Estimation of population structure in coastal Douglas-fir [Pseudotsuga menziesii (Mirb.) Franco var. menziesii] using allozyme and microsatellite markers

Tree Genetics and Genomes

Volumn 5, Issue 4, 2009, Pages 641-658

  Krutovsky, Konstantin V ^a,b   St Clair, John Bradley ^c   Saich, Robert ^a   Hipkins, Valerie D ^a   Neale, David B ^d  

^a PACIFIC SOUTHWEST RESEARCH STATION   (United States)

^b TEXAS A AND M UNIVERSITY   (United States)

^c PACIFIC NORTHWEST RESEARCH STATION   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Allozyme; Genetic markers; Microsatellites; Population structure; Pseudotsuga menziesii var. menziesii; Simple sequence repeats; SSR

Indexed keywords

PSEUDOTSUGA; PSEUDOTSUGA MENZIESII; PSEUDOTSUGA MENZIESII VAR. MENZIESII;

EID: 70349817292     PISSN: 16142942     EISSN: 16142950     Source Type: Journal    
DOI: 10.1007/s11295-009-0216-y     Document Type: Article

References (103)

1. Aagaard JE, Krutovskii KV, Strauss SH (1998a) RAPDs and allozymes exhibit similar levels of diversity and differentiation among populations and races of Douglas-fir. Heredity 81:69-78
2. Aagaard JE, Krutovskii KV, Strauss SH (1998b) RAPD markers of mitochondrial origin exhibit lower population diversity and higher differentiation than RAPDs of nuclear origin in Douglas-fir. Mol Ecol 7:801-812
3. Adams WT, Neale DB, Doerksen AH, Smith DB (1990) Inheritance and linkage of isozyme variants from seed and bud tissues in coastal Douglas-fir [Pseudotsuga menziesii var. menziesii (Mirb.) Franco]. Silvae Genet 39:153-167
4. Aitken SN, Adams WT (1997) Spring cold hardiness under strong genetic control in Oregon populations of coastal Douglas-fir. Can J For Res 27:1773-1778
5. Altukhov YP (1991) The role of balancing selection and overdominance in maintaining allozyme polymorphism. Genetica 85:79-90
6. Altukhov YP (2006) Intraspecific genetic diversity. Springer, Berlin
7. Amarasinghe V, Carlson JE (2002) The development of microsatellite DNA markers for genetic analysis in Douglas-fir. Can J For Res 32:1904-1915
8. Andersen JR, Schrag T, Melchinger AE, Zein I, Lubberstedt T (2005) Validation of Dwarf8 polymorphisms associated with flowering time in elite European inbred lines of maize (Zea mays L.). Theor Appl Genet 111:206-217
9. Anekonda TS, Adams WT, Aitken SN, Neale DB, Jermstad KD, Wheeler NC (2000) Genetics of cold-hardiness in a cloned full-sib family of coastal Douglas-fir. Can J For Res 30:837-840
10. Antao T, Lopes A, Lopes RJ, Beja-Pereira A, Luikart G (2008) LOSITAN: a workbench to detect molecular adaptation based on a Fst-outlier method. BMC Bioinformatics 9:323
11. Aranzana MJ, Kim S, Zhao K, Bakker E, Horton M, Jakob K, Lister C, Molitor J, Shindo C, Tang C, Toomajian C, Traw B, Zheng H, Bergelson J, Dean C, Marjoram P, Nordborg M (2005) Genome-wide association mapping in Arabidopsis identifies previously known flowering time and pathogen resistance genes. PLoS Genet 1(5):e60. doi:10.1371
12. Ball RD (2007) Statistical analysis and experimental design, Ch8. In: Oraguzie NC, Rikkerink EHA, Gardiner SE, de Silva HN (eds) Association mapping in plants. Springer, New York
13. Beaumont MA, Balding DJ (2004) Identifying adaptive genetic divergence among populations from genome scans. Mol Ecol 13:969-980
14. Beaumont MA, Nichols RA (1996) Evaluating loci for use in the genetic analysis of population structure. Proc R Soc Lond B Biol Sci 263:1619-1626
15. Campbell RK (1979) Genecology of Douglas-fir in a watershed in the Oregon Cascades. Ecology 60(5):1036-1050
16. Campbell RK, Sorensen FC (1978) Effect of test environment on expression of clines and on delimitation of seed zones in Douglas-fir. Theor Appl Genet 51:233-246
17. Campbell RK, Sugano AI (1975) Phenology of bud burst in Douglas-fir related to provenance, photoperiod, chilling and flushing temperature. Bot Gaz 136:290-298
