Sundar Lab

Functional Genomics of Model Plants

NSF funded Rice Microbiome Project << New

We have been using insertional mutagenesis for the identification of gene expression pattern and function in plants. Our approach utilizes gene and enhancer trap mutagenesis by transposons (Sundaresan et al. 1995), which together with sequencing of flanking DNA to establish an FST database (Parinov et al. 1999), provides a powerful tool for functional genomics (Parinov and Sundaresan 2000; Ramachandran and Sundaresan 2000). The original application of this strategy was in Arabidopsis. We are now applying this strategy in rice, which is an important model plant for monocots, and whose genome has been recently sequenced. A high-efficiency strategy for generating large numbers of transposon knockouts in rice has been established in our laboratory (Kolesnik et al. 2004; Kumar et al. 2005), which will be useful for the large scale analysis of gene function in rice as well as other cereal crops. A second area of research in functional genomics is the identification of small RNAs in rice and maize. This is a component of the transcriptome which has an important function in the control of gene expression as well as in epigenetic silencing, whose importance has only been recognized in the past few years. We have developed computational methods for identification of micro RNAs in Arabidopsis (Adai et al. 2005). Now we are extending these methods to rice and maize, in collaboration with Dr. Vicki Vance and Dr. Lew Bowman (U. South Carolina) who are generating large numbers of small RNA sequences from these plants. These studies will eventually lead to a map of the small RNA transcriptome in large plant genomes to identify their specific and global functions.

Transposition of maize elements
in rice plants.

(Left) rice plants expressing the Green Fluorescent protein (GFP).
(Right), insertion and re-excision of dSpm element from the GFP gene generates bright fluorescent green sectors on a dark leaf sheath

Genetics of Gametogenesis and Embryogenesis

Mutant and expression screens have provided a rich harvest of information on genes regulating fundamental plant processes. These include several genes regulating vegetative and reproductive development characterized by our laboratory (e.g. Yang et al. 1999; Tantikanjana et al. 2000; Rajani and Sundaresan, 2001; Kumaran et al. 2002). The current focus of our laboratory is on genes that are required for gametogenesis and early embryogenesis, many of which are genes involved in the regulation of cell cycle or cell division patterns (e.g. Yang and Sundaresan, 2000). In collaboration with Dr. Sheila McCormick (USDA) we are studying gametophyte mutants in Arabidopsis generated in our laboratory. A partial analysis of the female gametophyte mutants has already been performed leading to the identification of over 100 genes involved in various aspects of embryo sac development and function (Pagnussat et al. 2005). A complementary strategy using microarrays has also been performed to identify another set of over 200 genes with potential functions in the female gametophyte (Yu et al. 2005). These studies should lead to applications in agriculture through control of a critical step in plant reproduction, as well as new insights into a fascinating biological process.


The tormoz (toz) mutation results in randomization of longitudinal planes of cell division during embryogenesis. The longitudinal division of the Embryo proper in wild-type Arabidopsis (left) is replaced by a transverse division (middle) or an oblique division (right). The TOZ gene was tagged with a Ds gene trap and found to encode a conserved nuclear protein.		This picture shows the tagging of a gene expressed in the egg apparatus of the female gametophyte of Arabidopsis, by a Ds gene trap insertion. The intense blue staining is due to the GUS reporter gene within the Ds element.