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Items: 36

1.

Adaptive introgression and maintenance of a trispecies hybrid complex in range-edge populations of Populus.

Chhatre VE, Evans LM, DiFazio SP, Keller SR.

Mol Ecol. 2018 Aug 2. doi: 10.1111/mec.14820. [Epub ahead of print]

PMID:
30071141
2.

Characterization of a large sex determination region in Salix purpurea L. (Salicaceae).

Zhou R, Macaya-Sanz D, Rodgers-Melnick E, Carlson CH, Gouker FE, Evans LM, Schmutz J, Jenkins JW, Yan J, Tuskan GA, Smart LB, DiFazio SP.

Mol Genet Genomics. 2018 Jul 18. doi: 10.1007/s00438-018-1473-y. [Epub ahead of print]

PMID:
30022352
3.

A 5-Enolpyruvylshikimate 3-Phosphate Synthase Functions as a Transcriptional Repressor in Populus.

Xie M, Muchero W, Bryan AC, Yee K, Guo HB, Zhang J, Tschaplinski TJ, Singan VR, Lindquist E, Payyavula RS, Barros-Rios J, Dixon R, Engle N, Sykes RW, Davis M, Jawdy SS, Gunter LE, Thompson O, DiFazio SP, Evans LM, Winkeler K, Collins C, Schmutz J, Guo H, Kalluri U, Rodriguez M, Feng K, Chen JG, Tuskan GA.

Plant Cell. 2018 Jul;30(7):1645-1660. doi: 10.1105/tpc.18.00168. Epub 2018 Jun 11.

4.

Large effect quantitative trait loci for salicinoid phenolic glycosides in Populus: Implications for gene discovery.

Woolbright SA, Rehill BJ, Lindroth RL, DiFazio SP, Martinsen GD, Zinkgraf MS, Allan GJ, Keim P, Whitham TG.

Ecol Evol. 2018 Mar 8;8(7):3726-3737. doi: 10.1002/ece3.3932. eCollection 2018 Apr.

5.

Agronomic performance of Populus deltoides trees engineered for biofuel production.

Macaya-Sanz D, Chen JG, Kalluri UC, Muchero W, Tschaplinski TJ, Gunter LE, Simon SJ, Biswal AK, Bryan AC, Payyavula R, Xie M, Yang Y, Zhang J, Mohnen D, Tuskan GA, DiFazio SP.

Biotechnol Biofuels. 2017 Nov 30;10:253. doi: 10.1186/s13068-017-0934-6. eCollection 2017.

6.

High-resolution genetic mapping of allelic variants associated with cell wall chemistry in Populus.

Muchero W, Guo J, DiFazio SP, Chen JG, Ranjan P, Slavov GT, Gunter LE, Jawdy S, Bryan AC, Sykes R, Ziebell A, Klápště J, Porth I, Skyba O, Unda F, El-Kassaby YA, Douglas CJ, Mansfield SD, Martin J, Schackwitz W, Evans LM, Czarnecki O, Tuskan GA.

BMC Genomics. 2015 Jan 23;16:24. doi: 10.1186/s12864-015-1215-z.

7.

Geographical barriers and climate influence demographic history in narrowleaf cottonwoods.

Evans LM, Allan GJ, DiFazio SP, Slavov GT, Wilder JA, Floate KD, Rood SB, Whitham TG.

Heredity (Edinb). 2015 Apr;114(4):387-96. doi: 10.1038/hdy.2014.115. Epub 2015 Jan 14.

8.

Population genomics of Populus trichocarpa identifies signatures of selection and adaptive trait associations.

Evans LM, Slavov GT, Rodgers-Melnick E, Martin J, Ranjan P, Muchero W, Brunner AM, Schackwitz W, Gunter L, Chen JG, Tuskan GA, DiFazio SP.

Nat Genet. 2014 Oct;46(10):1089-96. doi: 10.1038/ng.3075. Epub 2014 Aug 24.

PMID:
25151358
9.

Genomic insights into salt adaptation in a desert poplar.

Ma T, Wang J, Zhou G, Yue Z, Hu Q, Chen Y, Liu B, Qiu Q, Wang Z, Zhang J, Wang K, Jiang D, Gou C, Yu L, Zhan D, Zhou R, Luo W, Ma H, Yang Y, Pan S, Fang D, Luo Y, Wang X, Wang G, Wang J, Wang Q, Lu X, Chen Z, Liu J, Lu Y, Yin Y, Yang H, Abbott RJ, Wu Y, Wan D, Li J, Yin T, Lascoux M, Difazio SP, Tuskan GA, Wang J, Liu J.

Nat Commun. 2013;4:2797. doi: 10.1038/ncomms3797. Erratum in: Nat Commun. 2014;5:3454. Jianquan, Liu [corrected to Liu, Jianquan].

PMID:
24256998
10.

Predicting whole genome protein interaction networks from primary sequence data in model and non-model organisms using ENTS.