18. Camus-Kulandaivelu L, Veyrieras J-B, Madur D, Combes V, Fourmann M, Barraud S, Dubreuil P, Gouesnard B, Manicacci D, Charcosset A (2006) Maize adaptation to temperate climate: relationship with population structure and polymorphism in the Dwarf8 gene. Genetics 172:2449-2463
19. Camus-Kulandaivelua L, Veyrierasa J-B, Gouesnardb B, Charcosseta A, Manicaccia D (2007) Evaluating the reliability of structure outputs in case of relatedness between individuals. Crop Sci 47:887-890
20. Carlson JE, Traore A, Agrama HA, Krutovsky KV (2007) Douglas-fir. In: Kole C (ed) Genome mapping and molecular breeding in plants, vol. 7: forest trees. Springer, Berlin, pp 199-210
21. Chakraborty R, De Andrade M, Daiger SP, Budowle B (1992) Apparent heterozygote deficiencies observed in DNA typing data and their implications in forensic applications. Ann Hum Genet 56:45-57
22. Criscione CD, Anderson JD, Sudimack D, Peng W, Jha B, Williams-Blangero S, Anderson TJC (2007) Disentangling hybridization and host colonization in parasitic roundworms of humans and pigs. Proc R Soc B 274:2669-2677
23. Devlin B, Roeder K (1999) Genomic control for association studies. Biometrics 55:997-1004
24. Devlin B, Roeder K, Wasserman L (2001) Genomic control, a new approach to genetic-based association studies. Theor Popul Biol 60:155-166
25. DeWoody J, Nason JD, Hipkins VD (2006) Mitigating scoring errors in microsatellite data from wild populations. Mol Ecol Notes 6(4):951-957
26. El-Kassaby YA (1991) Genetic variation within and among conifer populations: review and evaluation of methods. In: Fineschi S, Malvolti ME, Cannata F, Hattemer HH (eds) Biochemical markers in the population genetics of forest trees. Proceedings of the International Workshop, Porano-Orvieto, Italy, October 1988. SPB Academic Publishing B. V., The Hague, pp 59-74
27. El-Kassaby YA, Sziklai O, Yeh FC (1982) Linkage relationships among 19 polymorphic allozyme loci in coastal Douglas-fir (Pseudotsuga menziesii var. 'menziesii'). Can J Genet Cytol 124:101-108
28. EPA (2004) Level III Ecoregions. Western Ecology Division, Corvalis, Oregon. Available at http://www.epa.gov/wed/pages/ecoregions/level_iii.htm. Revised March 2007
29. Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611-262
30. Falush D, Stephens M, Pritchard JK (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164:1567-1587
31. González-Martínez SC, Krutovsky KV, Neale DB (2006) Forest tree population genomics and adaptive evolution. New Phytol 170(2):227-238
32. González-Martínez SC, Wheeler NC, Ersoz E, Nelson CD, Neale DB (2007) Association genetics in Pinus taeda L. I. Wood property traits. Genetics 175(1):399-409
33. González-Pérez MA, Sosa PA, Rivero E, González-González EA, Naranjo A (2009) Molecular markers reveal no genetic differentiation between Myrica rivas-martinezii and M. faya (Myricaceae). Ann Bot 103:79-86
34. Goudet J (1995) FSTAT (vers. 1.2): a computer program to calculate F-statistics. J Heredity 86:485-486
35. Goudet J (2001) FSTAT, a program to estimate and test gene diversities and fixation indices (version 2.9.3). Available at http://www.unil.ch/izea/softwares/fstat.html
36. Goudet J, Raymond M, de Meeüs T, Rousset F (1996) Testing differentiation in diploid populations. Genetics 144:1931-1938
37. Hamrick JL, Godt MJ, Sherman-Broyles SL (1992) Factors influencing levels of genetic diversity in woody plant species. New Forest 6:95-124
38. Hardy OJ, Vekemans X (2002) SPAGeDi: a versatile computer program to analyse spatial genetic structure at the individual or population levels. Mol Ecol Notes 2:618-620
39. Hedrick PW (2005) A standardized genetic differentiation measure. Evolution 59:1633-1638
40. Howe GT, Jayawickrama KJ, Cherry ML, Johnson GR, Wheeler NC (2006) Breeding Douglas-fir. In: Janick J (ed) Plant breeding reviews, vol 27. Wiley, New York, pp 245-353
