Jeffrey Doyle

My research lies in the area of plant molecular systematics, molecular evolution, and comparative genomics. I am especially interested in the origin and evolution of polyploidy, a key process that has shaped the genomes of all flowering plants through multiple rounds of whole genome duplication and diploidization.

Interest in polyploidy intersects with my other research interests. Among these are systematics and evolution of the legume family (Leguminosae, Fabaceae), the third largest family of flowering plants and of great economic and ecological importance due to its ability to nodulate—form symbioses with bacteria capable of fixing atmospheric nitrogen into forms usable by plants. There are still questions about how and when nodulation evolved in the legumes and other families, and how polyploidy, which is a generator of evolutionary novelty, might have played a role in the origin or refinement of nodulation.

Within legumes, much of my career has been spent on understanding relationships in the genus Glycine, which includes not only the annual soybean and its East Asian wild progenitor, but also a group of perennial species with diploids native to Australia, where new collections in remote areas, coupled with phylogenetic and phylogenomic studies, continues to identify new species. Perennial Glycine also includes an extensive allopolyploid complex whose polyploid species have colonized islands of the Pacific thousands of miles from Australia, exhibiting the invasiveness typical of many polyploids.

Studies of Glycine allopolyploid “triads” (a polyploid and its two diploid progenitors) have elucidated the molecular underpinnings of their greater photosynthetic capacity, photoprotection, and enhanced nodulation. Allopolyploidy couples hybridization with genome doubling, and the Glycine allopolyploids have had around 300,000 years to diverge since their origins, making it difficult to determine how much of their evolution is due to genome doubling, per se.

For that, autopolyploids, synthesized in the laboratory, are of great use, and I have been involved in several studies using the model plant, Arabidopsis thaliana. These studies have shown, among other things, that cell and nucleus size increase upon polyploidization, but that nuclear size does not control cell size, and that cytoplasmic interactions and dosage responses that shape the retention or loss of genes duplicated by polyploidy take place immediately upon genome doubling. Most recently, I have been involved in studies using single cell approaches to study polyploidy.

Selected journal articles

Bombarely A., J. E. Coate, and J. J. Doyle. 2014. Mining transcriptomic data to study the origins and evolution of a plant allopolyploid complex. PeerJ 2:e391; DOI 10.7717/peerj.391

Cannon, S. B., M. R. McKain, A. Harkess, M. N. Nelson, S. Dash, M. K. Deyholos, Y. Peng, B. Joyce, C. N. Stewart Jr., M. Rolf, T. Kutchan, X. Tan, C. Chen, Y. Zhang, E. Carpenter, G. K-S. Wong, J. J. Doyle, and J. Leebens-Mack. 2015. Multiple polyploidy events in the early radiation of nodulating and non-nodulating legumes. Molecular Biology and Evolution 32:193-210 (first published online October 27, 2014. doi: 10.1093/molbev/msu296

Coate, J. E. and J. J. Doyle. 2015. Variation in transcriptome size: are we getting the message? Chromosoma 124:27-43 doi:10.1007/s00412-014-0496-3

Coate, J. E., M. Schreyer, D. Kum, and J. J. Doyle. 2020. Robust transcriptional cytonuclear coordination in nascent Arabidopsis thaliana polyploids. Genes 11:134; doi:10.3390/genes11020134.

Doyle, J. J. 2016. Chasing unicorns: Nodulation origins and the paradox of novelty. American Journal of Botany 103:1865-1868 DOI:10.3732/ajb.1600260.

Doyle, J. J. and J. E. Coate. 2019. Polyploidy, the nucleotype, and novelty: The impact of genome doubling on the biology of the cell. International Journal of Plant Sciences 180: 1-52. doi: https://doi.org/10.1086/700636

Doyle, J. J. and J. E. Coate. 2020. Autopolyploidy: an epigenetic macromutation. American Journal of Botany. https://doi-org.proxy.library.cornell.edu/10.1002/ajb2.1513

Doyle, J. J. and S. Sherman-Broyles. 2017. Double trouble: Taxonomy and definitions of polyploidy. New Phytologist 213:487-493. DOI: 10.1111/nph.14276.

