Scanning the genome for gene SNPs related to climate adaptation and estimating selection at the molecular level in boreal black spruce

Molecular Ecology

Volumn 20, Issue 8, 2011, Pages 1702-1716

  Prunier, Julien ^a   Laroche, Jérôme ^a   Beaulieu, Jean ^a,b   Bousquet, Jean ^a  

^a UNIVERSITÉ LAVAL   (Canada)

^b NATURAL RESOURCES CANADA   (Canada)

Author keywords

adaptive divergence; climate; genome scan; natural selection; outlier loci; spruces

Indexed keywords

PLANT DNA; RAIN;

ADAPTATION; ARTICLE; CANADA; CLIMATE; DNA SEQUENCE; EXPRESSED SEQUENCE TAG; GENETIC SELECTION; GENETICS; GENOTYPE; PLANT GENOME; POPULATION GENETICS; QUANTITATIVE TRAIT; SINGLE NUCLEOTIDE POLYMORPHISM; SPRUCE; TEMPERATURE;

ADAPTATION, PHYSIOLOGICAL; CANADA; CLIMATE; DNA, PLANT; EXPRESSED SEQUENCE TAGS; GENETICS, POPULATION; GENOME, PLANT; GENOTYPE; PICEA; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT, HERITABLE; RAIN; SELECTION, GENETIC; SEQUENCE ANALYSIS, DNA; TEMPERATURE;

CONIFEROPHYTA; PICEA MARIANA;

EID: 79953164600     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2011.05045.x     Document Type: Article

References (93)

