The University of Queensland

Techniques for Small Non-Coding RNA Analysis in Seeds of Forest Tree Species

Liu, Yang and El-Kassaby, Yousry A. (2020). Techniques for Small Non-Coding RNA Analysis in Seeds of Forest Tree Species. Plant Epigenetics and Epigenomics: Methods and Protocols. (pp. 217-225) New York, NY United States: Humana Press. doi: 10.1007/978-1-0716-0179-2_15

Roles of the Environment in Plant Life-History Trade-offs

Liu, Yang, Walck, Jeffrey L. and El-Kassaby, Yousry A. (2017). Roles of the Environment in Plant Life-History Trade-offs. Advances in Seed Biology. (pp. 3-24) London, United Kingdom: InTech. doi: 10.5772/intechopen.70312

Decoupling of height growth and drought or pest resistance tradeoffs is revealed through multiple common-garden experiments of lodgepole pine

Liu, Yang, Erbilgin, Nadir, Cappa, Eduardo Pablo, Chen, Charles, Ratcliffe, Blaise, Wei, Xiaojing, Klutsch, Jennifer G, Ullah, Aziz, Azcona, Jaime Sebastian, Thomas, Barb R and El-Kassaby, Yousry A (2023). Decoupling of height growth and drought or pest resistance tradeoffs is revealed through multiple common-garden experiments of lodgepole pine. Evolution, 77 (3), 893-906. doi: 10.1093/evolut/qpad004

Conservation prioritization based on past cascading climatic effects on genetic diversity and population size dynamics: Insights from a temperate tree species

Liu, Yang (2022). Conservation prioritization based on past cascading climatic effects on genetic diversity and population size dynamics: Insights from a temperate tree species. Diversity and Distributions, 28 (12), 2712-2728. doi: 10.1111/ddi.13490

Multiple-trait analyses improved the accuracy of genomic prediction and the power of genome-wide association of productivity and climate change-adaptive traits in lodgepole pine

Cappa, Eduardo P., Chen, Charles, Klutsch, Jennifer G., Sebastian-Azcona, Jaime, Ratcliffe, Blaise, Wei, Xiaojing, Da Ros, Letitia, Ullah, Aziz, Liu, Yang, Benowicz, Andy, Sadoway, Shane, Mansfield, Shawn D., Erbilgin, Nadir, Thomas, Barb R. and El-Kassaby, Yousry A. (2022). Multiple-trait analyses improved the accuracy of genomic prediction and the power of genome-wide association of productivity and climate change-adaptive traits in lodgepole pine. BMC Genomics, 23 (1) 536, 1-20. doi: 10.1186/s12864-022-08747-7

Pest defences under weak selection exert a limited influence on the evolution of height growth and drought avoidance in marginal pine populations

Liu, Yang, Erbilgin, Nadir, Ratcliffe, Blaise, Klutsch, Jennifer G., Wei, Xiaojing, Ullah, Aziz, Cappa, Eduardo Pablo, Chen, Charles, Thomas, Barb R. and El-Kassaby, Yousry A. (2022). Pest defences under weak selection exert a limited influence on the evolution of height growth and drought avoidance in marginal pine populations. Proceedings of the Royal Society B: Biological Sciences, 289 (1982) 20221034, 1-9. doi: 10.1098/rspb.2022.1034

Improving lodgepole pine genomic evaluation using spatial correlation structure and SNP selection with single-step GBLUP

Cappa, Eduardo P., Ratcliffe, Blaise, Chen, Charles, Thomas, Barb R., Liu, Yang, Klutsch, Jennifer, Wei, Xiaojing, Azcona, Jaime Sebastian, Benowicz, Andy, Sadoway, Shane, Erbilgin, Nadir and El-Kassaby, Yousry A. (2022). Improving lodgepole pine genomic evaluation using spatial correlation structure and SNP selection with single-step GBLUP. Heredity, 128 (4), 209-224. doi: 10.1038/s41437-022-00508-2

Integrating genomic information and productivity and climate-adaptability traits into a regional white spruce breeding program

Cappa, Eduardo P., Klutsch, Jennifer G., Sebastian-Azcona, Jaime, Ratcliffe, Blaise, Wei, Xiaojing, Ros, Letitia Da, Liu, Yang, Chen, Charles, Benowicz, Andy, Sadoway, Shane, Mansfield, Shawn D., Erbilgin, Nadir, Thomas, Barb R. and El-Kassaby, Yousry A. (2022). Integrating genomic information and productivity and climate-adaptability traits into a regional white spruce breeding program. PLoS ONE, 17 (3 March) e0264549, 1-28. doi: 10.1371/journal.pone.0264549