41. Jermstad KD, Reem AM, Wheeler NC, Neale DB (1994) Inheritance of restriction fragment length polymorphisms, random amplified polymorphic DNAs and isozymes in coastal Douglas-fir. Theor Appl Genet 89:758-766
42. Jermstad KD, Bassoni DL, Jech KS, Wheeler NC, Neale DB (2001a) Mapping of quantitative trait loci controlling adaptive traits in coastal Douglas-fir. I. Timing of vegetative bud flush. Theor Appl Genet 102:1142-1151
43. Jermstad KD, Bassoni DL, Wheeler NC, Anekonda TS, Aitken SN (2001b) Mapping of quantitative trait loci controlling adaptive traits in coastal Douglas-fir. II. Spring and fall cold-hardiness. Theor Appl Genet 102:1152-1158
44. Jermstad KD, Bassoni DL, Jech KS, Ritchie GA, Wheeler NC (2003) Mapping of quantitative trait loci controlling adaptive traits in coastal Douglas-fir. III. QTL by environment interactions. Genetics 165:1489-1506
45. Johnson PCD, Haydon DT (2007) Maximum-likelihood estimation of allelic dropout and false allele error rates from microsatellite genotypes in the absence of reference data. Genetics 175:827-842
46. Johnson GR, Sorenson FC, St Clair JB, Cronn RC (2004) Pacific Northwest forest tree seed zones: a template for native plants? Nativ Plants J 5:131-140
47. Jordan MA, Snell HL (2008) Historical fragmentation of islands and genetic drift in populations of Galápagos lava lizards (Microlophus albemarlensis complex). Mol Ecol 17:1224-1237
48. Kettle CJ, Hollingsworth PM, Jaffré T, Moran B, Ennos RA (2007) Identifying the early genetic consequences of habitat degradation in a highly threatened tropical conifer, Araucaria nemorosa Laubenfels. Mol Ecol 16:3581-3591
49. Khasa DP, Jaramillo-Correa JP, Jaquish B, Bousquet J (2006) Contrasting microsatellite variation between subalpine and western larch, two closely related species with different distribution patterns. Mol Ecol 15:3907-3918
50. Krutovskii KV, Politov DV, Altukhov YP (1995) Isozyme study of population genetic structure, mating system and phylogenetic relationships of the five stone pine species (subsection Cembrae, section Strobus, subgenus Strobus). In: Baradat P, Adams WT, Mller-Starck G (eds) Population genetics and genetic conservation of forest trees. Proceedings of the International Symposium, Carcans Maubuisson, France, 24-28 August 1992. SPB Academic Publishing, Amsterdam, The Netherlands, pp 279-304
51. Krutovsky KV, Neale DB (2005a) 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, Zvolen, Slovakia, pp 369-390 Available online at http://www.fao.org/DOCREP/003/X6884E/X6884E00.HTM
52. Krutovsky KV, Neale DB (2005b) Nucleotide diversity and linkage disequilibrium in cold hardiness and wood quality related candidate genes in Douglas-fir. Genetics 171:2029-2041
53. Langergraber KE, Siedel H, Mitani JC, Wrangham RW, Reynolds V, Hunt K, Vigilant L (2007) The genetic signature of sex-biased migration in patrilocal chimpanzees and humans. PLoS ONE 2(10):e973. doi:10.1371/journal.pone.0000973
54. Ledig FT (1986) Heterozygosity, heterosis and fitness in outbreeding plants. In: Soule ME (ed) Conservation biology: the science of scarcity and diversity. Sinauer, Sunderland, Massachusetts, pp 77-104
55. Ledig FT (1998) Genetic variation in Pinus. In: Richardson DM (ed) Ecology and biogeography of Pinus. Cambridge University Press, Cambridge, UK, pp 251-280
56. Leinonen T, O'Hara RB, Cano JM, Merila J (2008) Comparative studies of quantitative trait and neutral marker divergence: a meta-analysis. J Evol Biol 21:1-17
57. Lewis PO, Zaykin D (2001) Genetic data analysis: computer program for the analysis of allelic data. Version 1.0 (d16c). Free program distributed by the authors over the Internet from http://lewis.eeb.uconn.edu/lewishome/software.html
