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Novel Insights into Plant Genome Evolution and Adaptation as Revealed through Transposable Elements and Non-Coding RNAs in Conifers.

Liu Y, El-Kassaby YA.

Genes (Basel). 2019 Mar 18;10(3). pii: E228. doi: 10.3390/genes10030228. Review.


In-depth transcriptome characterization uncovers distinct gene family expansions for Cupressus gigantea important to this long-lived species' adaptability to environmental cues.

Zhou SS, Xing Z, Liu H, Hu XG, Gao Q, Xu J, Jiao SQ, Jia KH, Jin YQ, Zhao W, Porth I, El-Kassaby YA, Mao JF.

BMC Genomics. 2019 Mar 13;20(1):213. doi: 10.1186/s12864-019-5584-6.


SNP variable selection by generalized graph domination.

Sun S, Miao Z, Ratcliffe B, Campbell P, Pasch B, El-Kassaby YA, Balasundaram B, Chen C.

PLoS One. 2019 Jan 24;14(1):e0203242. doi: 10.1371/journal.pone.0203242. eCollection 2019.


Genomic selection of juvenile height across a single-generational gap in Douglas-fir.

Thistlethwaite FR, Ratcliffe B, Klápště J, Porth I, Chen C, Stoehr MU, El-Kassaby YA.

Heredity (Edinb). 2019 Jan 10. doi: 10.1038/s41437-018-0172-0. [Epub ahead of print]


Quantitative Genetics and Genomics Converge to Accelerate Forest Tree Breeding.

Grattapaglia D, Silva-Junior OB, Resende RT, Cappa EP, Müller BSF, Tan B, Isik F, Ratcliffe B, El-Kassaby YA.

Front Plant Sci. 2018 Nov 22;9:1693. doi: 10.3389/fpls.2018.01693. eCollection 2018. Review.


Author Correction: Sexual homomorphism in dioecious trees: extensive tests fail to detect sexual dimorphism in Populus.

McKown AD, Klápště J, Guy RD, Soolanayakanahally RY, La Mantia J, Porth I, Skyba O, Unda F, Douglas CJ, El-Kassaby YA, Hamelin RC, Mansfield SD, Cronk QCB.

Sci Rep. 2018 Nov 22;8(1):17410. doi: 10.1038/s41598-018-35443-y.


Temporal quantification of mating system parameters in a coastal Douglas-fir seed orchard under manipulated pollination environment.

Song J, Ratcliffe B, Kess T, Lai BS, Korecký J, El-Kassaby YA.

Sci Rep. 2018 Aug 2;8(1):11593. doi: 10.1038/s41598-018-30041-4.


Ecological genomics of variation in bud-break phenology and mechanisms of response to climate warming in Populus trichocarpa.

McKown AD, Klápště J, Guy RD, El-Kassaby YA, Mansfield SD.

New Phytol. 2018 Oct;220(1):300-316. doi: 10.1111/nph.15273. Epub 2018 Jul 2.


Development of high transferability cpSSR markers for individual identification and genetic investigation in Cupressaceae species.

Huang LS, Sun YQ, Jin Y, Gao Q, Hu XG, Gao FL, Yang XL, Zhu JJ, El-Kassaby YA, Mao JF.

Ecol Evol. 2018 Apr 20;8(10):4967-4977. doi: 10.1002/ece3.4053. eCollection 2018 May.


Genomic-based multiple-trait evaluation in Eucalyptus grandis using dominant DArT markers.

Cappa EP, El-Kassaby YA, Muñoz F, Garcia MN, Villalba PV, Klápště J, Marcucci Poltri SN.

Plant Sci. 2018 Jun;271:27-33. doi: 10.1016/j.plantsci.2018.03.014. Epub 2018 Mar 14.


Multienvironment genomic variance decomposition analysis of open-pollinated Interior spruce (Picea glauca x engelmannii).

El-Dien OG, Ratcliffe B, Klápště J, Porth I, Chen C, El-Kassaby YA.

