My training is as a plant systematist, studying the evolutionary relationships of flowering plants. Beginning with my doctoral work I have been interested in genome duplication, and my work in this area involves comparative genomics of polyploid species. 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 involved in cell wall synthesis, aimed at developing alfalfa (a polyploid) as a biofuels crop, particularly soybean and its wild relatives. Soybean and, particularly, its wild relatives have been the focus of much work, developing the latter into a model system for studying natural allopolyploidy.
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 in plants, including such topics as the role of polyploidy in shaping the floral and photosynthetic transcriptomes. Much of my research has focused on polyploid complexes in the genus Glycine, which includes the cultivated soybean (G. max). The genus is itself an ancient polyploid, and several projects are aimed at understanding two ancient polyploidy events that shaped its genome. More recent cycles of allopolyploidy have occurred in the Australian perennial subgenus. Genomic studies are aimed at investigating the effect of both ancient and recent polyploidy on regions of the genome that harbor disease resistance genes (R-genes). Dissecting the genome origins of the neopolyploids has revealed at least nine different allopolyploid genome combinations involving around nine different diploid genomes. Primary molecular phylogenetic work on diploid species is addressing the possible hybrid origins of diploid species. We are studying the evolution of gene expression in fixed hybrid allopolyploid plants, and investigating the consequences of altered expression on morphology and physiology. The evolution of autopolyploidy is being studied in alfalfa and its allies (Medicago); a current project is aimed at understanding the diversity at genes involved in biomass production. Student projects also have centered on the origin of polyploids, with current work on another legume genus, Amorpha, and a noxious polyploid weed, johnsongrass (Sorghum halepense); an additional collaborative project with a plant breeder in Israel involves the origin of the polyploid “dragon fruit” cactus (Selenicereus megalanthus). The legume family as a whole has also been a focus of phylogenetic work. Knowledge of legume phylogeny is important for understanding the origin of nitrogen fixing symbioses ("nodulation"), which our work suggests may have originated several times in the family. Studies of low copy nuclear genes are useful for understanding patterns of gene family evolution and for phylogeny reconstruction at low taxonomic levels, and also for testing hypotheses of multiple origins of nodulation.
Molecular systematics and evolution
- Coate, J. E., Luciano, A. K., Seralathan, V., Minchew, K. J., Owens, T. G., & Doyle, J. J. (2012). Anatomical, biochemical and photosynthetic responses to recent allopolyploidy in Glycine dolichocarpa. American Journal of Botany. 99:55-67.
- Coate, J. E., Schlueter, J. A., Whaley, A., & Doyle, J. J. (2011). Comparative evolution of photosynthetic genes in response to polyploid and non-polyploid duplication. Plant Physiology. 155:2081-2095.
- Havananda, T., Brummer, E. C., & Doyle, J. J. (2011). Complex patterns of autopolyploid evolution in alfalfa and allies (Medicago sativa: Leguminosae). American Journal of Botany. 98:1633-1646.
- Coate, J. E., & Doyle, J. J. (2011). Divergent evolutionary fates of major photosynthetic gene networks following gene and whole genome duplications. Plant Signaling and Behavior. 6:594-597.
- Tel-Zur, N. Y., Mizrahi, A., Cisneros, A., Mouyal, J., Schneider, B., & Doyle, J. J. (2011). Phenotypic and genomic characterization of vine cacti collection (Cactaceae). Genetic Resources of Crop Evolution. 7:1075-1085.
- Doyle, J. J. (2011). Phylogenetic perspectives on the origins of nodulation. Molecular Plant-Microbe Interactions. 24:1289-1295.
- Egan, A. N., & Doyle, J. J. (2010). A comparison of global, gene-specific, and relaxed clock methods in a comparative genomics framework: dating the polyploid history of soybean (Glycine max). Systematic Biology. 59:534-547.
- Doyle, J. J., & Egan, A. N. (2010). Dating the origins of polyploidy events. New Phytologist. 186:73–85.
- Parra-Gonzalez, L. S., Straub, C. K., Doyle, J. J., Ortega, P. E., Salvo-Garrido, H. E., & Maureira-Butler, I. J. (2010). Development of microsatellite markers in Lupinus luteus (Fabaceae) and cross-species amplification in other lupine species.. American Journal of Botany. 97:e72-e74.
- Sakiroglu, M. J., Doyle, J. J., & Brummer, E. C. (2010). Inferring population structure and genetic diversity of broad range of wild diploid alfalfa (Medicago sativa L.) accessions using SSR markers. Theoretical and Applied Genetics. 121:403–415.
- Ratnaparkhe, M. B., Singh, R. J., & Doyle, J. J. (2011). Glycine. Wild Crop Relatives: Genomic and Breeding Resources, Legume Crops and Forages. C. Kole (ed.), Springer-Verlag Berlin Heidelberg,
- Sakiroglu, M., Doyle, J. J., & Brummer, E. C. (2010). The population genetic structure of diploid Medicago sativa L. germplasm. p. 143-148 Sustainable use of genetic diversity in forage and turf breeding. C. Huyghe (ed.), Springer, Berlin, Germany
- Wendel, J. F., & Doyle, J. J. (2005). Polyploidy and evolution in plants. p. 97-117 Plant Diversity and Evolution: Genotypic and Phenotypic Variation in Higher Plants. R. Henry (ed.), CABI Publishing, Oxon, UK
- Doyle, J. J. (2004). Legume phylogeny:context for the family, major groups, and the relationships of crop and model species. p. 30-59 Legume Crop Genomics. R. F. Wilson, H. T. Stalker, and E. C. Brummer (ed.), AOCS Press, Cambridge, IL, USA