Professor, School of Integrative Plant Science Plant Biology Section Plant Breeding and Genetics Section
My field is systematics, a very broad discipline defined as “the scientific study of the kinds and diversity of organisms and of any and all relationships among them,” and dealing primarily with phylogenetic pattern and the evolutionary process that shape that pattern. Beginning with my doctoral work I have been interested in genome duplication, and my work in this area involves comparative genomics of polyploid plant species, both naturally occurring taxa and laboratory synthesized plants. Most of this work involves the large and economically important legume family ("beans"), where projects include studies addressing the origin of nodulation (symbiotic nitrogen fixation) and the study of gene families.
View my talk from the Botany 2021 Conference: How many coalescent genes does an organelle genome comprise?
Legume systematics and origin of nodulation
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
Awards & Honors
- 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)
- PLBIO 4831: Concepts and Techniques in Plant Molecular Biology
- PLBIO 7440: Graduate Research in Plant Biology
- PLBRG 7900: Graduate-Level Dissertation
240 Emerson Hall
Ithaca, NY 14853
jjd5 [at] cornell.edu