Mol Breed. 2018;38(3):26. doi: 10.1007/s11032-018-0784-3. Epub 2018 Feb 15.


Genomic prediction accuracies in space and time for height and wood density of Douglas-fir using exome capture as the genotyping platform.

Thistlethwaite FR, Ratcliffe B, Klápště J, Porth I, Chen C, Stoehr MU, El-Kassaby YA.

BMC Genomics. 2017 Dec 2;18(1):930. doi: 10.1186/s12864-017-4258-5.


The gibberellin GID1-DELLA signalling module exists in evolutionarily ancient conifers.

Du R, Niu S, Liu Y, Sun X, Porth I, El-Kassaby YA, Li W.

Sci Rep. 2017 Nov 30;7(1):16637. doi: 10.1038/s41598-017-11859-w.


Dynamic Gene-Resource Landscape Management of Norway Spruce: Combining Utilization and Conservation.

Lstibůrek M, El-Kassaby YA, Skrøppa T, Hodge GR, Sønstebø JH, Steffenrem A.

Front Plant Sci. 2017 Oct 18;8:1810. doi: 10.3389/fpls.2017.01810. eCollection 2017.


Practical application of genomic selection in a doubled-haploid winter wheat breeding program.

Song J, Carver BF, Powers C, Yan L, Klápště J, El-Kassaby YA, Chen C.

Mol Breed. 2017;37(10):117. doi: 10.1007/s11032-017-0715-8. Epub 2017 Sep 3.


High throughput sequencing of small RNAs reveals dynamic microRNAs expression of lipid metabolism during Camellia oleifera and C. meiocarpa seed natural drying.

Feng JL, Yang ZJ, Chen SP, El-Kassaby YA, Chen H.

BMC Genomics. 2017 Jul 20;18(1):546. doi: 10.1186/s12864-017-3923-z.


Sexual homomorphism in dioecious trees: extensive tests fail to detect sexual dimorphism in Populus .

McKown AD, Klápště J, Guy RD, Soolanayakanahally RY, La Mantia J, Porth I, Skyba O, Unda F, Douglas CJ, El-Kassaby YA, Hamelin RC, Mansfield SD, Cronk QCB.

Sci Rep. 2017 May 12;7(1):1831. doi: 10.1038/s41598-017-01893-z. Erratum in: Sci Rep. 2018 Nov 22;8(1):17410.


Regulatory crosstalk between microRNAs and hormone signalling cascades controls the variation on seed dormancy phenotype at Arabidopsis thaliana seed set.

Liu Y, El-Kassaby YA.

Plant Cell Rep. 2017 May;36(5):705-717. doi: 10.1007/s00299-017-2111-6. Epub 2017 Feb 14.


Single-Step BLUP with Varying Genotyping Effort in Open-Pollinated Picea glauca.

Ratcliffe B, El-Dien OG, Cappa EP, Porth I, Klápště J, Chen C, El-Kassaby YA.

G3 (Bethesda). 2017 Mar 10;7(3):935-942. doi: 10.1534/g3.116.037895.


Impact of temperature shifts on the joint evolution of seed dormancy and size.

Liu Y, Barot S, El-Kassaby YA, Loeuille N.

Ecol Evol. 2016 Nov 27;7(1):26-37. doi: 10.1002/ece3.2611. eCollection 2017 Jan.


Simple Genetic Distance-Optimized Field Deployments for Clonal Seed Orchards Based on Microsatellite Markers: As a Case of Chinese Pine Seed Orchard.

Yuan H, Niu S, El-Kassaby YA, Li Y, Li W.

PLoS One. 2016 Jun 16;11(6):e0157646. doi: 10.1371/journal.pone.0157646. eCollection 2016.


De Novo Transcriptome Assembly and Characterization for the Widespread and Stress-Tolerant Conifer Platycladus orientalis.

Hu XG, Liu H, Jin Y, Sun YQ, Li Y, Zhao W, El-Kassaby YA, Wang XR, Mao JF.