1. Acheré V, Favre JM, Besnard G, Jeandroz S, (2005) Genomic organization of molecular differentiation in Norway spruce (Picea abies). Molecular Ecology, 14, 3191-3201.
2. Aitken SN, Yeaman S, Holliday JA, Wang T, Curtis-McLane S, (2008) Adaptation, migration or extirpation: climate change outcomes for tree populations. Evolutionary Applications, 1, 95-111.
3. Bannister P, Neumer G, (2001) Frost resistance and the distribution of conifers. In: Conifer Cold Hardiness (eds, Bigras FJ, Colombo SJ,). pp. 3-21. Kluwer Academic Publisher, Dordrecht, The Netherlands.
4. Beaulieu J, Perron M, Bousquet J, (2004) Multivariate patterns of adaptive genetic variation and seed source transfer in Picea mariana. Canadian Journal of Forest Research, 34, 531-545. (Pubitemid 38784053)
5. Beaumont MA, Balding DJ, (2004) Identifying adaptive genetic divergence among populations from genome scans. Molecular Ecology, 13, 969-980. (Pubitemid 38390600)
6. Beaumont MA, Nichols RA, (1996) Evaluating loci for use in the genetic analysis of population structure. Proceedings of the Royal Society B: Biological Sciences, 263, 1619-1626. (Pubitemid 27055553)
7. Bedon F, Grima-Pettenati J, Mackay J, (2007) Conifer R2R3-MYB transcription factors: sequence analyses and gene expression in wood-forming tissues of white spruce (Picea glauca). BMC Plant Biology, 7, 17.
8. Bigras F, Colombo SJ, (2001) Conifer Cold Hardiness. Kluwer Academic Publishers, Dordrecht, The Netherlands.
9. Blödner C, Skroppa T, Johnsen O, Polle A, (2005) Freezing tolerance in two Norway spruce (Picea abies [L.] Karst.) progenies is physiologically correlated with drought tolerance. Journal of Plant Physiology, 162, 549-558. (Pubitemid 40588932)
10. Bonin A, Taberlet P, Miaud C, Pompanon F, (2006) Explorative genome scan to detect candidate loci for adaptation along a gradient of altitude in the common frog (Rana temporaria). Molecular Biology and Evolution, 23, 773-783.
11. Bouillé M, Bousquet J, (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. American Journal of Botany, 92, 63-73. (Pubitemid 40113108)
12. Bouillé M, Senneville S, Bousquet J, (2011) Discordant mtDNA and cpDNA spruce phylogenies indicate geographic speciation and reticulation as driving factors for the diversification of the genus Picea. Tree Genetics and Genomes, in press. DOI:.
13. Bousquet J, Isabel N, Pelgas B, et al. (2007) Spruce. In: Genome Mapping and Molecular Breeding in Plants (ed., Kole C,). pp. 93-114. Springer-Verlag, Berlin Heidelberg, Germany.
14. Campbell D, Bernatchez L, (2004) Genomic scan using AFLP markers as a means to assess the role of directional selection in the divergence of sympatric whitefish ecotypes. Molecular Biology and Evolution, 21, 945-956. (Pubitemid 38529736)
15. Capriotti E, Fariselli P, Calabrese R, Casadio R, (2005) Predicting protein stability changes from sequences using support vector machines. Bioinformatics, 21, 54-58.
16. Clarke B, Murray J, (1962) Changes of gene-frequency in Cepaea nemoralis (L.)-estimation of selective values. Heredity, 17, 445-465.
17. Cockerham CC, Weir BS, (1993) Estimation of gene flow from F-statistics. Evolution, 47, 855-863.
18. Curtis CF, Cook LM, Wood RJ, (1978) Selection for and against insecticide resistance and possible methods of inhibiting evolution of resistance in mosquitos. Ecological Entomology, 3, 273-287.
19. Cwynar LC, McDonald GM, (1987) Geographical variation of lodgepole pine in relation to population history. American Naturalist, 129, 463-469. (Pubitemid 19319213)
20. Davis MB, Shaw RG, (2001) Range shifts and adaptive responses to Quaternary climate change. Science, 292, 673-679. (Pubitemid 32385531)
21. Dong CH, Agarwal M, Zhang YY, Xie Q, Zhu JK, (2006) The negative regulator of plant cold responses, HOS1, is a RING E3 ligase that mediates the ubiquitination and degradation of ICE1. Proceedings of the National Academy of Sciences of the United States of America, 103, 8281-8286. (Pubitemid 43801089)
22. Dyke AS, (2004) An outline of north American deglaciation with emphasis on central and northern Canada. In: Quaternary Glaciations Extent and Chronology, Part II: North America (eds, Ehlers J, Gibbard PL,). pp. 373-424. Elsevier B.V., New York, New York.
23. Eckert AJ, Bower AD, Wegrzyn JL, et al. (2009) Association genetics of coastal douglas-fir (Pseudotsuga menziesii var. menziesii, Pinaceae). I. Cold-hardiness related traits. Genetics, 182, 1289-1302.
