Yousry El-Kassaby | Faculty Profile

Research Areas:

Biotechnology, Genetics, Genomics

Research
Publications

Research Areas:

Tree domestication
Tree improvement delivery system
Seed orchards’ genetics
Tree breeding
Association genetics and genomic selection

Projects

Development of advanced generation seed orchard designs

In situ wood quality assessment

Seed orchard’s genetic efficiency

Seed dormancy

Association genetics of biofuel attributes

Genomic selection

Awards

International Union of Forest Research Organizations Scientific Achievement Award 2010
Professor Honoris Causa – The Czech University of Life Sciences Praue 2011
Canadian Forestry Scientific Achievement Award 2017

Selected Publications

L Feng, J Sun, YA El-Kassaby, X Yang, X Tian, T Wang (2022). Predicting potential habitat of a plant species with small populations under climate change: Ostrya rehderiana. Forests 13:129.

EP Cappa, B Ratcliffe, C Chen, BR Thomas, Y Liu, J Klutsch, X Wei, JS Azcona, A Benowicz, S Sadoway, N Erbilgin, YA El-Kassaby (2022). Improving lodgepole pine genomic evaluation using spatial correlation structure and SNP selection with single-step GBLUP. Heredity https://doi.org/10.1038/s41437-022-00508-2

Q Tian, YA El-Kassaby, W Li (2022). Revealing the genetic structure and differentiation in endangered species of Pinus bungeana by genome-wide SNP markers. Forests 13:326.

J-X Zhang, H-M Liu, B-N Yang, H-L Wang, S-H Niu, YA El-Kassaby, W Li (2022). Phytohormone profiles and related gene expressions after endodormancy release in developing Pinus tabuliformis male strobili. Plant Sci 316:111167.

Z Yiyang, X Li, J Xie, XW Jie, S Chen, X Zhang, S Liu, J Wu, YA El-Kassaby, D Zhang (2022). Transposable elements: distribution, polymorphism, and climate adaptation in Populus Front. Plant Sci. 13:814718.

Cappa, E.P., Klutsch, J.G., Sebastian-Azcona, J., Ratcliffe, B., Wei, X., Da Ros, L., Ullah, A., Liu, Y., Chen, C., Benowicz, A., Sadoway, S., Mansfield, S.D., Erbilgin, N., Thomas, B.R., El-Kassaby, Y.A. (2022). Integrating genomic information and productivity and climate-adaptability traits into a regional white spruce breeding program. PLOS One 17(3):e0264549

304. Chen, Panfei, Y Song, X Liu, L Xiao, C Bu, P Liu, L Zhao, PK Ingvarsson, HX Wu, YA El-Kassaby, D Zhang. (2022). LncRNA PMAT–PtoMYB46 module represses PtoMATE and PtoARF2 promoting Pb2+ uptake and plant growth in poplar. J Hazard Mat https://doi.org/10.1016/j.jhazmat.2022.128769

Piot, A, YA El-Kassaby, I Porth. (2022). Genomics-based systems and multi-disciplinary approaches to unlock complex gene networks underlying wood formation. Current For Reports doi.org/10.1007/s40725-022-00162-1

Stejskal, J, J Klápště, J Čepl, YA El‑Kassaby, M Lstibůrek. (2022). Effect of clonal testing on the efficiency of genomic evaluation in forest tree breeding. Sci Reports 12:3033

Xu, J, Luo H, S-S Zhou, S-Q Jiao. K-K Jia, S Nie, H Liu, W Zhao, X-R Wang, YA El-Kassaby, I Porth, J-F Mao. (2022). UV-B and UV-C radiation trigger both common and distinctive signal perceptions and transmissions in Pinus tabuliformis Carr. Tree Physiol https://doi.org/10.1093/treephys/tpac021

Zhou, C, Y Guo, Y Chen, H Zhang, YA El-Kassaby, W Li. (2022). Genome wide association study identifies candidate genes related to the earlywood tracheid properties in Picea crassifolia Kom. Forests 13:332.

Ning, K, T Zhou, Y Wang, YA El-Kassaby, Y Ma. (2022). The complete chloroplast genome of Euonymus alatus (Celastraceae). Mitochondrial DNA B: Resour 7:707-708.

F du Toit, NC Coops, TRH Goodbody, M Stoehr, YA El-Kassaby (2021). Deriving internal crown geometric features of Douglas-fir from airborne laser scanning in a realized-gain trial. Forestry 94:442-454 doi.org/10.1093/forestry/cpaa046

K Ning, T Zhou, CZ Jiang, HM Wu, JL Jiang, J Chen, YA El-Kassaby, Y Ma (2021). Rapid and efficient leaf regeneration propagation system for Euonymus bungeanus. Biologia Plamtarum 65:118-125. DOI:10.32615/bp.2020.166

Y Guo, S Niu, YA El-Kassaby, Wei Li (2021). Transcriptome-wide isolation and expression of NF-Y gene family in male cone development and hormonal treatment of Pinus tabuliformis Physiologia Plantarum 171:34-47.

Yang, B, S Niu, YA El-Kassaby, W Li (2021). Monitoring genetic diversity across Pinus tabuliformis seed orchard generations using SSR markers Can J For Res 51:1-7 doi.org/10.1139/cjfr-2020-0479

Guo, Y, Y Feng, F-F Fu, YA El-Kassaby, T Wang, G Wang (2021). Eliciting increased flavonoids content in Ginkgo biloba leaves through exogenous salicylic acid and methyl jasmonate treatments Can J For Res 51:1-8 doi.org/10.1139/cjfr-2020-0468

Guo Y, T Wang, F-F Fu, YA El-Kassaby, G Wang (2021). Metabolome and transcriptome analyses reveal the regulatory mechanisms of photosynthesis in developing Ginkgo biloba leaves Int. J. Mol. Sci. 22:2601 doi.org/10.3390/ijms22052601

Guo, Y, Wang, M, Gao, C, Fu, F-F, Wang, T, El-Kassaby, YA, Wang, G. (2021). Amino acid metabolism reprogramming in response to changing growth environment in Ginkgo biloba leaves. Food Science and Technology 144:111276 doi.org/10.1016/j.lwt.2021.111276

L Xuan, G Wei, YA El-Kassaby, Y Fang (2021). Hybridization and introgression in sympatric and allopatric populations of four oak species BMC Plant Biology 21:266 doi.org/10.1186/s12870-021-03007-4

Y Song; P Chen; A Xuan; C Bu; P Liu; PK Ingvarsson; YA El-Kassaby; D Zhang (2021). Integration of genome wide association studies and co-expression networks reveal roles of PtoWRKY 42 -PtoUGT76C1-1 in trans-zeatin metabolism and cytokinin sensitivity in poplar New Phytology doi: 10.1111/nph.17469

J Xu, S Nie, C-Q Xu, H Liu, K-H Jia, S-S Zhou, W Zhao, X-Q Zhou, YA El-Kassaby, X-R Wang, I Porth, J-F Mao (2021). UV-B-induced molecular mechanisms of stress physiology responses in the major northern Chinese conifer Pinus tabuliformis Carr. Tree Physiology doi:10.1093/treephys/tpaa180

Y Zhao, J Xie, S Wang, W Xu, S Chen, X Song, M Lu, YA El-Kassaby, D Zhang (2021). Synonymous mutation in Growth Regulating Factor 15 of miR396a target sites enhances photosynthetic efficiency and heat tolerance in poplar J Experimental Bot doi:10.1093/jxb/erab120

K-H Jia, H Liu, R-G Zhang, J Xu, S-S Zhou, S-Q Jiao, X-M Yan, X-C Tian, T-L Shi, H Luo, Z-C Li, Y-T Bao, S Nie, J-F Guo, I Porth, YA El-Kassaby, X-R Wang, C Chen, Y Van de Peer, W Zhao, J-F Mao (2021). Chromosome-scale assembly and evolution of the tetraploid Salvia splendens (Lamiaceae) genome Hortic Res 8:177 doi.org/10.1038/s41438-021-00614-y

S-P Cheng, K-H Jia, R-G Zhang, Z-C Li, S-S Zhou, T-L Shi, A-C Ma, C-W Yu, C Gao, G-L Cao, H Liu, W Zhao, S Nie, J-F Guo, S-Q Jiao, X-C Tian, X-M Yan, Y-T Bao, Q-Z Yun, I Porth, YA El-Kassaby, X-R Wang, Z Li, Y Van de Peer, J-F Mao (2021). Haplotype-resolved genome assembly and allele specific gene expression of cultivated ginger Hort Res 8:88. doi.org/10.1038/s41438-021-00599-8

S-S Zhou, X-M Yan, K-F Zhang, H Liu, J Xu, S Nie, K-H Jia, S-Q Jiao, W Zhao, Y-J Zhao, I Porth, YA El-Kassaby, T Wang, J-F Mao (2021). A comprehensive annotation dataset of intact LTR retrotransposons of 300 plant genomes. Scientific Data 8:174 doi.org/10.1038/s41597-021-00968-x