PLoS One. 2016 Feb 16;11(2):e0148985. doi: 10.1371/journal.pone.0148985. eCollection 2016.


Implementation of the Realized Genomic Relationship Matrix to Open-Pollinated White Spruce Family Testing for Disentangling Additive from Nonadditive Genetic Effects.

Gamal El-Dien O, Ratcliffe B, Klápště J, Porth I, Chen C, El-Kassaby YA.

G3 (Bethesda). 2016 Jan 22;6(3):743-53. doi: 10.1534/g3.115.025957.


Changes in hormone flux and signaling in white spruce (Picea glauca) seeds during the transition from dormancy to germination in response to temperature cues.

Liu Y, Müller K, El-Kassaby YA, Kermode AR.

BMC Plant Biol. 2015 Dec 18;15:292. doi: 10.1186/s12870-015-0638-7.


Evolutionary Quantitative Genomics of Populus trichocarpa.

Porth I, Klápště J, McKown AD, La Mantia J, Guy RD, Ingvarsson PK, Hamelin R, Mansfield SD, Ehlting J, Douglas CJ, El-Kassaby YA.

PLoS One. 2015 Nov 23;10(11):e0142864. doi: 10.1371/journal.pone.0142864. eCollection 2015.


A transcriptomics investigation into pine reproductive organ development.

Niu S, Yuan H, Sun X, Porth I, Li Y, El-Kassaby YA, Li W.

New Phytol. 2016 Feb;209(3):1278-89. doi: 10.1111/nph.13680. Epub 2015 Sep 25.


A comparison of genomic selection models across time in interior spruce (Picea engelmannii × glauca) using unordered SNP imputation methods.

Ratcliffe B, El-Dien OG, Klápště J, Porth I, Chen C, Jaquish B, El-Kassaby YA.

Heredity (Edinb). 2015 Dec;115(6):547-55. doi: 10.1038/hdy.2015.57. Epub 2015 Jul 1.


Colonization history, host distribution, anthropogenic influence and landscape features shape populations of white pine blister rust, an invasive alien tree pathogen.

Brar S, Tsui CK, Dhillon B, Bergeron MJ, Joly DL, Zambino PJ, El-Kassaby YA, Hamelin RC.

PLoS One. 2015 May 26;10(5):e0127916. doi: 10.1371/journal.pone.0127916. eCollection 2015.


Prediction accuracies for growth and wood attributes of interior spruce in space using genotyping-by-sequencing.

Gamal El-Dien O, Ratcliffe B, Klápště J, Chen C, Porth I, El-Kassaby YA.

BMC Genomics. 2015 May 9;16:370. doi: 10.1186/s12864-015-1597-y.


Using Populus as a lignocellulosic feedstock for bioethanol.

Porth I, El-Kassaby YA.

Biotechnol J. 2015 Apr;10(4):510-24. doi: 10.1002/biot.201400194. Epub 2015 Feb 11. Review.


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.


Association genetics, geography and ecophysiology link stomatal patterning in Populus trichocarpa with carbon gain and disease resistance trade-offs.

McKown AD, Guy RD, Quamme L, Klápště J, La Mantia J, Constabel CP, El-Kassaby YA, Hamelin RC, Zifkin M, Azam MS.

Mol Ecol. 2014 Dec;23(23):5771-90. doi: 10.1111/mec.12969. Epub 2014 Nov 8.


Population structure of mountain pine beetle symbiont Leptographium longiclavatum and the implication on the multipartite beetle-fungi relationships.

Tsui CK, Farfan L, Roe AD, Rice AV, Cooke JE, El-Kassaby YA, Hamelin RC.

PLoS One. 2014 Aug 25;9(8):e105455. doi: 10.1371/journal.pone.0105455. eCollection 2014.


Genome-wide association implicates numerous genes underlying ecological trait variation in natural populations of Populus trichocarpa.

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.

New Phytol. 2014 Jul;203(2):535-53. doi: 10.1111/nph.12815. Epub 2014 Apr 22.