24. Eckert AJ, Bower AD, Gonzalez-Martinez SC, et al. (2010) Back to nature: ecological genomics of loblolly pine (Pinus taeda, Pinaceae). Molecular Ecology, 19, 3789-3805.
25. Endler J, (1986) Natural Selection in the Wild. Princeton University Press, Princeton.
26. Eveno E, Collada C, Guevara MA, et al. (2008) Contrasting patterns of selection at Pinus pinaster Ait. drought stress candidate genes as revealed by genetic differentiation analyses. Molecular Biology and Evolution, 25, 417-437. (Pubitemid 351231615)
27. Excoffier L, Laval G, Schneider S, (2005) Arlequin ver. 3.0: an integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online, 2005, 1.
28. Excoffier L, Hofer T, Foll M, (2009) Detecting loci under selection in a hierarchically structured population. Heredity, 103, 285-298.
29. Fan J, Oliphant A, Shen R, et al. (2003) Highly parallel SNP genotyping. Cold Spring Harbor Symposia on Quantitative Biology, 68, 69-78. (Pubitemid 38955554)
30. Gamache I, Jaramillo-Correa JP, Payette S, Bousquet J, (2003) Diverging patterns of mitochondrial and nuclear DNA diversity in subarctic black spruce: imprint of a founder effect associated with postglacial colonization. Molecular Ecology, 12, 891-901. (Pubitemid 36524284)
31. Garcia-Gil MR, Mikkonen M, Savolainen O, (2003) Nucleotide diversity at two phytochrome loci along a latitudinal cline in Pinus sylvestris. Molecular Ecology, 2003, 1195-1206. (Pubitemid 36573121)
32. Gérardi S, Jaramillo-Correa JP, Beaulieu J, Bousquet J, (2010) From glacial refugia to modern populations: new assemblages of organelle genomes generated by differential cytoplasmic gene flow in transcontinental black spruce. Molecular Ecology, 19, 5265-5280.
33. Gilmour SJ, Zarka DG, Stockinger EJ, et al. (1998) Low temperature regulation of the Arabidopsis CBF family of AP2 transcriptional activators as an early step in cold-induced COR gene expression. Plant Journal, 16, 433-442.
34. Govindaraju DR, (1988) Life histories, neighborhood sizes, and variance structure in some North American conifers. Biological Journal of the Linnean Society, 35, 69-78.
35. Guillet-Claude C, Isabel N, Pelgas B, Bousquet J, (2004) The evolutionary implications of knox-I gene duplications in conifers: correlated evidence from phylogeny, gene mapping, and analysis of functional divergence. Molecular Biology and Evolution, 21, 2232-2245. (Pubitemid 39488894)
36. Guy CL, (1990) Cold-acclimation and freezing stress tolerance-role of protein-metabolism. Annual Review of Plant Physiology and Plant Molecular Biology, 41, 187-223. (Pubitemid 120024682)
37. Heuertz M, De Paoli E, Kallman T, et al. (2006) Multilocus patterns of nucleotide diversity, linkage disequilibrium and demographic history of Norway spruce [Picea abies (L.) Karst]. Genetics, 174, 2095-2105. (Pubitemid 46011597)
38. Holliday JA, Ralph SG, White R, Bohlmann J, Aitken SN, (2008) Global monitoring of autumn gene expression within and among phenotypically divergent populations of Sitka spruce (Picea sitchensis). New Phytologist, 178, 103-122. (Pubitemid 351341338)
39. Holliday JA, Ritland K, Aitken SN, (2010) Widespread, ecologically relevant genetic markers developed from association mapping of climate-related traits in Sitka spruce (Picea sitchensis). New Phytologist, 188, 501-514.
40. Howe GT, Aitken SN, Neale DB, et al. (2003) From genotype to phenotype: unraveling the complexities of cold adaptation in forest trees. Canadian Journal of Botany, 81, 1247-1266. (Pubitemid 38390482)
41. Hu HH, Dai MQ, Yao JL, et al. (2006) Overexpressing a NAM, ATAF, and CUC (NAC) transcription factor enhances drought resistance and salt tolerance in rice. Proceedings of the National Academy of Sciences of the United States of America, 103, 12987-12992.
42. Hurme P, Sillanpaa MJ, Arjas E, Repo T, Savolainen O, (2000) Genetic basis of climatic adaptation in Scots pine by Bayesian quantitative trait locus analysis. Genetics, 156, 1309-1322.
43. Ingram J, Bartels D, (1996) The molecular basis of dehydration tolerance in plants. Annual Review of Plant Physiology and Plant Molecular Biology, 47, 377-403.
44. Isabel N, Beaulieu J, Bousquet J, (1995) Complete congruence between gene diversity estimates derived from genotypic data at enzyme and random amplified polymorphic DNA loci in black spruce. Proceedings of the National Academy of Sciences of the United States of America, 92, 6369-6373.
