Cornell University Department of Plant Breeding and Genetics

Our lab uses systematics, phylogenetics, and comparative genomics to address diverse questions in plant evolution. A primary focus of the lab is on polyploidy (whole genome duplication), which is one of the most important mechanisms of evolution in plants. For a given polyploid species, we use molecular variation to trace the origins of its genome genome, to identify its one or more diploid progenitor species and genotypes, to date its origins, and to understand the process by which it formed. We also study the consequences of polyploidy at the genomic, genetic, morphological, and physiological levels in synthetic and natural polyploids, particularly in crop species and their relatives. Much work in the lab involves the legume family, including investigating the history of ancient polyploidy in the family and elucidating the evolution of nodulation. Understanding relationships and polyploid origins in the Medicago sativa (alfalfa) polyploid complex is a current focus of work whose ultimate goal is the identification of genes for increasing biomass in alfalfa for use in biofuel production. Comparative genomics of Glycine, which includes the soybean (G. max) and its immediate progenitor (G. soja), as well as some 25 perennial Australian species, is a major topic in the lab. Polyploidy again is a key topic for Glycine, from understanding its ancient polyploid origin and the impact of this event in shaping its genome, to developing the perennial species as a model system for understanding recent polyploidy. In addition, as the secondary germplasm pool for soybean, the perennials are a potential source of genes for drought and disease resistance. Other projects in the lab have involved polyploid domesticates such as oca (Oxalis tuberosa) and tef (Eragrostis tef) and polyploid weeds such as johnsongrass (Sorghum halepense).

Courses Taught

BioPL 447, Molecular Systematics; BioPL 482.4 Plant gene evolution and phylogeny; BioG 201 Sophomore Seminar in Biology

Selected publications:

Choi, H-K, M. A. Luckow, J. J. Doyle, and D. R. Cook. 2006. Development of nuclear gene-derived markers linked to legume genetic maps. Molecular Genetics & Genomics (in press).
Cui, L., P. K. Wall, J. H. Leebens-Mack, B. G. Lindsay, D. E. Soltis, J. J. Doyle, P. S. Soltis, J. E. Carlson, K. Arumuganathan, A. Barakat, V. A. Albert, H. Ma, and C. W. dePamphilis. 2006. Widespread genome duplications throughout the history of flowering plants. Genome Research 16: 738-749.
Doyle, J. J., J. L. Doyle, J. T. Rauscher, and A. H. D. Brown. 2004. Evolution of the perennial soybean polyploid complex (Glycine subgenus Glycine): A study of contrasts. Biological Journal of the Linnean Society 82:583-597.
Joly, S., J. T. Rauscher, S. L. Sherman-Broyles, A. H. D. Brown, and J. J. Doyle. 2004. Evolutionary dynamics and preferential expression of homoeologous 18S-5.8S-26S nuclear ribosomal genes in natural and artificial Glycine allopolyloids. Molecular Biology and Evolution 21: 1409-1421.
Pfeil, B. E., J. A. Schlueter, R. C. Shoemaker, and J. J. Doyle. 2005. Placing paleopolyploidy in relation to taxon divergence: a phylogenetic analysis in legumes using 39 gene families. Systematic Biology 54:441-454.
Schlueter, J. A., P. Dixon, C. Granger, D. Grant, L. Clark, J. J. Doyle, and R. C. Shoemaker. 2004. Mining EST databases to resolve evolutionary events in major crop species. Genome 47:868-876.
Shoemaker, R. C., J. Schlueter, and J. J. Doyle. 2006. Paleopolyploidy and gene duplication in soybean and other legumes. Current Opinion in Plant Biology 9:104-109.
Straub, S. C. K., B. E. Pfeil, and J. J. Doyle. 2006. Testing the polyploid past of soybean using a low-copy nuclear gene: Is Glycine (Fabaceae: Papilonoideae) an auto- or allopolyploid? Molecular Phylogenetics and Evolution 39:580-584.

© 2006 Department of Plant Breeding and Genetics, Cornell University