Z-J Yang, X-H Wu, L-M Huang, W-W Xie, Y Chen, YA El-Kassaby, J-L Feng (2021). Soil bacteria to regulate Phoebe bournei seedlings growth and soil sustainable utilization under NPK fertilization Plants 10:1868. doi.org/10.3390/plants10091868

T Zhou, K Ning, W Zhang, X Lu, D Zhang, YA El-Kassaby, T Wang, J Fan, H Jiang, F Cao (2021). Phenotypic variation of floral organs in flowering crabapples and its taxonomic significance BMC Plant Biology 21:503 doi.org/10.1186/s12870-021-03227-8

J Korecký, J Čepl, J Stejskal, Z Faltinová, J Dvořák, M Lstibůrek, YA El-Kassaby (2021). Genetic diversity of Norway spruce ecotypes assessed by GBS-derived SNPs Scientific Reports 11:23119 doi.org/10.1038/s41598-021-02545-z

Q Xia, H Sun, YA El-Kassaby, W Li (2021). Characterization of Pinus densiflora var. zhangwuensis S.J.Zhang, C.X.Li & X.Y.Yuan complete chloroplast genome Mitochondrial DNA Part B 6:3515-3516 doi.org/10.1080/23802359.2021.2005486

Z-J Yang, X-H Wu, L-H Chen, L-M Huang, Y Chen, J Wu, YA El-Kassaby, SC Grossnickle, J-L Feng (2021). Fertilization regulates accumulation and allocation of biomass and nutrients in Phoebe bournei seedlings Agriculture 11:1187 doi.org/10.3390/agriculture11121187

X Li, Y Li, YA El-Kassaby, Y Fang (2021). Characterization of the complete chloroplast genome of Quercus acrodonta (Fagaceae) Mitochondrial DNA Part B 12:3320-3321.

L Xuan, Y Li, SP Sylvester, M Zang, YA El-Kassaby, Y Fang (2021). Evolutionary patterns of nucleotide substitution rates in plastid genomes of Quercus Ecology and Evolution 11:13401-13414 DOI: 10.1002/ece3.8063

B Yang, H Sun, J Qi, S Niu, YA El-Kassaby, W Li (2020). Improved genetic distance-based spatial deployment can effectively minimize inbreeding in seed orchard For Ecosystems 7:10

YA El-Kassaby, B Ratcliffe, O Gamal El-Dien, S Sun, C Chen, EP Cappa, I Porth (2020). Genomic selection in Canadian spruces In: IM Porth and AR De la Torre (eds.), The Spruce Genome, Compendium of Plant Genomes, Springer Nature Switzerland AG. Pp. 115-127. ttps://doi.org/10.1007/978-3-030-21001-4_8

du Toit, F, NC Coops, P Tompalski, TRH Goodbody, YA El-Kassaby, M Stoehr, D Turner, A Lucieer (2020). Characterizing variations in growth characteristics between Douglas-fir with different genetic gain levels using Airborne Laser Scanning TREES doi:10.1007/s00468-019-01946-y

T Zhou, XW Zhang, LD Zhang,YA El-Kassaby, JJ Fan, H Jiang, BG Wang, LF Cao (2020). A binary-based matrix model for Malus corolla symmetry and its variational significance Front. Plant Sci. 11:416

A Xuan, Y Song, C Bu, P Chen, YA El-Kassaby, D Zhang (2020). Changes in DNA methylation in response to 6-benzylaminopurine affect allele-specific gene expression in Populus tomentosa. Int. J. Mol. 21:2117

X-G HU, S-S ZHOU, Y YANG, H LIU, S ANIL, Q WANG, W ZHAO, Q GAO, YA EL-KASSABY, T WANG, Y LI, J-F MAO (2020). Transcriptome-wide identification and profiling of miRNAs in a stress-tolerant conifer Sabina chinensis J Biosci 45:41.

Y Liu, YA El-Kassaby (2020). Ecological drivers of plant life-history traits: Assessment of seed mass and germination variation using climate cues and nitrogen resources in conifer species Ecological Indicators 117:106517.

FR Thistlethwaite, O Gamal El-Dien, B Ratcliffe, J Klápště, I Porth, C Chen, MU Stoehr, PK Ingvarsson, YA El-Kassaby (2020). Linkage disequilibrium vs. pedigree: genomic selection prediction accuracy in conifer species PLOS ONE 15(6): e0232201.

Grubinger, S; NC Coops; M Stoehr, YA El-Kassaby, A Lucieer; D Turner (2020). Height and effective LAI are key metrics for modeling realized gains in Douglas-fir (Pseudotsuga menziesii) using laser scanning data from unmanned aircraft systems (UAS) For Ecol Manage 473:118284.

Fu,F-F, Y Peng, G Wang, YA El-Kassaby, F Cao (2020). Integrative analysis of the metabolome and transcriptome reveals seed germination mechanism in Punica granatum L. J. Integr. Agric. 19:2-16.

Feng, J-L, Y Jiang, Z-J Yang, S-P Chen, YA El-Kassaby, H Chen (2020). Marker-assisted selection in C. oleifera hybrid papulation Silvae Genetica 69:63-72.

Z-J Yang, X-H Wu, SC Grossnickle, L-H Chen, X-X Yu, YA El-Kassaby, J-L Feng (2020). Formula fertilization promotes Phoebe bournei robust seedling cultivation Forests 11:781

F-S Yang, S Nie, H Liu, T-L Shi, X-C Tian, S-S Zhou, Y-T Bao, K-H Jia, J-F Guo, W Zhao, N An, R-G Zhang, Q-Z Yun, X-Z Wang, C Mannapperuma, I Porth, YA El-Kassaby, NR Street, X-R Wang, Y Van de Peer, J-F Mao. (2020). Chromosome-level genome assembly of a parent species of widely cultivated azaleas. Nat. Commun. 11:5269.

J-M Park, H-I Kang, D-B Yeom, K-S Kang, YA El-Kassaby, K-M Lee. (2020). Gender, reproductive output covariation and their role on gene diversity of Pinus koraiensis seed orchard crops. BMC Plant Biology 20:418.

J Klápště, A Kremer, K Burg, P Garnier-Géré, O Gamal El-Dien, B. Ratcliffe, YA El-Kassaby, I Porth. (2020). Quercus species divergence is driven by natural selection on evolutionarily less integrated traits. Heredity https://doi.org/10.1038/s41437-020-00378-6

Y Guo, C Gao, M Wang, F-F Fu, YA El-Kassaby, T Wang, G Wang. (2020). Metabolome and transcriptome analyses reveal flavonoids biosynthesis differences in Ginkgo biloba associated with environmental conditions. Ind Crops Prod 158:112963

IM Porth, A R. De la Torre, YA El-Kassaby. (2020). Prospects: The Spruce Genome, a Model for Understanding Gymnosperm Evolution and Supporting Tree Improvement Efforts. In: IM Porth and AR De la Torre (eds.), The Spruce Genome, Compendium of Plant Genomes, Springer Nature Switzerland AG. Pp. 215-217. ttps://doi.org/10.1007/978-3-030-21001-4_8

Liu, Y, YA El-Kassaby (2020). Transcriptome-wide analysis of introgression-resistant regions reveals genetic divergence genes under positive selection in Populus trichocarpa. Heredity 126:442–462.

Guo, Y, T Wang, F-F Fu, G Wang, YA El-Kassaby (2020). Temporospatial flavonoids metabolism variation in Ginkgo Biloba leaves Frontiers in Genetics doi.org/10.3389/fgene.2020.589326

Y Liu and YA El-Kassaby (2020). Techniques for small non-coding RNA analysis in seeds of forest tree species In: Spillane C., McKeown P. (eds) Plant Epigenetics and Epigenomics. Methods in Molecular Biology, vol 2093. Humana, New York, NY

Y-Q Sun, W Zhao, C-Q Xu, YA El-Kassaby, AR De La Torre, J-F Mao (2020). Genetic variation related to high elevation adaptation revealed by long-term common garden experiments in Pinus yunnanensis Frontiers in Genetics 10:1405

M Lstibůrek, S Schueler, YA El-Kassaby, GR Hodge, J Stejskal, J Korecký, P Škorpík, H Konrad, T Geburek (2020). In situ forest gene resources management accelerates adaptive response to climate change Frontiers in Genetics 11:28

A Piot, J Prunier, N Isabel, J Klápště, YA El-Kassaby, JCV Aguilar, I Porth (2020). Genomic diversity evaluation of Populus trichocarpa germplasm for rare variant genetic association studies Frontiers in Genetics 10:1384

K-H Jia, W Zhao, PA Maier, X-G Hu, Y-Q Jin, S-S Zhou, S-Q Jiao, X-R Wang, YA El-Kassaby, T Wang, J-F Mao (2020). Landscape genomics predicts climate change related genetic offset for the widespread Platycladus orientalis (Cupressaceae) Evolutionary Applications 13:665-676.