58. Li P, Adams WT (1989) Range-wide patterns of allozyme variation in Douglas-fir (Pseudotsuga menziesii). Can J For Res 19:149-161
59. Li P, Adams WT (1993) Genetic control of bud phenology in pole-size trees and seedlings of coastal Douglas-fir. Can J For Res 23:1043-1051
60. Liu KJ, Goodman M, Muse S, Smith JS, Buckler E, Doebley J (2003) Genetic structure and diversity among maize inbred lines as inferred from DNA microsatellites. Genetics 165:2117-2128
61. Manel S, Brthier P, Luikart G (2002) Detecting wildlife poaching: identifying the origin of individuals with Bayesian assignment tests and multilocus genotypes. Conserv Biol 16:650-659
62. Marquardt PE, Epperson BK (2004) Spatial and population genetic structure of microsatellites in white pine. Mol Ecol 13:3305-3315
63. Meirmans PG (2006) Using the AMOVA framework to estimate a standardized genetic differentiation measure. Evolution 60:2399-2402
64. Merkle SA, Adams WT (1987) Pattern of allozyme variation within and among Douglas-fir breeding zones in southwest Oregon. Can J For Res 17:402-407
65. Miller CR, Joyce P, Waits LP (2002) Assessing allelic dropout and genotype reliability using maximum likelihood. Genetics 160:357-366
66. Moran GF, Adams WT (1989) Microgeographical patterns of allozyme differentiation in Douglas-fir from southwest Oregon. For Sci 35:3-15
67. Neale DB, Weber JC, Adams WT (1984) Inheritance of needle tissue isozymes in Douglas-fir. Can J Genet Cytol 26:459-468
68. Nei M (1972) Genetic distance between populations. Am Nat 106:283-292
69. Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New York
70. Omernik JM (1995) Ecoregions: a spatial framework for environmental management. In: Davis WS, Simon TP (eds) Biological assessment and criteria: tools for water resource planning and decision making. Lewis, Boca Raton, FL, pp 49-62
71. Pande B, Krutovsky KV, Jermstad KD, Howe GT, St. Clair JB, Wheeler NC, Neale DB (2007) Candidate gene-based association genetics in Douglas-fir (Poster #502). In: Plant & Animal Genome XV. The International Conference on the Status of Plant and Animal Genome Research, Final Program and Abstracts Guide, January 13-17, 2007. San Diego, CA, USA, p 227. http://www.intl-pag.org/15/abstracts/PAG15_P05j_502.html
72. Pater DE, Bryce SE, Thorson TD, Kagan J, Chappel C, Omernik JM, Azevedo SH, Woods AJ (1998) Ecoregions of western Washington and Oregon. Map scale 1:1,350,000. US Geological Survey, Reston, VI
73. Petit RJ, El Mousadik A, Pons O (1998) Identifying populations for conservation on the basis of genetic markers. Conserv Biol 12:844-855
74. Petit E, Balloux F, Goudet J (2001) Sex biased dispersal in a migratory bat: a characterization using sex-specific demographic parameters. Evolution 55:635-640
75. Pompanon F, Bonin A, Bellemain E, Taberlet P (2005) Genotyping errors: causes, consequences and solutions. Nat Rev Genet 6:847-859
76. Pritchard JK, Donnelly P (2001) Case-control studies of association in structured or admixed populations. Theor Popul Biol 60:227-237
77. Pritchard JK, Rosenberg NA (1999) Use of unlinked genetic markers to detect population stratification in association studies. Am J Hum Genet 65:220-228
78. Pritchard JK, Wen W (2004) Documentation for structure software: version 2. http://pritch.bsd.uchicago.edu/software/readme_structure2_1.pdf
79. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945-959
80. Rajora OH, Rahman MH, Buchert GP, Dancik BP (2000) Microsatellite DNA analysis of genetic effects of harvesting in old-growth eastern white pine (Pinus strobus) in Ontario, Canada. Mol Ecol 9:339-348
81. Rajora OP, Mann IK, Shi Y-Z (2005) Genetic diversity and population structure of boreal white spruce (Picea glauca) in pristine conifer-dominated and mixedwood forest stands. Can J Bot 83:1096-1105
