205 1219
59. E Lerceteau AE Szmidt B Andersson 2001 Detection of quantitative trait loci in Pinus sylvestris L. across years Euphytica 121 117 122
60. M Lynch TJ Crease 1990 The analysis of population survey data on DNA sequence variation Mol Biol Evol 7 377 394
61. XF Ma AE Szmidt XR Wang 2006 Genetic structure and evolutionary history of a diploid hybrid pine Pinus densata inferred from the nucleotide variation at seven gene loci Mol Biol Evol 23 807 816
62. JH McDonald M Kreitman 1991 Adaptive protein evolution at the Adh locus in Drosophila Nature 351 652 654
63. JK McKay RG Latta 2002 Adaptive population divergence: markers, QTL and traits Trends Ecol Evol 17 285 291
64. G McVean P Awadalla P Fearnhead 2002 A coalescent-based method for detecting and estimating recombination from gene sequences Genetics 160 1231 1241
65. Morgenstern EK (1996) In: Morgenstern EK (ed) Geographic variation in forest trees: genetic basis and application of knowledge in silviculture. UBC, Washington, p 214
66. JM Mouillon P Gustafsson P Harryson 2006 Structural investigation of disordered stress proteins. Comparison of full-length dehydrins with isolated peptides of their conserved segments Plant Physiol 141 638 650
67. O Muona A Harju 1989 Effective population sizes, genetic variability, and mating system in natural stands and seed orchards of Pinus sylvestris Silvae Genet 38 221 228
68. DB Neale O Savolainen 2004 Association genetics of complex traits in conifers Trends Plant Sci 9 325 330
69. Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New York
70. M Nylander J Svensson ET Palva BV Welin 2001 Stress-induced accumulation and tissue-specific localization of dehydrins in Arabidopsis thaliana Plant Mol Biol 45 263 279
71. D Pot L McMillan C Echt G Le Provost P Garnier-Gere S Cato C Plomion 2005 Nucleotide variation in genes involved in wood formation in two pine species New Phytol 167 101 112
72. T Puhakainen MW Hess P Makela J Svensson P Heino ET Palva 2004 Overexpression of multiple dehydrin genes enhances tolerance to freezing stress in Arabidopsis Plant Mol Biol 54 743 753
73. T Pyhäjärvi MR García-Gil T Knürr M Mikkonen W Wachowiak O Savolainen 2007 Demographic history has influenced nucleotide diversity in European Pinus sylvestris populations Genetics 177 1713 1724
74. T Pyhäjärvi MJ Salmela O Savolainen 2008 Colonization routes of Pinus sylvestris inferred from distribution of mitochondrial DNA variation Tree Genet Genom 4 247 254
75. S Ramos-Onsins J Rozas 2002 Statistical properties of new neutrality tests against population growth Mol Biol Evol 19 2092 2100
76. T Rorat 2006 Plant dehydrins-tissue location, structure and function Cell Mol Biol Lett 11 536 556
77. K Roselius W Stephan T Stadler 2005 The relationship of nucleotide polymorphism, recombination rate and selection in wild tomato species Genetics 171 753 763
78. J Rozas JC Sanchez-DelBarrio X Messeguer R Rozas 2003 DnaSP, DNA polymorphism analyses by the coalescent and other methods Bioinformatics 19 2496 2497
79. PC Sabeti DE Reich JM Higgins HZP Levine DJ Richter SF Schaffner SB Gabriel JV Platko NJ Patterson GJ McDonald HC Ackerman SJ Campbell D Altshuler R Cooper D Kwiatkowski R Ward ES Lander 2002 Detecting recent positive selection in the human genome from haplotype structure Nature 419 832 837
80. O Savolainen T Pyhäjärvi T Knürr 2007 Gene flow and local adaptation in trees Ann Rev Ecol 38 595 619
81. O Savolainen T Pyhäjärvi 2007 Genomic diversity in forest trees Curr Opin Plant Biol 10 1 6
82. MM Seppänen T Cardi MB Hyökki E Pehu 2000 Characterization and expression of cold-induced glutathione S-transferase in freezing tolerant Solanum commersonii, sensitive S. tuberosum and their interspecific somatic hybrids Plant Science 153 125 133
83. N Soranzo R Alia J Provan W Powell 2000 Patterns of variation at a mitochondrial sequence-tagged-site locus provides new insights into the postglacial history of European Pinus sylvestris populations Mol Ecol 9 1205 1211
84. F Tajima 1989 Statistical method for testing the neutral mutation hypothesis by DNA polymorphism Genetics 123 585 595
85. MI Tenaillon J U'Ren O Tenaillon BS Gaut 2004 Selection versus demography: a multilocus investigation of the domestication process in maize Mol Biol Evol 21 1214 1225
86. JD Thompson TJ Gibson F Plewniak F Jeanmougin DG Higgins 1997 The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools Nucleic Acids Res 24 4876 4882
87. P Tiffin BS Gaut 2001 Sequence diversity in the tetraploid Zea perennis and the closely related diploid Z. diploperennis: insights from four nuclear loci Genetics 158 401 412
88. G Watterson 1975 On the number of segregating sites in genetical models without recombination Theor Popul Biol 7 256 276
89. A Welling ET Palva 2006 Molecular control of cold acclimation in trees Physiol Plantarum 127 167 181
90. A Welling P Rinne A Vihera-Aarnio S Kontunen-Soppela P Heino ET Palva 2004 Photoperiod and temperature differentially regulate the expression of two dehydrin genes during overwintering of birch (Betula pubescens Ehrh.) J Exp Bot 55 507 516
91. ME Wisniewski CL Bassett J Renaut R Farrell T Tworkoskii TS Artlip 2006 Differential regulation of two dehydrin genes from peach (Prunus persica) by photoperiod, low temperature and water deficit Tree Physiol 26 575 584
92. SI Wright B Charlesworth 2004 The HKA test revisited: a maximum-likelihood-ratio test of the standard neutral model Genetics 168 1071 1076
93. SI Wright BS Gaut 2005 Molecular population genetics and the search for adaptive evolution in plants Mol Biol Evol 22 3 506 519
94. SI Wright B Lauga D Charlesworth 2003 Subdivision and haplotype structure in natural populations of Arabidopsis lyrata Mol Ecol 12 1247 1263
95. K Yamaguchi-Shinozaki K Shinozaki 2006 Transcriptional regulatory networks in cellular responses and tolerance to dehydration and cold stresses Ann Rev Plant Biol 57 781 803
96. TW Yang LJ Zhang TG Zhang H Zhang SJ Xu LZ An 2005 Transcriptional regulation network of cold-responsive genes in higher plants Plant Science 169 987 995
97. R Yazdani JE Nilsson C Plomion G Mathur 2003 Marker trait association for autumn cold acclimation and growth rhythm in Pinus sylvestris Scand J For Res 18 29 38
98. ZM Yin T Rorat BM Szabala A Ziolkowska S Malepszy 2006 Expression of a Solanum sogarandinum SK3-type dehydrin enhances cold tolerance in transgenic cucumber seedlings Plant Sci 170 1164 1172