J Xu, S Nie, C-Q Xu, H Liu, K-H Jia, S-S Zhou, W Zhao, X-Q Zhou, I Porth, YA El-Kassaby, X-R Wang, J-F Mao (2020). UV-B induced molecular mechanisms of stress physiology responses in the major Northern Chinese conifer Pinus tabuliformis Carr. Tree Physiology doi:10.1093/treephys/tpaa180

Y Liu and YA El-Kassaby (2019). Phenotypic plasticity of natural Populus trichocarpa populations in response to temporally environmental change in a common garden BMC Evolutionary Biology 19:231

X-G Hu; J-F Mao; YA El-Kassaby; K-H Jia; S-Q Jiao; S-S Zhou; Y Li; NC Coops; T Wang (2019). Local adaptation and response of Platyclades orientalis populations to climate change. iForests 10:622 doi.org/10.3390/f10080622

Jin, Y., W. Zhao, S. Nie, S.-S. Liu, Y.A. El-Kassaby, X.-R. Wang, J.-F. Mao (2019). Genome-wide variant identification and high-density genetic map construction using RADseq for Platycladus orientalis (Cupressaceae) G3: Genes|Genomes|Genetics 9:3663 doi.org/10.1534/g3.119.400684

W Lu, L Xiao, M Quan, Q Wang, YA El‐Kassaby, Q Du, D Zhang (2019). Linkage‐linkage disequilibrium dissection of the epigenetic quantitative trait loci (epiQTLs) underlying growth and wood properties in Populus New Phytol doi.org/10.1111/nph.16220

S-S Zhou; Z Xing; H Liu; X-G Hu; Q Gao; J Xu, S-Q Jiao; K-H Jia; Y-Q Jin; W Zhao; I Porth; YA El-Kassaby; J-F Mao (2019). In-depth transcriptome characterization uncovers distinct gene family expansions for Cupressus gigantea important to this long-lived species adaptability to environmental cues. BMC Genomics 20:213.

YA El-Kassaby, Q Wang, T Wang, B Ratcliffe, Q-X Bi, Z Wang, J-F Mao, W Guan (2019). Concept for gene conservation strategy for the endangered Chinese yellowhorn, Xanthoceras sorbifolium, based on simulation of pairwise kinship coefficient For Ecol Manage 432:976-982

S Sun, Z Miao, B Ratcliffe, P Campell, B Pasch, YA El-Kassaby, B Balsundaram, C Chen. (2019). SNP variable selection by generalized graph domination. PLoS ONE 14:e0203242

Thistlethwaite, F.R., Ratcliffe, B., Klápště, J., Porth, I., Chen, C., Stoehr, M.U., El-Kassaby, Y.A, (2019). Genomic selection of juvenile height across a single generational gap in Douglas-fir Heredity doi.org/10.1038/s41437-018-0172-0

Ren-Bin Zhu, Qing Wang, Wen-Bin Guan, Yanjia Mao, Bin Tian, Ji-Min Cheng, Yousry A. El-Kassaby (2019). Conservation of genetic diversity hotspots of the high valued relic yellowhorn (Xanthoceras sorbifolium) considering climate change predictions Ecology and Evolution 9:3251-3263.

K Chaloupková, J Stejskal, YA El-Kassaby, J Frampton, M Lstibůrek (2019). Current advances in seed orchard layouts: two case studies in conifers Forests 10:93

Y Liu, YA El-Kassaby (2019). Novel insights into plant genome evolution and adaptation as revealed through transposable elements and non-coding RNAs in conifers Genes 10:228.

Y Guo, Y Lu, YA El-Kassaby, L Feng, G Wang, T Wang (2019). Predicting growth and habitat responses of Ginkgo biloba L. to climate change Ann. For. Sci. 76:101

McKown, A; Klapšte, J; Guy, R; Corea, O; Fritsche, S; Ehlting, J; El-Kassaby, YA; Mansfield, SD (2019). A role for SPEECHLESS in the integration of leaf stomatal patterning with the growth vs disease trade-off in poplar New Phytologist 223:1888-1903.

El-Kassaby, Y.A.; Thistlethwaite, F.R. (2018). Genomics-based selective breeding of forest trees Atlas of Science- atlasofscience.org

O Gamal El-Dien, B Ratcliffe, J Klápště, I Porth, C Chen, YA El-Kassaby (2018). Multi-environment genomic variance decomposition analysis of open-pollinated Interior spruce (Picea glauca x engelmannii) Mol Breeding 38:26.

Cappa,E.P.; P.V. Villalba; Y.A. El-Kassaby; M.N. Garcia; J. Klápště; F. Muñoz; S.M. Poltri (2018). Genomic-based multiple-trait evaluation in Eucalyptus grandis using dominant DArT markers Plant Science 271:27-33.

L-S Huang, Y-Q Sun, Y Jin, Q Gao, X-G Hu, F-L Gao, X-L Yang, J-J Zhu, YA El-Kassaby, J-F Mao (2018). Development of high transferability cpSSR markers for individual identification and genetic investigation in Cupressaceae species DOI: 10.1002/ece3.4053 Ecology and Evolution 8:4967-4977.

Y Liu and YA El-Kassaby (2018). Evapotranspiration and favorable growing degree-days are key to tree height growth and ecosystem functioning: Meta-analyses of Pacific Northwest historical data Scientific Reports 8:8228.

L-S Huang, J-Y Song, Y-Q Sun, S-Q Jiao, S-S Zhou, Y Jin, X-L Yang, J-J Zhu, F-L Gao, YA El-Kassaby, J-F Mao (2018). Pollination dynamics in a Platycladus orientalis seed orchard as revealed by partial pedigree reconstruction Can J For Res 48:1-6.

McKown AD; J Klápště; RD Guy; YA El-Kassaby; SD Mansfield (2018). Ecological genomics of variation in bud break phenology and mechanisms of response to climate warming in Populus trichocarpa New Phytol 220:300-316..

Porth, I; F Maghuly; YA El-Kassaby; S Mansfield (2018). Localization of gene expression, tissue specificity of Populus xylosyltransferase genes by isolation and functional characterization of their promoters Plant Cell Tissue and Organ Culture 134:503-508.

J. Stejskal; M. Lstibůrek; J. Klápště; J. Čepl; Y.A. El-Kassaby (2018). Effect of genomic prediction on response to selection in forest tree breeding Tree Genet Genomes 14:74.

Wang Q, Zhu R, Cheng J, Deng Z, Guan W, El-Kassaby YA (2018). Species association in Xanthoceras sorbifolium Bunge communities and selection for agroforestry establishment Agroforestry Systems doi.org/10.1007/s10457-018-0265-z

J Song, B Ratcliffe, T Kess, BS Lai, J Korecký, YA El-Kassaby (2018). Temporal quantification of mating system parameters in a coastal Douglas-fir seed orchard under manipulated pollination environment Scientific Reports 8:11593 | DOI:10.1038/s41598-018-30041-4

Grattapaglia, D, OB Silva-Junior, RT Resende, EP Cappa, BSF Müller, B Tan, F Isik, B Ratcliffe, YA E-Kassaby. (2018). Quantitative genetics and genomics converge to accelerate forest tree breeding Frontiers in Plant Science (accepted).

J.H. Sønstebø, M.M. Tollefsrud, T. Myking, A. Steffenrem, A.E. Nilsen, Ø.M. Edvardsen, O.R. Johnskås, Y.A. El-Kassaby (2018). Genetic diversity of Norway spruce (Picea abies) seed orchard crops: effects of clone number, seed year, and pollen contamination For Ecol Manage 411:132-141.

X-G Hu, T Wang, S-S Liu, S-Q Jiao, K-H Jia, S-S Zhou, Y Jin, Y Li, YA El-Kassaby, J-F Mao (2017). Predicting future seed sourcing of Platycladus orientalis for future climates using climate niche models iForest 8:471.

Park J-M, Kwon S-H, Lee H-J, Na S-J, El-Kassaby YA, Kang K-S (2017). Integrating fecundity variation and genetic relatedness in estimating seed crops genetic diversity: Pinus koraiensis seed orchard as an example Can J For Res 47: 366–37

P Wu, G Wang, YA El-Kassaby, P Wang, X Zou, X Ma. (2017). Solubilization of aluminum-bound phosphorus by root cell walls: evidence from Chinese fir, Cunninghamia lanceolata (Lamb.) Hook. Can J For Res 47:419–423.

Y. Liu, Y.A. El-Kassaby (2017). Regulatory cross-talk between microRNAs and hormone signalling cascades controls the variation on seed dormancy phenotype at Arabidopsis thaliana seed set Plant Cell Reports 36:705-717.