45. Jaramillo-Correa JP, Beaulieu J, Bousquet J, (2001) Contrasting evolutionary forces driving population structure at expressed sequence tag polymorphisms, allozymes and quantitative traits in white spruce. Molecular Ecology, 10, 2729-2740. (Pubitemid 33136576)
46. Jaramillo-Correa JP, Beaulieu J, Bousquet J, (2004) Variation in mitochondrial DNA reveals multiple distant glacial refugia in black spruce (Picea mariana), a transcontinental North American conifer. Molecular Ecology, 13, 2735-2747. (Pubitemid 39151630)
47. Joost S, Bonin A, Bruford MW, et al. (2007) A spatial analysis method (SAM) to detect candidate loci for selection: towards a landscape genomics approach to adaptation. Molecular Ecology, 16, 3955-3969. (Pubitemid 47397327)
48. Kelley JL, Madeoy J, Calhoun JC, Swanson W, Akey JM, (2006) Genomic signatures of positive selection in humans and the limits of outlier approaches. Genome Research, 16, 980-989. (Pubitemid 44162257)
49. Kimchi-Sarfaty C, (2007) A 'silent' polymorphism in the MDR1 gene changes substrate specificity. Science, 315, 525-528. (Pubitemid 46175758)
50. Kimura M, (1968) Evolutionary rate at molecular level. Nature, 217, 624-626.
51. King RB, Lawson R, (1995) Color-pattern variation in Lake-Erie water snakes-the role of gene flow. Evolution, 49, 885-896. (Pubitemid 3002802)
52. Laberge MJ, Payette S, Bousquet J, (2000) Life span and biomass allocation of stunted black spruce clones in the subarctic environment. Journal of Ecology, 88, 584-593. (Pubitemid 30647573)
53. Ladd AN, Cooper TA, (2002) Finding signals that regulate alternative splicing in the post genomic era. Genome Biology, 3, reviews0008.0001-0016.
54. Laval G, Excoffier L, (2004) SIMCOAL 2.0: a program to simulate genomic diversity over large recombining regions in a subdivided population with a complex history. Bioinformatics, 20, 2485-2487. (Pubitemid 39429927)
55. Legendre P, Legendre L, (1998) Numerical Ecology, 2nd edn. Elsevier, Amsterdam & New York.
56. Lewontin RC, Krakauer J, (1973) Distribution of gene frequency as a test of theory of selective neutrality of polymorphisms. Genetics, 74, 175-195.
57. Lu PL, Chen NZ, An R, et al. (2007) A novel drought-inducible gene, ATAF1, encodes a NAC family protein that negatively regulates the expression of stress-responsive genes in Arabidopsis. Plant Molecular Biology, 63, 289-305. (Pubitemid 46058730)
58. Luikart G, England PR, Tallmon D, Jordan S, Taberlet P, (2003) The power and promise of population genomics: from genotyping to genome typing. Nature Reviews Genetics, 4, 981-994. (Pubitemid 37474645)
59. Mayewski PA, Rohling EE, Stager JC, et al. (2004) Holocene climate variability. Quaternary Research, 62, 243-255. (Pubitemid 39499957)
60. Morgenstern EK, (1969a) Genetic variation in seedlings of Picea mariana (Mill.) BSP: I. Correlation with ecological factors. Silvae Genetica, 18, 151-161.
61. Morgenstern EK, (1969b) Genetic variation in seedlings of Picea mariana (Mill.) BSP: II. Variation patterns. Silvae Genetica, 18, 161-167.
62. Morgenstern EK, (1996) Geographic Variation in Forest Trees: Genetic Basis and Application of Knowledge in Silviculture. UBC Press, Vancouver.
63. Murray BG, (1998) Nuclear DNA amounts in gymnosperms. Annals of Botany, 82, 3-15. (Pubitemid 29014736)
64. Namroud MC, Beaulieu J, Juge N, Laroche J, Bousquet J, (2008) Scanning the genome for gene single nucleotide polymorphisms involved in adaptive population differentiation in white spruce. Molecular Ecology, 17, 3599-3613.
65. Namroud MC, Guillet-Claude C, Mackay J, Isabel N, Bousquet J, (2010) Molecular evolution of regulatory genes in spruces from different species and continents: heterogenous patterns of linkage disequilibrium and selection but correlated recent demographic changes. Journal of Molecular Evolution, 70, 371-386.
66. Nosil P, Funk DJ, Ortiz-Barrientos D, (2009) Divergent selection and heterogeneous genomic divergence. Molecular Ecology, 18, 375-402.
67. Pavy N, Paule C, Parsons L, et al. (2005) Generation, annotation, analysis and database integration of 16,500 white spruce EST clusters. BMC Genomics, 6, 144.
68. Pavy N, Parsons LS, Paule C, Mackay J, Bousquet J, (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, Article No. 174.
69. Pavy N, Pelgas B, Beauseigle S, et al. (2008) 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.
70. Payette S, (1993) The range limit of boreal tree species in Quebec-Labrador-an ecological and paleoecological interpretation. Review of Palaeobotany and Palynology, 79, 7-30.
