A 34K SNP genotyping array for Populus trichocarpa: Design, application to the study of natural populations and transferability to other Populus species

Molecular Ecology Resources

Volumn 13, Issue 2, 2013, Pages 306-323

  Geraldes, A ^a   Difazio, S P ^b   Slavov, G T ^b,c   Ranjan, P ^d   Muchero, W ^e   Hannemann, J ^f   Gunter, L E ^e   Wymore, A M ^e   Grassa, C J ^a   Farzaneh, N ^a   Porth, I ^a   Mckown, A D ^a   Skyba, O ^a   Li, E ^a   Fujita, M ^a   Klapste J ^a   Martin, J ^g   Schackwitz, W ^g   Pennacchio, C ^g   Rokhsar, D ^g   Friedmann, M C ^a   Wasteneys, G O ^a   Guy, R D ^a   El Kassaby, Y A ^a   Mansfield, S D ^a   Cronk, Q C B ^a   Ehlting, J ^f   Douglas, C J ^a   Tuskan, G A ^e,g   more..

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^b WEST VIRGINIA UNIVERSITY   (United States)

^c ABERYSTWYTH UNIVERSITY   (United Kingdom)

^d UNIVERSITY OF TENNESSEE   (United States)

^e OAK RIDGE NATIONAL LABORATORY   (United States)

^f UNIVERSITY OF VICTORIA   (Canada)

^g DOE JOINT GENOME INSTITUTE   (United States)

Author keywords

Genotype accuracy; High throughput SNP genotyping; Hybridization; Populus balsamifera; Populus trichocarpa

Indexed keywords

ARTICLE; CHROMOSOME MAP; CLASSIFICATION; DNA MICROARRAY; EVALUATION; GENETICS; GENOTYPE; METHODOLOGY; POPULUS; SINGLE NUCLEOTIDE POLYMORPHISM;

CHROMOSOME MAPPING; GENOTYPE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMORPHISM, SINGLE NUCLEOTIDE; POPULUS;

POPULUS; POPULUS BALSAMIFERA; POPULUS TRICHOCARPA; TACAMAHACA;

EID: 84873999865     PISSN: 1755098X     EISSN: 17550998     Source Type: Journal    
DOI: 10.1111/1755-0998.12056     Document Type: Article

References (55)