Blaise Ratcliffe, Omnia Gamal El-Dien, Eduardo P. Cappa, Ilga Porth, Jaroslav Klápste, Charles Chen, Yousry A. El-Kassaby (2017). Single-step BLUP with varying genotyping effort in open-pollinated Picea glauca G3: Genes | Genomes | Genetics 7:935.

Q Wang, W-B Guan, MHG Wong, S Ranjitkar, W-N Sun, Y Pan, YA El-Kassaby, L-X Shen (2017). Tree size predicts vascular epiphytic richness of traditional cultivated tea plantations in Southwestern China Global Ecology and Conservation 10:147–153.

McKown, A.D., Klápště, J., Guy, R.D., Soolanayakanahally, R.Y., La Mantia, J., Porth, I., Skyba, O., Unda, F., Douglas, C.J., El-Kassaby, Y.A., Hamelin, R.C., Mansfield, S.D., Cronk, Q.C.B. (2017). Sexual homomorphism in dioecious trees: extensive tests fail to detect sexual dimorphism in Populus. Scientific Reports 7:1831 DOI:10.1038/s41598-017-01893-z

J-L Feng, Z-J Yang, S-P Chen, YA El-Kassaby, Hui Chen (2017). Signaling pathway in development of Camellia oleifera nurse seedling grafting union Trees Struct. Funct. 31:1543-1558.

J-L Feng; Z-J Yang; S-P Chen; YA El-Kassaby; Hui Chen (2017). High throughput sequencing of small RNAs reveals dynamic microRNAs expression of lipid metabolism during Camellia oleifera and C. meiocarpa seed natural drying BMC Genomics 18:546 DOI 10.1186/s12864-017-3923-z

J-L Feng, Z-J Yang, W-W Bai, S-P Chen, W-Q Xu, YA El-Kassaby, H Chen (2017). Transcriptome comparative analysis of two Camellia species reveals lipid metabolism during mature seed natural drying Trees Struct. Funct. 31:1827-1848.

J Song, BF Carver, C Powers, L Yan, J Klápště, YA El-Kassaby, C Chen (2017). Practical application of genomic selection in a doubled-haploid winter wheat breeding program Mol Breed 37:117. DOI 10.1007/s11032-017-0715-8

R. Du, S. Niu, Y. Liu, X. Sun, I. Porth, YA El-Kassaby and W Li (2017). The gibberellin GID1-DELLA signalling module exists in evolutionarily ancient conifers Scientific Reports 7: 16637 | DOI:10.1038/s41598-017-11859-w

Q Wang, L Yang, S Ranjitkar, J-J Wang, X-R Wang, D-X Zhang, Z-Y Wang, Y-Z Huang, Y-M Zhou, Z-X Deng, L Yi, X-F Luan, YA El-Kassaby, W-B Guan (2017). Distribution and in situ conservation of a relic Chinese oil woody species yellowhorn Xanthoceras sorbifolium Bunge Can J For Res 47:1450-1456. doi.org/10.1139/cjfr-2017-0210

M Lstibůrek, YA El-Kassaby, T Skrøpa, GR Hodge, JH Sønstebø, A Steffenrem (2017). Dynamic gene-resource landscape management of Norway spruce: combining utilization and conservation Frontiers in Plant Science 8:1810 doi: 10.3389/fpls.2017.01810

Q Wang, Y Huang, Z Wang, YA El-Kassaby, W Guan (2017). Fruit shape and reproductive self and cross compatibility for the performance of fruit set in an andromonoecious species: Xanthoceras sorbifolium Bunge Tree Genet Genomes 13:116 https://doi.org/10.1007/s11295-017-1198-9

Yang Liu and Yousry A. El-Kassaby (2017). Global analysis of small RNA dynamics during seed development of Picea glauca and Arabidopsis thaliana populations reveals insights on their evolutionary trajectories Frontiers in Plant Science 8:1719. doi: 10.3389/fpls.2017.01719

E.P. Cappa, Y.A. El-Kassaby, F. Muñoz, M.N. Garcia, P.V. Villalba, J. Klápště, S.N.M.i Poltri (2017). Improving accuracy of breeding values by incorporating genomic information in spatial-competition mixed models Mil Breeding - DOI 10.1007/s11032-017-0725-6

Y. Liu, J.L. Walck and Y.A. El-Kassaby (2017). Roles of the Environment in Plant Life-History Tradeoffs In: Advances in Seed Biology (J. Jimenez-Lopez, ed.). InTech Open Access Publisher. ISBN: 978-953-51-5602-4

Thistlethwaite FR, Ratcliffe B, Klápstě J, Porth I, Chen C, Stoehr MU, El-Kassaby YA (2017). Genomic prediction accuracies in space and time for height and wood density of Douglas-fir using exome capture as the genotyping platform BMC Genomics 18:930. DOI 10.1186/s12864-017-4258-5

Steve Grossnickle and Yousry A. El-Kassaby (2016). Bareroot versus Container Stocktypes: An Ecophysiological Performance Comparison New Forests 47:1-51. DOI 10.1007/s11056-015-9476-6

O. Gamal El-Dien, B. Ratcliffe, J. Klápště, I. Porth, C. Chen, Y.A. El-Kassaby (2016). Implementation of the realized genomic relationship matrix to open-pollinated white spruce family testing for disentangling additive from non-additive genetic effects Genes, Genomes, Genetics DOI: 10.1534/g3.115.025957

Xian-Ge Hu, Hui Liu, YuQing Jin, Yan-Qiang Sun, Yue Li, Wei Zhao, Yousry A. El-Kassaby, Xiao-Ru Wang, Jian-Feng Mao (2016). De novo transcriptome assembly and characterization for the widespread and stress-tolerant conifer Platycladus orientalis PLoS ONE DOI:10.1371/journal.pone.0148985

H. Yuan, S. Niu, Y.A. El-Kassaby, Y. L., W. Li (2016). Simple genetic distance-optimized field deployments for clonal seed orchards based on microsatellite markers: as a case of Chinese pine seed orchard PLoS ONE 11(6): e0157646. doi:10.1371/journal.pone.0157646

X-G Hu, H Liu, J-Q Zhang, Y-Q Sun, Y Jin, W Zhao, YA El-Kassaby, X-R Wang, J-F Mao (2016). Global transcriptome analysis of Sabina chinensis (Cupressaceae), a valuable reforestation conifer Mol Breeding 36:99 DOI 10.1007/s11032-016-0526-3

I. PORTH, P. GARNIER-GÉRÉ, J. KLÁPŠTĔ, C. SCOTTI-SAINTAGNE, Y.A. EL-KASSABY, K. EL BURG, A. KREMER (2016). Species-specific alleles at a β-tubulin gene show significant associations with leaf morphological variation within Quercus petraea and Q. robur populations Tree Genetics and Genomes 12:81 DOI 10.1007/s11295-016-1041-8

Chaloupková, K, J Stejskal, YA El-Kassaby, M Lstibůrek (2016). Optimum neighbourhood seed orchard design Tree Genetics and Genomes 12:105 DOI 10.1007/s11295-016-1067-y

El-Kassaby YA, J Klapste (2016). Tree Breeding – Challenges and Opportunities. In: Forestry for the Curious – Why Study Forestry? (K Viadya, ed.), Chapter 7. The Curious Academic Publishing. ISBN: 978-1-925128-52-9.

Y. Liu, T. Wang, and Y. A. El-Kassaby (2016). Contributions of dynamic environmental signals during life-cycle transitions to early life-history traits in lodgepole pine (Pinus contorta Dougl.) Biogeosciences 13:1-14 doi:10.5194/bg-13-1-2016

Korecký J, El-Kassaby YA (2016). Pollination dynamics variation in a Douglas-fir seed orchard as revealed by microsatellite analysis Silva Fennica 50:1682.

