* Corresponding author
# Equal contribution
Research Paper
45. H-W Chen#, C-C Chien#, C-R Lee*. 2024 ?. Distinct types of selection and genetic architecture shape molecular variation during the domestication of vegetable crops. Plant Physiology doi:10.1093/plphys/kiae245
44. 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
43. P-S Chien, P-H Chen, C-R Lee*, T-J Chiou*. 2023 Sep. 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
42. 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
41. P-W Ong, Y-P Lin, H-W Chen, C-Y Lo, M Burlyaeva, T Noble, R Nair, R Schafleitner, M Vishnyakova, E Bishop-von-Wettberg, M Samsonova, S Nuzhdin, C-T Ting, C-R Lee*. 2023 Jun. Environment as a limiting factor of the historical global spread of mungbean. eLife accepted doi:10.7554/eLife.85725
40. J Li*, C-R Lee*. 2023 July. The role of gene presence-absence variations on genetic incompatibility in Oryza sativa. New Phytologist 239(2):778-791
39. Y-P Lin, C-Y Lu, C-R Lee*. 2023 Oct. The past contribution and future fate of genetic variants under climate change in an island population of Musa itinerans. American Naturalist 202(4):558-570
38. Y-J Chen, BH Cheah, C-Y Lin, Y-T Ku, C-H Kuo, Y-Y Zhang, B-R Chen, O Nean, C-H Hsieh, P-M Yeh, FKS Yeo, Y-P Lin, W-P Chuang, C-R Lee, H-M Ting. 2023 Jan. Inducible chemical defenses in wild mungbean confer resistance to Spodoptera litura and possibly at the expense of drought tolerance. Environmental and Experimental Botany 205:105100
37. M Bavykina, N Kostina, C-R Lee, R Schafleitner, E Bishop-von Wettberg, SV Nuzhdin, M Samsonova, V Gursky, K Kozlov. 2022 Dec. Modeling of flowering Time in Vigna radiata with artificial image objects, convolutional neural network and random forest. Plants 11(23):3327
36. A Ageev, C-R Lee, C-T Ting, R Schafleitner, E Bishop-von Wettberg, SV Nuzhdin, M Samsonova, K Kozlov. 2021 Nov. Modeling of Flowering Time in Vigna radiata with Approximate Bayesian Computation. Agronomy 11: 2317
35. LN Carley, JP Mojica, B Wang, C-Y Chen, Y-P Lin, KVSK Prasad, E Chan, C-W Hsu, R Keith, CL Nunez, CF Olson-Manning, CA Rushworth, MR Wagner, J Wang, P-M Yeh, M Reichelt, K Ghattas, J Gershenzon, C-R Lee*, T Mitchell-Olds*. 2021 Aug. Ecological factors influence balancing selection on leaf chemical profiles of a wildflower. Nature Ecology & Evolution 5:1135-1144
34. Y-P Lin, T Mitchell-Olds, C-R Lee*. 2021 Apr. The ecological, genetic, and genomic architecture of local adaptation and population differentiation in Boechera stricta. Proceedings of the Royal Society B 288:20202472
33. K Kozlov, A Sokolkova, C-R Lee, C-T Ting, R Schafleitner, E Bishop-von Wettberg, S Nuzhdin, M Samsonova*. 2020 Oct. Dynamical climatic model for time to flowering in Vigna radiata. BMC Plant Biology 20:202
32. A Sokolkova, M Burlyaeva, T Valiannikova, M Vishnyakova, R Schafleitner, C-R Lee, C-T Ting, RM Nair, S Nuzhdin, M Samsonova*, E Bishop-von Wettberg*. 2020 Oct. Genome-wide association study in accessions of the mini-core collection of mungbean (Vigna radiata) from the World Vegetable Gene Bank (Taiwan). BMC Plant Biology 20:363
31. H Matsumura#*, M-C Hsiao#, Y-P Lin, A Toyoda, N Taniai, K Tarora, N Urasaki, SS Anand, NPS Dhillon, R Schafleitner, C-R Lee*. 2020 June. Long-read bitter gourd (Momordica charantia) genome and the genomic architecture of nonclassic domestication. PNAS 117:14543-14551