1. Aitken S, 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.
2. Barrett JC, Fry B, Maller J, Daly MJ (2005) Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics, 21, 263-265.
3. Brayshaw TC (1965) Native Poplars of Southern Alberta and their Hybrids. Department of Forestry, Publication 1109, Canada.
4. Cervera MT, Storme V, Soto A et al. (2005) Intraspecific and interspecific genetic and phylogenetic relationships in the genus Populus based on AFLP markers. TAG. Theoretical and Applied Genetics., 111, 1440-1456.
5. Cronk QCB (2005) Plant eco-devo: the potential of poplar as a model organism. New Phytologist, 166, 39-48.
6. Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin, 19, 11-15.
7. Du Z, Zhou X, Ling Y, Zhang Z, Su Z (2010) agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Research, 38, W64-W70.
8. Earl DA, vonHoldt BM (2011) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genetics Resources, 4, 359-361.
9. Eckenwalder JE (1996) Systematics and evolution of Populus. In: Biology of Populus and its Implications for Management and Conservation (eds Stettler RF, Bradshaw HD, Heilman PE & Hinckley TM), pp. 7-32. NRC Research Press, National Research Council of Canada Ottawa, ON, Canada.
10. Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software structure: a simulation study. Molecular Ecology, 14, 2611-2620.
11. 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.
12. Floate KD (2004) Extent and patterns of hybridization among the three species of Populus that constitute the riparian forest of southern Alberta, Canada. Canadian Journal of Botany, 82, 253-264.
13. Geraldes A, Pang J, Thiessen N et al. (2011) SNP discovery in black cottonwood (Populus trichocarpa) by population transcriptome resequencing. Molecular Ecology Resources, 11(Suppl 1), 81-92.
14. Glenn TC (2011) Field guide to next-generation DNA sequencers. Molecular Ecology Resources, 11, 759-769.
15. Goudet J (2005) hierfstat, a package for r to compute and test hierarchical F-statistics. Molecular Ecology Notes, 5, 184-186.
16. Hamzeh M, Dayanandan S (2004) Phylogeny of Populus (Salicaceae) based on nucleotide sequences of chloroplast TRNT-TRNF region and nuclear rDNA. American Journal of Botany, 91, 1398-1408.
17. Harfouche A, Meilan R, Kirst M et al. (2012) Accelerating the domestication of forest trees in a changing world. Trends in Plant Science, 17, 64-72.
18. 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.
19. Ingvarsson PK, Street NR (2010) Association genetics of complex traits in plants. New Phytologist, 189, 909-922.
20. Ingvarsson PK, Garcia MV, Luquez V, Hall D, Jansson S (2008) Nucleotide polymorphism and phenotypic associations within and around the phytochrome B2 locus in European Aspen (Populus tremula, Salicaceae). Genetics, 178, 2217-2226.
21. Ismail M, Soolanayakanahally RY, Ingvarsson PK et al. (2012) Comparative Nucleotide Diversity Across North American and European Populus Species. Journal of Molecular Evolution, 74, 257-272.
22. Jansson S, Douglas CJ (2007) Populus: A Model System for Plant Biology. Annual Review of Plant Biology, 58, 435-458.
23. Keller SR, Olson MS, Silim S, Schoeder W, Tiffin P (2010a) Genomic diversity, population structure, and migration following rapid range expansion in the Balsam Poplar, Populus balsamifera. Molecular Ecology, 19, 1212-1226.
24. Keller SR, Soolanayakanahally RY, Guy RD, Silim SN, Olson MS, Tiffin P (2010b) Climate-driven adaptive divergence in ecophysiology and phenology during the post-glacial expansion of balsam poplar, Populus balsamifera L. American Journal of Botany, 98, 99-108.
25. Levsen ND, Tiffin P, Olson MS (2012) Pleistocene Speciation in the Genus Populus (Salicaceae). Systematic Biology, 61, 401-412.
26. Li H, Ruan J, Durbin R (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Research, 18, 1851-1858.
27. Li M, Wang IX, Li Y et al. (2011) Widespread RNA and DNA sequence differences in the Human Transcriptome. Science, 333, 53-58.
28. Little E Jr (1971) Atlas of United States trees. In: Conifers and Important Hardwoods, Vol. 1. US Department of Agriculture, Forest Service Miscellaneous Publication, Washington, DC.
29. Luquez V, Hall D, Albrectsen BR et al. (2008) Natural phenological variation in aspen (Populus tremula): the SwAsp collection. Tree Genetics & Genomes, 4, 279-292.