Y Liu, S Barot, YA El-Kassaby, N Loeuille (2016). Impact of temperature shifts on the joint evolution of seed dormancy and size Ecology and Evolution DOI: 10.1002/ece3.2611

Y Liu, YA El-Kassaby (2016). Landscape of fluid sets of hairpin-derived 21-/24-nt-long small RNAs at seed set uncovers special epigenetic features in Picea glauca Genome Biology and Evolution 82–92 doi:10.1093/gbe/evw283

Yang Liu, Kerstin Muller, Yousry A. El-Kassaby, Allison Kermode, (2015). Changes in hormone flux and signaling in white spruce (Picea glauca) seeds during the transition from dormancy to germination in response to temperature cues BMC Plant Biology DOI 10.1186/s12870-015-0638-7

O. Gamal El-Dien, B. Ratcliffe, J. Klápště, C. Chen, I. Porth, Y.A. El-Kassaby (2015). Prediction accuracy of growth and wood attributes of interior spruce in space using genotyping-by-sequencing BMC Genomics DOI 10.1186/s12864-015-1597-y

Porth, I, J Klápště, AD McKown, J La Mantia, RD Guy, PK Ingvarsson, R Hamelin, SD Mansfield, J Ehlting, CJ Douglas, YA El-Kassaby (2015). Evolutionary quantitative genomics of Populus trichocarpa. PLoS ONE DOI:10.1371/journal.pone.0142864

B Ratcliffe, O Gamal El-Dien, J Klápště, I Porth, C Chen, B Jaquish, YA. El-Kassaby (2015). A comparison of genomic selection models across time in interior spruce (Picea engelmannii x glauca) using unordered SNP imputation methods Heredity doi:10.1038/hdy.2015.57

S Niu, H Yuan, X Sun, I Porth, Y Li, YA El-Kassaby, W Li (2015). A transcriptomics investigation into pine reproductive organ development New Phytol DOI: 10.1111/nph.13680

K Demertzis, L Iliadis, S Avramidis, YA El-Kassaby (2015). The use of machine learning in predicting interior spruce wood density utilizing progeny testing information Neural Computing and Applications DOI 10.1007/s00521-015-2075-9

Guibin Wang, Fuliang Cao, Guangyu Wang, Yousry A. El-Kassaby (2015). Role of Temperature and Soil Moisture Conditions on Flavonoid Production and Biosynthesis-Related Genes in Ginkgo (Ginkgo biloba L.) Leaves Nat Prod Chem Res 3:1 doi.org/10.4172/2329-6836.1000162

Lstibůrek M, J Stejskal, A Misevicius, J Korecký, YA El-Kassaby (2015). Expansion of the minimum-inbreeding seed orchard design to operational scale. Tree Genetics and Genomes 11:12

Yousry A. El-Kassaby, Tomas Funda, Cherdsak Liewlaksaneeyanawin (2015). Increasing Breeding without Breeding (BwB) efficiency: full- vs. partial-pedigree reconstruction in lodgepole pine SOJ Genetic Science 2:1-6.

S Brar, CKM Tsui, B Dhillon, M-J Bergeron, DL Joly, YA El-Kassaby, RC Hamelin (2015). Colonization history, host distribution, anthropogenic influence and landscape features shape populations of white pine blister rust, an invasive alien tree pathogen PLoS ONE DOI:10.1371/journal.pone.0127916

Porth I, YA El-Kassaby (2015). Using poplar as a lignocellulosic feedstock for bioethanol. Biotech J DOI 10.1002/biot.201400194

Tony Kess and Yousry A. El-Kassaby (2015). Estimates of pollen contamination and selfing in a coastal Douglas-fir seed orchard Scand J For Res DOI: 10.1080/02827581.2015.1012112

Ilga Porth, Mark Boyland, Suborna Ahmed, Yousry A. El-Kassaby, Gary Bull (2015). Forest Genomics Research and Development in Canada: Priorities for Developing an Economic Framework The Forest Chronicle 91:1-13.

Muchero W, DiFazio SP, Guo J, Chen J-G, Ranjan P, Slavov GT, Gunter LE, Jawdy S, Bryan AC, Sykes R, Ziebell A, Klápste J, Porth I, Skyba O, Unda F, El-Kassaby YA, Douglas CJ, Mansfield SD, Martin J, Schackwitz W, Evans LM, Czarnecki O, Tuskan GA. (2015). High-resolution genetic mapping of allelic variants associated with cell wall chemistry in Populus BMC Genomics 16:24.

Liu Y, YA El-Kassaby (2015). Timing of seed germination correlated with temperature-based environmental conditions during seed development in conifers. Seed Science Research 25:29-45.

McKowna AD, RD Guy, L Quamme, J Klápště, J La Mantia, CP Constabel, YA El-Kassaby, RC Hamelin, M Zifkin, MS Azam (2014). Association genetics, geography, and ecophysiology link stomatal patterning in Populus trichocarpa with carbon gain and disease resistance trade-offs. Mol Ecol (in press) doi: 10.1111/mec.12969

Tsui CK-M, Farfan L, Roe AD, Rice AV, Cooke JEK, El-Kassaby YA, Hamelin RC. (2014). Population structure of mountain pine beetle symbiont Leptographium longiclavatum and the implication on the multipartite beetle-fungi relationships. PLoS ONE 9[8]:e105455

Korecký J, Lstibůrek M, El-Kassaby YA. (2014). Congruence between theory and practice: Reduced contamination rate following phenotypic pre-selection within the Breeding without Breeding framework. Scand J For Res doi.org/10.1080/02827581.2014.945616

Alfaro, R., B. Fady, G.G. Vendramin, I. Dawson, R.A. Fleming, C.Sáenz-Romero, R.A. Lindig-Cisneros, T. Murdock, B. Vinceti, C.M. Navarro, T. Skrøppa, G. Baldinelli, Y.A. El-Kassaby and J. Loo. (2014). The role of forest genetic resources in responding to biotic and abiotic factors in the context of anthropogenic climate change. Forest Ecology and Management doi.org/10.1016/j.foreco.2014.04.006

El-Kassaby, Y.A., M. Fayed, J. Klápště and M. Lstibůrek. (2014). Randomized, replicated, staggered clonal-row (R2SCR) seed orchard design. Tree Genetics and Genomes DOI 10.1007/s11295-014-0703-7

McKown, A.D., J. Klápště, R.D. Guy, A. Geraldes, I. Porth, J. Hannemann, M. Friedmann, W. Muchero, G.A. Tuskan, J. Ehlting, Q.C.B. Cronk, Y.A. El-Kassaby, S.D. Mansfield and C.J. Douglas. (2014). Genome-wide association implicates numerous genes underlying ecological trait variation in natural populations of Populus trichocarpa New Phytol 203:535-553

Porth, I.and Y.A. El-Kassaby (2014). Current status of the development of genetically modified (GM) forest trees world-wide: a comparison with the development of other GM plants in agriculture CAB Reviews 9, No. 008 doi: 10.1079/PAVSNNR20149008

Porth I and YA El-Kassaby (2014). Assessment of the Genetic Diversity in Forest Tree Populations Using Molecular Markers Diversity 6:283-295.

Funda,T., C. Liewlaksaneeyanawin and Y.A. El-Kassaby (2014). Determination of Paternal and Maternal Parentage in Lodgepole Pine Seed: Full versus Partial Pedigree Reconstruction Can. J. For. Res. 44: 1122–1127 (2014) dx.doi.org/10.1139/cjfr-2014-0145

Xu,Y., G. Wang, F. Cao, C. Zhu, G. Wang, Y.A. El-Kassaby (2014). Light Intensity Affects the Growth and Flavonol Biosynthesis of Ginkgo (Ginkgo biloba L.) New Forests DOI 10.1007/s11056-014-9435-7

Ratcliffe, B., F.J. Hart, J. Klápšte, B. Jaquish, S.D. Mansfield and Y.A. El-Kassaby. (2014). Genetics of wood quality attributes in western larch Annals of Forest Science 71:415-424.

Klápšte, J., M. Lstiburek and Y.A. El-Kassaby. (2014). Estimates of genetic parameters and breeding values from western larch open-pollinated families using marker-based relationship Tree Genetics and Genomes 10:241–249 DOI 10.1007/s11295-013-0673-1

McKown, A.D., R.D. Guy, J. Klápšte, A. Geraldes, M. Friedmann, Q.C.B. Cronk, Y.A. El-Kassaby, S.D. Mansfield and C.J. Douglas. (2014). Geographical and environmental gradients shape phenotypic trait variation and genetic structure in Populus trichocarpa New Phytologist 201:1263-1276.

Porth, I., J. Klápšte, A.D. McKown, J. LaMantia, R.C. Hamelin, O. Skyba, F. Unda, M.C. Friedmann, Q.C.B. Cronk, J. Ethling, R.D. Guy, S.D. Mansfield, Y.A. El-Kassaby and C.J. Douglas. (2014). Extensive functional pleiotropy of REVOLUTA substantiated through forward genetics Plant Physiology 164:548-554.

T Kess, YA El-Kassaby (2014). Jackknife resampling for precision measurement of direct gene flow estimates. Scan J For Res DOI:10.1080/02827581.2014.965196

El-Kassaby YA, J Klapste (2014). Genomic selection and clonal forestry revival Proceedings of the Third International Conference of the IUFRO unit 2.09.02 on “Woody Plant Production Integrating Genetic and Vegetative Propagation Technologies“ September 18-12, 2014 ▪ Vitoria-Gasteiz, Spain (Park YS, JM Bonga, eds.). pp. 98-100.

Liu Y, A. Kermode, Y.A. EL-Kassaby (2013). The role of moist-chilling and thermo-priming on the germination characteristics of white spruce (Picea glauca) seed Seed Sci. & Technol. 41:1-15

Porth, I., J. Klápšte, O. Skyba, M.C. Friedmann, J. Hannemann, J. Ehlting, Y.A. El-Kassaby, S.D. Mansfield and C.J. Douglas (2013). Network analysis reveals the relationship between wood properties, gene expression levels and genotypes of natural Populus trichocarpa accessions New Phytologist 200:727-742.