Correction to: Phenotypic plasticity of natural Populus trichocarpa populations in response to temporally environmental change in a common garden (BMC Evolutionary Biology, (2019), 19, 1, (231), 10.1186/s12862-019-1553-6)

Liu, Yang and El-Kassaby, Yousry A. (2021). Correction to: Phenotypic plasticity of natural Populus trichocarpa populations in response to temporally environmental change in a common garden (BMC Evolutionary Biology, (2019), 19, 1, (231), 10.1186/s12862-019-1553-6). BMC Ecology and Evolution, 21 (1) 155, 155. doi: 10.1186/s12862-021-01884-9

Transcriptome-wide analysis of introgression-resistant regions reveals genetic divergence genes under positive selection in Populus trichocarpa

Liu, Yang and El-Kassaby, Yousry A. (2021). Transcriptome-wide analysis of introgression-resistant regions reveals genetic divergence genes under positive selection in Populus trichocarpa. Heredity, 126 (3), 442-462. doi: 10.1038/s41437-020-00388-4

Ecological drivers of plant life-history traits: Assessment of seed mass and germination variation using climate cues and nitrogen resources in conifers

Liu, Yang and El-Kassaby, Yousry A. (2020). Ecological drivers of plant life-history traits: Assessment of seed mass and germination variation using climate cues and nitrogen resources in conifers. Ecological Indicators, 117 106517, 1-11. doi: 10.1016/j.ecolind.2020.106517

Phenotypic plasticity of natural Populus trichocarpa populations in response to temporally environmental change in a common garden

Liu, Yang and El-Kassaby, Yousry A. (2019). Phenotypic plasticity of natural Populus trichocarpa populations in response to temporally environmental change in a common garden. BMC Evolutionary Biology, 19 (1) 231, 231. doi: 10.1186/s12862-019-1553-6

A roadmap for urban evolutionary ecology

Rivkin, L. Ruth, Santangelo, James S., Alberti, Marina, Aronson, Myla F. J., de Keyzer, Charlotte W., Diamond, Sarah E., Fortin, Marie-Josée, Frazee, Lauren J., Gorton, Amanda J., Hendry, Andrew P., Liu, Yang, Losos, Jonathan B., MacIvor, J. Scott, Martin, Ryan A., McDonnell, Mark J., Miles, Lindsay S., Munshi-South, Jason, Ness, Robert W., Newman, Amy E. M., Stothart, Mason R., Theodorou, Panagiotis, Thompson, Ken A., Verrelli, Brian C., Whitehead, Andrew, Winchell, Kristin M. and Johnson, Marc T. J. (2019). A roadmap for urban evolutionary ecology. Evolutionary Applications, 12 (3), 384-398. doi: 10.1111/eva.12734

Novel insights into plant genome evolution and adaptation as revealed through transposable elements and non-coding RNAs in conifers

Liu, Yang and El-Kassaby, Yousry A. (2019). Novel insights into plant genome evolution and adaptation as revealed through transposable elements and non-coding RNAs in conifers. Genes, 10 (3) 228. doi: 10.3390/genes10030228

Evapotranspiration and favorable growing degree-days are key to tree height growth and ecosystem functioning: Meta-Analyses of Pacific Northwest historical data

Liu, Yang and El-Kassaby, Yousry A. (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 (1) 8228. doi: 10.1038/s41598-018-26681-1

Global Analysis of Small RNA Dynamics during Seed Development of Picea glauca and Arabidopsis thaliana Populations Reveals Insights on their Evolutionary Trajectories

Liu, Yang and El-Kassaby, Yousry A. (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

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

Liu, Yang and El-Kassaby, Yousry A. (2017). Regulatory crosstalk between microRNAs and hormone signalling cascades controls the variation on seed dormancy phenotype at Arabidopsis thaliana seed set. Plant Cell Reports, 36 (5), 705-717. doi: 10.1007/s00299-017-2111-6

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

Liu, Yang, Barot, Sébastien, El-Kassaby, Yousry A. and Loeuille, Nicolas (2017). Impact of temperature shifts on the joint evolution of seed dormancy and size. Ecology and Evolution, 7 (1), 26-37. doi: 10.1002/ece3.2611

Landscape of fluid sets of hairpin-derived 21-/24-nt-long small RNAs at seed set uncovers special epigenetic features in Picea glauca

Liu, Yang and El-Kassaby, Yousry A. (2017). 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, 9 (1), 82-92. doi: 10.1093/gbe/evw283

Contributions of dynamic environmental signals during life-cycle transitions to early life-history traits in lodgepole pine (Pinus contorta Dougl.)