71. Pelgas B, Bousquet J, Beauseigle S, Isabel N, (2005) A composite linkage map from two crosses for the species complex Picea mariana x Picea rubens and analysis of synteny with other Pinaceae. Theoretical and Applied Genetics, 111, 1466-1488. (Pubitemid 41618648)
72. Pelgas B, Beauseigle S, Acheré V, et al. (2006) Comparative genome mapping among Picea glauca, P. mariana x P. rubens and P. abies, and correspondence with other Pinaceae. Theoretical and Applied Genetics, 113, 1371-1393. (Pubitemid 44705019)
73. Pelgas B, Bousquet J, Meirmans P, Ritland K, Isabel N, (2011) QTL mapping in white spruce: gene maps and genomics regions underlying adaptive traits across pedigrees, years and environments. BMC Genomics. (in press).
74. Perry DJ, Bousquet J, (2001) Genetic diversity and mating system of post-fire and post-harvest black spruce: an investigation using codominant sequence-tagged-site (STS) markers. Canadian Journal of Forest Research, 31, 32-40. (Pubitemid 32185337)
75. Pritchard JK, Stephens M, Donnelly P, (2000) Inference of population structure using multilocus genotype data. Genetics, 155, 945-959. (Pubitemid 30397141)
76. Régnière J, (1996) Generalized approach to landscape-wide seasonal forecasting with temperature-driven simulation models. Environmental Entomology, 25, 869-881.
77. Root TL, Price JT, Hall KR, et al. (2003) Fingerprints of global warming on wild animals and plants. Nature, 421, 57-60. (Pubitemid 36077083)
78. Scotti-Saintagne C, Bodenes C, Barreneche T, et al. (2004) Detection of quantitative trait loci controlling bud burst and height growth in Quercus robur L. Theoretical and Applied Genetics, 109, 1648-1659. (Pubitemid 40024930)
79. Shen R, Fan J, Campbell D, et al. (2005) High-throughput SNP genotyping on universal bead arrays. Mutation Research, 573, 70-82. (Pubitemid 40514402)
80. Shinozaki K, Yamaguchi-Shinozaki K, (2000) Molecular responses to dehydration and low temperature: differences and cross-talk between two stress signaling pathways. Current Opinion in Plant Biology, 3, 217-223. (Pubitemid 30308351)
81. Shinozaki K, Yamaguchi-Shinozaki K, Seki M, (2003) Regulatory network of gene expression in the drought and cold stress responses. Current Opinion in Plant Biology, 6, 410-417. (Pubitemid 37195741)
82. Storey JD, Tibshirani R, (2003) Statistical significance for genomewide studies. Proceedings of the National Academy of Sciences of the United States of America, 100, 9440-9445. (Pubitemid 37033947)
83. Storz JF, (2005) Using genome scans of DNA polymorphism to infer adaptive population divergence. Molecular Ecology, 14, 671-688. (Pubitemid 40346460)
84. Tajima F, (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, 123, 585-595. (Pubitemid 19274682)
85. Thomashow MF, (1999) Plant cold acclimation: freezing tolerance genes and regulatory mechanisms. Annual Review of Plant Physiology and Plant Molecular Biology, 50, 571-599. (Pubitemid 129491974)
86. Thornton KR, Jensen JD, Becquet C, Andolfatto P, (2007) Progress and prospects in mapping recent selection in the genome. Heredity, 98, 340-348. (Pubitemid 46801773)
87. Viereck LA, Johnston WF, (1990) Picea mariana (Mill.) B.S.P. black spruce. In: Silvics of North America: Volume 1. Conifers (eds., Burns RM, Honkala BH,), pp. 227-237. United States Department of Agriculture, Forest Service, Agriculture Handbook 654, Washington DC, USA.
88. Wang RL, Stec A, Hey J, Lukens L, Doebley J, (1999) The limits of selection during maize domestication. Nature, 398, 236-239.
89. Wheeler NC, Jermstad KD, Krutovsky K, et al. (2005) Mapping of quantitative trait loci controlling adaptive traits in coastal Douglas-fir. IV. Cold-hardiness QTL verification and candidate gene mapping. Molecular Breeding, 15, 145-156. (Pubitemid 40374272)
90. Williams JW, Shuman BN, Webb T III, Bartlein PJ, Leduc PL, (2004) Late-quaternary vegetation dynamics in North America: scaling from taxa to biomes. Ecological Monographs, 74, 309-334. (Pubitemid 39182897)
91. Williamson SH, Hubisz MJ, Clark AG, et al. (2007) Localizing recent adaptive evolution in the human genome. PLoS Genetics, 3, 901-915.
92. Wright SI, Gaut BS, (2005) Molecular population genetics and the search for adaptive evolution in plants. Molecular Biology and Evolution, 22, 506-519. (Pubitemid 40299500)
93. Yamaguchi-Shinozaki K, Shinozaki K, (2006) Transcriptional regulatory networks in cellular responses and tolerance to dehydration and cold stresses. Annual Review of Plant Biology, 57, 781-803. (Pubitemid 44061045)