Rodgers-Melnick E, Culp M, DiFazio SP.

BMC Genomics. 2013 Sep 10;14:608. doi: 10.1186/1471-2164-14-608.

11.

Genome-wide association mapping for wood characteristics in Populus identifies an array of candidate single nucleotide polymorphisms.

Porth I, Klapšte J, Skyba O, Hannemann J, McKown AD, Guy RD, DiFazio SP, Muchero W, Ranjan P, Tuskan GA, Friedmann MC, Ehlting J, Cronk QC, El-Kassaby YA, Douglas CJ, Mansfield SD.

New Phytol. 2013 Nov;200(3):710-26. doi: 10.1111/nph.12422. Epub 2013 Jul 26.

12.

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

Geraldes A, Difazio SP, Slavov GT, Ranjan P, Muchero W, Hannemann J, Gunter LE, Wymore AM, Grassa CJ, Farzaneh N, Porth I, McKown AD, Skyba O, Li E, Fujita M, Klápště J, Martin J, Schackwitz W, Pennacchio C, Rokhsar D, Friedmann MC, Wasteneys GO, Guy RD, El-Kassaby YA, Mansfield SD, Cronk QC, Ehlting J, Douglas CJ, Tuskan GA.

Mol Ecol Resour. 2013 Mar;13(2):306-23. doi: 10.1111/1755-0998.12056. Epub 2013 Jan 11.

PMID:
23311503
13.

Revisiting the sequencing of the first tree genome: Populus trichocarpa.

Wullschleger SD, Weston DJ, DiFazio SP, Tuskan GA.

Tree Physiol. 2013 Apr;33(4):357-64. doi: 10.1093/treephys/tps081. Epub 2012 Oct 25.

PMID:
23100257
14.

Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest tree Populus trichocarpa.

Slavov GT, DiFazio SP, Martin J, Schackwitz W, Muchero W, Rodgers-Melnick E, Lipphardt MF, Pennacchio CP, Hellsten U, Pennacchio LA, Gunter LE, Ranjan P, Vining K, Pomraning KR, Wilhelm LJ, Pellegrini M, Mockler TC, Freitag M, Geraldes A, El-Kassaby YA, Mansfield SD, Cronk QC, Douglas CJ, Strauss SH, Rokhsar D, Tuskan GA.

New Phytol. 2012 Nov;196(3):713-25. doi: 10.1111/j.1469-8137.2012.04258.x. Epub 2012 Aug 3.

15.

Identification of quantitative trait loci and candidate genes for cadmium tolerance in Populus.

Induri BR, Ellis DR, Slavov GT, Yin T, Zhang X, Muchero W, Tuskan GA, DiFazio SP.

Tree Physiol. 2012 May;32(5):626-38. doi: 10.1093/treephys/tps032. Epub 2012 Apr 21.

PMID:
22522179
16.

Gene flow and simulation of transgene dispersal from hybrid poplar plantations.

DiFazio SP, Leonardi S, Slavov GT, Garman SL, Adams WT, Strauss SH.

New Phytol. 2012 Mar;193(4):903-15. doi: 10.1111/j.1469-8137.2011.04012.x. Epub 2012 Jan 4.

17.

Contrasting patterns of evolution following whole genome versus tandem duplication events in Populus.

Rodgers-Melnick E, Mane SP, Dharmawardhana P, Slavov GT, Crasta OR, Strauss SH, Brunner AM, Difazio SP.

Genome Res. 2012 Jan;22(1):95-105. doi: 10.1101/gr.125146.111. Epub 2011 Oct 5.

18.

Population substructure in continuous and fragmented stands of Populus trichocarpa.

Slavov GT, Leonardi S, Adams WT, Strauss SH, DiFazio SP.

Heredity (Edinb). 2010 Oct;105(4):348-57. doi: 10.1038/hdy.2010.73. Epub 2010 Jun 9.

19.

Cytogenetic analysis of Populus trichocarpa--ribosomal DNA, telomere repeat sequence, and marker-selected BACs.

Islam-Faridi MN, Nelson CD, DiFazio SP, Gunter LE, Tuskan GA.

Cytogenet Genome Res. 2009;125(1):74-80. doi: 10.1159/000218749. Epub 2009 Jul 14.

PMID:
19617699
20.

Extensive pollen flow in two ecologically contrasting populations of Populus trichocarpa.

Slavov GT, Leonardi S, Burczyk J, Adams WT, Strauss SH, Difazio SP.

Mol Ecol. 2009 Jan;18(2):357-73. doi: 10.1111/j.1365-294X.2008.04016.x.

PMID:
19076277
21.

Emerging use of gene expression microarrays in plant physiology.

Wullschleger SD, Difazio SP.

Comp Funct Genomics. 2003;4(2):216-24. doi: 10.1002/cfg.277.

22.

Extending genomics to natural communities and ecosystems.

Whitham TG, Difazio SP, Schweitzer JA, Shuster SM, Allan GJ, Bailey JK, Woolbright SA.

