Genomics of the Zygotic Transition in Rice
Fig: Rice fertilized zygote (2.5 hours)
The fusion of two highly differentiated cells, the egg cell and the sperm cell, results in a totipotent zygote: a single cell
with the capacity to develop into an entirely new organism. In this respect, the zygote can be considered to be the ultimate
stem cell. In both plants and animals, early embryo development is dependent on maternal transcripts deposited in the egg cell
before fertilization. The degradation of these maternal transcripts and the initiation of zygotic transcription take place during
the Maternal to Zygotic Transition (MZT). Regulation of the MZT in plants and animals is critical to successful reproduction.
We are studying the transcriptomes of rice zygotes to answer the following questions: When and how does the maternal to zygotic
transition occur in rice...
The Rice Microbiome and its effect on the Transcriptome
Fig: Rhizosphere of rice plant
Plants, much like humans and other animals, harbor rich communities of
potentially beneficial bacteria. The collective genomes of this complex
microbial network, termed the metagenome, encode diverse metabolic
capabilities unfounded within plants, essentially offering a functional
extension to the host plant's genome. Soil microbes in close proximity to
plant roots (termed the rhizosphere) have been shown to promote plant
disease suppression and nutrient acquisition.
Using rice (Oryza sativa) as a model, we are answering questions based
around how plants recruit and moderate their associated root microbiomes.
Unraveling the composition and maintenance of the rice microbiome is not only
important for bolstering our basic understanding of host-microbe interactions:
it is of great agronomic and ecological importance as well...
Patterning and Gamete Specification in the Embryo Sac of Arabidopsis and Rice
Fig: Arabidopsis embryo sac
Development of the gametophyte, the haploid generation of the plant life-cycle, is important for plant reproduction and
seed formation. In flowering plants, the female gametophyte is called the embryo sac. It consists of only four cell types,
including two gametes, which are the result of a precise developmental program.
Until recently, relatively little was known about the molecular mechanisms that establish developmental pattern in the
embryo sac, in part due to the relative inaccessibility of the gametophyte and the limited availability of informative mutants.
Experimental evidence has now been obtained that signaling by the hormone auxin, acting through an asymmetric distribution in the
ovule, is the key to position based cell identity in the embryo sac...
Functional Genomics of Model Plants
Fig: 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
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.
miRNA Candidates in A. thaliana
Genetics of Gametogenesis in Arabidopsis
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
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.
Mutant and expression screens have provided a rich harvest of information on genes regulating fundamental plant processes.
They 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 have characterized gametophyte mutants in Arabidopsis that were generated in our laboratory, 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 help us understand a critical step in plant reproduction, and potentially
lead to applications in agriculture through control of seed production.