82. Raymond M, Rousset F (1995a) GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism. J Heredity 86:248-249
83. Raymond M, Rousset F (1995b) An exact test for population differentiation. Evolution 49:1280-1283
84. Rosenberg NA, Burke T, Elo K, Feldman MW, Freidlin PJ, Groenen MAM, Hillel J, Maki-Tanila A, Tixier-Boichard M, Vignal A, Wimmers K, Weigend S (2001) Empirical evaluation of genetic clustering methods using multilocus genotypes from 20 chicken breeds. Genetics 159:699-713
85. Rousset F (1997) Genetic differentiation and estimation of gene flow from F-statistics under isolation by distance. Genetics 145:1219-1228
86. Rousset F (2008) GENEPOP'007: a complete re-implementation of the GENEPOP software for Windows and Linux. Mol Ecol Res 8(1):103-106
87. Ryynänen HJ, Tonteri A, Vasemägi A, Primmer CR (2007) A comparison of biallelic markers and microsatellites for the estimation of population and conservation genetic parameters in Atlantic salmon (Salmo salar). J Heredity 98:692-704
88. Slavov GT, Howe GT, Yakovlev I, Edwards KJ, Krutovskii KV, Tuskan GA, Carlson JE, Strauss SH, Adams WT (2004) Highly variable SSR markers in Douglas-fir: Mendelian inheritance and map locations. Theor Appl Genet 108:873-880
89. St. Clair JB (2006) Genetic variation in fall cold hardiness in coastal Douglas-fir in western Oregon and Washington. Can J Bot 84:1110-1121
90. St. Clair JB, Mandel NL, Vance-Borland KW (2005) Genecology of Douglas-fir in western Oregon and Washington. Ann Bot 96:1199-1214
91. Steiner KC (1979) Variation in bud-burst timing among populations of interior Douglas-fir. Silvae Genet 28:76-79
92. Strobeck C (1987) Average number of nucleotide differences in a sample from a single subpopulation: a test for population subdivision. Genetics 117(149):153
93. Thomas BR, MacDonald SE, Hick M, Adams DL, Hodgetts RB (1999) Effects of reforestation methods on genetic diversity of lodgepole pine: an assessment using microsatellite and randomly amplified polymorphic DNA markers. Theor Appl Genet 98:793-801
94. Thornsberry JM, Goodman MM, Doebley J, Kresovich S, Nielsen D et al (2001) Dwarf8 polymorphisms associate with variation in flowering time. Nat Genet 28:286-289
95. Turakulov R, Easteal S (2003) Number of SNPS loci needed to detect population structure. Hum Hered 55:37-45
96. US DOI BLM (2005) Final Programmatic Environmental Impact Statement (PEIS) on wind energy development on Bureau of Land Management (BLM)-administered lands in the Western United States. Appendix F: Ecoregions of the 11 Western States and Distribution by Ecoregion of Wind Energy Resources on BLM-Administered Lands Within Each State. http://windeis.anl.gov/documents/fpeis/maintext/Vol2/appendices/appendix_f/Vol2AppF_1.pdf
97. van Oosterhout C, Hutchinson WF, Wills DPM, Shipley P (2004) MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data. Mol Ecol Notes 4:535-538 http://www.microchecker.hull.ac.uk/index.jsp
98. Viard F, El-Kassaby YA, Ritland K (2001) Diversity and genetic structure in populations of Pseudotsuga menziesii (Pinaceae) at chloroplast microsatellite loci. Genome 44:336-344
99. Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38:1358-1370
100. Wheeler NC, Jermstad KD, Krutovsky KV, Aitken SN, Howe GT, Krakowski J, Neale DB (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
101. Wilson LM, Whitt SR, Ibanez AM, Rocheford TR, Goodman M, Buckler E (2004) Dissection of maize kernel composition and starch production by candidate gene association. Plant Cell 16:2719-2733
102. Yu J, Buckler ES IV (2006) Genetic association mapping and genome organization of maize. Curr Opin Biotechnol 17:155-160
103. Yu J, Pressoir G, Briggs WH, Vroh Bi I, Yamasaki M, Doebley JF, McMullen MD, Gaut BS, Nielsen DM, Holland JB, Kresovich S, Buckler ES (2006) A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet 38:203-208