30. Y-P Lin*, C-Y Lu, C-R Lee*. 2020 Apr. The climatic association of population divergence and future extinction risk of Solanum pimpinellifolium. AoB Plants 12(2):plaa012
29. EM Demmings, B Williams, C-R Lee, PB Burgos, S Yang, C-F Hwang, BI Reisch, DH Chitwood, JP Londo*. 2019 Nov. Quantitative trait locus analysis of leaf morphology indicates conserved shape loci in grapevine. Frontiers in Plant Science 10:1373
28. B Wang*, JP Mojica, N Perera, C-R Lee, JT Lovell, A Sharma, C Adam, A Lipzen, K Barry, DS Rokhsar, J Schmutz, T Mitchell-Olds*. 2019 June. Ancient polymorphisms contribute to genome-wide variation by long-term balancing selection and divergent sorting in Boechera stricta. Genome Biology 20:126
27. M Burlyaeva, M Vishnyakova, M Gurkina, K Kozlov, C-R Lee, C-T Ting, R Schafleitner, S Nuzhdin, M Samsonova, E von Wettberg*. 2019 April. Collections of Mungbean [Vigna radiata (L.) R. Wilczek] and urdbean [V. mungo (L.) Hepper] in Vavilov Institute (VIR): traits diversity and trends in the breeding process over the last 100 years. Genetic Resources and Crop Evolution 66(4):767-781
26. C-W Hsu, C-Y Lo, C-R Lee*. 2019 May. On the post-glacial spread of human commensal Arabidopsis thaliana: journey to the east. New Phytologist 222:1447-1457
25. C-R Lee*, J-W Hsieh, ME Schranz, T Mitchell-Olds. 2018 July. The functional change and deletion of FLC homologs contribute to the evolution of rapid flowering in Boechera stricta. Frontiers in Plant Science 9:1078
24. P Vaidya, A McDurmon, E Mattoon, M Keefe, L Carley, C-R Lee, R Bingham, JT Anderson. 2018 April. Ecological causes and consequences of flower color polymorphism in a self-pollinating plant (Boechera stricta). New Phytologist 218:380-392
23. C-R Lee*#, B Wang#, J Mojica, T Mandáková, 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, T Mitchell-Olds*. 2017 April. Young inversion with multiple linked QTLs under selection in a hybrid zone. Nature Ecology & Evolution 1: 0119
22. C-R Lee*, H Svardal, A Farlow, M Exposito-Alonso, W Ding, P Novikova, C Alonso-Blanco, D Weigel, M Nordborg*. 2017 February. On the post-glacial spread of human commensal Arabidopsis thaliana. Nature Communications 8: 14458
21. P Fransz, G Linc, C-R Lee, SA Aflitos, JR Lasky, C Toomajian, A Hoda, J Peters, P van Dam, X Ji, M Kuzak, T Gerats, I Schubert, K Schneeberger, V Colot, R Martienssen, M Koornneef, M Nordborg, TE Juenger, H de Jong, ME Schranz. 2016 October. Molecular, genetic and evolutionary analysis of a paracentric inversion in Arabidopsis thaliana. The Plant Journal 88(2):159-178
20. LJ Leamy, C-R Lee, Q Song, I Mujacic, Y Luo, CY Chen, C Li, S Kjemtrup, B-H Song. 2016 August. Environmental versus geographical effects on genomic variation in wild soybean (Glycine soja) across its native range in northeast Asia. Ecology and Evolution 6(17):6332-6344
19. N Yao#, C-R Lee#, K Semagn, M Sow, F Nwilene, O Kolade, R Bocco, O Oyetunji, T Mitchell-Olds, MN Ndjiondjop. 2016. QTL mapping in three rice populations uncovers major genomic regions associated with African rice gall midge resistance. PLoS One 11(8): e0160749
18. The 1001 Genomes Consortium. 2016. 1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana. Cell 166:481-491
17. T Kawakatsu, SC Huang, F Jupe, E Sasaki, RJ Schmitz, MA Urich, R Castanon, JR. Nery, C Barragan, Y He, H Chen, M Dubin, C-R Lee, C Wang, F Bemm, C Becker, R O’Neil, RC O’Malley, DX Quarless, The 1001 Genomes Consortium, NJ Schork, D Weigel, M Nordborg, and JR Ecker. 2016. Epigenomic diversity in a global collection of Arabidopsis thaliana accessions. Cell 166:492-505