Cappa, E.P., Y.A. El-Kassaby, M.N. Garcia, C. Acuña, N.M.G. Borralho, D. Grattapaglia and S.N.M. Poltri. (2013). Impacts of population structure and analytical models in a genome-wide association studies of complex traits in forest trees: A case study in Eucalyptus globulus. PLoS ONE 8:e81267

Iliadis, L., S.D. Mansfield, S. Avramidis and Y.A. El-Kassaby (2013). Predicting Douglas-fir wood density by artificial neural networks (ANN) based on progeny testing information. Holzforschung 67:771-777.

Fundova, I., B. Jaquish and Y.A. El-Kassaby. (2013). Quick wood density assessment using drilling resistance technology NSERC, ForValueNet Res Note No 24.

El-Kassaby, Y.A., F. Isik and R.W. Whetten. (2013). Modern advances in tree breeding Springer Science+Business Media Dordrecht. DOI 10.1007/978-94-007-7076-8_18 In: (Fenning, T., ed.) Challenges and Opportunities for the World's Forests in the 21st Century.

Liu, Y., A. Kermode and Y.A. El-Kassaby. (2013). The role of moist-chilling and thermo-priming on the germination characteristics of white spruce (Picea glauca) seed. -Seed Sci. Tech. 41:1-15.

Geraldes, A., S.P. DiFazio, G.T. Slavov, P. Ranjan, W. Muchero, J. Hannemann, L.E. Gunter, A. Wymore, C. Grassa, N. Farzaneh, I. Porth, A.D. McKown, O. Skyba, E. Li, M. Fujita, J. Klápšte, J. Martin, W. Schackwitz, C. Pennacchio, D.niel Rokhsar, M.C. Friedmann, G.O. Wasteneys, R.D. Guy, Y.A. El-Kassaby, S.D. Mansfield, Q.C.B. Cronk, J. Ehlting, C.J. Douglas, and G.A. Tuskan. (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.

Porth, I., J. Klápšte, O. Skyba, B.S.K. Lai, A. Geraldes, W. Muchero, G.A. Tuskan, C.J. Douglas, Y.A. El-Kassaby and S.D. Mansfield. (2013). Populus trichocarpa cell wall chemistry and ultrastructure trait variation, genetic control and genetic correlations. New Phytologist 197:777-790.

Korecky, J., J. Klapste, M. Lstiburek, J. Kobliha, C.D. Nelson and Y.A, El-Kassaby. (2013). Comparison of genetic parameters from marker-based relationship, sib-ship and combined models in Scots pine multi-site open-pollinated tests. - Tree Genetics and Genomes 9:1227-1235. Tree Genet. Genomes (in press). DOI 10.1007/s11295-013-0630-z

Baltunis B.S., J.H. Russell, A. Van Niejenhuis, J. Barker and Y.A. El-Kassaby. (2013). Genetic analysis and clonal stability of two yellow cypress clonal populations in British Columbia Silvae Genetica 62:173-187.

Chen, C., S.E. Mitchell, R.J. Elshire, E.S. Buckler and Y.A. El-Kassaby. (2013). Mining conifers’ mega-genome using rapid and efficient multiplexed high-throughput genotyping-by-sequencing (GBS) SNP discovery platform. -Tree Genetics and Genomes DOI 10.1007/s11295-013-0657-1

Bao, H. , E. Li, S.D. Mansfield, Q.C.B. Cronk, Y.A. El-Kassaby and C.J. Douglas. (2013). The developing xylem transcriptome and genome-wide analysis of alternative splicing in Populus trichocarpa (black cottonwood) populations -BMC Genomics 14:359

Porth, I., J. Klapste, O. Skyba, J. Hannemann, A.D. McKown, R.D. Guy, S.P. DiFazio, W. Muchero, P. Ranjan, G.A. Tuskan, M.C. Friedmann, J. Ehlting, Q.C.B. Cronk, Y.A. El-Kassaby, C.J. Douglas and S.D. Mansfield (2013). Genome-wide association mapping for wood characteristics in Populus identifies an array of candidate single nucleotide polymorphisms. -New Phytologist 200:710-726.

La Mantia, J., J. Klápšte, Y.A. El-Kassaby, S. Azam, R.D. Guy, C.J. Douglas, S.D. Mansfield, and R. Hamelin (2013). Association analysis identifies Melampsora x columbiana poplar leaf rust resistance SNPs PLoS ONE 8:e78423

El-Kassaby, Y.A. (2012). Breeding without breeding: From no pedigree to pedigree-free model. -Lee, H. et al. (eds.), International Symposium Commemorating the 100th Anniversary of Dr. S.K. Hyun's Birth. Seoul, Korea (Feb. 21, 2012). pp. 61-71.

Ding, C., L. McAuley, M.J. Meitner, Y.A. El-Kassaby. (2012). Evaluating interior spruce seed deployment with GIS-based modeling using British Columbia’s Prince George Seed Planning Zone as a model. -Silvae Genet. 61:271-279.

Tomas Funda, Milan Lstiburek, Jaroslav Klápšte, Yousry A. El-Kassaby (2012). OPTIMIZATION OF GENETIC GAIN AND DIVERSITY IN SEED ORCHARD CROPS CONSIDERING GERMINATION VARIATION -Scand. J. For. Res. 27:787-793.

Yousry A. El-Kassaby, Jaroslav Klápšte and Robert D. Guy (2012). Breeding without Breeding: selection using the genomic best linear unbiased predictor method (GBLUP) New Forests 43:631-637.

Slavov, G.T., DiFazio, S.P., Martin, J., Schackwitz, W., Muchero, W., Rodgers-Melnick, E., Lipphardt, M.F., Pennacchio, C.P., Hellsten, U., Pennacchio, L., Gunter, L.E., Ranjan, P., Vining, K., Pomraning, K.R., Wilhelm, L.J., Pellegrini, M., Mockler, T., Freitag, M., Geraldes, A., El-Kassaby, Y.A., Mansfield, S.D., Cronk, Q.C.B., Douglas, C.J., Strauss, S.H., Rokhsar, D., Tuskan. G.A. (2012). Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest tree Populus trichocarpa. New Phytologist. 196:713–725.

Wang, J., Y.A. El-Kassaby and K. Ritland. (2012). Estimating selfing rates from reconstructed pedigrees using multilocus genotype data. Mol. Ecol. 21:100-116.

Lstiburek, M.; J. Klaste; J. Kobliha and Y.A. El-Kassaby. (2012). Breeding without Breeding: Effect of gene flow on fingerprinting effort -Tree Genetics and Genomes 8:873-877.

Funda, T and Y.A. El-Kassaby (2012). Seed Orchards Genetics -CAB Reviews 7, No. 013 doi: 10.1079/PAVSNNR20127013

Tomas Funda, Cherdsak Liewlaksaneeyanawin, Irena Fundova, Ben S.K. Lai, Chris G. Walsh, Annette Van Niejenhuis, Cathy Cook, Hilary Graham, Michael U. Stoehr, Jack Woods, and Yousry A. El-Kassaby (2011). Congruence between clonal reproductive investment and success as revealed by DNA-based pedigree reconstruction in conifers seed orchards - Can. J. For. Res. 41: 380–389.

El-Kassaby, Y. A., Mansfield, S. D., Isik, F., Stoehr, M. (2011). In situ wood quality assessment in Douglas-fir Tree Genetics and Genomes 7:553-561.

Lstiburek, M, K. Ivanková, J. Kadlec, J. Kobliha, J. Klápšte, Y.A. El-Kassaby. (2011). Breeding without breeding: minimum fingerprinting effort with respect to the effective population size. -Tree Genetics and Genomes 7:1069-1078.

El-Kassaby, Y.A., E.P. Cappa, C. Liewlaksaneeyanawin, J. Klápšte and M. Lstiburek. (2011). Breeding without breeding: is a complete pedigree necessary for efficient breeding? -PLoS ONE 6(10): e25737. doi:10.1371/journal.pone.0025737.

Stoehr, MU and Y.A. El-Kassaby (2011). Challenges facing the forest industry in relation to seed dormancy and seed quality -Springer Science+Business Media, LLC 2011 -Allison R. Kermode (ed.), Seed Dormancy: Methods and Protocols, Methods in Molecular Biology, vol. 773, DOI 10.1007/978-1-61779-231-1_1, Chapter 1. pp 3-15.

Cappa, E.P., M. Lstiburek, A.D. Yanchuk and Y.A. El-Kassaby. (2011). Two-dimensional penalized splines via Gibbs sampling to account for spatial variability in forest genetic trials with small amount of information available. -Silvae Genet. 60:25-35.

Kang, K.S., C.S. Kim and Y.A. El-Kassaby. (2010). Clonal variation in acorn production and its effect on effective population size in a Quercus acutissima seed orchard. -Silvae Genet. 59:170-175.