Science. 2008 Apr 25;320(5875):492-5. doi: 10.1126/science.1153918.

PMID:
18436780
23.

Genome structure and emerging evidence of an incipient sex chromosome in Populus.

Yin T, Difazio SP, Gunter LE, Zhang X, Sewell MM, Woolbright SA, Allan GJ, Kelleher CT, Douglas CJ, Wang M, Tuskan GA.

Genome Res. 2008 Mar;18(3):422-30. doi: 10.1101/gr.7076308. Epub 2008 Feb 6.

24.

Genome-wide analysis of Aux/IAA and ARF gene families in Populus trichocarpa.

Kalluri UC, Difazio SP, Brunner AM, Tuskan GA.

BMC Plant Biol. 2007 Nov 6;7:59.

25.

A dense linkage map of hybrid cottonwood (Populus fremontii x P. angustifolia) contributes to long-term ecological research and comparison mapping in a model forest tree.

Woolbright SA, Difazio SP, Yin T, Martinsen GD, Zhang X, Allan GJ, Whitham TG, Keim P.

Heredity (Edinb). 2008 Jan;100(1):59-70. Epub 2007 Sep 26.

26.

Efficiency of gene silencing in Arabidopsis: direct inverted repeats vs. transitive RNAi vectors.

Filichkin SA, DiFazio SP, Brunner AM, Davis JM, Yang ZK, Kalluri UC, Arias RS, Etherington E, Tuskan GA, Strauss SH.

Plant Biotechnol J. 2007 Sep;5(5):615-26. Epub 2007 Jun 15.

27.

Forest genomics grows up and branches out.

Brunner AM, DiFazio SP, Groover AT.

New Phytol. 2007;174(4):710-3. No abstract available.

28.

A physical map of the highly heterozygous Populus genome: integration with the genome sequence and genetic map and analysis of haplotype variation.

Kelleher CT, Chiu R, Shin H, Bosdet IE, Krzywinski MI, Fjell CD, Wilkin J, Yin T, DiFazio SP, Ali J, Asano JK, Chan S, Cloutier A, Girn N, Leach S, Lee D, Mathewson CA, Olson T, O'connor K, Prabhu AL, Smailus DE, Stott JM, Tsai M, Wye NH, Yang GS, Zhuang J, Holt RA, Putnam NH, Vrebalov J, Giovannoni JJ, Grimwood J, Schmutz J, Rokhsar D, Jones SJ, Marra MA, Tuskan GA, Bohlmann J, Ellis BE, Ritland K, Douglas CJ, Schein JE.

Plant J. 2007 Jun;50(6):1063-78. Epub 2007 May 3.

29.

The Populus homeobox gene ARBORKNOX1 reveals overlapping mechanisms regulating the shoot apical meristem and the vascular cambium.

Groover AT, Mansfield SD, DiFazio SP, Dupper G, Fontana JR, Millar R, Wang Y.

Plant Mol Biol. 2006 Aug;61(6):917-32.

PMID:
16927204
30.

A framework for community and ecosystem genetics: from genes to ecosystems.

Whitham TG, Bailey JK, Schweitzer JA, Shuster SM, Bangert RK, LeRoy CJ, Lonsdorf EV, Allan GJ, DiFazio SP, Potts BM, Fischer DG, Gehring CA, Lindroth RL, Marks JC, Hart SC, Wimp GM, Wooley SC.

Nat Rev Genet. 2006 Jul;7(7):510-23. Review.

PMID:
16778835
32.

Large-scale heterospecific segregation distortion in Populus revealed by a dense genetic map.

Yin TM, DiFazio SP, Gunter LE, Riemenschneider D, Tuskan GA.

Theor Appl Genet. 2004 Aug;109(3):451-63. Epub 2004 May 27.

PMID:
15168022
33.

Poplar genomics is getting popular: the impact of the poplar genome project on tree research.

Tuskan GA, DiFazio SP, Teichmann T.

Plant Biol (Stuttg). 2004 Jan-Feb;6(1):2-4.

PMID:
15095128
34.

Mycorrhizal symbionts of Populus to be sequenced by the United States Department of Energy's Joint Genome Institute.

Lammers P, Tuskan GA, DiFazio SP, Podila GK, Martin F.

Mycorrhiza. 2004 Feb;14(1):63-4. Epub 2003 Dec 20. No abstract available.

PMID:
14689288
35.

Genomics and the tree physiologist.

Wullschleger SD, Tuskan GA, DiFazio SP.

Tree Physiol. 2002 Dec;22(18):1273-6.

PMID:
12490424
36.

Structure and expression of duplicate AGAMOUS orthologues in poplar.

Brunner AM, Rottmann WH, Sheppard LA, Krutovskii K, DiFazio SP, Leonardi S, Strauss SH.

Plant Mol Biol. 2000 Nov;44(5):619-34.

PMID:
11198423

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