Adaptation Genomics

Our approach involves whole genome sequencing and large scale transcriptome resequencing in populations. Population genomics is then coupled with functional and bioinformatic analysis, using mainly Populus trichocarpa and P. balsamifera (species from the Pacific Northwest and central and eastern Canada respectively). In early work we used comparative transcriptomics to identify 500,000 single nucleotide polymorphisms (snps) and used those to determine the genomic architecture of adaptation in this species. Subsequently we expanding the work to include whole genome sequencing of c. 400 genotypes which allowed us to operate with c. 2 million snps.

Poplar team: Armando Geraldes - population genomics of black cottonwood trees (Populus trichocarpa); Charles Hefer - bioinformatics and genomics, POPCAN project (Douglas/Cronk lab); Daisie Huang - evolutionary genomics of Salicaceae, POPCAN project
Former: Nyssa Temmel (PhD student), Julia Nowak (PhD student)

Funding: Genome BC, Genome Canada, NSERC

Partners: Genome Sciences Centre (Vancouver), Oak Ridge National Laboratory (Tennessee)

Major project: Genome Canada "POPCAN project: genetic improvement of poplar trees as a Canadian bioenergy feedstock: clean energy from the poplar tree" (Project leaders: Carl Douglas, UBC and Shawn Mansfield, UBC)

Sample publications:
Suarez‐Gonzalez, A., Hefer, C. A., Christe, C., Corea, O., Lexer, C., Cronk, Q. C., & Douglas, C. J. (2016). Genomic and functional approaches reveal a case of adaptive introgression from Populus balsamifera (balsam poplar) in P. trichocarpa (black cottonwood). Molecular ecology 25(11): 2427-2442

Geraldes A, Hefer C A, Capron A, Kolosova N, Martinez-Nuñez F, Soolanayakanahally RY, Stanton B, Guy RD, Mansfield SD, Douglas CJ, Cronk QCB (2015) Recent Y chromosome divergence despite ancient origin of dioecy in poplars (Populus). Molecular Ecology DOI: 101111/mec13126

Huang D, Hefer C, Kolosova N, Douglas C, Cronk QC (2014) Whole plastome sequencing reveals deep plastid divergence and cytonuclear discordance between closely related balsam poplars, Populus balsamifera and P. trichocarpa (Salicaceae). New Phytologist 204 (3), 693-703.

Percy DM, Argus GW, Cronk QC, Fazekas AJ, Kesanakurti PR, Burgess KS, Husband BC, Newmaster SG, Barrett SCH and Graham SW (2014). Understanding the spectacular failure of DNA barcoding in willows (Salix): Does this result from a trans-specific selective sweep? Molecular Ecology 23 (19), 4737-4756.

Geraldes A, Farzaneh N, Grassa CJ, McKown AD, Guy RD, Mansfield SD, Douglas CJ, Cronk QC (2014) Landscape genomics of Populus trichocarpa: the role of hybridization, limited gene flow and natural selection in shaping patterns of population structure. Evolution 68 (11), 3260-3280.

McKown AD, RDGuy, J Klápště, A Geraldes, M Friedmann, QCB Cronk, YA El‐Kassaby, SD Mansfield, and CJ Douglas. (2014) Geographical and environmental gradients shape phenotypic trait variation and genetic structure in Populus trichocarpa. New Phytologist 201: 1263-1276.

McKown AD, Klápště J, Guy RD, Geraldes A, Porth I, Hannemann J, Friedmann M, Muchero W, Tuskan GA, Ehlting J, Cronk QC, El-Kassaby YA, Mansfield SD, Douglas CJ. (2014) Genome-wide association implicates numerous genes underlying ecological trait variation in natural populations of Populus trichocarpa. New Phytol. 203: 535–553, doi: 10.1111/nph.12815.

Porth I, Klápště J, McKown AD, La Mantia J, Hamelin RC, Skyba O, Unda F, Friedmann MC, Cronk QCB, Ehlting J, Guy RD, Mansfield SD, El-Kassaby YA, & Douglas CJ. (2014). Extensive functional pleiotropy of REVOLUTA substantiated through forward genetics. Plant Physiology, 164(2), 548-554.