B S LAI, T FUNDA, C LIEWLAKSANEEYANAWIN, J KLAPSTE, A VAN NIEJENHUIS, C COOK, M U STOEHR, J WOODS, Y A EL-KASSABY (2010). Pollination Dynamics in a Douglas-fir Seed Orchard as Revealed by Pedigree Reconstruction -Annals of Forest Science 67. DOI: 10.1051/forest/2010044

Massah, N., J. Wang, J.H. Russell, A. van Niejenhuis and Y.A. El-Kassaby. (2010). Genealogical relationship among members of selection and production populations of yellow-cedar (Callitropsis nootkatensis) in the absence of parental information. J. Hered. 101:154-163.

Yousry A. El-Kassaby, Tomas Funda, and Ben S.K. Lai (2010). Female Reproductive Success Variation in a Pseudotsuga menziesii Seed Orchard as Revealed by Pedigree Reconstruction from a Bulk Seed Collection -J Hered. 101:164-168.

Lstiburek, M. and Y.A. El-Kassaby. (2010). Minimum-Inbreeding Seed Orchard Design -For. Sci. 56:603-608.

El-Kassaby, Y.A. and J.A. Prado (eds.) (2010). Forests and genetically modified trees -Food and Agriculture Organization of the United nations, Rome, Italy. 235pp.

El-Kassaby, Y.A. (2010). Pedigree Reconstruction: An Alternative to Systematic Breeding. - In: Molecular Approaches in Natural Resource Conservation and Management (DeWoody, J.A. et al., eds). Cambridge University Press. 285-286pp.

Ding, C., Meitner, M., El-Kassaby, Y., and McAuley, L. (2009). GIS-based forest seed deployment tracking over time and space. In Proceedings, 2009 ESRI International Users conference, July 2009, San Diego, California. (CD), ESRI Press.

B. Bains, F. Isik, W. Strong, B. Jaquish, J.A. McLean, and Y.A. El-Kassaby. (2009). Genetic resistance of spruce to gall forming adelgids (Hemiptera: Adelgidae). - Can. J. For. Res. 39:2536-2541.

T. Funda, M. Lstiburek, P. Lachout, J. Klapste, Y.A. El-Kassaby (2009). GENETIC GAIN-DIVERSITY OPTIMIZATION FOR SEED ORCHARD CROPS -Tree Genetics and Genomes DOI 10.1007/s1 1295-009-0211-3

El-Kassaby, Y.A. and M. Lstiburek (2009). Breeding without breeding -Genet. Res. 91:111-120.

El-Kassaby,Y.A., D. Kolotelo and D. Reid (2009). Understanding Lodgepole Pine Seed Germination for Improved Utilization -Seed Sci. & Tech. 37: 316-328.

El-Kassaby, Y.A. (2008). Breeding without breeding: an unorthodox concept. -In: Adaptation, Breeding and Conservation in the Era of Forest Tree Genomics and Environmental Change. IUFRO-CTIA 2008 Joint Meeting, Quebec City (Bousquet, J. and J.D. Simpsom, eds.). pp. 4-8.

C. Chen, C. Liewlaksaneeyanawin, T. Funda, A. Kenawy, C.H. Newton and Y.A. El-Kassaby (2008). Development and characterization of microsatellite loci in western larch (Larix occidentalis Nutt.) -Mol. Ecol. Res. 9:843-845.

Funda, T., C. Chen, C. Liewlaksaneeyanawin, A. Kenawy, and Y.A. El-Kassaby (2008). Pedigree and Mating System Analyses in a Western Larch (Larix occidentalis Nutt.) Experimental Population -Ann. For. Sci. 65:705. DOI:10.1051/forest:2008055

El-Kassaby, Y.A., M.U Stoehr, D. Reid, C.G. Walsh and T.E. Lee. (2007). Clonal-row vs. random seed orchard designs: interior spruce mating system evaluation. - Can. J. For. Res. 37:690-696.

El-Kassaby, Y.A., F. Perscher, F. and D. Lindgren. (2007). Advanced generation seed orchards turnover as affected by breeding advance, time to sexual maturity, and costs: special reference to Pinus sylvestris in Sweden. -Scand. J. For. Res. 22:88-98.

El-Kassaby, Y.A. and D. Lindgren. (2007). Increasing the efficiency of Breeding Without Breeding through phenotypic pre-selection in open pollinated progenies. -In: Joint Meeting of the South. For. Tree Improve. Conf. and the Western For. Genetics Association, June, 2007. Galveston, Taxes. pp 15-19.

El-Kassaby, Y.A. and D. Reid. (2007). Is randomization necessary in seed orchards? - In: Joint Meeting of the South. For. Tree Improve. Conf. and the Western For. Genetics Association, June, 2007. Galveston, Taxes. pp 63-67.

El-Kassaby, Y.A. and S.D. Mansfield (2007). The use of genetically modified trees in forests: opportunities and challenges -In: Challenges and Opportunities of Forest Research in the Policy Making Process. The Chinese Academy of Forestry (CAF) and the International Union of Forest Research Organizations (IUFRO) Symposium, Beijing, PRC (May 29, 2007). pp. 2-13.

El-Kassaby,Y.A., M. Lstiburek, C. Liewlaksaneeyanawin, G.T. Slavov and G.T. Howe. (2007). Breeding without breeding: approach, example, and proof of concept. -In: Proc. IUFRO, Low input breeding and genetic conservation of forest tree species. Antalya, Turkey. pp. 43-54. http://www.akdeniz.edu.tr/english/iufro/2007.pdf

Perscher, F., D. Lindgren and Y.A. El-Kassaby, Y.A. (2006). Is linear deployment of clones optimal under different clonal outcrossing contributions in seed orchards? - Tree Genetics and Genomics 2:25-29.

Lstiburek, M., T. Mullin and Y.A. El-Kassaby. (2005). The impacts of positive assortative mating, differential success of somatic embryogenesis, and multi-trait selection on the outcome of clonal forestry programs. - Can. J. For. Res. 36:1376-1384.

El-Kassaby, Y.A. and J. Krakowski. (2005). Forest biotechnology deliverables: availability and benefits. -In: North American Conf. on forest biotechnology. New Century, New Trees: Biotechnology as a Tool for Forestry in North America (McCord, S. and R. Kellison, eds.), Nov. 16-17, Research Triangle Park, S.C., USA. 53-69pp.

El-Kassaby Y.A., K. Ritland, C.E. Ritland, S.N. Aitken, J. Bohlmann, and J. Krakowski. (2005). Forest genetics. -In: Forestry handbook (S.B. Watts and L. Tolland, eds.), 5th ed. Faculty of Forestry, The University of British Columbia, Vancouver, BC. 474-486pp.

Kang, K.S., Y.A. El-Kassaby, S.U. Han, and C.S Kim. (2005). Genetic gain and diversity under different thinning scenarios in a breeding seedling seed orchard of Quercus accutissima. For. Ecol. Manage. 212:405-410.

Krakowski, J, A. Benowicz, J.H. Russell and Y.A. El-Kassaby. (2005). Effects of serial propagation, donor age and genotype on Chamaecyparis nootkatensis physiology and growth traits. Can. J. For. Res. 35:623-632.

Krakowski, J. and Y.A. El-Kassaby. (2005). Lodgepole pine and white spruce germination: effects of stratification and simulated aging. Silvae Genet. 54:138-144.

Beland, J.D., J. Krakowski, C.E. Ritland, K. Ritland, and Y.A. El-Kassaby. (2005). Genetic structure and mating system of northern Arbutus menziesii populations. Can. J. Botany 83:1581-1589.

Krakowski, J., Y.S. Park, and Y.A. El-Kassaby. (2005). Early testing of Douglas-fir: wood density and ring width. For. Genet. 12:99-105.

Kang, K.S., Y.A. EL-Kassaby, M.S. Chung, C.S. Kim, Y.J. Kang and B.S. Kang. (2005). Fertility variation and effective number in a clonal seed orchard of Cryptomeria japonica. Silvae Genet. 54:104-107.

Ritland, K., M.D. Meagher, D.G.W. Edwards and Y.A. El-Kassaby. (2005). Isozyme variation and the conservation genetics of Garry oak. Can. J. Bot. 83:1478-1487.

Wilkin, J.E., S.F. Shamoun, C.E. Ritland, K. Ritland, and Y.A. El-Kassaby. (2005). Population genetics of Gaultheria shallon in British Columbia and the implications for management using biocontrol. Can. J. Bot. 83:501-509.

El-Kassaby, Y.A. and G.R. Askew. (2004). A method for estimating expected genetic diversity of vegetatively propagated populations produced from commonly used mating designs. -In: Plantation forest biotechnology for the 21st century (Walter, C. and M. Carson, eds). Research Signpost, Kerala, India. pp. 129-146.

El-Kassaby, Y.A., A. Benowicz, and D.G.W. Edwards. (2004). Genetic variation in germination attributes and response to accelerated aging in western hemlock seeds. Seed Technol. 26:38-50.