Geographical and environmental gradients shape phenotypic trait variation and genetic structure in Populus trichocarpa.

McKown AD, Guy RD, Klápště J, Geraldes A, Friedmann M, Cronk QC, El-Kassaby YA, Mansfield SD, Douglas CJ.

New Phytol. 2014 Mar;201(4):1263-76. doi: 10.1111/nph.12601. Epub 2013 Nov 25.


Extensive functional pleiotropy of REVOLUTA substantiated through forward genetics.

Porth I, Klápste J, McKown AD, La Mantia J, Hamelin RC, Skyba O, Unda F, Friedmann MC, Cronk QC, Ehlting J, Guy RD, Mansfield SD, El-Kassaby YA, Douglas CJ.

Plant Physiol. 2014 Feb;164(2):548-54. doi: 10.1104/pp.113.228783. Epub 2013 Dec 5.


Impacts of population structure and analytical models in genome-wide association studies of complex traits in forest trees: a case study in Eucalyptus globulus.

Cappa EP, El-Kassaby YA, Garcia MN, Acuña C, Borralho NM, Grattapaglia D, Marcucci Poltri SN.

PLoS One. 2013 Nov 25;8(11):e81267. doi: 10.1371/journal.pone.0081267. eCollection 2013.


Association analysis identifies Melampsora ×columbiana poplar leaf rust resistance SNPs.

La Mantia J, Klápště J, El-Kassaby YA, Azam S, Guy RD, Douglas CJ, Mansfield SD, Hamelin R.

PLoS One. 2013 Nov 13;8(11):e78423. doi: 10.1371/journal.pone.0078423. eCollection 2013.


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.


Network analysis reveals the relationship among wood properties, gene expression levels and genotypes of natural Populus trichocarpa accessions.

Porth I, Klápště J, Skyba O, Friedmann MC, Hannemann J, Ehlting J, El-Kassaby YA, Mansfield SD, Douglas CJ.

New Phytol. 2013 Nov;200(3):727-42. doi: 10.1111/nph.12419. Epub 2013 Jul 29.


The developing xylem transcriptome and genome-wide analysis of alternative splicing in Populus trichocarpa (black cottonwood) populations.

Bao H, Li E, Mansfield SD, Cronk QC, El-Kassaby YA, Douglas CJ.

BMC Genomics. 2013 May 29;14:359. doi: 10.1186/1471-2164-14-359.


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.


Populus trichocarpa cell wall chemistry and ultrastructure trait variation, genetic control and genetic correlations.

Porth I, Klápště J, Skyba O, Lai BS, Geraldes A, Muchero W, Tuskan GA, Douglas CJ, El-Kassaby YA, Mansfield SD.

New Phytol. 2013 Feb;197(3):777-90. doi: 10.1111/nph.12014. Epub 2012 Dec 20.


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.


Comparative nucleotide diversity across North American and European populus species.

Ismail M, Soolanayakanahally RY, Ingvarsson PK, Guy RD, Jansson S, Silim SN, El-Kassaby YA.

J Mol Evol. 2012 Jun;74(5-6):257-72. doi: 10.1007/s00239-012-9504-5. Epub 2012 May 6.


Population structure and migration pattern of a conifer pathogen, Grosmannia clavigera, as influenced by its symbiont, the mountain pine beetle.

Tsui CK, Roe AD, El-Kassaby YA, Rice AV, Alamouti SM, Sperling FA, Cooke JE, Bohlmann J, Hamelin RC.

Mol Ecol. 2012 Jan;21(1):71-86. doi: 10.1111/j.1365-294X.2011.05366.x. Epub 2011 Nov 25.


Estimating selfing rates from reconstructed pedigrees using multilocus genotype data.

Wang J, El-Kassaby YA, Ritland K.

Mol Ecol. 2012 Jan;21(1):100-16. doi: 10.1111/j.1365-294X.2011.05373.x. Epub 2011 Nov 22.


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