Cornell University Department of Plant Breeding and Genetics

I have been intrigued by what determines a phenotype for many years, by the interplay of genetic, environmental and stochastic factors. My research integrates molecular and quantitative genetics, comparative genomics, and plant physiology to investigate basic biological questions with strong applicability to the farmer’s field. Most of my work has been in the area of plant-metal interactions: investigating how toxic metals such as aluminum influence root development and understanding the processes and genes that plants employ to protect root growth potential. Previously, I studied epigenetic regulatory mechanisms in maize, which is where I first became aware of phenotypic variation and fell in love with genetics.

The primary emphasis of my research program now is assessing unintended effects of transgenic crop improvement on plant composition, quality and performance. According to the National Agricultural Statistical Service, transgenic crops made up a majority of US acreage planted in 2007. In spite of this (or perhaps because of this), a debate rages between supporters and opponents of transgenic crops regarding the demonstrated or presumed safety of these varieties to people, animals and the environment. Two important concepts in the debate over transgenic crop safety are substantial equivalence (SE) and generally regarded as safe (GRAS). SE is the concept that a transgenic variety is so highly similar to its non-transgenic parent, that it can be considered to be the same. Opponents of transgenic crop improvement have criticized this concept for being without statistical merit or utility for risk assessment. In the plant improvement context, GRAS means that we accept that the products of conventional plant breeding (i.e., new varieties) are safe. Thus, the differences that exist between conventionally improved plant cultivars represent a threshold that is acceptable to consumers, regulators and other stakeholders. We will assess the differences between conventionally and transgenically modified tomatoes from a standpoint of GRAS, to evaluate SE in a statistically rigorous manner. I am using fruit ripening in tomato as a model system of known agronomic importance and using genomic, proteomic, and metabolomic methodologies and agronomic performance metrics. This project is supported by USDA Agricultural Research Service base funds.

I am also conducting research in the molecular genetic bases of aluminum stress tolerance in maize roots. This is a largely natural problem related to acid soils and is a major limitation on crop yield and thus food security. The latter project has been supported by extramural grants from National Science Foundation Plant Genome, USDA National Research Initiative and the Generation Challenge Program of the Consultative Group on International Agricultural Research (CGIAR).

I participate in the teams that teach CSS/BIO PL 642 (Plant Mineral Nutrition) and PB 406 (Plant Breeding Methods Laboratory).

Publications:
Kobayashi Y*, Hoekenga OA*, Ito H, Nakashima M, Saito S, Shaff JE, Maron LG, Pineros MA, Kochian LV, Koyama H. 2007. Characterization of AtALMT1 expression in aluminum inducible malate release and its role for rhizotoxic stress tolerance in Arabidopsis thaliana. Plant Physiology (in press). * co-first authors.

Magalhães JV, Liu J, Guimaraes CT, Lana UG, Alves VM, Wang YH, Schaffert RE, Hoekenga OA, Pineros MA, Shaff JE, Klein PE, Carneiro NP, Coelho CM, Trick HN, Kochian LV. 2007. Nature Genetics 39(9): 1156-61. A gene in the multidrug and toxic compound extrusion (MATE) family confers aluminum tolerance in sorghum.

Küpper H, Ort-Seib L, Sivaguru M, Hoekenga OA, Kochian LV. 2007. Plant Journal 50(1): 159-175. A method for cellular localization of gene expression via quantitative in situ hybridization in plants.

Hoekenga OA, Maron LG, Piñeros MA, Cançado GM, Shaff J, Kobayashi Y, Ryan PR, Dong B, Delhaize E, Sasaki T, Matsumoto H, Yamamoto Y, Koyama H, Kochian LV. 2006. Proceedings of the National Academy of Sciences (USA) 103:9783-43. AtALMT1, which encodes a malate transporter, is identified as one of several genes critical for aluminum tolerance in Arabidopsis.

Kochian LV, Piñeros MA, and Hoekenga OA. 2005. Plant and Soil 274(1):173-202. The physiology, genetics and molecular biology of plant aluminum resistance and toxicity.

Kochian LV, Hoekenga OA, and Piñeros MA, 2004. Annual Review of Plant Biology 55 (459-493) How do crop plants tolerate acid soils? Mechanisms of aluminum tolerance and phosphorous efficiency.

Hoekenga OA, Vision TJ, Shaff JE, Monforte AJ, Lee GP, Howell SH, and Kochian LV, 2003. Plant Physiology 132(2): 936-948. Identification and characterization of aluminum tolerance loci in Arabidopsis (Landsberg erecta x Columbia) by quantitative trait locus mapping. A physiologically simple but genetically complex trait.

Kochian LV, Pence NS, Letham DLD, Piñeros MA, Magalhães JV, Hoekenga OA, and Garvin DF, 2002. Plant and Soil 247(1): 109-119.Mechanisms of toxic metal resistance in plants: aluminum and heavy metals.

Hoekenga OA, Muszynski MG, and Cone KC, 2000. Genetics 155(4): 1889-1902. Developmental patterns of chromatin structure and DNA methylation responsible for epigenetic expression of a maize regulatory gene.

© 2006 Department of Plant Breeding and Genetics, Cornell University