Vibha Srivastava - Professor

Phone: 479-575-4872 (Office)
Address: 115 Plant Science Bldg I University of Arkansas I Fayetteville AR 72701


University of Arkansas | Crop, Soil & Environmental Sciences

 Cluster Identification:
- Plant Productivity ‘Set-Points’ Cluster
- Plant Interactions with Other Organisms Cluster

Research Areas/Expertise:
- Gene Regulation & Signal Transduction
- Plant Genetics/ Breeding
- Plant Cell Walls
- Plant Tissue Culture
- Transformation Technologies

Research Summary | Selected Publications | Lab Members | Key Collaborators | Research Projects | Links

Research Summary:

Our laboratory is developing DNA recombination based strategies for genetic engineering.  Specifically, we use FLP-FRT and Cre-lox systems for developing site-specific transgene integration approaches using rice as a model crop.  We also work on the role of DNA methylation in gene expression. In this project, we use Arabidopsis Phytochrome A epiallele, phyA’, that is suppressed due to cytosine methylations in gene coding region. We are using forward genetics approach to understand the mechanism of phyA’ suppression.

Selected Publications:

Rangani G, Khodakovskaya M, Alimohammadi M, Hoecker U, Srivastava V (2012) Site-specific methylation in gene coding region underlies transcriptional silencing of the Phytochrome A epiallele in Arabidopsis thaliana. Plant Mol Biol. DOI: 10.1007/s11103-012-9906-1

Nicholson SJ, Hoecker U, Srivastava V (2011) A novel Phytochrome B allele in Arabidopsis thaliana exhibits partial mutant phenotype: a short deletion in N-terminal extension reduces Phytochrome B activity. Plant Growth Regulation 65:207–212.

Akbudak MA and Srivastava V (2011) Improved FLP recombinase, FLPe, efficiently removes marker gene from transgene locus developed by Cre-lox mediated site-specific gene integration in rice. Mol. Biotechnol. 9:82-89.

Khattri A, Nandy S, and Srivastava V (2011) Heat-inducible Cre-lox system for marker excision in transgenic rice. J. Biosci. 36:37-42.

Lab Members:


Jamie Thomas
Program Associate I; 479-575-6690

no photo Shan Zhou

Soumen Nandy
Post Doctoral Associate; 479-575-2783

Key Collaborators

1)     Manoharan Muthusamy, University of Arkansas-Pine Bluff

2)      Mariya Khodakovskaya, University of Arkansas-Little Rock

3)      Xingyou Gu, South Dakota State University

4)      Kan Wang, Iowa State University

5)      James Thomson, USDA

Research Projects

I. Site Specific Gene Integration

Our laboratory is developing DNA recombination (Cre-lox and FLP-FRT) based plant transformation approaches such as site-specific gene integration and marker gene deletions.  These approaches are useful in optimizing the production of single-copy events and minizing transgene silencing.  When these approaches are used in combination with particle bombardment, single copy clones are produced at a higher rate, which express the gene-of-interest.  Thus, incidence of gene silencing is greatly reduced.  The site-specific integration approach is also useful for gene stacking as precise integrations of multiple gene copies results in proper expression of each copy.  These transformation approaches were developed using Cre-lox and FlP-FRT systems, but can be practiced with alternative recombination systems that function robustly in the plant cells.  Following transformation stratgies have been developed using particle bombardment for DNA delivery:

(i) Resolving complex multi-copy insertions to a single-copy via Cre-lox recombination.

(ii) Site-specific transgene integration via Cre-lox or FLP-FRT recombination

(iii) Marker gene deletion via Cre-lox or FLP-FRT recombination

(iv) Marker-free site-specific gene integration using FLP-FRT and Cre-lox recombination systems.

II. Epigenetic Mechanisms Associated With DNA Methylation in Exonic Sequences

We isolated phyA (phytochrome A gene) epi-allele, phyA', from a transgenic line of Arabidopsis containing multiple copies of PHYA transgene. phyA' is transcriptionally suppressed and highly stable in the absence of transgene locus. CG hypermethylation in exon 1 was found to be associated with its transcriptional suppression.  Further, methylation of a specific CG site rather than methylation density within the coding region was found to be critical for phyA' suppression.  Since, regulatory elements of PHYA gene are not predicted to be within the coding region, this type of gene regulation is distinct from that of promoter methylation.  Most of the well known epigenetic modifiers were ruled out to have any role in phyA' regulation; thus, transcriptional silencing mediated by exonic methylations might recruit a novel epigenetic pathway.  We are interested in understanding the underlying mechanism.


WT                 phyA'             phyA-211