Research Summary

My lab focuses on the regulation of root system development in Arabidopsis thaliana. Plant root systems are developmentally plastic, and respond to environmental conditions by adding lateral roots to the system at appropriate locations. We characterized lateral root formation in detail, and showed that there are several developmental stages that can be independently regulated to alter root system morphology. We also characterized root system responses to various growth conditions, and demonstrated that lateral root formation is strongly repressed by osmotica and specific combinations of nutrients. The osmotic and nutrient cues used in our assays must trigger different signaling mechanisms in the root system, as one represses lateral root initiation while the other targets a later stage in lateral root formation. Forward and reverse genetic screens, expression profiling and quantitative genetic analyses based on both assays lead to identification of novel signaling molecules that are critical for the regulation of root system morphology. For example, our work implicated phospholipid signaling in the regulation of lateral root formation. We also showed that the phytohormone abscisic acid (ABA) is an intrinsic regulator of lateral root development, contrary to previous ideas that ABA functions solely in stress responses. Our studies also defined a putative nitrate transporter as a component of a signaling pathway coordinating lateral root initiation with nutritional cues, demonstrating for the first time that nutrient transporters in plants may have signaling roles independent of nutrient transport. Finally, analysis of natural variation in root system morphology identified QTLs that regulate intrinsic lateral root development programs and the sensitivity of the root system to osmotica. In the upcoming years, my lab will focus on the roles of phospholipid and hormonal signaling in the regulation of lateral root formation and its modulation by environmental cues.

Selected Publications

Fitz Gerald, J.N., Lehti-Shiu, M.D., Ingram, P.A., Deak, K.I., Biesiada, T., and Malamy, J.E. (2006) Identification of quantitative trait loci that regulate Arabidopsis root system size and plasticity. Genetics. 2006 172:485-98. (PubMed)

Little, D., Rao, H., Oliva, S., Daniel-Vedele, F., Krapp, A., and Malamy, J.E. (2005) The putative high-affinity nitrate transporter NRT2.1 represses lateral root initiation in response to nutritional cues. Proc. Natl. Acad. Sci. USA 102, 13693-13598. (PubMed)

Deak, K.I. and Malamy, J.E. (2005) Osmotic regulation of root system architecture. Plant J. 43, 17-28.

Malamy, J. (2005) Intrinsic and environmental factors regulating root system growth. Plant, Cell and Env. 28, 67-77. (PubMed)

Malamy, J. E. and Ryan, K. S. (2001). "Environmental regulation of lateral root initiation in Arabidopsis." Plant Physiol 127: 899-909. (PubMed)

Wysocka-Diller, J. W., Helariutta, Y., Fukaki, H., Malamy, J. E. and Benfey, P. N. (2000). "Molecular analysis of SCARECROW function reveals a radial patterning mechanism common to root and shoot." Development 127: 595-603. (PubMed)

Malamy, J. and Benfey, P. (1997) Down and out in Arabidopsis: lateral root formation. Trends in Plant Sci. 2: 390-396.

Malamy, J. and Benfey, P. (1997) Organization and cell differentiation in lateral roots of Arabidopsis thaliana. Development 124: 33-44. (PubMed)