30. Meirmans PG, Lamothe M, Perinet P, Isabel N (2007) Species-specific single nucleotide polymorphism markers for detecting hybridization and introgression in poplar. Canadian Journal of Botany, 85, 1082-1091.
31. Meirmans PG, Lamothe M, Gros-Louis MC et al. (2010) Complex patterns of hybridization between exotic and native North American poplar species. American Journal of Botany, 97, 1688-1697.
32. Miller JM, Kijas JW, Heaton MP, McEwan JC, Coltman DW (2012) Consistent divergence times and allele sharing measured from cross-species application of SNP chips developed for three domestic species. Molecular Ecology Resources, 12, 1145-1150.
33. Myles S, Chia J-C, Hurwitz B et al. (2010) Rapid genomic characterization of the genus Vitis. PLoS ONE, 5, e8219.
34. Neale DB, Kremer A (2011) Forest tree genomics: growing resources and applications. Nature Reviews Genetics, 12, 111-122.
35. Nei M (1987) Molecular Evolutionary Genetics. Columbia University Press, New York.
36. Nieminen K, Robischon M, Immanen J, Helariutta Y (2011) Towards optimizing wood development in bioenergy trees. New Phytologist, 194, 46-53.
37. Patterson N, Price AL, Reich D (2006) Population Structure and Eigenanalysis. PLoS Genetics, 2, e190.
38. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics, 155, 945-959.
39. Rockman MV (2008) Reverse engineering the genotype-phenotype map with natural genetic variation. Nature, 456, 738-744.
40. Slavov GT, DiFazio SP, Martin J et al. (2012) Genome Resequencing Reveals Multiscale Geographic Structure and Extensive Linkage Disequilibrium in the Forest Tree Populus trichocarpa. New Phytologist, 196, 713-725.
41. Soolanayakanahally RY, Guy RD, Silim SN, Drewes EC, Schroeder WR (2009) Enhanced assimilation rate and water use efficiency with latitude through increased photosynthetic capacity and internal conductance in balsam poplar (Populus balsamifera L.). Plant, Cell & Environment, 32, 1821-1832.
42. Stanton BJ, B Neale D, Li S (2010) Populus breeding: from the classical to the genomic approach. In: Genetics and Genomics of Populus (eds Jansson S, Rishikesh BP & Groover AT), pp. 309-348. Springer, New York.
43. Studer MH, DeMartini JD, Davis MF et al. (2011) Lignin content in natural Populus variants affects sugar release. PNAS, 108, 6300-6305.
44. Talbot P, Thompson SL, Schroeder W, Isabel N (2011) An efficient single nucleotide polymorphism assay to diagnose the genomic identity of poplar species and hybrids on the Canadian praries. Canadian Journal of Forest Research, 41, 1102-1111.
45. Thompson SL, Lamothe M, Meirmans PG, Périnet P, Isabel N (2010) Repeated unidirectional introgression towards Populus balsamifera in contact zones of exotic and native poplars. Molecular Ecology, 19, 132-145.
46. Tuskan GA (1998) Short-rotation woody crop supply systems in the United States: What do we know and what do we need to know? Biomass and Bioenergy, 14, 307-315.
47. Tuskan GA, DiFazio S, Jansson S et al. (2006) The Genome of Black Cottonwood, Populus trichocarpa (Torr & Gray). Science, 313, 1596-1604.
48. Viereck LA, Foote JM (1970) The status of Populus balsamifera and P. trichocarpa in Alaska. Canadian Field-Naturalist, 84, 169-173.
49. Weber JC, Stettler RF (1981) Isoenzyme variation among 10 populations of Populus trichocarpa Torr & Gray in the Pacific Northwest. Silvae Genetica, 30, 82-87.
50. Weber JC, Stettler RF, Heilman PE (1985) Genetic variation and productivity of Populus trichocarpa and its hybrids. I. Morphology and phenology of 50 native clones. Canadian Journal of Forest Research, 15, 376-383.
51. Wegrzyn JL, Eckert AJ, Choi M et al. (2010) Association genetics of traits controlling lignin and cellulose biosynthesis in black cottonwood (Populus trichocarpa, Salicaceae) secondary xylem. New Phytologist, 188, 515-532.
52. Xie CY, Ying CC, Yanchuk AD, Holowachuk DL (2009) Ecotypic mode of regional differentiation caused by restricted gene migration: a case in black cottonwood (Populus trichocarpa) along the Pacific Northwest coast. Canadian Journal of Forest Research, 39, 519-526.
53. Xie C-Y, Carlson MR, Ying CC (2012) Ecotypic mode of regional differentiation of black cottonwood (Populus trichocarpa) due to restricted gene migration: further evidence from a field test on the northern coast of British Columbia. Canadian Journal of Forest Research, 42, 400-405.
54. Yan H, Yuan W, Velculescu VE, Vogelstein B, Kinzler KW (2002) Allelic variation in human gene expression. Science, 297, 1143.
55. 1 hybrids. Genetics, 177, 1987-1996.