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Cheng-Ruei Lee Professor

Ph.D., Duke University, USA

Specialty: Evolutionary Genetics, Evolutionary Genomics, Quantitative Genetics, Genetic Mapping

E-mail: chengrueilee@ntu.edu.tw

Laboratory: Life Science Building R1129

Telephone: 886-2-3366-2535

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Current Research Interests

The genetic and genomic changes underlying weedy plant evolution. The evolution of wild relatives of important economical species.

Laboratory Introduction

Our lab is interested in any topic broadly related with evolutionary and ecological genetics and genomics, specifically, how do genes, genomes, environments, complex traits, and natural selection interact with and shape the patterns of each other? What is your favorite species? Let's explore the interesting story behind it!We use a highly integrative and interdisciplinary approach for our research, incorporating knowledge and techniques in field ecology, population genetics, quantitative genetics, molecular biology, genomics, and bioinformatics. Perspective students are expected to be enthusiastic about evolution. Having prior knowledge of any of these fields is great, but not necessary.We are interested in (but not limited to) these important questions:

  1. Does local adaptation facilitate speciation?

  2. Why is there genetic variation, and what maintains it?

  3. What are the factors shaping geographical patterns of genomic variation?

  4. Some genomic regions are more polymorphic than others. Why?

  5. What are the genomic regions or genes controlling adaptive traits?

  6. Are they few genes each with large effect, or many genes each with small effect?

  7. Does the adaptive allele come from novel mutation or standing genetic variation?

In addition, we are also interested in the evolution and relationship of human-associated plants with their wild relatives, including the weed Arabidopsis thaliana and economically important species such as rice and soybean. Our group highly welcome those who are interested in ecological and evolutionary genetics and genomics!

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Selected Publications

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  1. N Fumia, R Nair, Y-P Lin, C-R Lee, H-W Chen, E Bishop-von-Wettberg, M Kantar, R Schafleitner*. 2023 Dec. Leveraging genomics and phenomics to accelerate improvement in mungbean: A case study in how to go from GWAS to selection. The Plant Phenome Journal doi:10.1002/ppj2.20088

  2. PS Chien, P-H Chen, C-R Lee*, T-J Chiou*. 2023 Sept. Transcriptome-wide association study coupled with eQTL analysis reveals the genetic connection between gene expression and flowering time in Arabidopsis. Journal of Experimental Botany 74(18):5653-5666

  3. Y-P Lin#, H-W Chen#, P-M Yeh, SS Anand, J Lin, J Li, T Noble, R Nair, R Schafleitner, M Samsonova, E Bishop-von-Wettberg, S Nuzhdin, CT Ting, RJ Lawn, C-R Lee*. 2023 Oct. Demographic history and distinct selection signatures of two domestication genes in mungbean. Plant Physiology 193(2):1197-1212

  4. ​Carley, L.N., Mojica, J.P., Wang, B., Chen, C.-Y., Lin, Y.-P., Prasad, K.V.S.K., Chan, E., Hsu, C.-W., Keith, R., Nuñez, C.L., Olson-Manning, C.F., Rushworth, C.A., Wagner, M.R., Wang, J., Yeh, P.-M., Reichelt, M., Ghattas, K., Gershenzon, J., Lee, C.-R.*, and Mitchell-Olds, T. (2021). Ecological factors influence balancing selection on leaf chemical profiles of a wildflower. Nature Ecology & Evolution.

  5. H. Matsumura, M.-C. Hsiao, Y.-P. Lin, A. Toyoda, N. Taniai, K. Tarora, N. Urasaki, S. S. Anand, N. P. S. Dhillon, R. Schafleitner, and C.-R. Lee*. Long-read bitter gourd (Momordica charantia) genome and the genomic architecture of nonclassic domestication.P.N.A.S. Jun 2020, 117 (25) 14543-14551; DOI: 10.1073/pnas.1921016117.

  6. Lee, C-R, B Wang , JP Mojica, T Mandakova, KVSK Prasad, JL Goicoechea, N Perera, U Hellsten, HN Hundley, J Johnson, J Grimwood, K Barry, S Fairclough, JW Jenkins, Y Yu, D Kudrna, J Zhang, J Talag, W Golser, K Ghattas, ME Schranz, R Wing, MA Lysak, J Schmutz, DS Rokhsar and T Mitchell-Olds. 2017. Young inversion with multiple linked QTLs under selection in a hybrid zone. Nature Ecology & Evolution 1: 0119

  7. Lee, C-R, H Svardal, A Farlow, M Exposito-Alonso, W Ding, P Novikova, C Alonso-Blanco, D Weigel, and M Nordborg. 2017. On the post-glacial spread of human commensal Arabidopsis thaliana. Nature Communications 8: 14458

  8. The 1001 Genomes Consortium. 2016. 1135 genomes reveal the global pattern of polymorphism in Arabidopsis thaliana. Cell 166:481-491

  9. Lee, C-R, JT Anderson, and T Mitchell-Olds. 2014. Unifying genetic canalization, genetic constraint, and genotype-by-environment interaction: QTL by genomic background by environment interaction of flowering time in Boechera stricta. PLoS Genetics 10(10):e1004727

  10. Lee, C-R and T Mitchell-Olds. 2013. Complex trait divergence contributes to environmental niche differentiation in ecological speciation of Boechera stricta. Molecular Ecology 22(8):2204-2217 

  11. Lee, C-R and T Mitchell-Olds. 2012. Environmental adaptation contributes to gene polymorphism across the Arabidopsis thaliana genome. Molecular Biology and Evolution 29(12):3721-3728 

  12. Prasad, K, B-H Song, C Olson-Manning, JT Anderson, C-R Lee, ME Schranz, AJ Windsor, MJ Clauss, AJ Manzaneda, I Naqvi, M Reichelt, J Gershenzon, SG Rupasinghe, MA Schuler, and T Mitchell-Olds. 2012. A gain-of-function polymorphism controlling complex traits and fitness in nature. Science 337:1081-1084

  13. Lee, C-R and T Mitchell-Olds. 2011. Quantifying effects of environmental and geographical factors on patterns of genetic differentiation. Molecular Ecology 20(22):4631- 4642

Courses Taught

  • EEB7002 Research Training

  • EEB5045 Population Genetics

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