El-Kassaby, Y.A. and J. Krakowski. (2004). Methods of cloning forest trees. In: Forest genetics and tree breeding in the age of genomics: progress and future, IUFRO Joint Conf. Div. 2. Li, B. and S. McKeand, eds. Nov. 16-17, Research Triangle Park, S.C., USA. pp. 327-332.

El-Kassaby, Y.A. and I. Moss. (2004). Clonal forestry: options, deliverables and benefits. In: Forest genetics and tree breeding in the age of genomics: progress and future, IUFRO Joint Conf. Div. 2. Li, B. and S. McKeand, eds. Nov. 16-17, Research Triangle Park, S.C., USA. pp. 55-64.

Sutton, B.C.S., S.M. Attree, Y.A. El-Kassaby, S.C. Grossnickle, and D.R. Polonenko. (2004). Commercialisation of somatic embryogenesis for plantation forestry. Plantation forest biotechnology for the 21st century (Walter, C. and M. Carson, eds). Research Signpost, Kerala, India. pp. 275-301.

Liewlaksaneeyanawin, C., Ritland, C., El-Kassaby, Y.A. and Ritland, K. (2004). Single-copy, species-transferable microsatellite markers developed from loblolly pine ESTs. Theor. Appl. Genetics 109: 361-369

El-Kassaby, Y.A. (2003). Clonal-row vs. random seed orchard designs: mating pattern and seed yield of western hemlock (Tsuga heterophylla (Raf.) Sarg.). For. Genet. 10:121-127.

El-Kassaby, Y.A., B.G. Dunsworth, and J. Krakowski. (2003). Genetic evaluation of alternative silvicultural systems in coastal montane forests: western hemlock and amabilis fir. Theor. Appl. Genet. 107:598-610.

Kang, K.S., Y.A. El-Kassaby, W.Y. Choi, S.U. Han, and C.S. Kim. (2003). Changes in genetic gain and diversity caused by genetic thinning in a clonal seed orchard of Pinus densiflora. Silvae Genet. 52:220-223.

Krakowski, J., S.N. Aitken, and Y.A. El-Kassaby. (2003). Inbreeding and conservation genetics in whitebark pine. Cons. Genet. 4:581-593.

Krakowski, J. and Y.A. El-Kassaby. (2003). Effects of stratification and simulated aging on germination of Douglas-fir seed from a clonal seed orchard. For. Genetics 10:65-70.

Krakowski, J. and Y.A. El-Kassaby. (2003). Impacts of alternative silviculture systems on the genetic diversity and mating systems of forest tree species. In: Silviculture and conservation of genetic resources for sustainable forest management. Proc. symp. N. Amer. For. Comm., Forest Genetic Res. and Silv. Working Groups, and IUFRO World Congress, Quebec City, PQ. Nat. Res. Canada, Can. For. Serv. Info. Rep. LAU-X-128 pp. 75-87.

Liewlaksaneeyanawin, C., C.E. Ritland, K. Ritland, and Y.A. El-Kassaby. (2003). Experimental analysis of the mating system of the white pine weevil, Pissodes strobi (Peck) (Coleoptera: Curculionidae). Can J. Zool. 81:424-429.

Benowicz, A., S.C. Grossnickle and Y.A. El-Kassaby. (2002). Field assessment of Douglas-fir somatic and zygotic seedlings with respect to gas exchange, water relations and frost hardiness. Can. J. For. Res. 32:1-7.

Liewlaksaneeyanawin, C., C.E. Ritland and Y.A. El-Kassaby. (2002). Inheritance of microsatellites in the white pine weevil, Pissodes strobi (Peck) (Coleoptera: Curculionidae). J. Hered. 93:67-70.

Kang, K.-S. and Y.A. El-Kassaby. (2002). Theoretical and applied considerations of correlated fertility between genders on genetic diversity: Pinus densiflora seed orchard as a model. Theor. Appl. Genet. 105:1183-1189.

Lewis, K.G., C. Liewlaksaneeyanawin, R.I. Alfaro, C. Ritland, K. Ritland, and Y.A. El-Kassaby. (2002). Sexual reproduction in the white pine weevil, Pissodes strobi (Peck) (Coleoptera: Curculionidae): Implications for population genetic diversity. J. Hered. 93:165-169.

Cherry, M.I. and Y.A. El-Kassaby. (2002). Performance of yellow-cedar (Chamaecyparis nootkatensis) seedlings originating from an abbreviated reproductive cycle. Can. J. For. Res. 32: 52-58.

El-Kassaby, Y.A., A. Benowicz, and D.G.W. Edwards. (2002). Genetic control of germination and aging: lessons for practice and conservation. In: 2002 IUFRO 2.09.00, Res.h Group for Seed Physiol. and Technol. Tree Seeds 2002. Thanos, C.A. et al. (eds.) Chania, Crete, Greece. pp. 70-78.

Benowicz, A., R.D. Guy and Y.A. El-Kassaby. (2000). Geographic pattern of genetic variation in photosynthetic capacity and growth in two hardwood species from British Columbia. Oecologia 123:168-174.

El-Kassaby, Y.A. (2000). Representation of Douglas-fir and western hemlock families in seedling crops as affected by seed biology and nursery crop management practices. For. Genetics 7:305-315.

El-Kassaby, Y.A. (2000). Effect of forest tree domestication on gene pools. In: Forest Conservation Genetics: Principles and Practice. (Young, A., D. Boshier and T. Boyle, eds.). Commonwealth Scientific and Industrial Research Organisation (CSIRO). CSIRO Publishing-CABI Publishing, Canberra, Australia. 13:197-213.

El-Kassaby, Y.A. (2000). Impacts of industrial forestry on genetic diversity of forest trees. In: Forest Genetics and Sustainability.Kluwer Academic Publishers. The Netherlands (Matyas, C. ed.). 63:155-169.

El-Kassaby, Y.A. and A. Benowicz. (2000). Effects of commercial thinning on genetic, plant species and structural diversity in second growth Douglas-fir (Psudotsuga menziesii (Mirb.) Franco) stands. For. Genetics. 7:193-203.

Glaubitz, J.C., Y.A. El-Kassaby and J. Carlson. (2000). Nuclear restriction fragment length ploymorphism analysis of genetic diversity in western red cedar. Can. J. For. Res. 30:379-389.

Lewis, K.G., Y.A. El-Kassaby, R.I. Alfaro and S. Barnes. (2000). Population genetic structure of Pissodes strobi (Coleoptera: Curculionidae) in British Columbia, Canada. Ann. Entomol. Soc. Am. 93:807-818.

Xu, P., C.C. Ying and Y.A. El-Kassaby. (2000). Multivariate approaches for determining the underlying major ecological factors characterizing growth of 43 Sitka spruce populations. Silvae Genet. 49:257-263.

Benowicz, A. and Y.A. El-Kassaby. (1999). Genetic variation in mountain hemlock (Tsuga mertensiana Bong.): quantitative and adaptive attributes. For. Ecol. Manage. 123:205-215.

El-Kassaby, Y.A. (1999). Phenotypic plasticity in western redcedar. For. Genetics 6:235-240.

El-Kassaby, Y.A. and G.R. Askew. (1998). Seed orchards and their genetics. In: Forest Genetics and Tree Breeding (Mandal, A.K. and G.L. Gibson, eds.). CBS Publishers abd Distributors, New Delhi, India. 6:103-111.

El-Kassaby, Y.A. and Edwards, D.G.W. (1998). Genetic control of germination and the effects of accelerated aging in mountain hemlock seeds and its relevance to gene conservation. For. Ecol. Manage. 112:203-211.

-EL-KASSABY, Y.A. and K. RITLAND. (1998). Isozymes: techniques, interpretation and applications to forest genetics. In: Mandal, A.K. and G.L. Gibson (eds.). CBS Publishers abd Distributors, New Delhi, India Forest Genetics and Tree Breeding.12:213-226.

Jaquish, B. and Y.A. El-Kassaby. (1998). Genetic variation of western larch in British Columbia and its conservation. J. Hered. 89:248-253.

Hamann, A., Y.A. El-Kassaby, M.P. Koshy and G. Namkoong. (1998). Multivariate analysis of allozymic and quantitative trait variation in Alnus rubra: geographic patterns and evolutionary implications. Can. J. For. Res. 28: 1557-1565.

El-Kassaby, Y.A. and K. Ritland. (1998). Isozymes: techniques, interpretation and applications to forest genetics In: Forest Genetics and Tree Breeding (Mandal, A.K., ed.). CBS Publishers and Distributors, New Delhi. pp.213-226.

El-Kassaby, Y. A. and Ritland, K. (1996). Genetic variation in low elevation Douglas-fir of British Columbia and its relevance to gene conservation. Biodiversity and Conservation 5:779-794.

El-Kassaby, Y.A. and Ritland, K. (1996). Impact of Selection and Breeding on the Genetic Diversity in Douglas-fir. Biodiversity and Conservation 5:795-813.