16. S Dixit, A Grondin, C-R Lee, A Henry, T Mitchell-Olds, and A Kumar. 2015. Understanding rice adaptation to varying agro-ecosystems: trait interactions and quantitative trait loci. BMC Genetics 16:86
15. C-R Lee*, 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
14. SP Gordon, H Priest, DL Des Marais, W Schackwitz, M Figueroa, J Martin, JN Bragg, L Tyler, C-R Lee, D Bryant, W Wang, J Messing, AJ Manzaneda, K Barry, DF Garvin, H Budak, M Tuna, T Mitchell-Olds, WF Pfender, TE Juenger, TC Mockler, and JP Vogel. 2014. Genome diversity in Brachypodium distachyon: Deep sequencing of highly diverse inbred lines. The Plant Journal 79(3):361-374
13. LJ Leamy, C-R Lee, V Cousins, I Mujacic, AJ Manzaneda, K Prasad, T Mitchell-Olds, and B-H Song. 2014. Large-scale adaptive divergence in Boechera fecunda, an endangered wild relative of Arabidopsis. Ecology and Evolution 4(16):3175-3186
12. JT Anderson, C-R Lee, T Mitchell-Olds. 2014. Strong selection genome-wide enhances fitness trade-offs across environments and episodes of selection. Evolution 68(1):16-31
11. C Topp, A Iyer-Pascuzzi, JT Anderson, C-R Lee, P Zurek, O Symonova, Y Zhen, Y Milyeko, T Galkovskyi, B Moore, J Harer, H Edelsbrunner, T Mitchell-Olds, J Weitz, and P Benfey. 2013. 3D phenotyping and quantitative trait locus mapping identify core regions of the rice genome controlling root architecture. PNAS 110(18):E1695-E1704
10. C-R Lee* 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
9. C Olson-Manning, C-R Lee, MD Rausher, and T Mitchell-Olds. 2013. Evolution of flux control in the glucosinolate pathway in Arabidopsis thaliana. Molecular Biology and Evolution 30(1):14-23
8. JT Anderson, C-R Lee, C Rushworth, R Colautti, and T Mitchell-Olds. 2013. Genetic tradeoffs and conditional neutrality contribute to local adaptation. Molecular Ecology 22(3):699-708
7. C-R Lee* and T Mitchell-Olds. 2012. Environmental adaptation contributes to gene polymorphism across the Arabidopsis thaliana genome. Molecular Biology and Evolution 29(12):3721-3728
6. 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
5. RI Colautti, C-R Lee, and T Mitchell-Olds. 2012. Origin, fate, and architecture of ecologically relevant genetic variation. Current Opinion in Plant Biology 15(2):199-204
4. C-R Lee and T Mitchell-Olds. 2011. Quantifying effects of environmental and geographical factors on patterns of genetic differentiation. Molecular Ecology 20(22):4631-4642 (Faculty 1000 - http://f1000.com/13357333)
3. JT Anderson, C-R Lee, and T Mitchell-Olds. 2011. Life history QTLs and natural selection on flowering time in Boechera stricta, a perennial relative of Arabidopsis. Evolution 65(3):771-787
2. CA Rushworth, B-H Song, C-R Lee, and T Mitchell-Olds. 2011. Boechera, a model system for ecological genomics. Molecular Ecology 20(23):4843-4857
1. S Fang, C-T Ting, C-R Lee, K-H Chu, C-C Wang, and S-C Tsaur. 2009. Molecular evolution and functional diversification of fatty acid desaturases after recurrent gene duplication in Drosophila. Molecular Biology and Evolution 26(7):1447-1456
Comment/Response
H Matsumura, M-C Hsiao, Y-P Lin, A Toyoda, N Taniai, K Tarora, N Urasaki, SS Anand, NPS Dhillon, R Schafleitner, C-R Lee*. 2020. REPLY TO RENNER: Meticulous investigation, not sequencing effort, leads to robust conclusion. PNAS 117: 24632-24633