Griesmann, M., Y. Chang, X. Liu, Y. Song, G. Haberer, M. B. Crook, B. Billault-Penneteau, D. Lauressergues, J. Keller, L. Imanishi, Y. P. Roswanjaya, W. Kohlen, P. Pujic, K. Battenberg, N. Alloisio, Y. Liang, H. Hilhorst, M. G. Salgado, V. Hocher, H. Gherbi, S. Svistoonoff, J. J. Doyle, S. He, Y. Xu, S. Xu, J. Qu, Q. Gao, X. Fang, Y. Fu, P. Normand, A. M. Berry, L. G. Wall, J-M. Ané, K. Pawlowski, X. Xu, H. Yang, M. Spannagl, K. F. X. Mayer, G. Ka-Shu Wong, M. Parniske, P-M. Delaux, S. Cheng. 2018. Phylogenomics reveals multiple losses of nitrogen-fixing root nodule symbiosis. Science. DOI: 10.1126/science.aat1743.

Harbert, R. S., A. H. D. Brown, and J. J. Doyle. 2014. Allopolyploidy, climate niche modeling, and evolutionary “success” in Glycine (Leguminosae). American Journal of Botany 101:710-721.

Powell, A. F. and J. J. Doyle. 2016. Enhanced rhizobial symbiotic capacity in an allopolyploid species of Glycine (Leguminosae). American Journal of Botany 103:1771-1782.

Powell, A. F. and J. J. Doyle. 2017. Non-additive transcriptomic responses to inoculation with rhizobia in a young allopolyploid compared with its diploid progenitors. Genes 8:357. doi:10.3390/genes8120357 http://www.mdpi.com/2073-4425/8/12/357/htm

Robinson, D. O., J. E. Coate, A. Singh, L. Hong, M. Bush, J. J. Doyle, and A. H. K. Roeder. 2018. Ploidy and size in the Arabidopsis sepal at multiple scales. The Plant Cell 30: 2308-2329. doi: 10.1105/tpc.18.00344.

Sherman-Broyles, S., A. Bombarely, and J. J. Doyle. 2017. Characterizing the allopolyploid species among the wild relatives of soybean: Utility of reduced representation genotyping methodologies. Journal of Systematics and Evolution 55:365-376. doi: 10.1111/jse.12268

Song, M. J., B. Potter, J. J. Doyle, and J. E. Coate. 2020. Gene balance predicts transcriptional responses immediately following ploidy change in Arabidopsis thaliana. The Plant Cell 32(5):1434-1448. doi: 10.1105/tpc.19.00832.

Sousa, F., Y.J. K. Bertrand, J. J. Doyle, B. Oxelman, and B. E. Pfeil. 2017. Using genomic location and coalescent simulation to investigate gene tree discordance in Medicago L. Systematic Biology 66:934-949. DOI: 10.1093/sysbio/syx035

Van Velzen, R., J. J. Doyle, and R. Geurts. 2018. A resurrected scenario: single gain and massive loss of nitrogen-fixing nodulation. Trends in Plant Science 24:49-57. doi: 10.1016/j.tplants.2018.10.005

• Named "Outstanding Educator" for being selected by Cornell Merrill Presidential Scholar Jennifer Sceppa ('96) as Cornell faculty member who most influenced her career.
• Named "Outstanding Educator" for being selected by Cornell Merrill Presidential Scholar Raymond Heung-Wing Mak ('01) as Cornell faculty member who most influenced his academic career.
• Named "Outstanding Educator" for being selected by Cornell Merrill Presidential Scholar Arthur Turko ('04) as Cornell faculty member who most influenced his academic career.
• Named "Outstanding Graduate Mentor" in 2007 by Plant Biology Graduate Student Organization
• Botanical Society of America Distinguished Fellow/Merit Award (2014)
• SUNY Chancellor's Award for Excellence in Faculty Service (2018)
• Asa Gray Award (highest award of American Society of Plant Taxonomists; 2020)