Groover A, Cronk Q (2013) From Nehemiah Grew to genomics: The emerging field of evo-devo research for woody plants. International Journal of Plant Sciences 174: 959-963.

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 QCB, El-Kassaby YA, Douglas CJ, Mansfield SD (2013) Genome-wide association mapping for wood characteristics in Populus identifies an array of candidate single nucleotide polymorphisms. New Phytologist: doi: 10.1111/nph.12422

Bao H, Li E, Mansfield SD, Cronk QC, El-Kassaby YA, Douglas CJ (2013) The developing xylem transcriptome and genome-wide analysis of alternative splicing in Populus trichocarpa (black cottonwood) populations. BMC Genomics 14: 359

Nowak JS, Douglas C, Cronk QC (2013) Abaxial greening phenotype in hybrid aspen. Plants 2: 279-301; doi:10.3390/plants2020279

Geraldes A, DiFazio SP, Slavov GT, Ranjan P, Muchero W, Hannemann J, Gunter LE, Wymore LE, Grassa CJ, Farzaneh N, Porth I, McKown AD, Skyba O, Li E, Fujita M, Klapště J, Martin J, Schackwitz W, Pennacchio C, Rokhsar D, Friedmann MC, Wasteneys GO, Guy RD, El-Kassaby YA, Mansfield SD, Cronk QCB, Ehlting J, Douglas CJ, and Tuskan GA (2013). 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 13: 306–323.

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. (2012) Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest tree Populus trichocarpa. New Phytologist 196: 713-25

  • Early work

Plant eco-devo: the potential of poplar as a model organism.
Cronk QC.
New Phytol. 2005 Apr;166(1):39-48. Review.

Use of Ecotilling as an efficient SNP discovery tool to survey genetic variation in wild populations of Populus trichocarpa.
Gilchrist EJ, Haughn GW, Ying CC, Otto SP, Zhuang J, Cheung D, Hamberger B, Aboutorabi F, Kalynyak T, Johnson L, Bohlmann J, Ellis BE, Douglas CJ, Cronk QC.
Mol Ecol. 2006 Apr; 15(5): 1367-78.

The genome of black cottonwood, Populus trichocarpa (Torr. & Gray).
Tuskan GA, Difazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S, Rombauts S, Salamov A, Schein J, Sterck L, Aerts A, Bhalerao RR, Bhalerao RP, Blaudez D, Boerjan W, Brun A, Brunner A, Busov V, Campbell M, Carlson J, Chalot M, Chapman J, Chen GL, Cooper D, Coutinho PM, Couturier J, Covert S, Cronk Q, Cunningham R, Davis J, Degroeve S, Déjardin A, Depamphilis C, Detter J, Dirks B, Dubchak I, Duplessis S, Ehlting J, Ellis B, Gendler K, Goodstein D, Gribskov M, Grimwood J, Groover A, Gunter L, Hamberger B, Heinze B, Helariutta Y, Henrissat B, Holligan D, Holt R, Huang W, Islam-Faridi N, Jones S, Jones-Rhoades M, Jorgensen R, Joshi C, Kangasjärvi J, Karlsson J, Kelleher C, Kirkpatrick R, Kirst M, Kohler A, Kalluri U, Larimer F, Leebens-Mack J, Leplé JC, Locascio P, Lou Y, Lucas S, Martin F, Montanini B, Napoli C, Nelson DR, Nelson C, Nieminen K, Nilsson O, Pereda V, Peter G, Philippe R, Pilate G, Poliakov A, Razumovskaya J, Richardson P, Rinaldi C, Ritland K, Rouzé P, Ryaboy D, Schmutz J, Schrader J, Segerman B, Shin H, Siddiqui A, Sterky F, Terry A, Tsai CJ, Uberbacher E, Unneberg P, Vahala J, Wall K, Wessler S, Yang G, Yin T, Douglas C, Marra M, Sandberg G, Van de Peer Y, Rokhsar D.
Science. 2006 Sep 15; 313(5793): 1596-604.

Copyright reserved