Liu, Yang, Wang, Tongli and El-Kassaby, Yousry (2016). Contributions of dynamic environmental signals during life-cycle transitions to early life-history traits in lodgepole pine (Pinus contorta Dougl.). Biogeosciences, 13 (10), 2945-2958. doi: 10.5194/bg-13-2945-2016

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, Yang, Müller, Kerstin, El-Kassaby, Yousry A. and Kermode, Allison R. (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, 15 (1) 292, 1-14. doi: 10.1186/s12870-015-0638-7

Timing of seed germination correlated with temperature-based environmental conditions during seed development in conifers

Liu, Yang and El-Kassaby, Yousry A. (2015). Timing of seed germination correlated with temperature-based environmental conditions during seed development in conifers. Seed Science Research, 25 (1), 29-45. doi: 10.1017/S0960258514000361

Expression patterns of ABA and GA metabolism genes and hormone levels during rice seed development and imbibition: a comparison of dormant and non-dormant rice cultivars

Liu, Yang, Fang, Jun, Xu, Fan, Chu, Jinfang, Yan, Cunyu, Schläppi, Michael R., Wang, Youping and Chu, Chengcai (2014). Expression patterns of ABA and GA metabolism genes and hormone levels during rice seed development and imbibition: a comparison of dormant and non-dormant rice cultivars. Journal of Genetics and Genomics, 41 (6), 327-338. doi: 10.1016/j.jgg.2014.04.004

The role of moist-chilling and thermo-priming on the germination characteristics of white spruce (Picea glauca) seed

Liu, Y., Kermode, A. and El-Kassaby, Y. A. (2013). The role of moist-chilling and thermo-priming on the germination characteristics of white spruce (Picea glauca) seed. Seed Science and Technology, 41 (3), 321-335. doi: 10.15258/sst.2013.41.3.01

Insights into salt tolerance from the genome of Thellungiella salsuginea

Wu, Hua-Jun, Zhang, Zhonghui, Wang, Jun-Yi, Oh, Dong-Ha, Dassanayake, Maheshi, Liu, Binghang, Huang, Quanfei, Sun, Hai-Xi, Xia, Ran, Wu, Yaorong, Wang, Yi-Nan, Yang, Zhao, Liu, Yang, Zhang, Wanke, Zhang, Huawei, Chu, Jinfang, Yan, Cunyu, Fang, Shuang, Zhang, Jinsong, Wang, Yiqin, Zhang, Fengxia, Wang, Guodong, Lee, Sang Yeol, Cheeseman, John M, Yang, Bicheng, Li, Bo, Min, Jiumeng, Yang, Linfeng, Wang, Jun ... Xie, Qi (2012). Insights into salt tolerance from the genome of Thellungiella salsuginea. Proceedings of the National Academy of Sciences of the United States of America, 109 (30), 12219-12224. doi: 10.1073/pnas.1209954109

ZEBRA2, encoding a carotenoid isomerase, is involved in photoprotection in rice

Chai, Chenglin, Fang, Jun, Liu, Yang, Tong, Hongning, Gong, Yanqing, Wang, Yiqin, Liu, Min, Wang, Youping, Qian, Qian, Cheng, Zhukuan and Chu, Chengcai (2011). ZEBRA2, encoding a carotenoid isomerase, is involved in photoprotection in rice. Plant Molecular Biology, 75 (3), 211-221. doi: 10.1007/s11103-010-9719-z

Genetic transformation of lipid transfer protein encoding gene in Phalaenopsis amabilis to enhance cold resistance

Qin, Xuyin, Liu, Yang, Mao, Shanjing, Li, Tianbi, Wu, Hsinkan, Chu, Chengcai and Wang, Youping (2011). Genetic transformation of lipid transfer protein encoding gene in Phalaenopsis amabilis to enhance cold resistance. Euphytica, 177 (1), 33-43. doi: 10.1007/s10681-010-0246-4